Iron in PDB 6vwy: Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)

All present enzymatic activity of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic):
1.2.7.4;

The structure of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic), PDB code: 6vwy was solved by E.C.Wittenborn, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	73.68 / 1.83
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.560, 147.360, 66.050, 90.00, 110.78, 90.00
R / Rfree (%)	14.7 / 17.8

The structure of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) also contains other interesting chemical elements:

Nickel

(Ni)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) (pdb code 6vwy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic), PDB code: 6vwy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:20.9 occ:1.00 FE1 A:SF4701 0.0 20.9 1.0 S3 A:SF4701 2.3 20.7 1.0 S2 A:SF4701 2.3 20.6 1.0 SG A:CYS51 2.3 20.1 1.0 S4 A:SF4701 2.3 18.8 1.0 FE2 A:SF4701 2.7 20.2 1.0 FE4 A:SF4701 2.7 19.9 1.0 FE3 A:SF4701 2.7 20.4 1.0 CB A:CYS51 3.2 18.3 1.0 NH2 A:ARG84 3.6 17.7 1.0 S1 A:SF4701 3.8 20.4 1.0 N A:ASN53 4.1 20.8 1.0 C A:CYS51 4.2 18.4 1.0 CB A:ASN53 4.3 23.0 1.0 CA A:CYS51 4.3 18.3 1.0 O A:CYS51 4.4 20.1 1.0 N A:ARG52 4.6 19.6 1.0 CA A:ASN53 4.6 20.9 1.0 N A:CYS54 4.7 18.1 1.0 SG A:CYS59 4.7 20.2 1.0 CZ A:ARG84 4.8 24.6 1.0 SG A:CYS74 4.9 21.8 1.0 SG A:CYS54 4.9 19.8 1.0 CB A:CYS59 4.9 23.8 1.0 C A:ASN53 4.9 26.0 1.0 CG A:ASN53 5.0 27.2 1.0

Iron binding site 2 out of 28 in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:20.2 occ:1.00 FE2 A:SF4701 0.0 20.2 1.0 S1 A:SF4701 2.3 20.4 1.0 SG A:CYS59 2.3 20.2 1.0 S3 A:SF4701 2.3 20.7 1.0 S4 A:SF4701 2.3 18.8 1.0 FE1 A:SF4701 2.7 20.9 1.0 FE4 A:SF4701 2.7 19.9 1.0 FE3 A:SF4701 2.8 20.4 1.0 CB A:CYS59 3.2 23.8 1.0 N A:VAL73 3.9 20.7 1.0 S2 A:SF4701 3.9 20.6 1.0 CA A:GLY57 4.2 21.9 1.0 N A:GLY57 4.3 21.3 1.0 CA A:GLY72 4.3 21.6 1.0 N A:CYS59 4.3 19.9 1.0 CA A:CYS59 4.4 21.8 1.0 CB A:CYS51 4.5 18.3 1.0 C A:GLY72 4.6 22.6 1.0 SG A:CYS51 4.6 20.1 1.0 SG A:CYS54 4.7 19.8 1.0 O A:CYS51 4.7 20.1 1.0 CB A:VAL73 4.7 24.0 1.0 N A:CYS74 4.7 21.5 1.0 SG A:CYS74 4.8 21.8 1.0 CA A:VAL73 4.8 20.8 1.0 CG2 A:VAL73 4.9 21.8 1.0 C A:MET56 4.9 24.3 1.0 C A:PRO58 5.0 20.3 1.0

Iron binding site 3 out of 28 in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:20.4 occ:1.00 FE3 A:SF4701 0.0 20.4 1.0 S1 A:SF4701 2.3 20.4 1.0 S2 A:SF4701 2.3 20.6 1.0 SG A:CYS74 2.3 21.8 1.0 S4 A:SF4701 2.3 18.8 1.0 FE1 A:SF4701 2.7 20.9 1.0 FE4 A:SF4701 2.7 19.9 1.0 FE2 A:SF4701 2.8 20.2 1.0 CB A:CYS74 3.3 19.2 1.0 N A:CYS74 3.9 21.5 1.0 S3 A:SF4701 3.9 20.7 1.0 NH2 A:ARG84 4.0 17.7 1.0 CG A:MET203 4.2 22.2 1.0 CA A:CYS74 4.2 20.5 1.0 CB A:ALA76 4.6 21.0 1.0 O A:HOH902 4.6 20.0 1.0 SG A:CYS54 4.6 19.8 1.0 N A:VAL73 4.6 20.7 1.0 SG A:CYS59 4.8 20.2 1.0 SG A:CYS51 4.8 20.1 1.0 CA A:GLY72 4.9 21.6 1.0 C A:GLY72 4.9 22.6 1.0 CB A:MET203 5.0 19.1 1.0

Iron binding site 4 out of 28 in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:19.9 occ:1.00 FE4 A:SF4701 0.0 19.9 1.0 SG A:CYS54 2.3 19.8 1.0 S2 A:SF4701 2.3 20.6 1.0 S3 A:SF4701 2.3 20.7 1.0 S1 A:SF4701 2.3 20.4 1.0 FE1 A:SF4701 2.7 20.9 1.0 FE2 A:SF4701 2.7 20.2 1.0 FE3 A:SF4701 2.7 20.4 1.0 CB A:CYS54 3.4 18.4 1.0 N A:CYS54 3.6 18.1 1.0 S4 A:SF4701 3.9 18.8 1.0 CA A:CYS54 4.0 19.9 1.0 O A:CYS54 4.1 20.7 1.0 N A:GLY57 4.2 21.3 1.0 C A:CYS54 4.3 20.9 1.0 C A:ASN53 4.4 26.0 1.0 CG A:MET203 4.6 22.2 1.0 CB A:MET56 4.7 20.6 1.0 N A:ASN53 4.7 20.8 1.0 CA A:GLY57 4.7 21.9 1.0 SG A:CYS59 4.8 20.2 1.0 SG A:CYS51 4.8 20.1 1.0 SG A:CYS74 4.8 21.8 1.0 CB A:MET203 4.8 19.1 1.0 CA A:ASN53 4.9 20.9 1.0 C A:MET56 4.9 24.3 1.0 N A:MET56 5.0 22.9 1.0

Iron binding site 5 out of 28 in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:22.4 occ:1.00 FE1 A:SF4702 0.0 22.4 1.0 SG B:CYS42 2.3 24.0 1.0 S2 A:SF4702 2.3 24.0 1.0 S4 A:SF4702 2.3 24.4 1.0 S3 A:SF4702 2.3 21.4 1.0 FE2 A:SF4702 2.7 22.9 1.0 FE3 A:SF4702 2.7 23.8 1.0 FE4 A:SF4702 2.7 23.4 1.0 CB B:CYS42 3.1 22.0 1.0 S1 A:SF4702 3.9 21.9 1.0 N B:GLY45 4.1 25.8 1.0 CB B:PHE44 4.3 21.8 1.0 O A:HOH1099 4.4 26.4 1.0 CA B:CYS42 4.6 27.0 1.0 SG A:CYS42 4.7 23.7 1.0 CA B:GLY45 4.7 22.5 1.0 SG A:CYS50 4.8 23.4 1.0 SG B:CYS50 4.8 23.2 1.0 C B:PHE44 4.9 23.2 1.0 CD2 B:PHE44 4.9 26.0 1.0 CB B:CYS50 4.9 22.7 1.0 CA B:PHE44 5.0 22.8 1.0 N B:PHE44 5.0 25.0 1.0 C B:CYS42 5.0 22.3 1.0

Iron binding site 6 out of 28 in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:22.9 occ:1.00 FE2 A:SF4702 0.0 22.9 1.0 S1 A:SF4702 2.3 21.9 1.0 SG A:CYS42 2.3 23.7 1.0 S4 A:SF4702 2.3 24.4 1.0 S3 A:SF4702 2.3 21.4 1.0 FE1 A:SF4702 2.7 22.4 1.0 FE4 A:SF4702 2.7 23.4 1.0 FE3 A:SF4702 2.7 23.8 1.0 CB A:CYS42 3.2 24.1 1.0 S2 A:SF4702 3.9 24.0 1.0 N A:GLY45 4.1 27.8 1.0 CB A:PHE44 4.3 21.2 1.0 O B:HOH1077 4.6 24.8 1.0 SG B:CYS42 4.6 24.0 1.0 CA A:CYS42 4.6 25.6 1.0 CA A:GLY45 4.7 23.0 1.0 SG B:CYS50 4.8 23.2 1.0 SG A:CYS50 4.8 23.4 1.0 CD2 A:PHE44 4.9 25.2 1.0 C A:PHE44 4.9 24.0 1.0 CB A:CYS50 4.9 22.2 1.0 CA A:PHE44 5.0 22.1 1.0 N A:PHE44 5.0 22.9 1.0

Iron binding site 7 out of 28 in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:23.8 occ:1.00 FE3 A:SF4702 0.0 23.8 1.0 S2 A:SF4702 2.3 24.0 1.0 S4 A:SF4702 2.3 24.4 1.0 SG B:CYS50 2.3 23.2 1.0 S1 A:SF4702 2.3 21.9 1.0 FE4 A:SF4702 2.7 23.4 1.0 FE1 A:SF4702 2.7 22.4 1.0 FE2 A:SF4702 2.7 22.9 1.0 CB B:CYS50 3.1 22.7 1.0 O B:HOH1077 3.7 24.8 1.0 S3 A:SF4702 3.8 21.4 1.0 CA B:CYS50 4.5 21.0 1.0 SG A:CYS50 4.6 23.4 1.0 SG B:CYS42 4.7 24.0 1.0 SG A:CYS42 4.8 23.7 1.0 CB B:PHE44 4.8 21.8 1.0 NE B:ARG52 5.0 54.2 1.0

Iron binding site 8 out of 28 in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:23.4 occ:1.00 FE4 A:SF4702 0.0 23.4 1.0 S3 A:SF4702 2.3 21.4 1.0 S2 A:SF4702 2.3 24.0 1.0 SG A:CYS50 2.3 23.4 1.0 S1 A:SF4702 2.3 21.9 1.0 FE3 A:SF4702 2.7 23.8 1.0 FE1 A:SF4702 2.7 22.4 1.0 FE2 A:SF4702 2.7 22.9 1.0 CB A:CYS50 3.1 22.2 1.0 O A:HOH1099 3.7 26.4 1.0 S4 A:SF4702 3.9 24.4 1.0 CA A:CYS50 4.5 19.1 1.0 SG B:CYS50 4.6 23.2 1.0 SG A:CYS42 4.8 23.7 1.0 SG B:CYS42 4.8 24.0 1.0 CB A:PHE44 4.8 21.2 1.0 NE B:ARG52 4.9 54.2 1.0 CB B:CYS42 5.0 22.0 1.0 CD A:ARG52 5.0 31.8 1.0

Iron binding site 9 out of 28 in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:30.1 occ:0.80 FE1 A:XCC703 0.0 30.1 0.8 FE1 A:CUV704 0.4 24.1 0.2 S2 A:CUV704 2.1 28.5 0.2 SG A:CYS340 2.3 23.1 0.5 S2 A:XCC703 2.3 25.4 0.8 S4 A:XCC703 2.3 26.2 0.8 S3 A:XCC703 2.4 48.9 0.8 SG A:CYS340 2.4 24.3 0.5 S4 A:CUV704 2.6 26.5 0.2 FE3 A:XCC703 2.6 29.2 0.8 FE3 A:CUV704 2.7 16.8 0.2 NI A:XCC703 2.9 42.7 0.2 FE4 A:XCC703 3.0 36.0 0.8 FE2 A:CUV704 3.1 17.0 0.2 CB A:CYS340 3.2 23.4 0.5 FE2 A:XCC703 3.3 50.2 0.8 CB A:CYS340 3.3 23.5 0.5 FE4 A:CUV704 3.4 17.2 0.2 NZ A:LYS556 3.5 27.0 0.5 NI A:CUV704 3.6 16.5 0.2 S1 A:XCC703 4.1 23.1 0.8 NE2 A:HIS266 4.1 26.6 0.5 CE2 A:TYR553 4.2 20.5 1.0 NZ A:LYS556 4.2 25.6 0.5 CE1 A:HIS266 4.2 25.6 0.5 SG A:CYS301 4.2 18.4 0.3 S1 A:CUV704 4.2 25.9 0.2 OH A:TYR553 4.5 31.7 1.0 CE1 A:HIS266 4.5 24.9 0.5 CE A:LYS556 4.6 22.4 0.5 NE2 A:HIS266 4.6 22.8 0.5 S3 A:CUV704 4.6 17.4 0.2 SG A:CYS448 4.6 25.8 0.5 CA A:CYS340 4.7 24.9 0.5 CA A:CYS340 4.7 24.8 0.5 SG A:CYS448 4.7 21.7 0.5 OG A:SER554 4.7 21.7 1.0 CZ A:TYR553 4.8 24.9 1.0 CE A:LYS556 4.9 23.1 0.5 CB A:SER554 4.9 22.5 1.0 SG A:CYS519 5.0 28.0 0.5

Iron binding site 10 out of 28 in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:50.2 occ:0.80 FE2 A:XCC703 0.0 50.2 0.8 NI A:CUV704 1.2 16.5 0.2 FE2 A:CUV704 1.7 17.0 0.2 SG A:CYS302 2.1 30.2 0.5 SG A:CYS302 2.2 29.2 0.5 NE2 A:HIS266 2.3 22.8 0.5 S3 A:XCC703 2.3 48.9 0.8 NI A:XCC703 2.4 42.7 0.2 NE2 A:HIS266 2.6 26.6 0.5 CE1 A:HIS266 2.7 25.6 0.5 FE1 A:CUV704 3.0 24.1 0.2 CD2 A:HIS266 3.1 23.9 0.5 SG A:CYS519 3.2 28.0 0.5 CB A:CYS302 3.2 27.5 0.5 FE1 A:XCC703 3.3 30.1 0.8 CB A:CYS302 3.4 27.2 0.5 CD2 A:HIS266 3.4 20.9 0.5 NZ A:LYS556 3.6 27.0 0.5 S3 A:CUV704 3.6 17.4 0.2 CE1 A:HIS266 3.7 24.9 0.5 SG A:CYS519 3.7 30.9 0.5 SG A:CYS301 3.7 18.4 0.3 CB A:CYS519 3.8 25.3 0.5 CB A:CYS519 3.8 25.6 0.5 ND1 A:HIS266 3.8 23.5 0.5 S4 A:XCC703 3.9 26.2 0.8 NZ A:LYS556 3.9 25.6 0.5 FE4 A:XCC703 4.0 36.0 0.8 S4 A:CUV704 4.0 26.5 0.2 FE4 A:CUV704 4.1 17.2 0.2 N A:CYS302 4.2 20.3 0.5 N A:CYS302 4.2 20.6 0.5 CG A:HIS266 4.2 23.8 0.5 CA A:CYS302 4.3 23.6 0.5 S1 A:XCC703 4.3 23.1 0.8 CA A:CYS302 4.3 23.6 0.5 CG A:HIS266 4.4 24.5 0.5 CE A:LYS556 4.5 23.1 0.5 S1 A:CUV704 4.5 25.9 0.2 FE3 A:CUV704 4.5 16.8 0.2 FE3 A:XCC703 4.5 29.2 0.8 SG A:CYS340 4.6 23.1 0.5 ND1 A:HIS266 4.6 24.6 0.5 S2 A:CUV704 4.6 28.5 0.2 O A:HOH912 4.6 37.1 1.0 N A:CYS519 4.7 21.8 0.5 N A:CYS519 4.7 21.9 0.5 SG A:CYS340 4.7 24.3 0.5 CA A:CYS519 4.9 24.3 0.5 CA A:CYS519 4.9 24.4 0.5 S2 A:XCC703 5.0 25.4 0.8 CB A:CYS301 5.0 24.4 0.7

E.C.Wittenborn, C.Guendon, M.Merrouch, M.Benvenuti, V.Fourmond, C.Leger, C.L.Drennan, S.Dementin. The Solvent-Exposed Fe-S D-Cluster Contributes to Oxygen-Resistance Indesulfovibrio Vulgarisni-Fe Carbon Monoxide Dehydrogenase. Acs Catalysis V. 10 7328 2020.
ISSN: ESSN 2155-5435
PubMed: 32655979
DOI: 10.1021/ACSCATAL.0C00934