Iron in PDB 7vxq: The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77

All present enzymatic activity of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77:
1.12.99.6;

The structure of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77, PDB code: 7vxq was solved by K.Nishikawa, K.Higuchi, T.Imanishi, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.49 / 1.77
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.39, 122.32, 99.91, 90, 103.12, 90
R / Rfree (%)	16.1 / 19.3

The structure of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Magnesium	(Mg)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 (pdb code 7vxq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77, PDB code: 7vxq:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:25.3 occ:1.00 FE A:NFU702 0.0 25.3 1.0 C2 A:NFU702 1.9 21.5 1.0 C3 A:NFU702 1.9 25.0 1.0 C1 A:NFU702 1.9 23.8 1.0 SG A:CYS64 2.2 22.7 1.0 SG A:CYS549 2.3 24.4 1.0 NI A:NFU702 2.6 27.5 1.0 O3 A:NFU702 3.0 24.1 1.0 N2 A:NFU702 3.0 21.2 1.0 N1 A:NFU702 3.1 24.7 1.0 CB A:CYS64 3.3 21.1 1.0 CB A:CYS549 3.4 23.6 1.0 C A:CMO703 3.4 25.9 0.3 NE2 A:HIS68 4.2 27.6 1.0 CD A:ARG479 4.2 23.1 1.0 CG1 A:VAL500 4.2 21.9 1.0 SG A:CYS546 4.3 30.3 1.0 CB A:CYS546 4.4 26.2 1.0 O A:CMO703 4.5 26.4 0.3 OG1 A:THR67 4.6 25.6 1.0 NH1 A:ARG479 4.6 24.6 1.0 CG A:PRO501 4.7 27.1 1.0 CA A:CYS64 4.7 24.6 1.0 CA A:CYS549 4.8 24.2 1.0 SG A:CYS61 4.8 28.4 1.0 CD A:PRO501 4.8 24.2 1.0 CB A:CYS61 4.9 28.6 1.0 CB A:ARG479 4.9 23.5 1.0 CD2 A:HIS68 4.9 25.9 1.0 CE1 A:HIS68 5.0 24.6 1.0

Iron binding site 2 out of 24 in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe403 b:29.1 occ:1.00 FE1 B:SF4403 0.0 29.1 1.0 S4 B:SF4403 2.2 29.4 1.0 S2 B:SF4403 2.3 29.5 1.0 SG B:CYS220 2.3 29.1 1.0 S3 B:SF4403 2.3 31.2 1.0 FE3 B:SF4403 2.6 31.8 1.0 FE2 B:SF4403 2.7 29.6 1.0 FE4 B:SF4403 2.8 29.3 1.0 CB B:CYS220 3.6 32.3 1.0 N B:LEU221 3.9 27.4 1.0 S1 B:SF4403 3.9 35.8 1.0 CA B:CYS220 4.0 29.0 1.0 N B:TYR222 4.2 29.5 1.0 CD1 B:PHE201 4.4 31.3 1.0 C B:CYS220 4.4 26.1 1.0 CB B:PHE201 4.4 31.1 1.0 ND1 B:HIS192 4.5 31.6 1.0 CB B:ARG197 4.5 31.0 1.0 CB B:TYR222 4.6 29.2 1.0 CA B:TYR222 4.7 28.4 1.0 CE1 B:HIS192 4.7 34.0 1.0 O B:ARG197 4.8 30.4 1.0 CG B:PHE201 4.8 35.0 1.0 SG B:CYS226 4.8 26.9 1.0 SG B:CYS195 4.9 30.6 1.0 C B:LEU221 4.9 29.1 1.0 C B:ARG197 4.9 28.2 1.0 CA B:LEU221 4.9 24.4 1.0

Iron binding site 3 out of 24 in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe403 b:29.6 occ:1.00 FE2 B:SF4403 0.0 29.6 1.0 S3 B:SF4403 2.3 31.2 1.0 S1 B:SF4403 2.3 35.8 1.0 S4 B:SF4403 2.3 29.4 1.0 SG B:CYS195 2.3 30.6 1.0 FE3 B:SF4403 2.6 31.8 1.0 FE4 B:SF4403 2.7 29.3 1.0 FE1 B:SF4403 2.7 29.1 1.0 CB B:CYS195 3.2 29.0 1.0 S2 B:SF4403 3.8 29.5 1.0 CB B:ARG197 4.1 31.0 1.0 ND1 B:HIS192 4.6 31.6 1.0 CA B:CYS195 4.6 29.6 1.0 N B:ARG197 4.7 28.9 1.0 CA B:ARG197 4.7 27.2 1.0 N B:ARG198 4.7 31.1 1.0 C B:ARG197 4.7 28.2 1.0 SG B:CYS226 4.7 26.9 1.0 CG1 B:VAL249 4.9 28.0 1.0 SG B:CYS220 4.9 29.1 1.0 CG B:ARG197 4.9 31.1 1.0 CH2 B:TRP247 4.9 30.4 1.0 C B:CYS195 4.9 34.9 1.0 CA B:HIS192 5.0 26.8 1.0

Iron binding site 4 out of 24 in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe403 b:31.8 occ:1.00 FE3 B:SF4403 0.0 31.8 1.0 ND1 B:HIS192 2.2 31.6 1.0 S2 B:SF4403 2.2 29.5 1.0 S4 B:SF4403 2.2 29.4 1.0 S1 B:SF4403 2.4 35.8 1.0 FE1 B:SF4403 2.6 29.1 1.0 FE2 B:SF4403 2.6 29.6 1.0 FE4 B:SF4403 2.7 29.3 1.0 CE1 B:HIS192 3.0 34.0 1.0 CG B:HIS192 3.3 30.7 1.0 CB B:HIS192 3.7 28.4 1.0 S3 B:SF4403 3.8 31.2 1.0 CA B:HIS192 4.0 26.8 1.0 NE2 B:HIS192 4.2 33.0 1.0 CG B:PRO229 4.4 30.6 1.0 CD B:PRO229 4.4 28.1 1.0 CD2 B:HIS192 4.4 33.5 1.0 SG B:CYS220 4.6 29.1 1.0 SG B:CYS195 4.6 30.6 1.0 CB B:CYS195 4.6 29.0 1.0 CD1 B:PHE201 4.7 31.3 1.0 SG B:CYS226 4.8 26.9 1.0 O B:HIS192 4.8 33.6 1.0 N B:PRO229 4.9 30.8 1.0 N B:HIS192 4.9 27.4 1.0 C B:HIS192 5.0 28.1 1.0

Iron binding site 5 out of 24 in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe403 b:29.3 occ:1.00 FE4 B:SF4403 0.0 29.3 1.0 S3 B:SF4403 2.3 31.2 1.0 S1 B:SF4403 2.3 35.8 1.0 SG B:CYS226 2.3 26.9 1.0 S2 B:SF4403 2.3 29.5 1.0 FE2 B:SF4403 2.7 29.6 1.0 FE3 B:SF4403 2.7 31.8 1.0 FE1 B:SF4403 2.8 29.1 1.0 CB B:CYS226 3.2 28.5 1.0 S4 B:SF4403 3.9 29.4 1.0 CA B:GLY228 4.5 28.4 1.0 N B:GLY228 4.5 27.0 1.0 CD B:PRO229 4.5 28.1 1.0 CA B:CYS226 4.6 28.6 1.0 CG2 B:VAL249 4.6 26.6 1.0 SG B:CYS220 4.7 29.1 1.0 SG B:CYS195 4.7 30.6 1.0 ND1 B:HIS192 4.8 31.6 1.0 N B:TYR222 4.8 29.5 1.0 C B:CYS226 4.8 28.9 1.0 N B:LEU221 4.9 27.4 1.0

Iron binding site 6 out of 24 in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe404 b:27.7 occ:1.00 FE1 B:F3S404 0.0 27.7 1.0 S2 B:F3S404 2.3 28.4 1.0 S1 B:F3S404 2.3 23.9 1.0 SG B:CYS258 2.3 28.7 1.0 S3 B:F3S404 2.3 22.9 1.0 FE3 B:F3S404 2.7 26.6 1.0 FE4 B:F3S404 2.7 25.5 1.0 CB B:CYS258 3.4 24.4 1.0 O A:HOH879 3.6 23.6 1.0 N B:CYS258 3.7 26.2 1.0 S4 B:F3S404 3.8 27.4 1.0 CA B:CYS258 4.0 23.9 1.0 OD1 B:ASN259 4.2 26.6 1.0 O B:HOH551 4.2 28.9 1.0 N B:ASN259 4.2 25.5 1.0 C B:CYS258 4.5 26.2 1.0 SG B:CYS235 4.7 29.3 1.0 C B:GLY257 4.8 26.6 1.0 CG B:ASN259 4.8 27.4 1.0 SG B:CYS255 4.8 26.0 1.0 O B:HOH508 4.9 32.4 1.0 CE A:LYS211 4.9 24.3 1.0 N B:GLY257 4.9 27.2 1.0 OE1 A:GLN216 5.0 27.0 1.0

Iron binding site 7 out of 24 in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe404 b:26.6 occ:1.00 FE3 B:F3S404 0.0 26.6 1.0 S4 B:F3S404 2.2 27.4 1.0 SG B:CYS235 2.3 29.3 1.0 S1 B:F3S404 2.3 23.9 1.0 S3 B:F3S404 2.3 22.9 1.0 FE4 B:F3S404 2.7 25.5 1.0 FE1 B:F3S404 2.7 27.7 1.0 CB B:CYS235 3.3 32.0 1.0 S2 B:F3S404 4.0 28.4 1.0 O B:HOH551 4.0 28.9 1.0 CD1 B:ILE191 4.1 26.0 1.0 CZ B:PHE240 4.4 26.9 1.0 CE1 B:PHE240 4.5 25.7 1.0 CA B:CYS235 4.7 28.4 1.0 SG B:CYS255 4.7 26.0 1.0 OD1 B:ASN259 4.7 26.6 1.0 SG B:CYS258 4.7 28.7 1.0 O B:HOH586 4.8 31.8 1.0 ND2 B:ASN259 4.9 26.4 1.0 CD B:PRO248 4.9 24.6 1.0 CG B:ASN259 5.0 27.4 1.0

Iron binding site 8 out of 24 in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe404 b:25.5 occ:1.00 FE4 B:F3S404 0.0 25.5 1.0 S3 B:F3S404 2.1 22.9 1.0 S4 B:F3S404 2.2 27.4 1.0 SG B:CYS255 2.3 26.0 1.0 S2 B:F3S404 2.3 28.4 1.0 FE3 B:F3S404 2.7 26.6 1.0 FE1 B:F3S404 2.7 27.7 1.0 CB B:CYS255 3.2 20.8 1.0 CA B:CYS255 3.6 24.2 1.0 N B:TYR256 3.8 24.3 1.0 N B:GLY257 3.9 27.2 1.0 S1 B:F3S404 3.9 23.9 1.0 C B:CYS255 4.2 27.4 1.0 CD1 B:ILE191 4.2 26.0 1.0 N B:CYS258 4.4 26.2 1.0 CA B:GLY257 4.5 30.4 1.0 NE2 A:GLN216 4.7 26.4 1.0 SG B:CYS235 4.7 29.3 1.0 SG B:CYS258 4.9 28.7 1.0 C B:TYR256 4.9 27.9 1.0 C B:GLY257 4.9 26.6 1.0 CG2 B:THR231 4.9 29.5 1.0 CA B:TYR256 4.9 26.5 1.0 N B:CYS255 5.0 24.5 1.0

Iron binding site 9 out of 24 in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe405 b:27.9 occ:1.00 FE1 B:SF4405 0.0 27.9 1.0 S4 B:SF4405 2.2 29.2 1.0 S3 B:SF4405 2.3 26.4 1.0 SG B:CYS22 2.3 26.5 1.0 S2 B:SF4405 2.3 24.5 1.0 FE3 B:SF4405 2.7 27.9 1.0 FE2 B:SF4405 2.7 30.9 1.0 FE4 B:SF4405 2.7 29.6 1.0 CB B:CYS22 3.3 23.0 1.0 N B:CYS22 3.7 29.3 1.0 S1 B:SF4405 3.8 28.0 1.0 CA B:CYS22 4.0 27.9 1.0 N B:GLY24 4.2 27.3 1.0 O B:HOH534 4.2 30.0 0.9 NE2 A:HIS214 4.2 27.4 1.0 O A:HOH954 4.4 33.8 1.0 CA B:GLY24 4.5 26.7 1.0 N B:THR23 4.5 29.6 1.0 C B:CYS22 4.6 31.0 1.0 SG B:CYS154 4.6 26.1 1.0 N B:CYS25 4.8 29.7 1.0 SG B:CYS120 4.8 30.5 1.0 CD2 A:HIS214 4.9 24.0 1.0 C B:GLU21 4.9 36.1 1.0 SG B:CYS25 4.9 30.1 1.0 CG A:ARG59 5.0 24.8 1.0

Iron binding site 10 out of 24 in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe405 b:30.9 occ:1.00 FE2 B:SF4405 0.0 30.9 1.0 S3 B:SF4405 2.2 26.4 1.0 S4 B:SF4405 2.3 29.2 1.0 S1 B:SF4405 2.3 28.0 1.0 SG B:CYS120 2.3 30.5 1.0 FE1 B:SF4405 2.7 27.9 1.0 FE3 B:SF4405 2.7 27.9 1.0 FE4 B:SF4405 2.8 29.6 1.0 CB B:CYS120 3.2 23.5 1.0 O A:HOH954 3.8 33.8 1.0 O B:HOH590 3.9 29.4 1.0 S2 B:SF4405 3.9 24.5 1.0 O B:HOH518 4.1 28.4 1.0 N B:CYS120 4.1 27.1 1.0 CA B:CYS120 4.2 27.2 1.0 SG B:CYS154 4.4 26.1 1.0 SG B:CYS22 4.9 26.5 1.0 SG B:CYS25 4.9 30.1 1.0 N B:CYS22 4.9 29.3 1.0 CA B:GLY82 5.0 27.6 1.0

T.Imanishi, K.Nishikawa, M.Taketa, K.Higuchi, H.Tai, S.Hirota, H.Hojo, T.Kawakami, K.Hataguchi, K.Matsumoto, H.Ogata, Y.Higuchi. Structural and Spectroscopic Characterization of Co Inhibition of [Nife]-Hydrogenase From Citrobacter Sp. S-77. Acta Crystallogr.,Sect.F V. 78 66 2022.
ISSN: ESSN 2053-230X
PubMed: 35102895
DOI: 10.1107/S2053230X22000188