Iron in PDB 3b51: Ni,Fe-Codh-600 Mv State

All present enzymatic activity of Ni,Fe-Codh-600 Mv State:
1.2.99.2;

The structure of Ni,Fe-Codh-600 Mv State, PDB code: 3b51 was solved by J.H.Jeoung, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.90 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.750, 74.660, 70.650, 90.00, 111.28, 90.00
R / Rfree (%)	15.7 / 18.3

The structure of Ni,Fe-Codh-600 Mv State also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Iron atom in the Ni,Fe-Codh-600 Mv State (pdb code 3b51). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 11 binding sites of Iron where determined in the Ni,Fe-Codh-600 Mv State, PDB code: 3b51:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 11 in the Ni,Fe-Codh-600 Mv State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ni,Fe-Codh-600 Mv State within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe1001 b:5.1 occ:1.00 FE1 X:SF41001 0.0 5.1 1.0 S3 X:SF41001 2.3 4.3 1.0 SG X:CYS56 2.3 4.9 1.0 S4 X:SF41001 2.3 4.3 1.0 S2 X:SF41001 2.3 4.4 1.0 FE3 X:SF41001 2.6 4.8 1.0 FE2 X:SF41001 2.7 5.1 1.0 FE4 X:SF41001 2.7 5.2 1.0 CB X:CYS56 3.1 5.8 1.0 S1 X:SF41001 3.9 4.3 1.0 N X:ILE69 4.0 5.4 1.0 CA X:CYS56 4.4 5.3 1.0 CB X:ILE69 4.4 4.7 1.0 CA X:GLY54 4.4 5.5 1.0 N X:CYS56 4.4 5.7 1.0 N X:GLY54 4.5 5.3 1.0 O X:CYS48 4.5 5.4 1.0 SG X:CYS51 4.6 4.7 1.0 SG X:CYS48 4.7 4.5 1.0 CB X:CYS48 4.7 5.7 1.0 CA X:GLY68 4.7 5.3 1.0 N X:CYS70 4.7 4.8 1.0 CA X:ILE69 4.7 5.1 1.0 SG X:CYS70 4.8 4.6 1.0 C X:GLY68 4.8 5.0 1.0 CG1 X:ILE69 4.9 4.8 1.0 C X:GLN53 5.0 5.6 1.0

Iron binding site 2 out of 11 in the Ni,Fe-Codh-600 Mv State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ni,Fe-Codh-600 Mv State within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe1001 b:5.1 occ:1.00 FE2 X:SF41001 0.0 5.1 1.0 SG X:CYS51 2.3 4.7 1.0 S4 X:SF41001 2.3 4.3 1.0 S3 X:SF41001 2.3 4.3 1.0 S1 X:SF41001 2.3 4.3 1.0 FE3 X:SF41001 2.7 4.8 1.0 FE1 X:SF41001 2.7 5.1 1.0 FE4 X:SF41001 2.8 5.2 1.0 CB X:CYS51 3.3 3.9 1.0 N X:CYS51 3.6 4.1 1.0 CA X:CYS51 3.9 4.2 1.0 S2 X:SF41001 3.9 4.4 1.0 O X:HOH1758 4.0 16.5 1.0 O X:CYS51 4.3 4.8 1.0 C X:CYS51 4.3 4.7 1.0 C X:HIS50 4.3 4.6 1.0 CG X:MET199 4.4 5.2 1.0 N X:GLY54 4.4 5.3 1.0 CB X:GLN53 4.6 6.1 1.0 N X:HIS50 4.8 5.0 1.0 SG X:CYS70 4.8 4.6 1.0 SG X:CYS56 4.8 4.9 1.0 CB X:MET199 4.8 5.0 1.0 SG X:CYS48 4.8 4.5 1.0 N X:GLN53 4.8 5.0 1.0 O X:HIS50 4.9 4.3 1.0 NE2 X:GLN53 4.9 8.2 1.0 CA X:GLY54 5.0 5.5 1.0 CA X:HIS50 5.0 4.5 1.0

Iron binding site 3 out of 11 in the Ni,Fe-Codh-600 Mv State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ni,Fe-Codh-600 Mv State within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe1001 b:4.8 occ:1.00 FE3 X:SF41001 0.0 4.8 1.0 S4 X:SF41001 2.3 4.3 1.0 S1 X:SF41001 2.3 4.3 1.0 S2 X:SF41001 2.3 4.4 1.0 SG X:CYS48 2.3 4.5 1.0 FE1 X:SF41001 2.6 5.1 1.0 FE2 X:SF41001 2.7 5.1 1.0 FE4 X:SF41001 2.7 5.2 1.0 CB X:CYS48 3.2 5.7 1.0 NH2 X:ARG80 3.6 6.2 1.0 S3 X:SF41001 3.9 4.3 1.0 N X:HIS50 4.0 5.0 1.0 C X:CYS48 4.2 5.0 1.0 O X:CYS48 4.2 5.4 1.0 CB X:HIS50 4.3 4.7 1.0 CA X:CYS48 4.3 4.8 1.0 N X:CYS51 4.5 4.1 1.0 CA X:HIS50 4.5 4.5 1.0 N X:ARG49 4.6 4.8 1.0 CB X:CYS56 4.6 5.8 1.0 SG X:CYS56 4.6 4.9 1.0 C X:HIS50 4.7 4.6 1.0 CZ X:ARG80 4.8 5.8 1.0 SG X:CYS70 4.9 4.6 1.0 SG X:CYS51 4.9 4.7 1.0 C X:ARG49 5.0 5.0 1.0 CG X:HIS50 5.0 5.0 1.0

Iron binding site 4 out of 11 in the Ni,Fe-Codh-600 Mv State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ni,Fe-Codh-600 Mv State within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe1001 b:5.2 occ:1.00 FE4 X:SF41001 0.0 5.2 1.0 S2 X:SF41001 2.3 4.4 1.0 S1 X:SF41001 2.3 4.3 1.0 SG X:CYS70 2.3 4.6 1.0 S3 X:SF41001 2.3 4.3 1.0 FE3 X:SF41001 2.7 4.8 1.0 FE1 X:SF41001 2.7 5.1 1.0 FE2 X:SF41001 2.8 5.1 1.0 CB X:CYS70 3.3 4.8 1.0 N X:CYS70 3.8 4.8 1.0 S4 X:SF41001 3.9 4.3 1.0 NH2 X:ARG80 4.1 6.2 1.0 O X:HOH1006 4.1 4.9 1.0 CA X:CYS70 4.2 5.0 1.0 CB X:ALA72 4.3 6.4 1.0 O X:HOH1758 4.4 16.5 1.0 N X:ILE69 4.6 5.4 1.0 CG X:MET199 4.6 5.2 1.0 SG X:CYS51 4.7 4.7 1.0 SG X:CYS56 4.8 4.9 1.0 SG X:CYS48 4.8 4.5 1.0 C X:ILE69 5.0 4.6 1.0 C X:GLY68 5.0 5.0 1.0

Iron binding site 5 out of 11 in the Ni,Fe-Codh-600 Mv State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Ni,Fe-Codh-600 Mv State within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe1002 b:5.8 occ:1.00 FE1 X:FES1002 0.0 5.8 1.0 S1 X:FES1002 2.2 5.5 1.0 S2 X:FES1002 2.2 5.0 1.0 SG X:CYS47 2.3 6.2 1.0 FE2 X:FES1002 2.6 6.3 1.0 CB X:CYS47 3.2 4.9 1.0 O X:HOH1079 3.6 5.2 1.0 CA X:CYS47 4.6 4.7 1.0 SG X:CYS39 4.7 5.9 1.0 CB X:PHE41 4.8 5.9 1.0 N X:GLY42 5.0 6.1 1.0

Iron binding site 6 out of 11 in the Ni,Fe-Codh-600 Mv State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Ni,Fe-Codh-600 Mv State within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe1002 b:6.3 occ:1.00 FE2 X:FES1002 0.0 6.3 1.0 S2 X:FES1002 2.2 5.0 1.0 S1 X:FES1002 2.3 5.5 1.0 SG X:CYS39 2.3 5.9 1.0 FE1 X:FES1002 2.6 5.8 1.0 CB X:CYS39 3.2 6.4 1.0 N X:GLY42 4.1 6.1 1.0 CB X:PHE41 4.3 5.9 1.0 O X:HOH1699 4.4 34.8 1.0 CA X:CYS39 4.6 6.4 1.0 CA X:GLY42 4.7 6.8 1.0 SG X:CYS47 4.7 6.2 1.0 CD2 X:PHE41 4.8 7.9 1.0 C X:PHE41 5.0 6.2 1.0 CB X:CYS47 5.0 4.9 1.0

Iron binding site 7 out of 11 in the Ni,Fe-Codh-600 Mv State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Ni,Fe-Codh-600 Mv State within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe1003 b:7.9 occ:0.80 FE1 X:WCC1003 0.0 7.9 0.8 S3 X:WCC1003 2.2 8.6 0.8 S2 X:WCC1003 2.2 8.0 0.8 SG X:CYS333 2.3 7.8 1.0 S4 X:WCC1003 2.3 8.4 0.8 FE3 X:WCC1003 2.4 8.3 0.8 FE4 X:WCC1003 2.5 9.3 0.8 CB X:CYS333 3.1 7.3 1.0 FE X:FE21004 3.2 10.8 0.6 NI X:WCC1003 3.2 10.8 0.6 FE X:FE21004 3.3 8.2 0.3 S1 X:WCC1003 3.6 7.6 0.8 NE2 X:HIS261 3.9 15.5 1.0 O X:HOH1887 3.9 10.2 0.6 CE1 X:HIS261 4.0 12.8 1.0 NZ X:LYS563 4.1 7.5 1.0 CA X:CYS333 4.5 7.2 1.0 SG X:CYS446 4.5 7.8 1.0 O X:HOH1120 4.6 9.4 1.0 CE X:LYS563 4.7 6.8 1.0 CE X:MET560 4.8 7.3 1.0 SG X:CYS476 4.8 13.0 1.0 CB X:HIS561 4.9 4.7 1.0 SG X:CYS294 5.0 10.9 1.0

Iron binding site 8 out of 11 in the Ni,Fe-Codh-600 Mv State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Ni,Fe-Codh-600 Mv State within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe1003 b:8.3 occ:0.80 FE3 X:WCC1003 0.0 8.3 0.8 S4 X:WCC1003 2.2 8.4 0.8 S1 X:WCC1003 2.2 7.6 0.8 S2 X:WCC1003 2.3 8.0 0.8 SG X:CYS446 2.4 7.8 1.0 FE1 X:WCC1003 2.4 7.9 0.8 FE4 X:WCC1003 2.6 9.3 0.8 NI X:WCC1003 2.6 10.8 0.6 CB X:CYS446 3.1 6.3 1.0 CA X:CYS446 3.4 6.8 1.0 N X:CYS446 3.6 6.6 1.0 S3 X:WCC1003 3.9 8.6 0.8 C X:GLY445 4.0 7.0 1.0 FE X:FE21004 4.1 8.2 0.3 SG X:CYS333 4.3 7.8 1.0 CA X:GLY445 4.5 6.5 1.0 CB X:HIS561 4.5 4.7 1.0 FE X:FE21004 4.5 10.8 0.6 O X:GLY445 4.6 8.0 1.0 SG X:CYS526 4.6 9.8 1.0 CE X:MET560 4.7 7.3 1.0 SG X:CYS476 4.7 13.0 1.0 O X:HOH1887 4.8 10.2 0.6 CB X:CYS476 4.9 9.6 1.0 C X:CYS446 4.9 6.1 1.0

Iron binding site 9 out of 11 in the Ni,Fe-Codh-600 Mv State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Ni,Fe-Codh-600 Mv State within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe1003 b:9.3 occ:0.80 FE4 X:WCC1003 0.0 9.3 0.8 S1 X:WCC1003 2.2 7.6 0.8 S2 X:WCC1003 2.2 8.0 0.8 S3 X:WCC1003 2.3 8.6 0.8 SG X:CYS476 2.3 13.0 1.0 FE1 X:WCC1003 2.5 7.9 0.8 FE3 X:WCC1003 2.6 8.3 0.8 FE X:FE21004 3.1 8.2 0.3 CB X:CYS476 3.3 9.6 1.0 NI X:WCC1003 3.4 10.8 0.6 O X:HOH1267 3.9 14.1 1.0 FE X:FE21004 3.9 10.8 0.6 S4 X:WCC1003 3.9 8.4 0.8 N X:CYS476 4.0 7.2 1.0 CA X:CYS476 4.2 8.0 1.0 CA X:CYS446 4.3 6.8 1.0 CB X:SER312 4.4 8.4 1.0 SG X:CYS294 4.5 10.9 1.0 OG X:SER312 4.5 9.3 1.0 CB X:CYS446 4.6 6.3 1.0 SG X:CYS526 4.7 9.8 1.0 SG X:CYS295 4.7 5.6 0.3 SG X:CYS446 4.7 7.8 1.0 SG X:CYS333 4.7 7.8 1.0 O X:GLY445 4.8 8.0 1.0 N X:CYS446 4.8 6.6 1.0 C X:GLY445 4.9 7.0 1.0 CB X:CYS294 4.9 7.8 1.0 CA X:SER312 4.9 7.7 1.0 C X:GLY475 5.0 6.5 1.0 CB X:CYS333 5.0 7.3 1.0 SG X:CYS295 5.0 10.7 0.7

Iron binding site 10 out of 11 in the Ni,Fe-Codh-600 Mv State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Ni,Fe-Codh-600 Mv State within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe1004 b:8.2 occ:0.30 FE X:FE21004 0.0 8.2 0.3 FE X:FE21004 1.3 10.8 0.6 S3 X:WCC1003 2.0 8.6 0.8 SG X:CYS295 2.1 10.7 0.7 SG X:CYS295 2.3 5.6 0.3 NI X:WCC1003 2.4 10.8 0.6 SG X:CYS526 2.7 9.8 1.0 O X:HOH1887 2.7 10.2 0.6 NE2 X:HIS261 3.1 15.5 1.0 S1 X:WCC1003 3.1 7.6 0.8 FE4 X:WCC1003 3.1 9.3 0.8 FE1 X:WCC1003 3.3 7.9 0.8 CB X:CYS295 3.3 7.1 0.3 CB X:CYS295 3.5 8.3 0.7 O X:HOH1267 3.5 14.1 1.0 CB X:CYS526 3.6 7.5 1.0 S4 X:WCC1003 3.7 8.4 0.8 CD2 X:HIS261 3.9 12.5 1.0 CE1 X:HIS261 4.0 12.8 1.0 FE3 X:WCC1003 4.1 8.3 0.8 N X:CYS295 4.2 8.0 0.7 N X:CYS295 4.2 7.6 0.3 CA X:CYS295 4.2 8.0 0.7 CA X:CYS295 4.3 7.2 0.3 N X:CYS526 4.4 6.4 1.0 CA X:GLY475 4.5 6.3 1.0 SG X:CYS476 4.6 13.0 1.0 NZ X:LYS563 4.6 7.5 1.0 CA X:CYS526 4.7 6.8 1.0 O X:HOH1761 4.8 24.8 1.0 S2 X:WCC1003 4.8 8.0 0.8 N X:CYS476 4.8 7.2 1.0 O X:HOH1102 4.9 7.2 1.0 SG X:CYS333 5.0 7.8 1.0

J.H.Jeoung, H.Dobbek. Carbon Dioxide Activation at the Ni,Fe-Cluster of Anaerobic Carbon Monoxide Dehydrogenase. Science V. 318 1461 2007.
ISSN: ISSN 0036-8075
PubMed: 18048691
DOI: 10.1126/SCIENCE.1148481