Cadmium in PDB 8wxd: Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis
Protein crystallography data
The structure of Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis, PDB code: 8wxd
was solved by
S.Yadav,
P.Parijat,
V.Krishnan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
58.35 /
2.00
|
Space group
|
P 2 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.593,
89.949,
216.408,
90,
90,
90
|
R / Rfree (%)
|
20.9 /
25.9
|
Other elements in 8wxd:
The structure of Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis also contains other interesting chemical elements:
Cadmium Binding Sites:
The binding sites of Cadmium atom in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis
(pdb code 8wxd). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the
Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis, PDB code: 8wxd:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
Cadmium binding site 1 out
of 6 in 8wxd
Go back to
Cadmium Binding Sites List in 8wxd
Cadmium binding site 1 out
of 6 in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis
 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 Shaft Pilin Pila From Streptococcus Sanguinis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd507
b:25.4
occ:0.85
|
OE2
|
A:GLU102
|
2.3
|
40.2
|
1.0
|
NA
|
A:NA504
|
2.4
|
23.9
|
1.0
|
NE2
|
A:HIS75
|
2.4
|
39.9
|
1.0
|
OE1
|
A:GLU102
|
2.6
|
35.4
|
1.0
|
CD
|
A:GLU102
|
2.8
|
33.9
|
1.0
|
CE1
|
A:HIS75
|
3.1
|
38.7
|
1.0
|
CD2
|
A:HIS75
|
3.7
|
36.8
|
1.0
|
CG
|
A:GLU102
|
4.2
|
30.3
|
1.0
|
ND1
|
A:HIS75
|
4.4
|
37.5
|
1.0
|
CG
|
A:HIS75
|
4.6
|
35.7
|
1.0
|
CE1
|
A:PHE76
|
4.9
|
25.4
|
1.0
|
|
Cadmium binding site 2 out
of 6 in 8wxd
Go back to
Cadmium Binding Sites List in 8wxd
Cadmium binding site 2 out
of 6 in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis
 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 Shaft Pilin Pila From Streptococcus Sanguinis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd508
b:31.4
occ:1.00
|
CL
|
A:CL510
|
2.3
|
32.5
|
1.0
|
ND1
|
A:HIS147
|
2.5
|
39.0
|
1.0
|
OG
|
A:SER38
|
2.5
|
34.6
|
1.0
|
NE2
|
A:HIS41
|
2.5
|
37.0
|
1.0
|
CE1
|
A:HIS147
|
3.3
|
39.3
|
1.0
|
CE1
|
A:HIS41
|
3.3
|
34.0
|
1.0
|
CB
|
A:SER38
|
3.4
|
37.1
|
1.0
|
CG
|
A:HIS147
|
3.6
|
36.0
|
1.0
|
CD2
|
A:HIS41
|
3.6
|
36.7
|
1.0
|
CB
|
A:HIS147
|
3.9
|
32.2
|
1.0
|
CA
|
A:HIS147
|
4.0
|
30.1
|
1.0
|
O
|
A:GLY146
|
4.3
|
28.9
|
1.0
|
O
|
A:GLU39
|
4.4
|
39.7
|
1.0
|
NE2
|
A:HIS147
|
4.4
|
38.5
|
1.0
|
ND1
|
A:HIS41
|
4.5
|
33.2
|
1.0
|
CA
|
A:SER38
|
4.6
|
39.6
|
1.0
|
CD2
|
A:HIS147
|
4.6
|
36.8
|
1.0
|
N
|
A:ALA148
|
4.6
|
26.7
|
1.0
|
N
|
A:SER38
|
4.6
|
38.1
|
1.0
|
CG
|
A:HIS41
|
4.7
|
36.3
|
1.0
|
C
|
A:HIS147
|
4.9
|
28.2
|
1.0
|
N
|
A:HIS147
|
5.0
|
30.1
|
1.0
|
|
Cadmium binding site 3 out
of 6 in 8wxd
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Cadmium Binding Sites List in 8wxd
Cadmium binding site 3 out
of 6 in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis
 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 Shaft Pilin Pila From Streptococcus Sanguinis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd509
b:39.0
occ:0.38
|
ND1
|
A:HIS47
|
2.5
|
30.4
|
1.0
|
CG
|
A:HIS47
|
3.4
|
28.0
|
1.0
|
CE1
|
A:HIS47
|
3.5
|
29.6
|
1.0
|
CB
|
A:HIS47
|
3.5
|
27.5
|
1.0
|
CD
|
A:PRO66
|
3.8
|
43.1
|
1.0
|
CD
|
A:LYS128
|
3.8
|
66.8
|
1.0
|
CG
|
A:PRO66
|
4.0
|
45.1
|
1.0
|
CG
|
A:LYS128
|
4.2
|
61.4
|
1.0
|
CD2
|
A:HIS47
|
4.5
|
27.1
|
1.0
|
NE2
|
A:HIS47
|
4.6
|
27.8
|
1.0
|
CB
|
A:LYS128
|
4.8
|
55.0
|
1.0
|
OH
|
A:TYR132
|
4.8
|
33.0
|
1.0
|
CE
|
A:LYS128
|
4.9
|
72.2
|
1.0
|
CA
|
A:GLY111
|
4.9
|
50.2
|
1.0
|
|
Cadmium binding site 4 out
of 6 in 8wxd
Go back to
Cadmium Binding Sites List in 8wxd
Cadmium binding site 4 out
of 6 in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis
 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 Shaft Pilin Pila From Streptococcus Sanguinis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd504
b:42.6
occ:0.46
|
ND1
|
B:HIS47
|
2.5
|
40.5
|
1.0
|
CE1
|
B:HIS47
|
3.3
|
41.4
|
1.0
|
CG
|
B:HIS47
|
3.3
|
37.3
|
1.0
|
CB
|
B:HIS47
|
3.6
|
35.5
|
1.0
|
OH
|
B:TYR132
|
3.8
|
40.3
|
1.0
|
CD
|
B:LYS128
|
3.8
|
72.5
|
1.0
|
CE
|
B:LYS128
|
3.9
|
77.1
|
1.0
|
CG
|
B:LYS128
|
4.1
|
68.6
|
1.0
|
CB
|
B:LYS128
|
4.3
|
62.5
|
1.0
|
NE2
|
B:HIS47
|
4.4
|
40.1
|
1.0
|
CD2
|
B:HIS47
|
4.4
|
37.7
|
1.0
|
CE2
|
B:TYR132
|
4.5
|
35.7
|
1.0
|
CZ
|
B:TYR132
|
4.6
|
36.7
|
1.0
|
CD
|
B:PRO66
|
4.8
|
45.7
|
1.0
|
|
Cadmium binding site 5 out
of 6 in 8wxd
Go back to
Cadmium Binding Sites List in 8wxd
Cadmium binding site 5 out
of 6 in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis
 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 Shaft Pilin Pila From Streptococcus Sanguinis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd505
b:39.6
occ:0.78
|
ND1
|
B:HIS75
|
2.5
|
41.8
|
1.0
|
CE1
|
B:HIS75
|
3.1
|
40.4
|
1.0
|
CG
|
B:HIS75
|
3.7
|
38.2
|
1.0
|
CB
|
B:HIS75
|
4.1
|
37.8
|
1.0
|
CA
|
B:HIS75
|
4.2
|
38.0
|
1.0
|
NE2
|
B:HIS75
|
4.4
|
38.2
|
1.0
|
O
|
B:HIS75
|
4.5
|
36.0
|
1.0
|
CD2
|
B:HIS75
|
4.6
|
37.5
|
1.0
|
C
|
B:HIS75
|
4.9
|
35.1
|
1.0
|
|
Cadmium binding site 6 out
of 6 in 8wxd
Go back to
Cadmium Binding Sites List in 8wxd
Cadmium binding site 6 out
of 6 in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis
 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 Shaft Pilin Pila From Streptococcus Sanguinis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd506
b:31.1
occ:1.00
|
O
|
B:HOH617
|
2.4
|
13.1
|
1.0
|
OG
|
B:SER38
|
2.4
|
37.7
|
1.0
|
NE2
|
B:HIS41
|
2.4
|
37.2
|
1.0
|
ND1
|
B:HIS147
|
2.5
|
31.1
|
1.0
|
CE1
|
B:HIS41
|
3.2
|
35.7
|
1.0
|
CE1
|
B:HIS147
|
3.3
|
31.8
|
1.0
|
CG
|
B:HIS147
|
3.5
|
30.3
|
1.0
|
CB
|
B:SER38
|
3.5
|
38.7
|
1.0
|
CD2
|
B:HIS41
|
3.6
|
37.5
|
1.0
|
CB
|
B:HIS147
|
3.8
|
28.5
|
1.0
|
CA
|
B:HIS147
|
3.9
|
26.8
|
1.0
|
O
|
B:GLY146
|
4.3
|
26.9
|
1.0
|
O
|
B:GLU39
|
4.4
|
40.0
|
1.0
|
ND1
|
B:HIS41
|
4.4
|
32.7
|
1.0
|
NE2
|
B:HIS147
|
4.5
|
32.9
|
1.0
|
N
|
B:ALA148
|
4.5
|
23.5
|
1.0
|
CD2
|
B:HIS147
|
4.6
|
31.5
|
1.0
|
CG
|
B:HIS41
|
4.6
|
34.8
|
1.0
|
CA
|
B:SER38
|
4.6
|
40.2
|
1.0
|
C
|
B:HIS147
|
4.8
|
24.7
|
1.0
|
N
|
B:SER38
|
4.8
|
39.5
|
1.0
|
N
|
B:HIS147
|
4.8
|
27.0
|
1.0
|
C
|
B:GLY146
|
5.0
|
28.1
|
1.0
|
|
Reference:
S.Yadav,
P.Parijat,
V.Krishnan.
Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis To Be Published.
Page generated: Thu Jul 10 15:57:48 2025
|