Cadmium in PDB 1m5q: Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum
Protein crystallography data
The structure of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum, PDB code: 1m5q
was solved by
C.Mura,
M.Phillips,
A.Kozhukhovsky,
D.Eisenberg,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.97 /
2.00
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
83.322,
172.427,
148.108,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.1 /
23.6
|
Other elements in 1m5q:
The structure of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum also contains other interesting chemical elements:
Cadmium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
28;
Binding sites:
The binding sites of Cadmium atom in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum
(pdb code 1m5q). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 28 binding sites of Cadmium where determined in the
Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum, PDB code: 1m5q:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Cadmium binding site 1 out
of 28 in 1m5q
Go back to
Cadmium Binding Sites List in 1m5q
Cadmium binding site 1 out
of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd2001
b:35.5
occ:0.93
|
NE2
|
A:HIS39
|
2.3
|
24.4
|
1.0
|
O
|
B:HOH3008
|
2.5
|
24.3
|
1.0
|
O
|
A:HOH4034
|
2.6
|
11.3
|
1.0
|
O
|
A:HOH4055
|
2.7
|
29.4
|
1.0
|
OE1
|
B:GLU84
|
2.7
|
43.9
|
1.0
|
OE2
|
B:GLU84
|
3.0
|
45.2
|
1.0
|
CD
|
B:GLU84
|
3.0
|
41.7
|
1.0
|
CD2
|
A:HIS39
|
3.1
|
20.5
|
1.0
|
CE1
|
A:HIS39
|
3.3
|
23.1
|
1.0
|
O
|
B:HOH3032
|
3.9
|
32.6
|
1.0
|
CG
|
B:GLU15
|
4.1
|
31.9
|
1.0
|
NE
|
A:ARG62
|
4.1
|
31.2
|
1.0
|
CG
|
B:GLU84
|
4.2
|
38.6
|
1.0
|
CG
|
A:HIS39
|
4.3
|
22.2
|
1.0
|
ND1
|
A:HIS39
|
4.4
|
22.7
|
1.0
|
OE2
|
B:GLU15
|
4.5
|
37.4
|
1.0
|
NH2
|
A:ARG62
|
4.6
|
28.8
|
1.0
|
CZ
|
A:ARG62
|
4.8
|
30.6
|
1.0
|
CD
|
B:GLU15
|
4.9
|
34.9
|
1.0
|
O
|
B:HOH3060
|
4.9
|
42.4
|
1.0
|
|
Cadmium binding site 2 out
of 28 in 1m5q
Go back to
Cadmium Binding Sites List in 1m5q
Cadmium binding site 2 out
of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd2007
b:37.4
occ:1.02
|
NE2
|
G:HIS39
|
2.1
|
25.7
|
1.0
|
O
|
G:HOH4058
|
2.5
|
39.6
|
1.0
|
OE1
|
A:GLU84
|
2.5
|
43.4
|
1.0
|
O
|
G:HOH4003
|
2.6
|
16.0
|
1.0
|
OE2
|
A:GLU84
|
2.8
|
43.7
|
1.0
|
CD
|
A:GLU84
|
2.9
|
42.4
|
1.0
|
CD2
|
G:HIS39
|
3.1
|
25.1
|
1.0
|
CE1
|
G:HIS39
|
3.1
|
24.6
|
1.0
|
O
|
G:HOH4059
|
4.0
|
46.8
|
1.0
|
CG
|
A:GLU15
|
4.1
|
32.8
|
1.0
|
O
|
A:HOH4041
|
4.1
|
38.0
|
1.0
|
NE
|
G:ARG62
|
4.2
|
28.6
|
1.0
|
ND1
|
G:HIS39
|
4.2
|
23.7
|
1.0
|
CG
|
G:HIS39
|
4.2
|
27.8
|
1.0
|
CG
|
A:GLU84
|
4.4
|
37.8
|
1.0
|
NH2
|
G:ARG62
|
4.5
|
28.9
|
1.0
|
OE1
|
A:GLU15
|
4.8
|
37.0
|
1.0
|
CZ
|
G:ARG62
|
4.8
|
30.5
|
1.0
|
|
Cadmium binding site 3 out
of 28 in 1m5q
Go back to
Cadmium Binding Sites List in 1m5q
Cadmium binding site 3 out
of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd2002
b:38.3
occ:0.91
|
NE2
|
B:HIS39
|
2.2
|
28.3
|
1.0
|
OE2
|
C:GLU84
|
2.3
|
43.5
|
1.0
|
OE1
|
C:GLU84
|
2.4
|
42.6
|
1.0
|
CD
|
C:GLU84
|
2.7
|
42.8
|
1.0
|
O
|
C:HOH194
|
2.7
|
46.0
|
1.0
|
O
|
B:HOH3003
|
2.7
|
21.6
|
1.0
|
CD2
|
B:HIS39
|
3.1
|
23.8
|
1.0
|
CE1
|
B:HIS39
|
3.2
|
25.4
|
1.0
|
OE2
|
C:GLU15
|
3.8
|
52.6
|
1.0
|
NE
|
B:ARG62
|
4.1
|
31.8
|
1.0
|
CG
|
C:GLU84
|
4.2
|
40.9
|
1.0
|
O
|
C:HOH177
|
4.2
|
36.9
|
1.0
|
ND1
|
B:HIS39
|
4.3
|
25.6
|
1.0
|
CG
|
B:HIS39
|
4.3
|
25.7
|
1.0
|
CD
|
C:GLU15
|
4.5
|
48.9
|
1.0
|
NH2
|
B:ARG62
|
4.6
|
28.2
|
1.0
|
CZ
|
B:ARG62
|
4.8
|
29.3
|
1.0
|
OE1
|
C:GLU15
|
4.8
|
52.5
|
1.0
|
CD
|
B:ARG62
|
4.9
|
29.2
|
1.0
|
|
Cadmium binding site 4 out
of 28 in 1m5q
Go back to
Cadmium Binding Sites List in 1m5q
Cadmium binding site 4 out
of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cd2003
b:44.8
occ:0.95
|
OE2
|
D:GLU84
|
2.4
|
37.3
|
1.0
|
OE1
|
D:GLU84
|
2.4
|
35.5
|
1.0
|
NE2
|
C:HIS39
|
2.4
|
31.1
|
1.0
|
O
|
C:HOH144
|
2.5
|
23.3
|
1.0
|
CD
|
D:GLU84
|
2.7
|
36.8
|
1.0
|
O
|
C:HOH179
|
2.8
|
41.8
|
1.0
|
CD2
|
C:HIS39
|
3.1
|
28.7
|
1.0
|
CE1
|
C:HIS39
|
3.6
|
30.8
|
1.0
|
NE
|
C:ARG62
|
4.0
|
30.2
|
1.0
|
O
|
D:HOH2040
|
4.0
|
37.5
|
1.0
|
CG
|
D:GLU15
|
4.2
|
39.3
|
1.0
|
CG
|
D:GLU84
|
4.2
|
35.7
|
1.0
|
NH2
|
C:ARG62
|
4.3
|
30.1
|
1.0
|
CG
|
C:HIS39
|
4.4
|
31.0
|
1.0
|
ND1
|
C:HIS39
|
4.6
|
33.4
|
1.0
|
CZ
|
C:ARG62
|
4.6
|
31.5
|
1.0
|
OE1
|
D:GLU15
|
4.8
|
46.2
|
1.0
|
CD
|
C:ARG62
|
5.0
|
30.1
|
1.0
|
|
Cadmium binding site 5 out
of 28 in 1m5q
Go back to
Cadmium Binding Sites List in 1m5q
Cadmium binding site 5 out
of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cd2004
b:44.1
occ:0.98
|
OE2
|
E:GLU84
|
2.2
|
38.6
|
1.0
|
NE2
|
D:HIS39
|
2.3
|
38.5
|
1.0
|
O
|
E:HOH2029
|
2.4
|
46.7
|
1.0
|
OE1
|
E:GLU84
|
2.5
|
40.1
|
1.0
|
O
|
D:HOH2005
|
2.6
|
18.0
|
1.0
|
CD
|
E:GLU84
|
2.6
|
40.2
|
1.0
|
CD2
|
D:HIS39
|
3.1
|
34.5
|
1.0
|
CE1
|
D:HIS39
|
3.4
|
38.6
|
1.0
|
NE
|
D:ARG62
|
4.0
|
26.1
|
1.0
|
CG
|
E:GLU84
|
4.1
|
38.5
|
1.0
|
CG
|
E:GLU15
|
4.2
|
38.5
|
1.0
|
CG
|
D:HIS39
|
4.3
|
35.6
|
1.0
|
NH2
|
D:ARG62
|
4.4
|
26.5
|
1.0
|
ND1
|
D:HIS39
|
4.4
|
38.7
|
1.0
|
CZ
|
D:ARG62
|
4.7
|
28.8
|
1.0
|
CD
|
D:ARG62
|
5.0
|
26.4
|
1.0
|
OE1
|
E:GLU15
|
5.0
|
45.6
|
1.0
|
|
Cadmium binding site 6 out
of 28 in 1m5q
Go back to
Cadmium Binding Sites List in 1m5q
Cadmium binding site 6 out
of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 6 of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cd2005
b:40.6
occ:1.00
|
NE2
|
E:HIS39
|
2.2
|
27.2
|
1.0
|
O
|
F:HOH5073
|
2.5
|
38.2
|
1.0
|
OE2
|
F:GLU84
|
2.5
|
39.3
|
1.0
|
O
|
E:HOH2008
|
2.5
|
15.4
|
1.0
|
OE1
|
F:GLU84
|
2.5
|
40.7
|
1.0
|
CD
|
F:GLU84
|
2.8
|
40.9
|
1.0
|
CD2
|
E:HIS39
|
3.0
|
27.9
|
1.0
|
CE1
|
E:HIS39
|
3.3
|
30.2
|
1.0
|
O
|
F:HOH5038
|
4.1
|
34.2
|
1.0
|
NE
|
E:ARG62
|
4.1
|
31.3
|
1.0
|
CG
|
E:HIS39
|
4.2
|
30.9
|
1.0
|
CG
|
F:GLU15
|
4.2
|
32.0
|
1.0
|
CG
|
F:GLU84
|
4.3
|
38.3
|
1.0
|
ND1
|
E:HIS39
|
4.4
|
29.8
|
1.0
|
NH2
|
E:ARG62
|
4.6
|
31.2
|
1.0
|
OE2
|
F:GLU15
|
4.7
|
40.5
|
1.0
|
CZ
|
E:ARG62
|
4.9
|
32.7
|
1.0
|
|
Cadmium binding site 7 out
of 28 in 1m5q
Go back to
Cadmium Binding Sites List in 1m5q
Cadmium binding site 7 out
of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 7 of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cd2006
b:37.0
occ:0.97
|
NE2
|
F:HIS39
|
2.2
|
26.6
|
1.0
|
OE1
|
G:GLU84
|
2.3
|
42.7
|
1.0
|
O
|
G:HOH4044
|
2.3
|
31.2
|
1.0
|
O
|
F:HOH5049
|
2.5
|
32.4
|
1.0
|
OE2
|
G:GLU84
|
2.6
|
41.5
|
1.0
|
O
|
F:HOH5016
|
2.6
|
14.2
|
1.0
|
CD
|
G:GLU84
|
2.8
|
39.5
|
1.0
|
CD2
|
F:HIS39
|
3.0
|
23.3
|
1.0
|
CE1
|
F:HIS39
|
3.4
|
25.8
|
1.0
|
O
|
G:HOH4062
|
4.0
|
46.3
|
1.0
|
NE
|
F:ARG62
|
4.0
|
28.7
|
1.0
|
CG
|
G:GLU15
|
4.1
|
36.7
|
1.0
|
O
|
G:HOH4016
|
4.1
|
27.5
|
1.0
|
CG
|
F:HIS39
|
4.2
|
25.8
|
1.0
|
CG
|
G:GLU84
|
4.3
|
36.5
|
1.0
|
NH2
|
F:ARG62
|
4.3
|
27.1
|
1.0
|
ND1
|
F:HIS39
|
4.4
|
26.2
|
1.0
|
O
|
F:HOH5056
|
4.7
|
37.8
|
1.0
|
CZ
|
F:ARG62
|
4.7
|
30.6
|
1.0
|
OE1
|
G:GLU15
|
4.7
|
44.0
|
1.0
|
O
|
G:HOH4028
|
4.8
|
37.0
|
1.0
|
CD
|
G:GLU15
|
5.0
|
41.8
|
1.0
|
|
Cadmium binding site 8 out
of 28 in 1m5q
Go back to
Cadmium Binding Sites List in 1m5q
Cadmium binding site 8 out
of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 8 of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Cd2008
b:38.6
occ:0.94
|
NE2
|
H:HIS39
|
2.4
|
29.2
|
1.0
|
O
|
I:HOH5064
|
2.5
|
31.4
|
1.0
|
O
|
H:HOH5061
|
2.6
|
38.0
|
1.0
|
O3
|
H:GOL4002
|
2.6
|
52.4
|
1.0
|
CD2
|
H:HIS39
|
3.3
|
26.4
|
1.0
|
C3
|
H:GOL4002
|
3.3
|
54.6
|
1.0
|
CE1
|
H:HIS39
|
3.4
|
27.1
|
1.0
|
OE1
|
I:GLU15
|
3.6
|
45.6
|
1.0
|
NZ
|
G:LYS91
|
4.1
|
39.3
|
1.0
|
C2
|
H:GOL4002
|
4.2
|
56.1
|
1.0
|
CG
|
H:HIS39
|
4.5
|
25.1
|
1.0
|
NH1
|
H:ARG62
|
4.5
|
29.0
|
1.0
|
ND1
|
H:HIS39
|
4.5
|
27.5
|
1.0
|
O
|
H:HOH5034
|
4.7
|
37.6
|
1.0
|
CE
|
G:LYS91
|
4.7
|
37.6
|
1.0
|
CD
|
I:GLU15
|
4.7
|
43.0
|
1.0
|
O2
|
H:GOL4002
|
4.8
|
57.8
|
1.0
|
CD
|
H:ARG62
|
4.8
|
23.6
|
1.0
|
O
|
G:HOH4040
|
4.8
|
40.9
|
1.0
|
|
Cadmium binding site 9 out
of 28 in 1m5q
Go back to
Cadmium Binding Sites List in 1m5q
Cadmium binding site 9 out
of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 9 of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Cd2014
b:40.8
occ:0.97
|
NE2
|
N:HIS39
|
2.3
|
25.5
|
1.0
|
OE2
|
H:GLU15
|
2.6
|
33.1
|
1.0
|
O
|
N:HOH5038
|
2.7
|
30.1
|
1.0
|
CD2
|
N:HIS39
|
3.1
|
23.2
|
1.0
|
CD
|
H:GLU15
|
3.2
|
37.6
|
1.0
|
OE1
|
H:GLU15
|
3.2
|
38.6
|
1.0
|
CE1
|
N:HIS39
|
3.4
|
26.4
|
1.0
|
NH1
|
N:ARG62
|
4.3
|
23.7
|
1.0
|
CG
|
N:HIS39
|
4.3
|
24.3
|
1.0
|
ND1
|
N:HIS39
|
4.4
|
25.8
|
1.0
|
CG
|
H:GLU15
|
4.5
|
33.4
|
1.0
|
O
|
A:HOH4049
|
4.6
|
37.3
|
1.0
|
CD
|
N:ARG62
|
4.8
|
26.5
|
1.0
|
O
|
A:HOH4052
|
4.9
|
40.0
|
1.0
|
|
Cadmium binding site 10 out
of 28 in 1m5q
Go back to
Cadmium Binding Sites List in 1m5q
Cadmium binding site 10 out
of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 10 of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Cd2009
b:46.1
occ:1.06
|
NE2
|
I:HIS39
|
2.3
|
32.9
|
1.0
|
OE1
|
J:GLU15
|
2.8
|
49.7
|
1.0
|
O
|
I:HOH5045
|
2.8
|
40.4
|
1.0
|
OE2
|
J:GLU15
|
3.0
|
50.2
|
1.0
|
CD
|
J:GLU15
|
3.1
|
46.4
|
1.0
|
CD2
|
I:HIS39
|
3.2
|
29.3
|
1.0
|
CE1
|
I:HIS39
|
3.3
|
32.6
|
1.0
|
CG
|
J:GLU15
|
4.3
|
41.5
|
1.0
|
NH1
|
I:ARG62
|
4.4
|
32.5
|
1.0
|
CG
|
I:HIS39
|
4.4
|
30.5
|
1.0
|
ND1
|
I:HIS39
|
4.4
|
32.9
|
1.0
|
O
|
F:HOH5053
|
4.6
|
31.6
|
1.0
|
NZ
|
F:LYS91
|
4.9
|
43.3
|
1.0
|
CD
|
I:ARG62
|
4.9
|
30.7
|
1.0
|
|
Reference:
C.Mura,
M.Phillips,
A.Kozhukhovsky,
D.Eisenberg.
Structure and Assembly of An Augmented Sm-Like Archaeal Protein 14-Mer Proc.Natl.Acad.Sci.Usa V. 100 4539 2003.
ISSN: ISSN 0027-8424
PubMed: 12668760
DOI: 10.1073/PNAS.0538042100
Page generated: Fri Jul 19 13:50:44 2024
|