Iron in PDB 7zxc: H96D Mutant of Recombinant Codh-II

All present enzymatic activity of H96D Mutant of Recombinant Codh-II:
1.2.7.4;

The structure of H96D Mutant of Recombinant Codh-II, PDB code: 7zxc was solved by Y.Basak, J.H.Jeoung, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.87 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.7, 75.24, 71.22, 90, 111.38, 90
R / Rfree (%)	16.3 / 20.5

The structure of H96D Mutant of Recombinant Codh-II 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 H96D Mutant of Recombinant Codh-II (pdb code 7zxc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 11 binding sites of Iron where determined in the H96D Mutant of Recombinant Codh-II, PDB code: 7zxc:
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 H96D Mutant of Recombinant Codh-II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of H96D Mutant of Recombinant Codh-II within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe701 b:8.3 occ:1.00 FE1 X:SF4701 0.0 8.3 1.0 S3 X:SF4701 2.2 6.2 1.0 SG X:CYS56 2.3 5.1 1.0 S4 X:SF4701 2.3 4.6 1.0 S2 X:SF4701 2.4 3.8 0.9 FE2 X:SF4701 2.7 7.3 1.0 FE3 X:SF4701 2.7 7.3 1.0 FE4 X:SF4701 2.8 7.1 1.0 CB X:CYS56 3.2 2.7 1.0 S1 X:SF4701 3.8 6.2 1.0 N X:ILE69 4.0 4.0 1.0 CB X:ILE69 4.3 5.3 1.0 CA X:GLY54 4.4 4.3 1.0 CA X:CYS56 4.4 4.3 1.0 N X:CYS56 4.4 5.5 1.0 O X:CYS48 4.5 4.9 1.0 N X:GLY54 4.5 8.2 1.0 N X:CYS70 4.6 6.3 1.0 SG X:CYS48 4.7 5.0 1.0 SG X:CYS51 4.7 6.0 1.0 CA X:ILE69 4.7 5.5 1.0 SG X:CYS70 4.8 6.0 1.0 CA X:GLY68 4.8 8.5 1.0 CB X:CYS48 4.8 3.3 1.0 C X:GLY68 4.8 9.0 1.0 CG1 X:ILE69 4.9 5.0 1.0

Iron binding site 2 out of 11 in the H96D Mutant of Recombinant Codh-II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of H96D Mutant of Recombinant Codh-II within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe701 b:7.3 occ:1.00 FE2 X:SF4701 0.0 7.3 1.0 S3 X:SF4701 2.3 6.2 1.0 S1 X:SF4701 2.3 6.2 1.0 S4 X:SF4701 2.3 4.6 1.0 SG X:CYS51 2.3 6.0 1.0 FE1 X:SF4701 2.7 8.3 1.0 FE3 X:SF4701 2.7 7.3 1.0 FE4 X:SF4701 2.8 7.1 1.0 CB X:CYS51 3.3 5.5 1.0 N X:CYS51 3.6 3.8 1.0 CA X:CYS51 3.9 4.6 1.0 S2 X:SF4701 3.9 3.8 0.9 O X:CYS51 4.2 3.8 1.0 C X:CYS51 4.3 3.2 1.0 C X:HIS50 4.3 7.0 1.0 CG X:MET199 4.3 6.0 1.0 N X:GLY54 4.4 8.2 1.0 N X:HIS50 4.7 6.3 1.0 CB X:GLN53 4.7 6.8 1.0 CB X:MET199 4.7 10.3 1.0 SG X:CYS70 4.8 6.0 1.0 SG X:CYS48 4.8 5.0 1.0 SG X:CYS56 4.8 5.1 1.0 N X:GLN53 4.9 6.0 1.0 CA X:HIS50 4.9 5.6 1.0 CA X:GLY54 4.9 4.3 1.0 C X:GLN53 5.0 9.3 1.0

Iron binding site 3 out of 11 in the H96D Mutant of Recombinant Codh-II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of H96D Mutant of Recombinant Codh-II within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe701 b:7.3 occ:1.00 FE3 X:SF4701 0.0 7.3 1.0 S1 X:SF4701 2.2 6.2 1.0 SG X:CYS48 2.3 5.0 1.0 S2 X:SF4701 2.3 3.8 0.9 S4 X:SF4701 2.3 4.6 1.0 FE1 X:SF4701 2.7 8.3 1.0 FE2 X:SF4701 2.7 7.3 1.0 FE4 X:SF4701 2.8 7.1 1.0 CB X:CYS48 3.2 3.3 1.0 NH2 X:ARG80 3.7 3.9 1.0 N X:HIS50 3.8 6.3 1.0 S3 X:SF4701 3.8 6.2 1.0 C X:CYS48 4.1 4.8 1.0 O X:CYS48 4.1 4.9 1.0 CB X:HIS50 4.2 5.3 1.0 CA X:CYS48 4.3 5.4 1.0 CA X:HIS50 4.4 5.6 1.0 N X:CYS51 4.5 3.8 1.0 N X:ARG49 4.5 6.1 1.0 SG X:CYS56 4.7 5.1 1.0 C X:HIS50 4.7 7.0 1.0 CB X:CYS56 4.7 2.7 1.0 C X:ARG49 4.8 9.2 1.0 CZ X:ARG80 4.8 7.7 1.0 SG X:CYS70 4.9 6.0 1.0 CG X:HIS50 5.0 3.4 1.0 SG X:CYS51 5.0 6.0 1.0 CA X:ARG49 5.0 6.6 1.0

Iron binding site 4 out of 11 in the H96D Mutant of Recombinant Codh-II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of H96D Mutant of Recombinant Codh-II within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe701 b:7.1 occ:1.00 FE4 X:SF4701 0.0 7.1 1.0 S2 X:SF4701 2.2 3.8 0.9 SG X:CYS70 2.3 6.0 1.0 S3 X:SF4701 2.3 6.2 1.0 S1 X:SF4701 2.3 6.2 1.0 FE1 X:SF4701 2.8 8.3 1.0 FE3 X:SF4701 2.8 7.3 1.0 FE2 X:SF4701 2.8 7.3 1.0 CB X:CYS70 3.3 5.5 1.0 N X:CYS70 3.7 6.3 1.0 S4 X:SF4701 4.0 4.6 1.0 CA X:CYS70 4.1 9.0 1.0 NH2 X:ARG80 4.2 3.9 1.0 O X:HOH1074 4.2 6.5 1.0 CB X:ALA72 4.5 7.0 1.0 CG X:MET199 4.6 6.0 1.0 N X:ILE69 4.6 4.0 1.0 SG X:CYS51 4.7 6.0 1.0 SG X:CYS56 4.8 5.1 1.0 SG X:CYS48 4.8 5.0 1.0 C X:ILE69 4.9 8.9 1.0 C X:CYS70 5.0 8.9 1.0 C X:GLY68 5.0 9.0 1.0

Iron binding site 5 out of 11 in the H96D Mutant of Recombinant Codh-II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of H96D Mutant of Recombinant Codh-II within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe702 b:8.4 occ:1.00 FE1 X:FES702 0.0 8.4 1.0 SG X:CYS47 2.2 8.1 1.0 S1 X:FES702 2.2 6.6 1.0 S2 X:FES702 2.2 7.7 1.0 FE2 X:FES702 2.7 8.3 1.0 CB X:CYS47 3.2 8.0 1.0 O X:HOH1258 3.6 7.6 1.0 CA X:CYS47 4.5 6.0 1.0 SG X:CYS39 4.7 7.7 1.0 CB X:PHE41 4.9 5.7 1.0

Iron binding site 6 out of 11 in the H96D Mutant of Recombinant Codh-II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of H96D Mutant of Recombinant Codh-II within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe702 b:8.3 occ:1.00 FE2 X:FES702 0.0 8.3 1.0 S2 X:FES702 2.2 7.7 1.0 S1 X:FES702 2.3 6.6 1.0 SG X:CYS39 2.3 7.7 1.0 FE1 X:FES702 2.7 8.4 1.0 CB X:CYS39 3.2 6.3 1.0 N X:GLY42 4.2 4.8 1.0 CB X:PHE41 4.4 5.7 1.0 CA X:CYS39 4.6 7.0 1.0 SG X:CYS47 4.7 8.1 1.0 CA X:GLY42 4.8 6.7 1.0 CD2 X:PHE41 4.8 8.8 1.0 CB X:CYS47 5.0 8.0 1.0

Iron binding site 7 out of 11 in the H96D Mutant of Recombinant Codh-II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of H96D Mutant of Recombinant Codh-II within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe703 b:14.2 occ:0.61 FE1 X:WCC703 0.0 14.2 0.6 S2 X:WCC703 2.2 12.9 0.8 SG X:CYS333 2.2 12.9 1.0 S3 X:WCC703 2.3 16.2 0.8 S4 X:WCC703 2.4 13.3 0.6 FE3 X:WCC703 2.4 14.5 0.7 FE4 X:WCC703 2.6 15.5 0.8 CB X:CYS333 3.0 12.0 1.0 NI X:WCC703 3.2 21.6 0.4 FE X:FE704 3.4 23.2 0.6 S1 X:WCC703 3.6 18.6 0.9 FE X:FE704 3.8 17.6 0.4 CE1 X:HIS261 3.8 13.5 1.0 NE2 X:HIS261 3.8 23.5 1.0 O X:HOH821 3.9 18.2 0.6 NZ X:LYS563 4.1 24.1 1.0 CA X:CYS333 4.4 10.8 1.0 SG X:CYS446 4.5 12.7 1.0 O X:HOH985 4.6 14.1 1.0 CE X:MET560 4.6 14.1 1.0 CE X:LYS563 4.7 11.7 1.0 CB X:HIS561 4.9 5.6 1.0 SG X:CYS476 4.9 17.0 1.0 CB X:CYS446 4.9 10.6 1.0 SG X:CYS294 5.0 19.9 1.0 CD2 X:HIS561 5.0 7.8 1.0

Iron binding site 8 out of 11 in the H96D Mutant of Recombinant Codh-II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of H96D Mutant of Recombinant Codh-II within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe703 b:14.5 occ:0.71 FE3 X:WCC703 0.0 14.5 0.7 S4 X:WCC703 2.1 13.3 0.6 S1 X:WCC703 2.2 18.6 0.9 S2 X:WCC703 2.2 12.9 0.8 SG X:CYS446 2.4 12.7 1.0 FE1 X:WCC703 2.4 14.2 0.6 FE4 X:WCC703 2.6 15.5 0.8 NI X:WCC703 2.7 21.6 0.4 CB X:CYS446 3.0 10.6 1.0 CA X:CYS446 3.4 11.6 1.0 N X:CYS446 3.6 11.0 1.0 S3 X:WCC703 3.8 16.2 0.8 C X:GLY445 4.0 8.3 1.0 FE X:FE704 4.1 17.6 0.4 SG X:CYS333 4.3 12.9 1.0 CB X:HIS561 4.5 5.6 1.0 CE X:MET560 4.5 14.1 1.0 SG X:CYS526 4.5 21.3 1.0 O X:GLY445 4.5 12.2 1.0 CA X:GLY445 4.5 10.3 1.0 FE X:FE704 4.6 23.2 0.6 O X:HOH821 4.7 18.2 0.6 SG X:CYS476 4.7 17.0 1.0 C X:CYS446 4.9 6.0 1.0 CB X:CYS476 4.9 11.5 1.0

Iron binding site 9 out of 11 in the H96D Mutant of Recombinant Codh-II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of H96D Mutant of Recombinant Codh-II within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe703 b:15.5 occ:0.75 FE4 X:WCC703 0.0 15.5 0.8 S1 X:WCC703 2.1 18.6 0.9 S3 X:WCC703 2.2 16.2 0.8 S2 X:WCC703 2.2 12.9 0.8 SG X:CYS476 2.4 17.0 1.0 FE3 X:WCC703 2.6 14.5 0.7 FE1 X:WCC703 2.6 14.2 0.6 FE X:FE704 3.2 17.6 0.4 CB X:CYS476 3.4 11.5 1.0 NI X:WCC703 3.4 21.6 0.4 O X:HOH950 3.8 23.5 1.0 FE X:FE704 3.9 23.2 0.6 S4 X:WCC703 3.9 13.3 0.6 N X:CYS476 4.0 11.5 1.0 CA X:CYS476 4.3 9.3 1.0 CA X:CYS446 4.3 11.6 1.0 SG X:CYS294 4.5 19.9 1.0 CB X:CYS446 4.5 10.6 1.0 CB X:SER312 4.6 14.1 1.0 SG X:CYS526 4.6 21.3 1.0 SG X:CYS295 4.7 13.1 0.4 OG X:SER312 4.7 9.7 1.0 O X:GLY445 4.7 12.2 1.0 SG X:CYS295 4.8 15.3 0.6 SG X:CYS446 4.8 12.7 1.0 SG X:CYS333 4.8 12.9 1.0 CB X:CYS294 4.9 16.8 1.0 N X:CYS446 4.9 11.0 1.0 C X:GLY445 4.9 8.3 1.0 C X:GLY475 5.0 9.5 1.0 CA X:CYS294 5.0 14.4 1.0

Iron binding site 10 out of 11 in the H96D Mutant of Recombinant Codh-II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of H96D Mutant of Recombinant Codh-II within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe704 b:17.6 occ:0.39 FE X:FE704 0.0 17.6 0.4 FE X:FE704 1.6 23.2 0.6 SG X:CYS295 2.0 15.3 0.6 SG X:CYS295 2.2 13.1 0.4 NI X:WCC703 2.3 21.6 0.4 SG X:CYS526 2.3 21.3 1.0 S3 X:WCC703 2.5 16.2 0.8 O X:HOH821 2.9 18.2 0.6 S1 X:WCC703 3.0 18.6 0.9 FE4 X:WCC703 3.2 15.5 0.8 O X:HOH950 3.3 23.5 1.0 NE2 X:HIS261 3.3 23.5 1.0 CB X:CYS295 3.3 15.9 0.4 CB X:CYS526 3.3 11.5 1.0 CB X:CYS295 3.5 16.5 0.6 FE1 X:WCC703 3.8 14.2 0.6 S4 X:WCC703 3.8 13.3 0.6 CD2 X:HIS261 4.0 24.9 1.0 N X:CYS526 4.0 8.0 1.0 FE3 X:WCC703 4.1 14.5 0.7 O X:HOH1196 4.2 18.9 0.5 CA X:GLY475 4.2 11.9 1.0 CA X:CYS526 4.3 6.7 1.0 CE1 X:HIS261 4.3 13.5 1.0 CA X:CYS295 4.3 15.5 0.6 CA X:CYS295 4.4 15.4 0.4 N X:CYS295 4.4 12.3 1.0 N X:CYS476 4.7 11.5 1.0 SG X:CYS476 4.7 17.0 1.0 O X:HOH1179 4.8 12.6 1.0 NZ X:LYS563 4.9 24.1 1.0 C X:GLY475 4.9 9.5 1.0 S2 X:WCC703 4.9 12.9 0.8

Y.Basak, J.H.Jeoung, L.Domnik, J.Ruickoldt, H.Dobbek. Substrate Activation at the Ni,Fe Cluster of Co Dehydrogenases: the Influence of the Protein Matrix Acs Catalysis 2022.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.2C02922