Iron in PDB 3ayx: Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition

All present enzymatic activity of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition:
1.12.5.1;

The structure of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition, PDB code: 3ayx was solved by Y.Shomura, K.S.Yoon, H.Nishihara, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.735, 116.327, 113.629, 90.00, 91.40, 90.00
R / Rfree (%)	13.9 / 16.9

The structure of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition 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 Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition (pdb code 3ayx). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition, PDB code: 3ayx:
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 Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:8.6 occ:1.00 C A:CMO603 1.8 8.0 1.0 C A:CYN605 1.9 9.0 1.0 C A:CYN604 1.9 7.4 1.0 SG A:CYS79 2.3 9.5 1.0 SG A:CYS593 2.3 10.6 1.0 O A:O606 2.4 11.9 0.5 NI A:NI602 2.6 12.8 1.0 O A:CMO603 2.9 10.1 1.0 N A:CYN605 3.0 8.1 1.0 N A:CYN604 3.1 8.6 1.0 CB A:CYS593 3.3 11.9 1.0 CB A:CYS79 3.4 10.1 1.0 O A:O609 3.5 7.8 0.5 O A:O610 3.7 8.0 0.6 O A:O607 4.0 8.3 0.6 SG A:CYS590 4.0 14.1 1.0 CB A:CYS590 4.1 12.4 1.0 NE2 A:HIS83 4.2 8.7 1.0 CD A:ARG523 4.2 9.7 1.0 CG1 A:VAL544 4.2 3.8 0.2 NH1 A:ARG523 4.4 9.1 1.0 SG A:CYS82 4.5 10.3 1.0 SG A:CYS76 4.6 11.7 1.0 CD A:PRO545 4.7 7.9 1.0 CB A:CYS76 4.7 12.1 1.0 CA A:CYS593 4.8 8.9 1.0 CA A:CYS79 4.9 10.0 1.0 NE A:ARG523 5.0 9.0 1.0 CE1 A:HIS83 5.0 9.2 1.0 CD2 A:HIS83 5.0 8.3 1.0

Iron binding site 2 out of 24 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:8.1 occ:1.00 FE1 B:F4S301 0.0 8.1 1.0 SG B:CYS23 2.2 8.0 1.0 S2 B:F4S301 2.3 8.0 1.0 S1 B:F4S301 2.3 8.1 1.0 SG B:CYS25 2.4 7.9 1.0 FE2 B:F4S301 2.6 7.9 1.0 FE4 B:F4S301 2.8 8.1 1.0 CB B:CYS23 3.4 9.1 1.0 CB B:CYS25 3.5 8.0 1.0 FE3 B:F4S301 3.5 7.7 1.0 N B:CYS23 3.6 8.1 1.0 N B:CYS25 3.6 7.5 1.0 S3 B:F4S301 3.7 7.7 1.0 CA B:CYS23 3.9 8.4 1.0 CA B:CYS25 4.1 7.0 1.0 N B:THR24 4.1 8.0 1.0 NE2 A:HIS230 4.2 7.4 1.0 C B:CYS23 4.2 8.5 1.0 SG B:CYS158 4.4 7.5 1.0 O B:HOH285 4.5 8.5 1.0 SG B:CYS121 4.6 8.4 1.0 C B:THR24 4.8 6.7 1.0 N B:CYS26 4.8 7.2 1.0 C B:GLU22 4.8 8.5 1.0 C B:CYS25 4.9 7.6 1.0 CD2 A:HIS230 4.9 7.2 1.0 CG A:ARG74 4.9 7.7 1.0

Iron binding site 3 out of 24 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:7.9 occ:1.00 FE2 B:F4S301 0.0 7.9 1.0 SG B:CYS121 2.3 8.4 1.0 S3 B:F4S301 2.3 7.7 1.0 S2 B:F4S301 2.3 8.0 1.0 S1 B:F4S301 2.3 8.1 1.0 FE1 B:F4S301 2.6 8.1 1.0 FE3 B:F4S301 2.8 7.7 1.0 FE4 B:F4S301 2.8 8.1 1.0 CB B:CYS121 3.3 8.2 1.0 O B:HOH288 3.9 9.4 1.0 N B:CYS121 4.0 7.3 1.0 SG B:CYS25 4.1 7.9 1.0 O B:HOH285 4.2 8.5 1.0 CA B:CYS121 4.2 7.8 1.0 CB B:CYS126 4.4 8.2 1.0 SG B:CYS126 4.4 7.9 1.0 N B:CYS23 4.5 8.1 1.0 SG B:CYS26 4.6 7.7 1.0 CA B:GLU22 4.7 8.4 0.2 CA B:GLU22 4.7 8.5 0.8 SG B:CYS23 4.8 8.0 1.0 CB B:GLU22 4.8 8.6 0.2 SG B:CYS158 4.8 7.5 1.0

Iron binding site 4 out of 24 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:7.7 occ:1.00 FE3 B:F4S301 0.0 7.7 1.0 SG B:CYS158 2.3 7.5 1.0 S2 B:F4S301 2.3 8.0 1.0 SG B:CYS126 2.3 7.9 1.0 S3 B:F4S301 2.4 7.7 1.0 FE2 B:F4S301 2.8 7.9 1.0 CB B:CYS158 3.3 7.9 1.0 CB B:CYS126 3.5 8.2 1.0 FE1 B:F4S301 3.5 8.1 1.0 CA B:CYS158 3.9 6.7 1.0 FE4 B:F4S301 4.0 8.1 1.0 SG B:CYS121 4.1 8.4 1.0 SG B:CYS25 4.1 7.9 1.0 CG A:ARG74 4.3 7.7 1.0 N B:CYS121 4.5 7.3 1.0 CB B:SER120 4.5 8.2 1.0 S1 B:F4S301 4.7 8.1 1.0 C B:CYS158 4.8 6.4 1.0 CA B:CYS126 4.9 8.3 1.0 N B:VAL127 4.9 7.7 1.0 N B:SER120 5.0 7.4 1.0 O B:GLY157 5.0 7.4 1.0

Iron binding site 5 out of 24 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:8.1 occ:1.00 FE4 B:F4S301 0.0 8.1 1.0 S1 B:F4S301 2.3 8.1 1.0 SG B:CYS26 2.3 7.7 1.0 SG B:CYS25 2.4 7.9 1.0 S3 B:F4S301 2.4 7.7 1.0 FE1 B:F4S301 2.8 8.1 1.0 FE2 B:F4S301 2.8 7.9 1.0 N B:CYS26 3.2 7.2 1.0 CB B:CYS26 3.5 8.2 1.0 CB B:CYS25 3.7 8.0 1.0 CA B:CYS26 3.8 6.6 1.0 C B:CYS25 3.9 7.6 1.0 O B:HOH288 3.9 9.4 1.0 FE3 B:F4S301 4.0 7.7 1.0 N B:CYS25 4.0 7.5 1.0 CA B:CYS25 4.1 7.0 1.0 S2 B:F4S301 4.2 8.0 1.0 CB B:PRO159 4.2 6.7 1.0 CA B:PRO159 4.4 6.2 1.0 OE2 B:GLU82 4.7 8.7 1.0 SG B:CYS23 4.7 8.0 1.0 O B:CYS25 4.8 6.9 1.0 N B:PRO159 4.8 6.6 1.0 O B:GLY157 4.9 7.4 1.0 SG B:CYS121 4.9 8.4 1.0 SG B:CYS158 4.9 7.5 1.0 CA B:CYS158 5.0 6.7 1.0 CA B:GLY119 5.0 6.8 1.0

Iron binding site 6 out of 24 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe308 b:7.4 occ:1.00 FE1 B:F3S308 0.0 7.4 1.0 S2 B:F3S308 2.2 7.6 1.0 S1 B:F3S308 2.3 7.5 1.0 S3 B:F3S308 2.3 7.4 1.0 SG B:CYS258 2.3 7.8 1.0 FE4 B:F3S308 2.7 7.2 1.0 FE3 B:F3S308 2.7 7.2 1.0 CB B:CYS258 3.2 8.3 1.0 CA B:CYS258 3.6 7.0 1.0 S4 B:F3S308 3.8 7.2 1.0 N B:ILE259 4.1 7.6 1.0 N B:GLY260 4.2 7.4 1.0 C B:CYS258 4.3 7.4 1.0 N B:CYS261 4.4 7.2 1.0 CG2 B:THR235 4.5 8.7 1.0 CG1 B:ILE195 4.5 11.4 1.0 O B:HOH680 4.7 13.5 1.0 CA B:GLY260 4.7 8.1 1.0 SG B:CYS261 4.8 7.8 1.0 SG B:CYS239 4.8 7.4 1.0 CG B:PRO251 4.8 7.6 1.0 N B:CYS258 4.8 7.6 1.0 CD1 B:ILE195 4.9 14.7 1.0 C B:GLY260 5.0 7.3 1.0

Iron binding site 7 out of 24 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe308 b:7.2 occ:1.00 FE3 B:F3S308 0.0 7.2 1.0 S4 B:F3S308 2.2 7.2 1.0 SG B:CYS261 2.3 7.8 1.0 S1 B:F3S308 2.3 7.5 1.0 S3 B:F3S308 2.3 7.4 1.0 FE4 B:F3S308 2.7 7.2 1.0 FE1 B:F3S308 2.7 7.4 1.0 CB B:CYS261 3.4 8.3 1.0 N B:CYS261 3.7 7.2 1.0 O A:HOH616 3.9 9.0 1.0 S2 B:F3S308 3.9 7.6 1.0 O B:HOH306 4.0 7.7 1.0 CA B:CYS261 4.0 7.4 1.0 NZ A:LYS227 4.0 8.6 1.0 C B:CYS261 4.5 8.0 1.0 N B:SER262 4.6 7.5 1.0 ND2 B:ASN237 4.6 7.5 1.0 SG B:CYS239 4.7 7.4 1.0 SG B:CYS258 4.7 7.8 1.0 C B:GLY260 4.9 7.3 1.0

Iron binding site 8 out of 24 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe308 b:7.2 occ:1.00 FE4 B:F3S308 0.0 7.2 1.0 S2 B:F3S308 2.2 7.6 1.0 S4 B:F3S308 2.2 7.2 1.0 S3 B:F3S308 2.3 7.4 1.0 SG B:CYS239 2.3 7.4 1.0 FE1 B:F3S308 2.7 7.4 1.0 FE3 B:F3S308 2.7 7.2 1.0 CB B:CYS239 3.2 7.5 1.0 S1 B:F3S308 3.9 7.5 1.0 ND2 B:ASN237 4.0 7.5 1.0 NE1 B:TRP244 4.2 7.3 1.0 CD1 B:ILE195 4.3 14.7 1.0 O B:HOH306 4.4 7.7 1.0 CG B:ASN237 4.5 7.2 1.0 CD B:PRO251 4.6 7.8 1.0 CG B:PRO251 4.6 7.6 1.0 CB B:ASN237 4.6 7.2 1.0 CA B:CYS239 4.7 7.1 1.0 SG B:CYS261 4.7 7.8 1.0 SG B:CYS258 4.8 7.8 1.0 CG1 B:ILE195 4.8 11.4 1.0

Iron binding site 9 out of 24 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe309 b:8.2 occ:1.00 FE1 B:SF4309 0.0 8.2 1.0 S4 B:SF4309 2.3 8.2 1.0 S3 B:SF4309 2.3 8.9 1.0 SG B:CYS199 2.3 8.0 1.0 S2 B:SF4309 2.3 8.4 1.0 FE4 B:SF4309 2.7 8.5 1.0 FE3 B:SF4309 2.7 8.3 1.0 FE2 B:SF4309 2.7 8.3 1.0 CB B:CYS199 3.1 8.3 1.0 S1 B:SF4309 3.9 8.7 1.0 CB B:ARG201 4.2 8.0 1.0 CG2 B:ILE252 4.4 9.6 1.0 CD1 B:ILE252 4.5 11.6 1.0 ND1 B:HIS196 4.5 9.1 1.0 CA B:CYS199 4.6 7.9 1.0 N B:ARG202 4.6 8.6 1.0 C B:ARG201 4.7 7.8 1.0 CA B:ARG201 4.7 7.8 1.0 N B:ARG201 4.7 7.9 1.0 SG B:CYS230 4.8 7.9 1.0 CG1 B:ILE252 4.9 10.1 1.0 SG B:CYS224 4.9 8.5 1.0 C B:CYS199 5.0 7.7 1.0 CA B:HIS196 5.0 9.3 1.0 CG B:ARG201 5.0 8.1 1.0

Iron binding site 10 out of 24 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe309 b:8.3 occ:1.00 FE2 B:SF4309 0.0 8.3 1.0 S3 B:SF4309 2.3 8.9 1.0 SG B:CYS224 2.3 8.5 1.0 S4 B:SF4309 2.3 8.2 1.0 S1 B:SF4309 2.3 8.7 1.0 FE4 B:SF4309 2.7 8.5 1.0 FE1 B:SF4309 2.7 8.2 1.0 FE3 B:SF4309 2.8 8.3 1.0 CB B:CYS224 3.4 8.6 1.0 N B:LEU225 3.8 7.7 1.0 CA B:CYS224 3.9 8.2 1.0 S2 B:SF4309 3.9 8.4 1.0 N B:TYR226 4.2 7.9 1.0 C B:CYS224 4.3 7.7 1.0 CB B:PHE205 4.4 10.5 1.0 CD2 B:PHE205 4.4 11.8 1.0 ND1 B:HIS196 4.4 9.1 1.0 CB B:TYR226 4.6 8.5 1.0 CB B:ARG201 4.7 8.0 1.0 CG B:PHE205 4.8 10.7 1.0 CA B:LEU225 4.8 7.5 1.0 C B:LEU225 4.8 7.3 1.0 CE1 B:HIS196 4.8 9.3 1.0 CA B:TYR226 4.8 8.4 1.0 SG B:CYS199 4.9 8.0 1.0 SG B:CYS230 4.9 7.9 1.0 O B:ARG201 4.9 9.2 1.0

Y.Shomura, K.S.Yoon, H.Nishihara, Y.Higuchi. Structural Basis For A [4FE-3S] Cluster in the Oxygen-Tolerant Membrane-Bound [Nife]-Hydrogenase Nature V. 479 253 2011.
ISSN: ISSN 0028-0836
PubMed: 22002607
DOI: 10.1038/NATURE10504