Iron in PDB 5xvb: [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An H2- Reduced Condition

The structure of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An H2- Reduced Condition, PDB code: 5xvb was solved by K.Nishikawa, H.Matsuura, N.D.Muhd Noor, H.Tai, S.Hirota, J.Kim, J.Kang, M.Tateno, K.S.Yoon, S.Ogo, Y.Shomura, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.02 / 1.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.730, 121.610, 98.880, 90.00, 102.65, 90.00
R / Rfree (%)	18.1 / 21.9

The structure of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An H2- Reduced Condition (pdb code 5xvb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An H2- Reduced Condition, PDB code: 5xvb:
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 [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 1 of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An H2- Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ L:Fe602 b:17.3 occ:1.00 FE L:NFU602 0.0 17.3 1.0 C3 L:NFU602 1.8 17.6 1.0 C2 L:NFU602 1.9 13.4 1.0 C1 L:NFU602 2.0 14.6 1.0 SG L:CYS64 2.4 16.9 1.0 SG L:CYS549 2.4 17.6 1.0 NI L:NFU602 2.7 23.0 1.0 O3 L:NFU602 2.9 18.5 1.0 N1 L:NFU602 3.0 16.2 1.0 N2 L:NFU602 3.1 13.6 1.0 CB L:CYS64 3.4 16.7 1.0 CB L:CYS549 3.5 19.1 1.0 CD L:ARG479 4.1 12.8 1.0 NE2 L:HIS68 4.2 15.3 1.0 CG1 L:VAL500 4.2 13.3 1.0 CB L:CYS546 4.4 15.0 1.0 SG L:CYS546 4.5 24.5 1.0 NH1 L:ARG479 4.5 12.7 1.0 CG L:PRO501 4.6 13.4 1.0 OG1 L:THR67 4.6 15.8 1.0 CA L:CYS64 4.7 17.3 1.0 CA L:CYS549 4.9 16.4 1.0 CB L:ARG479 4.9 14.8 1.0 CD L:PRO501 4.9 13.0 1.0 CD2 L:HIS68 5.0 13.5 1.0 CB L:CYS61 5.0 18.9 1.0 NE L:ARG479 5.0 13.7 1.0

Iron binding site 2 out of 24 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 2 of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An H2- Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe500 b:18.9 occ:1.00 FE1 S:SF4500 0.0 18.9 1.0 S4 S:SF4500 2.2 24.9 1.0 S2 S:SF4500 2.2 23.2 1.0 S3 S:SF4500 2.2 23.6 1.0 SG S:CYS220 2.4 19.4 1.0 FE3 S:SF4500 2.7 21.7 1.0 FE2 S:SF4500 2.8 18.8 1.0 FE4 S:SF4500 2.9 17.1 1.0 CB S:CYS220 3.5 22.0 1.0 S1 S:SF4500 3.8 24.2 1.0 N S:LEU221 3.8 14.9 1.0 CA S:CYS220 4.0 17.4 1.0 N S:TYR222 4.0 19.1 1.0 C S:CYS220 4.3 17.3 1.0 CB S:PHE201 4.4 19.7 1.0 CB S:TYR222 4.4 17.5 1.0 CD1 S:PHE201 4.4 23.3 1.0 CB S:ARG197 4.6 19.5 1.0 CA S:TYR222 4.6 16.5 1.0 ND1 S:HIS192 4.7 20.5 1.0 O S:ARG197 4.8 20.0 1.0 C S:LEU221 4.8 19.5 1.0 CA S:LEU221 4.8 17.3 1.0 CG S:PHE201 4.8 22.8 1.0 C S:ARG197 4.9 19.8 1.0 SG S:CYS226 4.9 17.1 1.0 CE1 S:HIS192 5.0 22.0 1.0

Iron binding site 3 out of 24 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An H2- Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe500 b:18.8 occ:1.00 FE2 S:SF4500 0.0 18.8 1.0 S1 S:SF4500 2.2 24.2 1.0 S3 S:SF4500 2.2 23.6 1.0 S4 S:SF4500 2.2 24.9 1.0 SG S:CYS195 2.4 18.8 1.0 FE3 S:SF4500 2.7 21.7 1.0 FE4 S:SF4500 2.7 17.1 1.0 FE1 S:SF4500 2.8 18.9 1.0 CB S:CYS195 3.2 20.8 1.0 S2 S:SF4500 3.7 23.2 1.0 CB S:ARG197 4.1 19.5 1.0 N S:ARG198 4.6 19.8 1.0 N S:ARG197 4.6 16.9 1.0 CA S:CYS195 4.6 21.3 1.0 C S:ARG197 4.6 19.8 1.0 CA S:ARG197 4.6 17.6 1.0 ND1 S:HIS192 4.7 20.5 1.0 C S:CYS195 4.8 24.0 1.0 SG S:CYS226 4.8 17.1 1.0 CH2 S:TRP247 4.9 16.6 1.0 CG2 S:VAL249 4.9 16.0 1.0 CG S:ARG197 4.9 18.2 1.0

Iron binding site 4 out of 24 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 4 of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An H2- Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe500 b:21.7 occ:1.00 FE3 S:SF4500 0.0 21.7 1.0 S2 S:SF4500 2.2 23.2 1.0 S1 S:SF4500 2.2 24.2 1.0 S4 S:SF4500 2.2 24.9 1.0 ND1 S:HIS192 2.3 20.5 1.0 FE1 S:SF4500 2.7 18.9 1.0 FE2 S:SF4500 2.7 18.8 1.0 FE4 S:SF4500 2.8 17.1 1.0 CE1 S:HIS192 3.1 22.0 1.0 CG S:HIS192 3.4 24.3 1.0 S3 S:SF4500 3.7 23.6 1.0 CB S:HIS192 3.8 16.1 1.0 CA S:HIS192 4.0 16.1 1.0 CD S:PRO229 4.1 18.9 1.0 NE2 S:HIS192 4.3 22.1 1.0 CG S:PRO229 4.3 19.5 1.0 CD2 S:HIS192 4.4 22.6 1.0 CB S:CYS195 4.7 20.8 1.0 O S:HIS192 4.7 23.4 1.0 N S:PRO229 4.8 20.6 1.0 SG S:CYS195 4.8 18.8 1.0 SG S:CYS220 4.8 19.4 1.0 CD1 S:PHE201 4.8 23.3 1.0 SG S:CYS226 4.9 17.1 1.0 C S:HIS192 4.9 18.1 1.0 CA S:GLY228 5.0 15.2 1.0

Iron binding site 5 out of 24 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 5 of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An H2- Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe500 b:17.1 occ:1.00 FE4 S:SF4500 0.0 17.1 1.0 S3 S:SF4500 2.2 23.6 1.0 S1 S:SF4500 2.2 24.2 1.0 S2 S:SF4500 2.2 23.2 1.0 SG S:CYS226 2.3 17.1 1.0 FE2 S:SF4500 2.7 18.8 1.0 FE3 S:SF4500 2.8 21.7 1.0 FE1 S:SF4500 2.9 18.9 1.0 CB S:CYS226 3.2 18.7 1.0 S4 S:SF4500 3.8 24.9 1.0 CA S:GLY228 4.3 15.2 1.0 CD S:PRO229 4.4 18.9 1.0 N S:GLY228 4.4 16.6 1.0 CA S:CYS226 4.6 16.6 1.0 CG1 S:VAL249 4.7 19.6 1.0 N S:TYR222 4.8 19.1 1.0 C S:CYS226 4.8 18.0 1.0 SG S:CYS195 4.8 18.8 1.0 ND1 S:HIS192 4.9 20.5 1.0 SG S:CYS220 4.9 19.4 1.0 N S:LEU221 4.9 14.9 1.0

Iron binding site 6 out of 24 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 6 of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An H2- Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe501 b:16.6 occ:1.00 FE1 S:F3S501 0.0 16.6 1.0 S3 S:F3S501 2.2 17.9 1.0 S1 S:F3S501 2.2 16.4 1.0 S2 S:F3S501 2.2 17.0 1.0 SG S:CYS258 2.4 20.0 1.0 FE3 S:F3S501 2.7 16.6 1.0 FE4 S:F3S501 2.7 16.5 1.0 CB S:CYS258 3.4 16.9 1.0 O L:HOH780 3.5 17.9 1.0 N S:CYS258 3.7 15.2 1.0 S4 S:F3S501 3.7 17.0 1.0 CA S:CYS258 4.0 15.1 1.0 OD1 S:ASN259 4.2 15.0 1.0 N S:ASN259 4.2 14.8 1.0 O S:HOH645 4.2 17.7 1.0 C S:CYS258 4.5 15.6 1.0 O S:HOH625 4.7 19.1 1.0 SG S:CYS235 4.8 17.9 1.0 CG S:ASN259 4.8 16.8 1.0 C S:GLY257 4.8 17.5 1.0 CE L:LYS211 4.8 13.4 1.0 OE1 L:GLN216 4.8 16.4 1.0 SG S:CYS255 5.0 16.4 1.0 N S:GLY257 5.0 18.3 1.0

Iron binding site 7 out of 24 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 7 of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An H2- Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe501 b:16.6 occ:1.00 FE3 S:F3S501 0.0 16.6 1.0 S4 S:F3S501 2.1 17.0 1.0 S1 S:F3S501 2.2 16.4 1.0 S3 S:F3S501 2.2 17.9 1.0 SG S:CYS235 2.3 17.9 1.0 FE1 S:F3S501 2.7 16.6 1.0 FE4 S:F3S501 2.8 16.5 1.0 CB S:CYS235 3.2 17.3 1.0 O S:HOH645 3.9 17.7 1.0 S2 S:F3S501 4.0 17.0 1.0 CD1 S:ILE191 4.2 15.1 1.0 CZ S:PHE240 4.3 15.8 1.0 CE1 S:PHE240 4.4 14.9 1.0 OD1 S:ASN259 4.6 15.0 1.0 CA S:CYS235 4.6 17.5 1.0 SG S:CYS258 4.8 20.0 1.0 CD S:PRO248 4.8 17.0 1.0 SG S:CYS255 4.9 16.4 1.0 CG S:PRO248 4.9 15.8 1.0 ND2 S:ASN259 4.9 15.7 1.0 CG S:ASN259 4.9 16.8 1.0 O S:HOH666 5.0 16.9 1.0

Iron binding site 8 out of 24 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An H2- Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe501 b:16.5 occ:1.00 FE4 S:F3S501 0.0 16.5 1.0 S3 S:F3S501 2.2 17.9 1.0 S4 S:F3S501 2.2 17.0 1.0 S2 S:F3S501 2.2 17.0 1.0 SG S:CYS255 2.4 16.4 1.0 FE1 S:F3S501 2.7 16.6 1.0 FE3 S:F3S501 2.8 16.6 1.0 CB S:CYS255 3.4 14.0 1.0 CA S:CYS255 3.6 13.8 1.0 N S:TYR256 3.7 15.8 1.0 N S:GLY257 3.9 18.3 1.0 S1 S:F3S501 4.0 16.4 1.0 C S:CYS255 4.1 18.9 1.0 CD1 S:ILE191 4.2 15.1 1.0 N S:CYS258 4.4 15.2 1.0 CA S:GLY257 4.5 16.8 1.0 NE2 L:GLN216 4.6 15.4 1.0 CA S:TYR256 4.8 16.2 1.0 SG S:CYS235 4.8 17.9 1.0 C S:TYR256 4.8 14.2 1.0 CG2 S:THR231 4.9 17.3 1.0 C S:GLY257 4.9 17.5 1.0 N S:CYS255 5.0 14.2 1.0 SG S:CYS258 5.0 20.0 1.0

Iron binding site 9 out of 24 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An H2- Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe502 b:21.1 occ:1.00 FE1 S:SF4502 0.0 21.1 1.0 S3 S:SF4502 2.2 22.3 1.0 S4 S:SF4502 2.2 22.8 1.0 S2 S:SF4502 2.2 20.8 1.0 SG S:CYS22 2.2 19.0 1.0 FE3 S:SF4502 2.8 19.8 1.0 FE4 S:SF4502 2.9 22.6 1.0 FE2 S:SF4502 2.9 21.6 1.0 CB S:CYS22 3.3 18.7 1.0 N S:CYS22 3.7 21.2 1.0 S1 S:SF4502 3.7 21.9 1.0 CA S:CYS22 4.0 21.0 1.0 O S:HOH669 4.1 17.9 0.8 N S:GLY24 4.1 18.6 1.0 NE2 L:HIS214 4.1 17.1 1.0 CA S:GLY24 4.4 18.7 1.0 C S:CYS22 4.4 19.5 1.0 N S:THR23 4.5 22.5 1.0 O L:HOH843 4.6 22.1 0.9 SG S:CYS154 4.7 18.6 1.0 CD2 L:HIS214 4.8 16.7 1.0 N S:CYS25 4.8 18.9 1.0 CG L:ARG59 4.9 14.7 1.0 C S:GLU21 4.9 25.2 1.0 SG S:CYS120 5.0 21.9 1.0

Iron binding site 10 out of 24 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An H2- Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe502 b:21.6 occ:1.00 FE2 S:SF4502 0.0 21.6 1.0 S3 S:SF4502 2.2 22.3 1.0 S1 S:SF4502 2.2 21.9 1.0 S4 S:SF4502 2.2 22.8 1.0 SG S:CYS120 2.3 21.9 1.0 FE3 S:SF4502 2.8 19.8 1.0 FE1 S:SF4502 2.9 21.1 1.0 FE4 S:SF4502 3.0 22.6 1.0 CB S:CYS120 3.0 19.6 1.0 O S:HOH678 3.8 17.2 0.9 S2 S:SF4502 3.8 20.8 1.0 O L:HOH843 3.9 22.1 0.9 O S:HOH622 3.9 16.8 1.0 N S:CYS120 4.0 16.9 1.0 CA S:CYS120 4.1 18.4 1.0 SG S:CYS154 4.5 18.6 1.0 CA S:GLY82 4.9 20.6 1.0 N S:CYS22 5.0 21.2 1.0 CG1 S:VAL126 5.0 21.4 1.0

N.D.M.Noor, H.Matsuura, K.Nishikawa, H.Tai, S.Hirota, J.Kim, J.Kang, M.Tateno, K.S.Yoon, S.Ogo, S.Kubota, Y.Shomura, Y.Higuchi. Redox-Dependent Conformational Changes of A Proximal [4FE-4S] Cluster in Hyb-Type [Nife]-Hydrogenase to Protect the Active Site From O2. Chem.Commun.(Camb.) V. 54 12385 2018.
ISSN: ESSN 1364-548X
PubMed: 30328414
DOI: 10.1039/C8CC06261G