Iron in PDB 5xvc: [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-Oxidized Condition

The structure of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-Oxidized Condition, PDB code: 5xvc 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)	37.86 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.970, 121.830, 99.170, 90.00, 102.93, 90.00
R / Rfree (%)	16.6 / 21.7

The structure of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-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 - 24;

Binding sites:

The binding sites of Iron atom in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-Oxidized Condition (pdb code 5xvc). 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 A Ferricyanide-Oxidized Condition, PDB code: 5xvc:
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 A Ferricyanide-Oxidized 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 A Ferricyanide-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ L:Fe602 b:7.7 occ:1.00 FE L:NFV602 0.0 7.7 1.0 C1 L:NFV602 1.8 7.7 1.0 O4 L:NFV602 1.8 12.9 1.0 C3 L:NFV602 1.9 4.7 1.0 C2 L:NFV602 1.9 8.0 1.0 SG L:CYS64 2.5 6.1 1.0 SG L:CYS549 2.5 9.3 1.0 O1 L:NFV602 2.9 10.6 1.0 N2 L:NFV602 2.9 4.5 1.0 NI L:NFV602 3.0 11.7 1.0 N3 L:NFV602 3.0 4.1 1.0 CB L:CYS64 3.4 7.4 1.0 CB L:CYS549 3.6 8.6 1.0 CD L:ARG479 4.1 6.1 1.0 NE2 L:HIS68 4.2 10.7 1.0 CG1 L:VAL500 4.2 7.7 1.0 CG2 L:THR67 4.4 3.5 1.0 CB L:CSO546 4.5 6.4 1.0 NH1 L:ARG479 4.5 4.3 1.0 CG L:PRO501 4.6 5.7 1.0 SG L:CSO546 4.7 11.8 1.0 CA L:CYS64 4.8 7.0 1.0 CB L:ARG479 4.8 5.4 1.0 CA L:CYS549 4.9 8.4 1.0 CD L:PRO501 4.9 6.3 1.0 CE1 L:HIS68 5.0 7.7 1.0 NE L:ARG479 5.0 5.6 1.0

Iron binding site 2 out of 24 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-Oxidized 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 A Ferricyanide-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe500 b:10.4 occ:1.00 FE1 S:SF4500 0.0 10.4 1.0 S4 S:SF4500 2.2 17.4 1.0 S2 S:SF4500 2.2 13.6 1.0 S3 S:SF4500 2.2 14.1 1.0 SG S:CYS220 2.3 11.0 1.0 FE3 S:SF4500 2.8 13.0 1.0 FE2 S:SF4500 2.9 12.2 1.0 FE4 S:SF4500 2.9 9.8 1.0 CB S:CYS220 3.5 14.0 1.0 S1 S:SF4500 3.8 13.6 1.0 N S:LEU221 3.9 8.3 1.0 N S:TYR222 4.0 7.9 1.0 CA S:CYS220 4.1 8.8 1.0 CB S:PHE201 4.4 10.6 1.0 C S:CYS220 4.4 9.1 1.0 CB S:TYR222 4.4 9.5 1.0 CD1 S:PHE201 4.5 13.9 1.0 CA S:TYR222 4.6 8.5 1.0 CB S:ARG197 4.6 9.8 1.0 C S:LEU221 4.8 13.2 1.0 ND1 S:HIS192 4.8 16.2 1.0 O S:ARG197 4.8 10.3 1.0 CG S:PHE201 4.8 15.3 1.0 CA S:LEU221 4.8 8.6 1.0 C S:ARG197 4.9 9.6 1.0

Iron binding site 3 out of 24 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-Oxidized 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 A Ferricyanide-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe500 b:12.2 occ:1.00 FE2 S:SF4500 0.0 12.2 1.0 S1 S:SF4500 2.2 13.6 1.0 S3 S:SF4500 2.2 14.1 1.0 S4 S:SF4500 2.2 17.4 1.0 SG S:CYS195 2.4 12.6 1.0 FE4 S:SF4500 2.8 9.8 1.0 FE1 S:SF4500 2.9 10.4 1.0 FE3 S:SF4500 2.9 13.0 1.0 CB S:CYS195 3.2 11.4 1.0 S2 S:SF4500 3.8 13.6 1.0 CB S:ARG197 4.1 9.8 1.0 N S:ARG198 4.5 9.8 1.0 N S:ARG197 4.5 7.8 1.0 CA S:CYS195 4.6 10.7 1.0 CA S:ARG197 4.6 9.6 1.0 C S:ARG197 4.7 9.6 1.0 C S:CYS195 4.8 14.0 1.0 CH2 S:TRP247 4.8 10.4 1.0 CG2 S:VAL249 4.8 5.3 1.0 CG S:ARG197 4.8 9.3 1.0 ND1 S:HIS192 4.9 16.2 1.0 SG S:CYS226 5.0 8.3 1.0

Iron binding site 4 out of 24 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-Oxidized 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 A Ferricyanide-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe500 b:13.0 occ:1.00 FE3 S:SF4500 0.0 13.0 1.0 S2 S:SF4500 2.2 13.6 1.0 S4 S:SF4500 2.2 17.4 1.0 S1 S:SF4500 2.2 13.6 1.0 ND1 S:HIS192 2.3 16.2 1.0 FE1 S:SF4500 2.8 10.4 1.0 FE4 S:SF4500 2.9 9.8 1.0 FE2 S:SF4500 2.9 12.2 1.0 CE1 S:HIS192 3.2 13.7 1.0 CG S:HIS192 3.3 14.2 1.0 CB S:HIS192 3.7 10.2 1.0 S3 S:SF4500 3.7 14.1 1.0 CA S:HIS192 4.0 11.1 1.0 CD S:PRO229 4.1 9.0 1.0 CG S:PRO229 4.3 9.9 1.0 NE2 S:HIS192 4.3 12.7 1.0 CD2 S:HIS192 4.4 12.7 1.0 CB S:CYS195 4.7 11.4 1.0 N S:PRO229 4.7 14.7 1.0 O S:HIS192 4.7 14.4 1.0 CA S:GLY228 4.8 8.1 1.0 C S:HIS192 4.9 10.6 1.0 SG S:CYS195 4.9 12.6 1.0 C S:GLY228 4.9 12.2 1.0 SG S:CYS220 4.9 11.0 1.0 CD1 S:PHE201 4.9 13.9 1.0 SG S:CYS226 4.9 8.3 1.0 N S:HIS192 5.0 10.0 1.0

Iron binding site 5 out of 24 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-Oxidized 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 A Ferricyanide-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe500 b:9.8 occ:1.00 FE4 S:SF4500 0.0 9.8 1.0 S3 S:SF4500 2.2 14.1 1.0 S1 S:SF4500 2.2 13.6 1.0 S2 S:SF4500 2.2 13.6 1.0 SG S:CYS226 2.3 8.3 1.0 FE2 S:SF4500 2.8 12.2 1.0 FE3 S:SF4500 2.9 13.0 1.0 FE1 S:SF4500 2.9 10.4 1.0 CB S:CYS226 3.2 7.2 1.0 S4 S:SF4500 3.8 17.4 1.0 CA S:GLY228 4.2 8.1 1.0 N S:GLY228 4.3 9.6 1.0 CD S:PRO229 4.4 9.0 1.0 CA S:CYS226 4.5 4.6 1.0 C S:CYS226 4.7 8.0 1.0 N S:TYR222 4.8 7.9 1.0 CG1 S:VAL249 4.8 6.3 1.0 SG S:CYS195 4.9 12.6 1.0 SG S:CYS220 4.9 11.0 1.0 O S:CYS226 5.0 12.3 1.0

Iron binding site 6 out of 24 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-Oxidized 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 A Ferricyanide-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe501 b:7.0 occ:1.00 FE1 S:F3S501 0.0 7.0 1.0 S2 S:F3S501 2.2 5.7 1.0 S1 S:F3S501 2.2 6.6 1.0 S3 S:F3S501 2.2 8.4 1.0 SG S:CYS258 2.4 10.6 1.0 FE4 S:F3S501 2.6 8.3 1.0 FE3 S:F3S501 2.6 8.1 1.0 CB S:CYS258 3.4 8.9 1.0 O L:HOH784 3.6 5.8 1.0 N S:CYS258 3.7 6.7 1.0 S4 S:F3S501 3.7 5.9 1.0 CA S:CYS258 4.0 5.6 1.0 N S:ASN259 4.2 7.0 1.0 O S:HOH647 4.2 4.3 1.0 OD1 S:ASN259 4.2 5.4 1.0 C S:CYS258 4.5 6.6 1.0 C S:GLY257 4.8 7.9 1.0 O S:HOH614 4.8 8.5 0.9 SG S:CYS235 4.8 9.0 1.0 CE L:LYS211 4.8 6.7 1.0 CG S:ASN259 4.8 8.1 1.0 OE1 L:GLN216 4.9 9.6 1.0 N S:GLY257 4.9 8.7 1.0 SG S:CYS255 4.9 8.8 1.0

Iron binding site 7 out of 24 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-Oxidized 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 A Ferricyanide-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe501 b:8.1 occ:1.00 FE3 S:F3S501 0.0 8.1 1.0 S4 S:F3S501 2.2 5.9 1.0 S1 S:F3S501 2.2 6.6 1.0 S3 S:F3S501 2.2 8.4 1.0 SG S:CYS235 2.4 9.0 1.0 FE1 S:F3S501 2.6 7.0 1.0 FE4 S:F3S501 2.7 8.3 1.0 CB S:CYS235 3.3 7.1 1.0 O S:HOH647 3.9 4.3 1.0 S2 S:F3S501 3.9 5.7 1.0 CD1 S:ILE191 4.2 11.3 1.0 CZ S:PHE240 4.3 6.6 1.0 CE1 S:PHE240 4.4 6.4 1.0 OD1 S:ASN259 4.6 5.4 1.0 CA S:CYS235 4.7 8.6 1.0 SG S:CYS258 4.8 10.6 1.0 SG S:CYS255 4.8 8.8 1.0 O S:HOH653 4.9 7.1 1.0 CG S:ASN259 4.9 8.1 1.0 ND2 S:ASN259 4.9 5.1 1.0 CD S:PRO248 5.0 4.6 1.0

Iron binding site 8 out of 24 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-Oxidized 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 A Ferricyanide-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe501 b:8.3 occ:1.00 FE4 S:F3S501 0.0 8.3 1.0 S3 S:F3S501 2.2 8.4 1.0 S4 S:F3S501 2.2 5.9 1.0 S2 S:F3S501 2.2 5.7 1.0 SG S:CYS255 2.5 8.8 1.0 FE1 S:F3S501 2.6 7.0 1.0 FE3 S:F3S501 2.7 8.1 1.0 CB S:CYS255 3.4 5.8 1.0 CA S:CYS255 3.7 4.8 1.0 N S:TYR256 3.8 5.2 1.0 S1 S:F3S501 3.8 6.6 1.0 N S:GLY257 3.9 8.7 1.0 C S:CYS255 4.2 8.4 1.0 CD1 S:ILE191 4.3 11.3 1.0 N S:CYS258 4.4 6.7 1.0 CA S:GLY257 4.5 8.1 1.0 NE2 L:GLN216 4.5 7.3 1.0 SG S:CYS235 4.8 9.0 1.0 CA S:TYR256 4.8 4.7 1.0 C S:TYR256 4.8 7.0 1.0 SG S:CYS258 4.9 10.6 1.0 C S:GLY257 4.9 7.9 1.0 OG1 S:THR231 5.0 17.3 1.0

Iron binding site 9 out of 24 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-Oxidized 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 A Ferricyanide-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe502 b:17.6 occ:1.00 FE2 S:8JU502 0.0 17.6 1.0 O S:8JU502 1.7 14.8 1.0 S3 S:8JU502 2.2 12.9 1.0 S2 S:8JU502 2.3 11.7 1.0 SG S:CYS120 2.3 13.1 1.0 FE3 S:8JU502 2.7 12.9 1.0 CB S:CYS120 3.1 11.0 1.0 FE4 S:8JU502 3.2 20.6 1.0 FE1 S:8JU502 3.3 12.6 1.0 O S:HOH619 3.7 10.9 1.0 N S:CYS120 3.8 12.2 1.0 O S:HOH669 3.9 10.2 0.8 S1 S:8JU502 3.9 19.1 1.0 CA S:CYS120 4.1 11.8 1.0 S4 S:8JU502 4.2 10.2 1.0 SG S:CYS154 4.6 8.1 1.0 N S:SER119 4.8 9.0 1.0 SG S:CYS25 4.8 12.2 1.0

Iron binding site 10 out of 24 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-Oxidized 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 A Ferricyanide-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe502 b:12.9 occ:1.00 FE3 S:8JU502 0.0 12.9 1.0 S2 S:8JU502 2.3 11.7 1.0 S4 S:8JU502 2.3 10.2 1.0 SG S:CYS154 2.3 8.1 1.0 S3 S:8JU502 2.3 12.9 1.0 FE1 S:8JU502 2.7 12.6 1.0 FE2 S:8JU502 2.7 17.6 1.0 CB S:CYS154 3.3 5.2 1.0 CA S:CYS154 3.5 5.3 1.0 O S:HOH669 3.8 10.2 0.8 O S:8JU502 3.9 14.8 1.0 C S:CYS154 3.9 6.8 1.0 O S:CYS154 4.3 4.9 1.0 CG L:ARG59 4.4 9.0 1.0 S1 S:8JU502 4.4 19.1 1.0 FE4 S:8JU502 4.4 20.6 1.0 N S:PRO155 4.4 7.4 1.0 SG S:CYS120 4.5 13.1 1.0 SG S:CYS22 4.5 11.7 1.0 O S:GLY153 4.5 8.7 1.0 NE2 L:HIS214 4.6 9.6 1.0 CD2 L:HIS214 4.6 6.8 1.0 CA S:PRO155 4.8 7.6 1.0 N S:CYS154 4.8 5.6 1.0 NE L:ARG59 4.9 10.9 1.0 SG S:CYS25 4.9 12.2 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