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Iron in PDB 5xvd: [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition

Protein crystallography data

The structure of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition, PDB code: 5xvd 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) 31.72 / 1.57
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.940, 118.980, 96.810, 90.00, 100.57, 90.00
R / Rfree (%) 12.1 / 16.6

Other elements in 5xvd:

The structure of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition also contains other interesting chemical elements:

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

Iron Binding Sites:

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 [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition (pdb code 5xvd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 32 binding sites of Iron where determined in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition, PDB code: 5xvd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 32 in 5xvd

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Iron binding site 1 out of 32 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe602

b:10.1
occ:1.00
 FE L:NFV602 0.0 10.1 1.0
C1 L:NFV602 1.8 9.0 1.0
C3 L:NFV602 1.8 8.5 1.0
O4 L:NFV602 1.9 13.2 1.0
C2 L:NFV602 1.9 9.1 1.0
SG L:CYS64 2.4 11.9 1.0
SG L:CYS549 2.4 10.8 1.0
NI L:NFV602 2.8 12.2 1.0
O1 L:NFV602 2.9 11.6 1.0
N3 L:NFV602 3.0 8.5 1.0
N2 L:NFV602 3.0 11.2 1.0
CB L:CYS64 3.3 11.1 1.0
CB L:CYS549 3.5 9.7 1.0
CD L:ARG479 4.2 9.6 1.0
NE2 L:HIS68 4.2 10.9 1.0
CG1 L:VAL500 4.3 12.7 1.0
NH1 L:ARG479 4.4 11.9 1.0
CB L:CSO546 4.5 13.0 1.0
OG1 L:THR67 4.5 13.5 1.0
SG L:CSO546 4.6 16.4 1.0
CA L:CYS64 4.8 11.6 1.0
CA L:CYS549 4.9 9.8 1.0
CB L:ARG479 4.9 8.9 1.0
CD L:PRO501 4.9 10.0 1.0
SG L:CYS61 5.0 12.1 1.0
NE L:ARG479 5.0 10.5 1.0

Iron binding site 2 out of 32 in 5xvd

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Iron binding site 2 out of 32 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:12.2
occ:1.00
 FE1 S:SF4401 0.0 12.2 1.0
S4 S:SF4401 2.2 12.5 1.0
S3 S:SF4401 2.2 11.9 1.0
S2 S:SF4401 2.2 12.3 1.0
SG S:CYS220 2.4 12.9 1.0
FE3 S:SF4401 2.7 12.8 1.0
FE2 S:SF4401 2.7 12.1 1.0
FE4 S:SF4401 2.8 12.1 1.0
CB S:CYS220 3.4 12.6 1.0
N S:LEU221 3.8 12.2 1.0
S1 S:SF4401 3.8 11.6 1.0
CA S:CYS220 4.0 11.2 1.0
N S:TYR222 4.2 11.5 1.0
C S:CYS220 4.3 11.9 1.0
CB S:PHE201 4.4 13.4 1.0
CB S:ARG197 4.5 11.3 1.0
ND1 S:HIS192 4.6 13.5 1.0
CD2 S:PHE201 4.6 15.3 1.0
CB S:TYR222 4.7 13.2 1.0
O S:ARG197 4.7 13.1 1.0
CA S:TYR222 4.8 11.3 1.0
CE1 S:HIS192 4.8 14.4 1.0
CA S:LEU221 4.8 11.7 1.0
C S:ARG197 4.8 12.0 1.0
C S:LEU221 4.8 12.5 1.0
SG S:CYS195 4.9 11.6 1.0
SG S:CYS226 4.9 12.1 1.0
CG S:PHE201 4.9 14.3 1.0

Iron binding site 3 out of 32 in 5xvd

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Iron binding site 3 out of 32 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:12.1
occ:1.00
 FE2 S:SF4401 0.0 12.1 1.0
S3 S:SF4401 2.2 11.9 1.0
S4 S:SF4401 2.2 12.5 1.0
S1 S:SF4401 2.2 11.6 1.0
SG S:CYS195 2.4 11.6 1.0
FE3 S:SF4401 2.7 12.8 1.0
FE4 S:SF4401 2.7 12.1 1.0
FE1 S:SF4401 2.7 12.2 1.0
CB S:CYS195 3.2 10.8 1.0
S2 S:SF4401 3.7 12.3 1.0
CB S:ARG197 4.1 11.3 1.0
ND1 S:HIS192 4.6 13.5 1.0
N S:ARG197 4.6 10.5 1.0
N S:ARG198 4.6 13.9 1.0
C S:ARG197 4.6 12.0 1.0
CA S:ARG197 4.6 11.7 1.0
CA S:CYS195 4.6 11.6 1.0
CG1 S:VAL249 4.8 11.8 1.0
CG S:ARG197 4.8 12.1 1.0
SG S:CYS226 4.8 12.1 1.0
C S:CYS195 5.0 11.6 1.0
CH2 S:TRP247 5.0 12.4 1.0
SG S:CYS220 5.0 12.9 1.0

Iron binding site 4 out of 32 in 5xvd

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Iron binding site 4 out of 32 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:12.8
occ:1.00
 FE3 S:SF4401 0.0 12.8 1.0
S2 S:SF4401 2.2 12.3 1.0
ND1 S:HIS192 2.2 13.5 1.0
S1 S:SF4401 2.2 11.6 1.0
S4 S:SF4401 2.2 12.5 1.0
FE2 S:SF4401 2.7 12.1 1.0
FE1 S:SF4401 2.7 12.2 1.0
FE4 S:SF4401 2.7 12.1 1.0
CE1 S:HIS192 3.0 14.4 1.0
CG S:HIS192 3.3 13.4 1.0
CB S:HIS192 3.7 12.2 1.0
S3 S:SF4401 3.7 11.9 1.0
CA S:HIS192 4.0 12.5 1.0
CD S:PRO229 4.2 12.1 1.0
NE2 S:HIS192 4.2 13.9 1.0
CG S:PRO229 4.3 12.0 1.0
CD2 S:HIS192 4.3 15.0 1.0
CB S:CYS195 4.6 10.8 1.0
SG S:CYS195 4.7 11.6 1.0
SG S:CYS220 4.7 12.9 1.0
O S:HIS192 4.7 14.2 1.0
SG S:CYS226 4.8 12.1 1.0
N S:PRO229 4.9 12.3 1.0
C S:HIS192 4.9 13.0 1.0
CD2 S:PHE201 5.0 15.3 1.0
N S:HIS192 5.0 12.4 1.0

Iron binding site 5 out of 32 in 5xvd

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Iron binding site 5 out of 32 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:12.1
occ:1.00
 FE4 S:SF4401 0.0 12.1 1.0
S1 S:SF4401 2.2 11.6 1.0
S2 S:SF4401 2.2 12.3 1.0
S3 S:SF4401 2.2 11.9 1.0
SG S:CYS226 2.4 12.1 1.0
FE2 S:SF4401 2.7 12.1 1.0
FE3 S:SF4401 2.7 12.8 1.0
FE1 S:SF4401 2.8 12.2 1.0
CB S:CYS226 3.3 10.7 1.0
S4 S:SF4401 3.8 12.5 1.0
CD S:PRO229 4.4 12.1 1.0
CA S:GLY228 4.6 10.8 1.0
N S:GLY228 4.6 10.9 1.0
CG2 S:VAL249 4.6 11.6 1.0
CA S:CYS226 4.7 9.9 1.0
N S:TYR222 4.8 11.5 1.0
ND1 S:HIS192 4.8 13.5 1.0
SG S:CYS195 4.8 11.6 1.0
SG S:CYS220 4.8 12.9 1.0
N S:LEU221 4.9 12.2 1.0
C S:CYS226 4.9 11.0 1.0

Iron binding site 6 out of 32 in 5xvd

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Iron binding site 6 out of 32 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:11.8
occ:1.00
 FE1 S:F3S402 0.0 11.8 1.0
S1 S:F3S402 2.2 12.0 1.0
S2 S:F3S402 2.2 11.4 1.0
S3 S:F3S402 2.2 11.8 1.0
SG S:CYS258 2.4 11.5 1.0
FE3 S:F3S402 2.6 12.0 1.0
FE4 S:F3S402 2.6 12.0 1.0
CB S:CYS258 3.5 11.1 1.0
N S:CYS258 3.7 11.3 1.0
O L:HOH850 3.7 13.4 1.0
S4 S:F3S402 3.7 13.0 1.0
CA S:CYS258 4.0 10.1 1.0
OD1 S:ASN259 4.2 12.6 1.0
N S:ASN259 4.2 10.6 1.0
O S:HOH568 4.2 13.3 1.0
C S:CYS258 4.5 10.2 1.0
SG S:CYS235 4.7 13.7 1.0
C S:GLY257 4.8 10.9 1.0
CG S:ASN259 4.8 11.1 1.0
SG S:CYS255 4.9 10.8 1.0
N S:GLY257 4.9 10.4 1.0
O S:HOH519 5.0 16.3 1.0
OE1 L:GLN216 5.0 13.8 1.0
CE L:LYS211 5.0 12.8 1.0

Iron binding site 7 out of 32 in 5xvd

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Iron binding site 7 out of 32 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:12.0
occ:1.00
 FE3 S:F3S402 0.0 12.0 1.0
S4 S:F3S402 2.2 13.0 1.0
S3 S:F3S402 2.2 11.8 1.0
S1 S:F3S402 2.2 12.0 1.0
SG S:CYS235 2.3 13.7 1.0
FE1 S:F3S402 2.6 11.8 1.0
FE4 S:F3S402 2.6 12.0 1.0
CB S:CYS235 3.3 12.6 1.0
S2 S:F3S402 3.9 11.4 1.0
O S:HOH568 4.0 13.3 1.0
CD1 S:ILE191 4.1 14.4 1.0
CZ S:PHE240 4.5 12.7 1.0
CE1 S:PHE240 4.5 12.8 1.0
OD1 S:ASN259 4.6 12.6 1.0
CA S:CYS235 4.7 11.7 1.0
SG S:CYS255 4.7 10.8 1.0
SG S:CYS258 4.8 11.5 1.0
ND2 S:ASN259 4.9 11.5 1.0
CG S:ASN259 4.9 11.1 1.0
O S:HOH632 5.0 16.6 1.0
CD S:PRO248 5.0 9.7 1.0

Iron binding site 8 out of 32 in 5xvd

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Iron binding site 8 out of 32 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:12.0
occ:1.00
 FE4 S:F3S402 0.0 12.0 1.0
S4 S:F3S402 2.2 13.0 1.0
S3 S:F3S402 2.2 11.8 1.0
S2 S:F3S402 2.2 11.4 1.0
SG S:CYS255 2.4 10.8 1.0
FE3 S:F3S402 2.6 12.0 1.0
FE1 S:F3S402 2.6 11.8 1.0
CB S:CYS255 3.4 11.1 1.0
CA S:CYS255 3.7 10.5 1.0
S1 S:F3S402 3.8 12.0 1.0
N S:TYR256 3.8 11.2 1.0
N S:GLY257 3.9 10.4 1.0
C S:CYS255 4.2 11.4 1.0
CD1 S:ILE191 4.2 14.4 1.0
N S:CYS258 4.4 11.3 1.0
CA S:GLY257 4.5 11.0 1.0
NE2 L:GLN216 4.7 12.4 1.0
SG S:CYS235 4.8 13.7 1.0
CG2 S:THR231 4.8 12.5 1.0
C S:TYR256 4.9 11.5 1.0
SG S:CYS258 4.9 11.5 1.0
CA S:TYR256 4.9 11.5 1.0
C S:GLY257 4.9 10.9 1.0

Iron binding site 9 out of 32 in 5xvd

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Iron binding site 9 out of 32 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:19.6
occ:0.33
 FE1 S:SF4403 0.0 19.6 0.3
FE1 S:8JU404 0.4 14.5 0.7
SG S:CYS22 2.0 11.8 0.7
S3 S:SF4403 2.2 17.6 0.3
S4 S:SF4403 2.2 19.5 0.3
S2 S:SF4403 2.2 18.1 0.3
S1 S:8JU404 2.2 18.2 0.7
S2 S:8JU404 2.2 14.3 0.7
SG S:CYS22 2.3 20.4 0.3
S4 S:8JU404 2.5 12.5 0.7
FE3 S:8JU404 2.8 12.3 0.7
FE4 S:SF4403 3.0 14.8 0.3
CB S:CYS22 3.0 12.6 0.7
CB S:CYS22 3.1 19.0 0.3
FE3 S:SF4403 3.1 18.0 0.3
FE2 S:SF4403 3.1 19.9 0.3
FE2 S:8JU404 3.3 18.7 0.7
N S:CYS22 3.4 14.8 0.7
N S:CYS22 3.4 17.1 0.3
FE4 S:8JU404 3.5 22.8 0.7
CA S:CYS22 3.7 13.6 0.7
CA S:CYS22 3.7 17.3 0.3
O S:8JU404 3.7 20.5 0.7
S1 S:SF4403 3.8 17.4 0.3
N S:GLY24 3.9 12.8 1.0
C S:CYS22 4.1 15.8 0.3
C S:CYS22 4.1 13.5 0.7
N S:THR23 4.1 14.4 1.0
S3 S:8JU404 4.3 15.1 0.7
CA S:GLY24 4.3 12.5 1.0
NE2 L:HIS214 4.3 12.3 1.0
C S:GLU21 4.6 16.9 1.0
N S:CYS25 4.7 13.8 0.3
N S:CYS25 4.7 12.6 0.7
O L:HOH1005 4.8 19.1 1.0
SG S:CYS154 4.8 12.0 0.7
O S:CYS22 4.8 15.4 0.3
O S:CYS22 4.8 12.3 0.7
C S:THR23 4.9 13.3 1.0
SG S:CYS25 4.9 18.4 0.7
C S:GLY24 5.0 13.3 1.0
CD2 L:HIS214 5.0 11.8 1.0
CA S:GLU21 5.0 17.6 1.0

Iron binding site 10 out of 32 in 5xvd

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Iron binding site 10 out of 32 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 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 [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:19.9
occ:0.33
 FE2 S:SF4403 0.0 19.9 0.3
FE2 S:8JU404 0.5 18.7 0.7
O S:8JU404 1.7 20.5 0.7
S1 S:SF4403 2.2 17.4 0.3
S4 S:SF4403 2.2 19.5 0.3
S3 S:SF4403 2.2 17.6 0.3
S2 S:8JU404 2.3 14.3 0.7
SG S:CYS120 2.3 16.2 0.7
SG S:CYS120 2.3 18.9 0.3
S3 S:8JU404 2.6 15.1 0.7
FE3 S:8JU404 2.8 12.3 0.7
FE3 S:SF4403 3.0 18.0 0.3
FE1 S:8JU404 3.0 14.5 0.7
FE4 S:SF4403 3.1 14.8 0.3
FE4 S:8JU404 3.1 22.8 0.7
CB S:CYS120 3.1 17.2 0.3
FE1 S:SF4403 3.1 19.6 0.3
CB S:CYS120 3.2 14.8 0.7
S1 S:8JU404 3.6 18.2 0.7
O S:HOH508 3.8 15.9 1.0
S2 S:SF4403 3.8 18.1 0.3
O L:HOH1005 3.9 19.1 1.0
N S:CYS120 4.1 13.3 0.3
N S:CYS120 4.1 11.7 0.7
O S:HOH644 4.2 17.0 1.0
CA S:CYS120 4.2 15.1 0.3
CA S:CYS120 4.3 13.1 0.7
S4 S:8JU404 4.3 12.5 0.7
SG S:CYS154 4.7 12.0 0.7
N S:CYS22 4.8 14.8 0.7
OD1 S:ASP81 4.8 24.0 0.7
N S:CYS22 4.8 17.1 0.3
CA S:GLY82 4.8 14.2 1.0
O S:GLN20 4.8 19.4 1.0
CA S:GLU21 4.9 17.6 1.0
SG S:CYS25 4.9 18.4 0.7
SG S:CYS154 5.0 17.2 0.3

Reference:

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
Page generated: Tue Aug 6 12:03:07 2024

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