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Cadmium in PDB 3vrc: Crystal Structure of Cytochrome C' From Thermochromatium Tepidum

Protein crystallography data

The structure of Crystal Structure of Cytochrome C' From Thermochromatium Tepidum, PDB code: 3vrc was solved by Y.Hirano, Y.Kimura, H.Suzuki, K.Miki, Z.-Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.310, 57.189, 54.225, 90.00, 94.81, 90.00
R / Rfree (%) 12.9 / 15.3

Other elements in 3vrc:

The structure of Crystal Structure of Cytochrome C' From Thermochromatium Tepidum also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Chlorine (Cl) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Cytochrome C' From Thermochromatium Tepidum (pdb code 3vrc). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Crystal Structure of Cytochrome C' From Thermochromatium Tepidum, PDB code: 3vrc:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 3vrc

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Cadmium binding site 1 out of 9 in the Crystal Structure of Cytochrome C' From Thermochromatium Tepidum


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Cytochrome C' From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:12.4
occ:0.80
 OE2 A:GLU82 2.2 17.7 1.0
CL A:CL206 2.5 18.5 1.0
OE1 A:GLU82 2.8 15.2 1.0
CD A:GLU82 2.9 13.6 1.0
O A:HOH460 4.3 25.3 1.0
C3 A:PEG207 4.3 18.9 1.0
CG A:GLU82 4.4 13.2 1.0
O A:HOH422 4.4 38.1 1.0
C4 A:PEG207 4.6 27.9 1.0

Cadmium binding site 2 out of 9 in 3vrc

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Cadmium binding site 2 out of 9 in the Crystal Structure of Cytochrome C' From Thermochromatium Tepidum


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Cytochrome C' From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:13.0
occ:0.70
 O A:HOH325 2.2 19.4 1.0
OD1 A:ASP131 2.3 13.8 1.0
O A:HOH320 2.3 15.0 1.0
O A:HOH501 2.3 14.6 0.5
O A:HOH319 2.4 15.1 1.0
O A:HOH501 2.4 13.4 0.5
O A:HOH371 2.5 13.3 1.0
CG A:ASP131 3.3 11.8 1.0
OD2 A:ASP131 3.6 12.8 1.0
O A:HOH348 4.1 17.1 0.7
O A:HOH463 4.2 24.2 0.5
CA A:GLN126 4.2 11.6 1.0
O A:HIS125 4.2 10.6 1.0
O A:GLN126 4.4 13.8 1.0
OXT A:ASP131 4.4 15.8 1.0
O A:ARG129 4.4 12.2 1.0
C A:ASP131 4.5 13.3 1.0
CB A:ASP131 4.6 12.8 1.0
O A:HOH387 4.7 16.3 0.5
C A:GLN126 4.7 11.2 1.0
C A:HIS125 4.7 9.4 1.0
N A:GLN126 4.8 10.3 1.0
O A:ASP131 4.8 15.1 1.0
O A:HOH523 4.8 19.2 0.3
O A:HOH463 4.8 20.8 0.5
CG A:GLN126 4.8 17.5 1.0
CA A:ASP131 4.9 13.0 1.0
N A:ASP131 5.0 12.2 1.0

Cadmium binding site 3 out of 9 in 3vrc

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Cadmium binding site 3 out of 9 in the Crystal Structure of Cytochrome C' From Thermochromatium Tepidum


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 Cytochrome C' From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:13.6
occ:0.50
 O A:HOH502 2.1 19.4 0.7
OD1 A:ASP116 2.3 20.5 1.0
O A:HOH337 2.3 17.0 1.0
O A:HOH402 2.7 29.5 1.0
CG A:ASP116 3.3 16.9 1.0
OD2 A:ASP116 3.5 19.3 1.0
O A:HOH388 3.7 24.5 1.0
O A:HOH462 4.0 31.6 0.5
O A:HOH384 4.3 24.9 1.0
O A:HOH312 4.4 12.3 1.0
O A:SER112 4.6 11.2 1.0
CB A:ASP116 4.6 14.5 1.0
N A:ASP116 4.6 11.4 1.0
O A:HOH466 4.7 28.1 0.5
CB A:ALA115 4.7 15.1 1.0
CA A:ASP116 4.8 11.7 1.0

Cadmium binding site 4 out of 9 in 3vrc

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Cadmium binding site 4 out of 9 in the Crystal Structure of Cytochrome C' From Thermochromatium Tepidum


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 Cytochrome C' From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:17.7
occ:0.30
 OE1 A:GLU76 2.2 24.2 1.0
OE2 A:GLU76 2.2 27.1 1.0
O A:HOH382 2.4 21.5 1.0
O A:HOH457 2.5 17.5 0.3
CD A:GLU76 2.5 26.5 1.0
CE A:LYS74 4.0 19.4 0.5
CG A:GLU76 4.1 29.4 1.0
CD A:PRO75 4.2 22.1 1.0
CD A:LYS74 4.4 17.2 0.5
CB A:LYS74 4.6 12.9 0.5
CG A:LYS74 4.7 14.1 0.5
N A:GLU76 4.8 18.2 1.0
O A:HOH468 4.8 26.7 1.0
CB A:LYS74 4.8 16.0 0.5
CG A:LYS74 4.8 14.2 0.5
N A:PRO75 4.9 16.9 1.0
CB A:GLU76 4.9 24.6 1.0
CG A:PRO75 5.0 27.3 1.0
NZ A:LYS74 5.0 22.4 0.5
CB A:PRO75 5.0 22.4 1.0

Cadmium binding site 5 out of 9 in 3vrc

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Cadmium binding site 5 out of 9 in the Crystal Structure of Cytochrome C' From Thermochromatium Tepidum


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 Cytochrome C' From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:17.8
occ:0.30
 O A:HOH486 1.4 20.0 0.5
OE1 A:GLU7 2.3 20.7 1.0
OE2 A:GLU7 2.3 26.6 1.0
CD A:GLU7 2.7 20.3 1.0
O A:HOH499 3.0 8.3 0.5
O A:HOH530 3.6 9.2 0.3
CG A:GLU7 4.2 16.0 1.0
O A:HOH412 4.4 28.5 1.0
O A:ASP2 4.4 28.3 1.0
N A:SER4 4.7 14.7 1.0
CA A:LEU3 4.8 16.0 1.0

Cadmium binding site 6 out of 9 in 3vrc

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Cadmium binding site 6 out of 9 in the Crystal Structure of Cytochrome C' From Thermochromatium Tepidum


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 Cytochrome C' From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd202

b:18.5
occ:0.30
 OD1 B:ASN108 1.5 28.2 0.5
O B:HOH518 1.6 15.0 0.3
O B:HOH302 1.6 13.2 0.5
O B:HOH311 2.5 20.6 0.5
O B:HOH424 2.7 23.6 0.5
CG B:ASN108 2.8 18.1 0.5
O B:HOH311 3.1 9.4 0.5
ND2 B:ASN108 3.6 22.6 0.5
O B:HOH424 3.9 18.0 0.5
CB B:ASN108 3.9 16.8 0.5
O B:HOH470 4.0 32.8 1.0
CB B:ASN108 4.2 14.3 0.5
O B:HOH394 4.2 16.2 0.5
O B:HOH429 4.2 14.7 0.5
O B:HOH529 4.4 19.6 0.3
O B:HOH380 4.5 12.3 0.5
ND2 B:ASN108 4.6 19.3 0.5
CG B:ASN108 4.9 17.4 0.5
O B:HOH472 4.9 24.0 1.0

Cadmium binding site 7 out of 9 in 3vrc

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Cadmium binding site 7 out of 9 in the Crystal Structure of Cytochrome C' From Thermochromatium Tepidum


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 Cytochrome C' From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd203

b:20.6
occ:0.30
 O B:HOH523 1.3 11.1 0.3
O B:HOH542 1.5 16.9 0.3
OD2 B:ASP37 2.4 22.2 1.0
O B:HOH435 2.4 31.5 1.0
OD1 B:ASP37 2.6 22.6 1.0
CG B:ASP37 2.8 16.7 1.0
O B:HOH310 4.2 15.0 1.0
CB B:ASP37 4.2 13.1 1.0
NH1 B:ARG40 4.3 20.8 0.8
O B:HOH524 4.4 16.0 0.3

Cadmium binding site 8 out of 9 in 3vrc

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Cadmium binding site 8 out of 9 in the Crystal Structure of Cytochrome C' From Thermochromatium Tepidum


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Cytochrome C' From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd204

b:45.4
occ:0.50
 O B:HOH473 1.3 78.9 0.3
O B:HOH378 2.1 6.0 0.3
O B:HOH379 2.3 21.9 1.0
O B:HOH537 2.4 15.4 0.3
O B:HOH378 2.7 8.5 0.3
O B:HOH344 2.9 23.2 1.0
OD1 B:ASP131 3.0 70.6 1.0
OD2 B:ASP131 3.5 92.1 1.0
CG B:ASP131 3.6 61.1 1.0
O B:HOH345 3.7 19.7 1.0
O B:HOH333 3.9 18.5 1.0
O B:HOH506 4.0 27.2 0.3
CA B:GLN126 4.2 13.7 1.0
CG B:GLN126 4.5 20.6 1.0
O B:HIS125 4.6 12.4 1.0
O B:GLN126 4.6 16.0 1.0
N B:GLN126 4.9 12.1 1.0
C B:GLN126 4.9 14.6 1.0
CB B:GLN126 4.9 17.4 1.0
O B:ARG129 4.9 14.7 1.0
C B:HIS125 5.0 12.9 1.0

Cadmium binding site 9 out of 9 in 3vrc

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Cadmium binding site 9 out of 9 in the Crystal Structure of Cytochrome C' From Thermochromatium Tepidum


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 Cytochrome C' From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd205

b:30.0
occ:0.30
 O B:HOH474 2.4 35.8 1.0
O B:HOH437 2.4 37.2 1.0
OD1 B:ASP63 2.6 29.7 1.0
OD2 B:ASP63 2.7 39.8 1.0
CG B:ASP63 3.0 31.5 1.0
NZ B:LYS64 4.0 57.9 1.0
N B:GLY61 4.3 22.8 1.0
CA B:GLY61 4.4 23.8 1.0
CB B:ASP63 4.5 30.3 1.0
CG B:LYS64 4.5 43.0 1.0
CD B:LYS64 4.6 53.2 1.0
CE B:LYS64 4.9 56.0 1.0
O B:HOH495 4.9 38.6 0.5

Reference:

Y.Hirano, Y.Kimura, H.Suzuki, K.Miki, Z.-Y.Wang. Structure Analysis and Comparative Characterization of the Cytochrome C' and Flavocytochrome C From Thermophilic Purple Photosynthetic Bacterium Thermochromatium Tepidum Biochemistry V. 51 6556 2012.
ISSN: ISSN 0006-2960
PubMed: 22827326
DOI: 10.1021/BI3005522
Page generated: Thu Jul 10 13:07:57 2025

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