Iron in PDB 3ayz: Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition

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

The structure of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition, PDB code: 3ayz 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 / 1.22
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.646, 116.664, 113.612, 90.00, 91.34, 90.00
R / Rfree (%)	13.9 / 17.1

The structure of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized 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 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Iron atom in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition (pdb code 3ayz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 32 binding sites of Iron where determined in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition, PDB code: 3ayz:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 32 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition


Mono view


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 Air-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:6.7 occ:1.00 C A:CMO603 1.8 6.8 1.0 C A:CYN605 1.9 6.5 1.0 C A:CYN604 1.9 6.7 1.0 O A:O606 2.2 12.7 1.0 SG A:CYS79 2.3 8.4 1.0 SG A:CYS593 2.3 7.7 1.0 NI A:3NI602 2.8 12.9 1.0 O A:CMO603 2.9 7.8 1.0 N A:CYN605 3.0 6.2 1.0 N A:CYN604 3.1 7.6 1.0 CB A:CYS593 3.4 9.6 1.0 CB A:CYS79 3.4 9.1 1.0 O A:O609 3.5 8.0 0.7 O A:O610 3.7 8.4 0.4 O A:O607 3.8 8.1 0.7 CB A:CYS590 4.2 14.0 1.0 SG A:CYS590 4.2 15.8 1.0 NE2 A:HIS83 4.2 7.2 1.0 CG1 A:VAL544 4.2 7.3 0.5 CD A:ARG523 4.2 7.8 1.0 NH1 A:ARG523 4.3 8.2 1.0 SG A:CYS82 4.4 8.9 1.0 CD A:PRO545 4.7 5.8 1.0 SG A:CYS76 4.7 12.4 1.0 CB A:CYS76 4.8 14.2 1.0 CA A:CYS593 4.8 6.7 1.0 CA A:CYS79 4.8 8.4 1.0 NE A:ARG523 4.9 7.4 1.0

Iron binding site 2 out of 32 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition


Mono view


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 Air-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:6.2 occ:0.59 FE1 B:F4S301 0.0 6.2 0.6 FE3 B:SF3302 0.0 6.2 0.4 SG B:CYS158 2.3 5.9 1.0 S2 B:F4S301 2.3 7.3 0.6 S1 B:SF3302 2.3 7.3 0.4 S1 B:F4S301 2.3 6.6 0.6 S3 B:SF3302 2.3 6.6 0.4 SG B:CYS126 2.3 6.2 1.0 FE2 B:F4S301 2.8 6.8 0.6 FE1 B:SF3302 2.8 6.8 0.4 CB B:CYS158 3.2 5.6 1.0 CB B:CYS126 3.5 5.9 1.0 FE4 B:F4S301 3.5 7.4 0.6 FE4 B:SF3302 3.5 7.4 0.4 CA B:CYS158 3.9 5.2 1.0 SG B:CYS121 4.0 7.0 1.0 FE3 B:F4S301 4.1 6.9 0.6 SG B:CYS25 4.2 7.6 1.0 CG A:ARG74 4.4 7.3 1.0 N B:CYS121 4.5 5.7 1.0 CB B:SER120 4.5 6.6 1.0 S3 B:F4S301 4.6 7.2 0.6 S2 B:SF3302 4.6 7.2 0.4 C B:CYS158 4.8 4.4 1.0 CA B:CYS126 4.9 6.4 1.0 O B:GLY157 4.9 5.6 1.0 N B:SER120 5.0 6.0 1.0 N B:VAL127 5.0 5.8 1.0

Iron binding site 3 out of 32 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized 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 Air-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:6.8 occ:0.59 FE2 B:F4S301 0.0 6.8 0.6 FE1 B:SF3302 0.0 6.8 0.4 S2 B:F4S301 2.3 7.3 0.6 S1 B:SF3302 2.3 7.3 0.4 SG B:CYS121 2.3 7.0 1.0 S3 B:F4S301 2.3 7.2 0.6 S2 B:SF3302 2.3 7.2 0.4 S1 B:F4S301 2.3 6.6 0.6 S3 B:SF3302 2.3 6.6 0.4 FE4 B:F4S301 2.6 7.4 0.6 FE4 B:SF3302 2.6 7.4 0.4 FE1 B:F4S301 2.8 6.2 0.6 FE3 B:SF3302 2.8 6.2 0.4 FE3 B:F4S301 2.9 6.9 0.6 CB B:CYS121 3.3 6.7 1.0 FE7 B:SF3302 3.8 10.7 0.4 O B:HOH311 3.8 10.2 1.0 N B:CYS121 4.0 5.7 1.0 SG B:CYS25 4.1 7.6 1.0 O B:HOH287 4.2 6.4 1.0 CA B:CYS121 4.2 6.2 1.0 SG B:CYS126 4.4 6.2 1.0 CB B:CYS126 4.4 5.9 1.0 N B:CYS23 4.5 6.6 1.0 SG B:CYS26 4.6 6.2 1.0 SG B:CYS23 4.7 6.8 1.0 SG B:CYS158 4.7 5.9 1.0 CA B:GLU22 4.7 6.6 0.5 CA B:GLU22 4.8 7.6 0.5 CB B:GLU22 4.9 9.3 0.5

Iron binding site 4 out of 32 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition


Mono view


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 Air-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:6.9 occ:0.59 FE3 B:F4S301 0.0 6.9 0.6 FE7 B:SF3302 1.3 10.7 0.4 SG B:CYS25 2.3 7.6 1.0 S3 B:F4S301 2.3 7.2 0.6 S2 B:SF3302 2.3 7.2 0.4 SG B:CYS26 2.3 6.2 1.0 S2 B:F4S301 2.6 7.3 0.6 S1 B:SF3302 2.6 7.3 0.4 FE4 B:F4S301 2.7 7.4 0.6 FE4 B:SF3302 2.7 7.4 0.4 FE2 B:F4S301 2.9 6.8 0.6 FE1 B:SF3302 2.9 6.8 0.4 N B:CYS26 3.1 6.1 1.0 CB B:CYS26 3.5 7.1 1.0 CB B:CYS25 3.6 6.2 1.0 CA B:CYS26 3.8 5.6 1.0 C B:CYS25 3.8 5.0 1.0 N B:CYS25 3.9 6.0 1.0 O B:HOH311 3.9 10.2 1.0 CA B:CYS25 4.0 5.3 1.0 FE1 B:F4S301 4.1 6.2 0.6 FE3 B:SF3302 4.1 6.2 0.4 S1 B:F4S301 4.2 6.6 0.6 S3 B:SF3302 4.2 6.6 0.4 CB B:PRO159 4.3 4.5 1.0 CA B:PRO159 4.4 4.1 1.0 OE2 B:GLU82 4.5 11.4 1.0 SG B:CYS23 4.6 6.8 1.0 O B:CYS25 4.8 5.5 1.0 N B:PRO159 4.9 4.5 1.0 C B:THR24 4.9 5.4 1.0 O B:GLY157 4.9 5.6 1.0 CG B:GLU82 5.0 10.2 1.0 CA B:CYS158 5.0 5.2 1.0 SG B:CYS158 5.0 5.9 1.0

Iron binding site 5 out of 32 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition


Mono view


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 Air-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:7.4 occ:0.59 FE4 B:F4S301 0.0 7.4 0.6 FE4 B:SF3302 0.0 7.4 0.4 SG B:CYS23 2.2 6.8 1.0 S1 B:F4S301 2.3 6.6 0.6 S3 B:SF3302 2.3 6.6 0.4 S3 B:F4S301 2.3 7.2 0.6 S2 B:SF3302 2.3 7.2 0.4 SG B:CYS25 2.3 7.6 1.0 FE2 B:F4S301 2.6 6.8 0.6 FE1 B:SF3302 2.6 6.8 0.4 FE3 B:F4S301 2.7 6.9 0.6 FE7 B:SF3302 3.2 10.7 0.4 CB B:CYS23 3.4 6.8 1.0 CB B:CYS25 3.4 6.2 1.0 FE1 B:F4S301 3.5 6.2 0.6 FE3 B:SF3302 3.5 6.2 0.4 N B:CYS25 3.6 6.0 1.0 N B:CYS23 3.7 6.6 1.0 S2 B:F4S301 3.7 7.3 0.6 S1 B:SF3302 3.7 7.3 0.4 CA B:CYS23 3.9 7.3 1.0 CA B:CYS25 4.1 5.3 1.0 N B:THR24 4.1 6.6 1.0 NE2 A:HIS230 4.1 5.6 1.0 C B:CYS23 4.2 6.9 1.0 SG B:CYS158 4.4 5.9 1.0 O B:HOH287 4.6 6.4 1.0 SG B:CYS121 4.6 7.0 1.0 N B:CYS26 4.7 6.1 1.0 C B:THR24 4.8 5.4 1.0 C B:GLU22 4.8 7.0 1.0 C B:CYS25 4.9 5.0 1.0 CD2 A:HIS230 4.9 6.1 1.0 O B:CYS23 5.0 7.8 1.0

Iron binding site 6 out of 32 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition


Mono view


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 Air-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:6.8 occ:0.41 FE2 B:F4S301 0.0 6.8 0.6 FE1 B:SF3302 0.0 6.8 0.4 S2 B:F4S301 2.3 7.3 0.6 S1 B:SF3302 2.3 7.3 0.4 SG B:CYS121 2.3 7.0 1.0 S3 B:F4S301 2.3 7.2 0.6 S2 B:SF3302 2.3 7.2 0.4 S1 B:F4S301 2.3 6.6 0.6 S3 B:SF3302 2.3 6.6 0.4 FE4 B:F4S301 2.6 7.4 0.6 FE4 B:SF3302 2.6 7.4 0.4 FE1 B:F4S301 2.8 6.2 0.6 FE3 B:SF3302 2.8 6.2 0.4 FE3 B:F4S301 2.9 6.9 0.6 CB B:CYS121 3.3 6.7 1.0 FE7 B:SF3302 3.8 10.7 0.4 O B:HOH311 3.8 10.2 1.0 N B:CYS121 4.0 5.7 1.0 SG B:CYS25 4.1 7.6 1.0 O B:HOH287 4.2 6.4 1.0 CA B:CYS121 4.2 6.2 1.0 SG B:CYS126 4.4 6.2 1.0 CB B:CYS126 4.4 5.9 1.0 N B:CYS23 4.5 6.6 1.0 SG B:CYS26 4.6 6.2 1.0 SG B:CYS23 4.7 6.8 1.0 SG B:CYS158 4.7 5.9 1.0 CA B:GLU22 4.7 6.6 0.5 CA B:GLU22 4.8 7.6 0.5 CB B:GLU22 4.9 9.3 0.5

Iron binding site 7 out of 32 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition


Mono view


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 Air-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:6.2 occ:0.41 FE1 B:F4S301 0.0 6.2 0.6 FE3 B:SF3302 0.0 6.2 0.4 SG B:CYS158 2.3 5.9 1.0 S2 B:F4S301 2.3 7.3 0.6 S1 B:SF3302 2.3 7.3 0.4 S1 B:F4S301 2.3 6.6 0.6 S3 B:SF3302 2.3 6.6 0.4 SG B:CYS126 2.3 6.2 1.0 FE2 B:F4S301 2.8 6.8 0.6 FE1 B:SF3302 2.8 6.8 0.4 CB B:CYS158 3.2 5.6 1.0 CB B:CYS126 3.5 5.9 1.0 FE4 B:F4S301 3.5 7.4 0.6 FE4 B:SF3302 3.5 7.4 0.4 CA B:CYS158 3.9 5.2 1.0 SG B:CYS121 4.0 7.0 1.0 FE3 B:F4S301 4.1 6.9 0.6 SG B:CYS25 4.2 7.6 1.0 CG A:ARG74 4.4 7.3 1.0 N B:CYS121 4.5 5.7 1.0 CB B:SER120 4.5 6.6 1.0 S3 B:F4S301 4.6 7.2 0.6 S2 B:SF3302 4.6 7.2 0.4 C B:CYS158 4.8 4.4 1.0 CA B:CYS126 4.9 6.4 1.0 O B:GLY157 4.9 5.6 1.0 N B:SER120 5.0 6.0 1.0 N B:VAL127 5.0 5.8 1.0

Iron binding site 8 out of 32 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized 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 Air-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:7.4 occ:0.41 FE4 B:F4S301 0.0 7.4 0.6 FE4 B:SF3302 0.0 7.4 0.4 SG B:CYS23 2.2 6.8 1.0 S1 B:F4S301 2.3 6.6 0.6 S3 B:SF3302 2.3 6.6 0.4 S3 B:F4S301 2.3 7.2 0.6 S2 B:SF3302 2.3 7.2 0.4 SG B:CYS25 2.3 7.6 1.0 FE2 B:F4S301 2.6 6.8 0.6 FE1 B:SF3302 2.6 6.8 0.4 FE3 B:F4S301 2.7 6.9 0.6 FE7 B:SF3302 3.2 10.7 0.4 CB B:CYS23 3.4 6.8 1.0 CB B:CYS25 3.4 6.2 1.0 FE1 B:F4S301 3.5 6.2 0.6 FE3 B:SF3302 3.5 6.2 0.4 N B:CYS25 3.6 6.0 1.0 N B:CYS23 3.7 6.6 1.0 S2 B:F4S301 3.7 7.3 0.6 S1 B:SF3302 3.7 7.3 0.4 CA B:CYS23 3.9 7.3 1.0 CA B:CYS25 4.1 5.3 1.0 N B:THR24 4.1 6.6 1.0 NE2 A:HIS230 4.1 5.6 1.0 C B:CYS23 4.2 6.9 1.0 SG B:CYS158 4.4 5.9 1.0 O B:HOH287 4.6 6.4 1.0 SG B:CYS121 4.6 7.0 1.0 N B:CYS26 4.7 6.1 1.0 C B:THR24 4.8 5.4 1.0 C B:GLU22 4.8 7.0 1.0 C B:CYS25 4.9 5.0 1.0 CD2 A:HIS230 4.9 6.1 1.0 O B:CYS23 5.0 7.8 1.0

Iron binding site 9 out of 32 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized 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 Air-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:10.7 occ:0.41 FE7 B:SF3302 0.0 10.7 0.4 FE3 B:F4S301 1.3 6.9 0.6 N B:CYS26 2.0 6.1 1.0 S3 B:F4S301 2.3 7.2 0.6 S2 B:SF3302 2.3 7.2 0.4 SG B:CYS26 2.3 6.2 1.0 SG B:CYS25 2.7 7.6 1.0 CB B:CYS26 2.8 7.1 1.0 CA B:CYS26 2.9 5.6 1.0 C B:CYS25 2.9 5.0 1.0 N B:CYS25 3.0 6.0 1.0 FE4 B:F4S301 3.2 7.4 0.6 FE4 B:SF3302 3.2 7.4 0.4 CA B:CYS25 3.2 5.3 1.0 OE2 B:GLU82 3.3 11.4 1.0 CB B:CYS25 3.4 6.2 1.0 C B:THR24 3.8 5.4 1.0 FE2 B:F4S301 3.8 6.8 0.6 FE1 B:SF3302 3.8 6.8 0.4 S2 B:F4S301 3.9 7.3 0.6 S1 B:SF3302 3.9 7.3 0.4 O B:CYS25 4.0 5.5 1.0 CD B:GLU82 4.1 8.1 1.0 C B:CYS26 4.1 5.0 1.0 O B:HOH311 4.2 10.2 1.0 CG B:GLU82 4.2 10.2 1.0 N B:THR24 4.4 6.6 1.0 O B:THR24 4.4 6.7 1.0 CB B:PRO159 4.4 4.5 1.0 CA B:THR24 4.4 6.3 1.0 N B:SER27 4.4 5.8 1.0 SG B:CYS23 4.7 6.8 1.0 CA B:PRO159 4.9 4.1 1.0

Iron binding site 10 out of 32 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized 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 Air-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe308 b:5.8 occ:1.00 FE1 B:F3S308 0.0 5.8 1.0 S2 B:F3S308 2.2 6.0 1.0 SG B:CYS258 2.3 6.1 1.0 S1 B:F3S308 2.3 5.9 1.0 S3 B:F3S308 2.3 5.7 1.0 FE4 B:F3S308 2.7 5.3 1.0 FE3 B:F3S308 2.7 5.6 1.0 CB B:CYS258 3.1 5.6 1.0 CA B:CYS258 3.6 4.9 1.0 S4 B:F3S308 3.9 5.6 1.0 N B:ILE259 4.1 5.3 1.0 N B:GLY260 4.2 5.3 1.0 C B:CYS258 4.3 4.9 1.0 N B:CYS261 4.4 5.6 1.0 CG2 B:THR235 4.5 7.7 1.0 CG1 B:ILE195 4.6 12.7 1.0 O B:HOH818 4.7 17.7 1.0 CA B:GLY260 4.7 6.1 1.0 SG B:CYS261 4.8 6.2 1.0 SG B:CYS239 4.8 5.5 1.0 N B:CYS258 4.8 5.5 1.0 CG B:PRO251 4.9 5.8 1.0 CD1 B:ILE195 4.9 18.1 1.0 C B:GLY260 5.0 5.7 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