Cadmium in PDB 6bmg: Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)
Protein crystallography data
The structure of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy), PDB code: 6bmg
was solved by
P.P.Samuel,
M.D.Miller,
W.Xu,
S.Alvarado,
G.N.Phillips Jr.,
J.S.Olson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
29.29 /
1.88
|
|
Space group
|
P 41 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.995,
85.995,
109.010,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
15.4 /
19
|
Other elements in 6bmg:
The structure of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) also contains other interesting chemical elements:
Cadmium Binding Sites:
The binding sites of Cadmium atom in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)
(pdb code 6bmg). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the
Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy), PDB code: 6bmg:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Cadmium binding site 1 out
of 9 in 6bmg
Go back to
Cadmium Binding Sites List in 6bmg
Cadmium binding site 1 out
of 9 in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd203
b:27.3
occ:1.00
|
O
|
A:ACT214
|
2.2
|
39.3
|
1.0
|
|
NE2
|
A:HIS35
|
2.3
|
27.9
|
1.0
|
|
O
|
B:HOH338
|
2.4
|
24.8
|
1.0
|
|
NE2
|
B:HIS116
|
2.4
|
28.7
|
1.0
|
|
O
|
A:ACT213
|
2.4
|
32.5
|
1.0
|
|
OXT
|
A:ACT213
|
2.5
|
34.4
|
1.0
|
|
C
|
A:ACT213
|
2.7
|
31.6
|
1.0
|
|
C
|
A:ACT214
|
2.9
|
49.6
|
1.0
|
|
OXT
|
A:ACT214
|
3.2
|
59.4
|
1.0
|
|
CE1
|
A:HIS35
|
3.2
|
27.2
|
1.0
|
|
CE1
|
B:HIS116
|
3.3
|
28.1
|
1.0
|
|
HE1
|
A:HIS35
|
3.3
|
32.7
|
1.0
|
|
CD2
|
A:HIS35
|
3.4
|
27.4
|
1.0
|
|
CD2
|
B:HIS116
|
3.4
|
28.4
|
1.0
|
|
HE1
|
B:HIS116
|
3.4
|
33.8
|
1.0
|
|
HE22
|
B:GLN128
|
3.5
|
36.5
|
0.7
|
|
HD2
|
B:HIS116
|
3.5
|
34.1
|
1.0
|
|
HD2
|
A:HIS35
|
3.5
|
32.9
|
1.0
|
|
O
|
A:HOH305
|
4.0
|
30.4
|
1.0
|
|
HH21
|
A:ARG31
|
4.1
|
32.7
|
1.0
|
|
HH22
|
A:ARG31
|
4.1
|
32.7
|
1.0
|
|
NE2
|
B:GLN128
|
4.2
|
30.4
|
0.7
|
|
HE21
|
B:GLN128
|
4.2
|
36.5
|
0.7
|
|
CH3
|
A:ACT213
|
4.3
|
35.7
|
1.0
|
|
CH3
|
A:ACT214
|
4.3
|
53.0
|
1.0
|
|
NH2
|
A:ARG31
|
4.3
|
27.2
|
1.0
|
|
ND1
|
A:HIS35
|
4.4
|
27.4
|
1.0
|
|
ND1
|
B:HIS116
|
4.4
|
27.9
|
1.0
|
|
CG
|
A:HIS35
|
4.5
|
27.5
|
1.0
|
|
H3
|
A:ACT214
|
4.5
|
63.6
|
1.0
|
|
CG
|
B:HIS116
|
4.5
|
27.6
|
1.0
|
|
O
|
A:HOH334
|
4.6
|
48.1
|
1.0
|
|
H2
|
A:ACT214
|
4.6
|
63.6
|
1.0
|
|
H2
|
A:ACT213
|
4.7
|
42.9
|
1.0
|
|
O
|
A:HOH313
|
4.7
|
27.8
|
1.0
|
|
H1
|
A:ACT213
|
4.7
|
42.9
|
1.0
|
|
H3
|
A:ACT213
|
4.7
|
42.9
|
1.0
|
|
O
|
B:PHE123
|
4.7
|
28.2
|
1.0
|
|
HA
|
B:PRO120
|
4.8
|
40.9
|
1.0
|
|
O
|
B:PRO120
|
4.8
|
50.7
|
1.0
|
|
HB2
|
B:PRO120
|
4.8
|
38.4
|
1.0
|
|
HA2
|
B:GLY124
|
4.9
|
33.1
|
1.0
|
|
HB3
|
B:PRO120
|
4.9
|
38.4
|
1.0
|
|
H1
|
A:ACT214
|
5.0
|
63.6
|
1.0
|
|
Cadmium binding site 2 out
of 9 in 6bmg
Go back to
Cadmium Binding Sites List in 6bmg
Cadmium binding site 2 out
of 9 in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd204
b:27.1
occ:1.00
|
OD2
|
A:ASP126
|
2.3
|
25.4
|
1.0
|
|
OXT
|
A:ACT210
|
2.4
|
32.2
|
1.0
|
|
OD1
|
A:ASP126
|
2.4
|
24.3
|
1.0
|
|
O
|
A:ACT210
|
2.6
|
31.7
|
1.0
|
|
CG
|
A:ASP126
|
2.7
|
25.3
|
1.0
|
|
C
|
A:ACT210
|
2.8
|
31.1
|
1.0
|
|
O
|
A:HOH335
|
4.0
|
39.6
|
1.0
|
|
CB
|
A:ASP126
|
4.2
|
23.5
|
1.0
|
|
O
|
A:HOH413
|
4.2
|
47.8
|
1.0
|
|
CH3
|
A:ACT210
|
4.3
|
35.8
|
1.0
|
|
O
|
A:HOH390
|
4.5
|
33.0
|
1.0
|
|
HB3
|
A:ASP126
|
4.6
|
28.2
|
1.0
|
|
O
|
A:HOH307
|
4.6
|
44.8
|
1.0
|
|
HB2
|
A:ASP126
|
4.6
|
28.2
|
1.0
|
|
H1
|
A:ACT210
|
4.6
|
43.0
|
1.0
|
|
H2
|
A:ACT210
|
4.7
|
43.0
|
1.0
|
|
HA
|
A:ASP126
|
4.7
|
29.1
|
1.0
|
|
O
|
A:HOH319
|
4.8
|
41.7
|
1.0
|
|
H3
|
A:ACT210
|
4.8
|
43.0
|
1.0
|
|
H
|
A:ASP126
|
4.9
|
29.8
|
1.0
|
|
CA
|
A:ASP126
|
5.0
|
24.2
|
1.0
|
|
Cadmium binding site 3 out
of 9 in 6bmg
Go back to
Cadmium Binding Sites List in 6bmg
Cadmium binding site 3 out
of 9 in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd205
b:29.2
occ:0.69
|
CD
|
A:CD205
|
0.0
|
29.2
|
0.7
|
|
HE1
|
A:HIS12
|
1.8
|
50.9
|
1.0
|
|
CD
|
A:CD205
|
2.3
|
36.0
|
0.3
|
|
OD1
|
A:ASP122
|
2.4
|
34.0
|
0.7
|
|
OD2
|
A:ASP122
|
2.5
|
39.1
|
0.7
|
|
CE1
|
A:HIS12
|
2.7
|
42.4
|
1.0
|
|
HZ1
|
A:LYS16
|
2.8
|
82.5
|
1.0
|
|
CG
|
A:ASP122
|
2.8
|
33.4
|
0.7
|
|
NE2
|
A:HIS12
|
3.4
|
47.9
|
1.0
|
|
HB2
|
A:ASP122
|
3.6
|
33.8
|
0.3
|
|
NZ
|
A:LYS16
|
3.6
|
68.8
|
1.0
|
|
HZ2
|
A:LYS16
|
3.8
|
82.5
|
1.0
|
|
ND1
|
A:HIS12
|
3.8
|
45.6
|
1.0
|
|
HD1
|
A:HIS12
|
4.0
|
54.7
|
1.0
|
|
HZ3
|
A:LYS16
|
4.0
|
82.5
|
1.0
|
|
CB
|
A:ASP122
|
4.4
|
28.1
|
0.7
|
|
HE3
|
A:LYS16
|
4.4
|
72.2
|
1.0
|
|
HB3
|
A:ASP122
|
4.4
|
33.8
|
0.3
|
|
CB
|
A:ASP122
|
4.4
|
28.2
|
0.3
|
|
CE
|
A:LYS16
|
4.5
|
60.1
|
1.0
|
|
O
|
A:HOH355
|
4.6
|
53.0
|
1.0
|
|
CD2
|
A:HIS12
|
4.6
|
43.7
|
1.0
|
|
HE2
|
A:LYS16
|
4.6
|
72.2
|
1.0
|
|
HB2
|
A:ASP122
|
4.7
|
33.8
|
0.7
|
|
HB3
|
A:ASP122
|
4.8
|
33.8
|
0.7
|
|
CG
|
A:HIS12
|
4.8
|
42.6
|
1.0
|
|
HA
|
A:ASP122
|
4.9
|
35.7
|
0.7
|
|
O
|
A:ASP122
|
4.9
|
32.5
|
0.7
|
|
HA
|
A:ASP122
|
5.0
|
34.8
|
0.3
|
|
Cadmium binding site 4 out
of 9 in 6bmg
Go back to
Cadmium Binding Sites List in 6bmg
Cadmium binding site 4 out
of 9 in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd205
b:36.0
occ:0.31
|
CD
|
A:CD205
|
0.0
|
36.0
|
0.3
|
|
NE2
|
A:HIS12
|
2.1
|
47.9
|
1.0
|
|
CD
|
A:CD205
|
2.3
|
29.2
|
0.7
|
|
HE1
|
A:HIS12
|
2.3
|
50.9
|
1.0
|
|
CE1
|
A:HIS12
|
2.5
|
42.4
|
1.0
|
|
CD2
|
A:HIS12
|
3.4
|
43.7
|
1.0
|
|
HZ1
|
A:LYS16
|
3.8
|
82.5
|
1.0
|
|
ND1
|
A:HIS12
|
3.8
|
45.6
|
1.0
|
|
OD2
|
A:ASP122
|
3.9
|
39.1
|
0.7
|
|
HD2
|
A:HIS12
|
3.9
|
52.4
|
1.0
|
|
HZ2
|
A:LYS16
|
4.0
|
82.5
|
1.0
|
|
CG
|
A:HIS12
|
4.2
|
42.6
|
1.0
|
|
NZ
|
A:LYS16
|
4.3
|
68.8
|
1.0
|
|
HD1
|
A:HIS12
|
4.4
|
54.7
|
1.0
|
|
O
|
A:HOH405
|
4.4
|
48.1
|
1.0
|
|
OD1
|
A:ASP122
|
4.6
|
34.0
|
0.7
|
|
CG
|
A:ASP122
|
4.7
|
33.4
|
0.7
|
|
HE3
|
A:LYS16
|
4.9
|
72.2
|
1.0
|
|
HZ3
|
A:LYS16
|
4.9
|
82.5
|
1.0
|
|
Cadmium binding site 5 out
of 9 in 6bmg
Go back to
Cadmium Binding Sites List in 6bmg
Cadmium binding site 5 out
of 9 in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd206
b:37.2
occ:0.54
|
O
|
A:HOH412
|
2.2
|
36.1
|
0.5
|
|
OD2
|
A:ASP122
|
2.4
|
24.1
|
0.3
|
|
O
|
A:HOH428
|
2.4
|
31.7
|
0.5
|
|
ND1
|
A:HIS119
|
2.4
|
24.9
|
1.0
|
|
O
|
A:ACT212
|
2.6
|
37.5
|
0.5
|
|
OXT
|
A:ACT212
|
2.6
|
39.6
|
0.5
|
|
C
|
A:ACT212
|
2.9
|
35.4
|
0.5
|
|
OD1
|
A:ASP122
|
3.0
|
24.7
|
0.3
|
|
CG
|
A:ASP122
|
3.0
|
25.7
|
0.3
|
|
HB3
|
A:HIS119
|
3.1
|
30.0
|
1.0
|
|
CG
|
A:HIS119
|
3.3
|
25.0
|
1.0
|
|
CE1
|
A:HIS119
|
3.4
|
25.9
|
1.0
|
|
HA
|
A:HIS119
|
3.4
|
29.9
|
1.0
|
|
HD3
|
A:LYS16
|
3.5
|
50.1
|
1.0
|
|
HE1
|
A:HIS119
|
3.5
|
31.1
|
1.0
|
|
CB
|
A:HIS119
|
3.6
|
25.0
|
1.0
|
|
HB3
|
A:ASP122
|
3.7
|
33.8
|
0.7
|
|
HE3
|
A:LYS16
|
3.7
|
72.2
|
1.0
|
|
HE2
|
A:LYS16
|
3.8
|
72.2
|
1.0
|
|
CA
|
A:HIS119
|
4.0
|
24.9
|
1.0
|
|
CE
|
A:LYS16
|
4.1
|
60.1
|
1.0
|
|
CD
|
A:LYS16
|
4.2
|
41.8
|
1.0
|
|
O
|
A:ARG118
|
4.4
|
27.9
|
1.0
|
|
CH3
|
A:ACT212
|
4.4
|
30.9
|
0.5
|
|
HB2
|
A:ASP122
|
4.4
|
33.8
|
0.7
|
|
O
|
A:HOH371
|
4.4
|
34.2
|
1.0
|
|
HB2
|
A:HIS119
|
4.5
|
30.0
|
1.0
|
|
NE2
|
A:HIS119
|
4.5
|
25.6
|
1.0
|
|
HG2
|
A:LYS16
|
4.5
|
40.7
|
1.0
|
|
CD2
|
A:HIS119
|
4.5
|
25.2
|
1.0
|
|
CB
|
A:ASP122
|
4.5
|
28.1
|
0.7
|
|
CB
|
A:ASP122
|
4.5
|
28.2
|
0.3
|
|
HB3
|
A:LYS16
|
4.5
|
37.2
|
1.0
|
|
H1
|
A:ACT212
|
4.7
|
37.1
|
0.5
|
|
HB2
|
A:ASP122
|
4.8
|
33.8
|
0.3
|
|
H2
|
A:ACT212
|
4.8
|
37.1
|
0.5
|
|
HB3
|
A:ASP122
|
4.8
|
33.8
|
0.3
|
|
CG
|
A:LYS16
|
4.9
|
33.9
|
1.0
|
|
N
|
A:HIS119
|
4.9
|
24.5
|
1.0
|
|
H3
|
A:ACT212
|
4.9
|
37.1
|
0.5
|
|
O
|
A:HOH433
|
4.9
|
54.1
|
1.0
|
|
OD2
|
A:ASP122
|
5.0
|
39.1
|
0.7
|
|
HD2
|
A:LYS16
|
5.0
|
50.1
|
1.0
|
|
Cadmium binding site 6 out
of 9 in 6bmg
Go back to
Cadmium Binding Sites List in 6bmg
Cadmium binding site 6 out
of 9 in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 6 of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd207
b:26.4
occ:1.00
|
NE2
|
B:HIS35
|
2.3
|
24.3
|
1.0
|
|
NE2
|
A:HIS116
|
2.3
|
27.3
|
1.0
|
|
O
|
A:ACT211
|
2.3
|
34.4
|
1.0
|
|
OXT
|
A:ACT209
|
2.4
|
28.6
|
1.0
|
|
O
|
A:ACT209
|
2.4
|
31.4
|
1.0
|
|
O
|
A:HOH357
|
2.4
|
23.9
|
1.0
|
|
C
|
A:ACT209
|
2.7
|
32.1
|
1.0
|
|
OXT
|
A:ACT211
|
2.8
|
60.8
|
1.0
|
|
C
|
A:ACT211
|
2.8
|
46.2
|
1.0
|
|
CE1
|
B:HIS35
|
3.2
|
24.9
|
1.0
|
|
CE1
|
A:HIS116
|
3.3
|
25.9
|
1.0
|
|
CD2
|
B:HIS35
|
3.3
|
26.0
|
1.0
|
|
CD2
|
A:HIS116
|
3.3
|
26.2
|
1.0
|
|
HE1
|
B:HIS35
|
3.3
|
29.9
|
1.0
|
|
HE1
|
A:HIS116
|
3.4
|
31.2
|
1.0
|
|
HD2
|
A:HIS116
|
3.5
|
31.5
|
1.0
|
|
HD2
|
B:HIS35
|
3.5
|
31.3
|
1.0
|
|
HE22
|
A:GLN128
|
3.8
|
37.2
|
1.0
|
|
O
|
A:HOH308
|
4.0
|
25.4
|
1.0
|
|
CH3
|
A:ACT209
|
4.2
|
37.7
|
1.0
|
|
HH21
|
B:ARG31
|
4.2
|
31.6
|
1.0
|
|
HH22
|
B:ARG31
|
4.3
|
31.6
|
1.0
|
|
CH3
|
A:ACT211
|
4.3
|
44.3
|
1.0
|
|
O
|
A:HOH384
|
4.3
|
48.8
|
1.0
|
|
ND1
|
B:HIS35
|
4.4
|
24.4
|
1.0
|
|
ND1
|
A:HIS116
|
4.4
|
26.8
|
1.0
|
|
CG
|
B:HIS35
|
4.4
|
24.4
|
1.0
|
|
CG
|
A:HIS116
|
4.5
|
25.5
|
1.0
|
|
NE2
|
A:GLN128
|
4.5
|
31.0
|
1.0
|
|
NH2
|
B:ARG31
|
4.5
|
26.3
|
1.0
|
|
H1
|
A:ACT209
|
4.5
|
45.2
|
1.0
|
|
O
|
A:PRO120
|
4.6
|
25.9
|
1.0
|
|
H3
|
A:ACT209
|
4.6
|
45.2
|
1.0
|
|
H2
|
A:ACT209
|
4.6
|
45.2
|
1.0
|
|
H2
|
A:ACT211
|
4.6
|
53.2
|
1.0
|
|
H1
|
A:ACT211
|
4.6
|
53.2
|
1.0
|
|
HE21
|
A:GLN128
|
4.7
|
37.2
|
1.0
|
|
HA
|
A:PRO120
|
4.7
|
29.3
|
1.0
|
|
O
|
A:PHE123
|
4.7
|
26.2
|
1.0
|
|
O
|
B:HOH303
|
4.8
|
31.2
|
1.0
|
|
O
|
A:HOH383
|
4.8
|
54.8
|
1.0
|
|
H3
|
A:ACT211
|
5.0
|
53.2
|
1.0
|
|
Cadmium binding site 7 out
of 9 in 6bmg
Go back to
Cadmium Binding Sites List in 6bmg
Cadmium binding site 7 out
of 9 in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 7 of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd208
b:49.1
occ:0.65
|
H1
|
A:MET0
|
2.4
|
83.8
|
1.0
|
|
O
|
A:HOH425
|
2.4
|
42.0
|
0.7
|
|
H2
|
A:MET0
|
2.4
|
83.8
|
1.0
|
|
NE2
|
A:HIS81
|
2.5
|
57.8
|
1.0
|
|
N
|
A:MET0
|
2.8
|
69.8
|
1.0
|
|
HB3
|
A:MET0
|
2.8
|
94.9
|
1.0
|
|
O
|
A:HOH438
|
2.9
|
52.4
|
0.7
|
|
CE1
|
A:HIS81
|
3.4
|
58.9
|
1.0
|
|
CA
|
A:MET0
|
3.4
|
74.4
|
1.0
|
|
HA
|
A:MET0
|
3.4
|
89.3
|
1.0
|
|
CB
|
A:MET0
|
3.4
|
79.1
|
1.0
|
|
HE1
|
A:HIS81
|
3.5
|
70.7
|
1.0
|
|
HG2
|
A:MET0
|
3.5
|
0.4
|
1.0
|
|
H3
|
A:MET0
|
3.5
|
83.8
|
1.0
|
|
CD2
|
A:HIS81
|
3.6
|
57.3
|
1.0
|
|
HD2
|
A:HIS81
|
3.8
|
68.8
|
1.0
|
|
CG
|
A:MET0
|
4.0
|
84.5
|
1.0
|
|
O
|
A:HOH324
|
4.1
|
50.4
|
1.0
|
|
O
|
A:HOH303
|
4.1
|
48.4
|
1.0
|
|
HB2
|
A:MET0
|
4.3
|
94.9
|
1.0
|
|
O
|
A:LYS79
|
4.5
|
32.8
|
1.0
|
|
HE2
|
A:MET0
|
4.5
|
0.6
|
1.0
|
|
ND1
|
A:HIS81
|
4.6
|
57.6
|
1.0
|
|
HG3
|
A:MET0
|
4.6
|
0.4
|
1.0
|
|
CG
|
A:HIS81
|
4.7
|
55.9
|
1.0
|
|
HE3
|
A:MET0
|
4.8
|
0.6
|
1.0
|
|
C
|
A:MET0
|
4.9
|
65.2
|
1.0
|
|
Cadmium binding site 8 out
of 9 in 6bmg
Go back to
Cadmium Binding Sites List in 6bmg
Cadmium binding site 8 out
of 9 in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 8 of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd203
b:27.9
occ:1.00
|
OE2
|
B:GLU38
|
2.2
|
31.1
|
1.0
|
|
O
|
B:ACT205
|
2.3
|
28.7
|
1.0
|
|
ND1
|
B:HIS36
|
2.4
|
25.3
|
1.0
|
|
OXT
|
B:ACT205
|
2.5
|
29.1
|
1.0
|
|
C
|
B:ACT205
|
2.7
|
29.7
|
1.0
|
|
CD
|
B:GLU38
|
2.9
|
31.8
|
1.0
|
|
OE1
|
B:GLU38
|
3.0
|
28.1
|
1.0
|
|
HB3
|
B:HIS36
|
3.1
|
28.3
|
1.0
|
|
HA
|
B:HIS36
|
3.3
|
26.0
|
1.0
|
|
CE1
|
B:HIS36
|
3.3
|
23.5
|
1.0
|
|
CG
|
B:HIS36
|
3.3
|
24.7
|
1.0
|
|
HE1
|
B:HIS36
|
3.4
|
28.2
|
1.0
|
|
CB
|
B:HIS36
|
3.6
|
23.6
|
1.0
|
|
HZ
|
B:PHE106
|
3.8
|
35.4
|
1.0
|
|
HE2
|
B:PHE106
|
3.9
|
32.5
|
1.0
|
|
CA
|
B:HIS36
|
3.9
|
21.8
|
1.0
|
|
CZ
|
B:PHE106
|
3.9
|
29.5
|
1.0
|
|
CE2
|
B:PHE106
|
4.0
|
27.0
|
1.0
|
|
O
|
B:HOH350
|
4.1
|
29.8
|
1.0
|
|
CH3
|
B:ACT205
|
4.3
|
40.9
|
1.0
|
|
O
|
B:HOH397
|
4.4
|
41.2
|
1.0
|
|
HD2
|
B:PRO37
|
4.4
|
36.2
|
1.0
|
|
O
|
B:HOH352
|
4.4
|
29.7
|
1.0
|
|
CG
|
B:GLU38
|
4.4
|
29.4
|
1.0
|
|
NE2
|
B:HIS36
|
4.4
|
25.5
|
1.0
|
|
CD2
|
B:HIS36
|
4.5
|
24.2
|
1.0
|
|
HB2
|
B:HIS36
|
4.5
|
28.3
|
1.0
|
|
O
|
B:HIS35
|
4.5
|
22.5
|
1.0
|
|
HG3
|
B:GLU38
|
4.6
|
35.3
|
1.0
|
|
H2
|
B:ACT205
|
4.7
|
49.1
|
1.0
|
|
CE1
|
B:PHE106
|
4.7
|
28.5
|
1.0
|
|
H3
|
B:ACT205
|
4.7
|
49.1
|
1.0
|
|
O
|
B:HOH314
|
4.7
|
42.2
|
1.0
|
|
H1
|
B:ACT205
|
4.7
|
49.1
|
1.0
|
|
C
|
B:HIS36
|
4.8
|
23.5
|
1.0
|
|
CD2
|
B:PHE106
|
4.8
|
24.3
|
1.0
|
|
H
|
B:GLU38
|
4.8
|
32.4
|
1.0
|
|
HG2
|
B:GLU38
|
4.9
|
35.3
|
1.0
|
|
HE1
|
B:PHE106
|
5.0
|
34.2
|
1.0
|
|
Cadmium binding site 9 out
of 9 in 6bmg
Go back to
Cadmium Binding Sites List in 6bmg
Cadmium binding site 9 out
of 9 in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 9 of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd204
b:45.7
occ:0.59
|
H1
|
B:MET0
|
2.4
|
82.6
|
1.0
|
|
NE2
|
B:HIS81
|
2.5
|
40.9
|
1.0
|
|
H2
|
B:MET0
|
2.5
|
82.6
|
1.0
|
|
O
|
B:HOH383
|
2.6
|
29.4
|
0.6
|
|
N
|
B:MET0
|
2.8
|
68.8
|
1.0
|
|
HB3
|
B:MET0
|
2.9
|
91.0
|
1.0
|
|
CE1
|
B:HIS81
|
3.3
|
43.4
|
1.0
|
|
HE1
|
B:HIS81
|
3.4
|
52.0
|
1.0
|
|
CD2
|
B:HIS81
|
3.5
|
40.3
|
1.0
|
|
CA
|
B:MET0
|
3.5
|
67.0
|
1.0
|
|
HG2
|
B:MET0
|
3.5
|
97.8
|
1.0
|
|
H3
|
B:MET0
|
3.5
|
82.6
|
1.0
|
|
CB
|
B:MET0
|
3.6
|
75.8
|
1.0
|
|
HA
|
B:MET0
|
3.6
|
80.5
|
1.0
|
|
HD2
|
B:HIS81
|
3.7
|
48.4
|
1.0
|
|
CG
|
B:MET0
|
4.1
|
81.5
|
1.0
|
|
O
|
B:LYS79
|
4.3
|
25.4
|
1.0
|
|
O
|
B:HOH311
|
4.4
|
40.0
|
1.0
|
|
O
|
B:HOH323
|
4.4
|
49.0
|
1.0
|
|
HB2
|
B:MET0
|
4.4
|
91.0
|
1.0
|
|
ND1
|
B:HIS81
|
4.5
|
40.9
|
1.0
|
|
CG
|
B:HIS81
|
4.6
|
39.4
|
1.0
|
|
HG3
|
B:MET0
|
4.6
|
97.8
|
1.0
|
|
HE2
|
B:MET0
|
4.8
|
0.5
|
1.0
|
|
HE3
|
B:MET0
|
4.9
|
0.5
|
1.0
|
|
C
|
B:MET0
|
5.0
|
53.5
|
1.0
|
|
Reference:
P.P.Samuel,
M.D.Miller,
W.Xu,
S.Alvarado,
G.N.Phillips Jr.,
J.S.Olson.
Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) To Be Published.
Page generated: Fri Jul 19 19:03:21 2024
|
