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Iron in PDB 3ze7: 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms

Enzymatic activity of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms

All present enzymatic activity of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms:
1.12.7.2;

Protein crystallography data

The structure of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms, PDB code: 3ze7 was solved by M.C.Marques, R.Coelho, I.A.C.Pereira, P.M.Matias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.78 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.297, 96.987, 103.855, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 19

Other elements in 3ze7:

The structure of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Iron atom in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms (pdb code 3ze7). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 14 binding sites of Iron where determined in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms, PDB code: 3ze7:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 14 in 3ze7

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Iron binding site 1 out of 14 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe284

b:13.9
occ:1.00
 FE1 A:SF4284 0.0 13.9 1.0
S2 A:SF4284 2.3 14.5 1.0
S3 A:SF4284 2.3 13.2 1.0
S4 A:SF4284 2.3 13.9 1.0
SG A:CYS238 2.4 13.7 1.0
FE3 A:SF4284 2.7 14.1 1.0
FE4 A:SF4284 2.7 13.5 1.0
FE2 A:SF4284 2.8 14.2 1.0
CB A:CYS238 3.3 12.6 1.0
S1 A:SF4284 3.9 13.4 1.0
CD A:PRO241 4.4 11.9 1.0
CA A:GLY240 4.5 9.1 1.0
N A:GLY240 4.5 8.5 1.0
CG1 A:VAL260 4.6 8.8 1.0
CA A:CYS238 4.6 10.4 1.0
SG A:CYS211 4.7 15.4 1.0
ND1 A:HIS208 4.7 12.8 1.0
SG A:CYS232 4.7 12.4 1.0
CB A:ARG233 4.7 9.8 1.0
N A:TYR234 4.8 14.6 1.0
N A:ARG233 4.8 8.4 1.0
C A:CYS238 4.8 12.8 1.0
CG2 A:VAL260 4.8 10.3 1.0
O A:CYS238 4.9 14.2 1.0
C A:ARG233 5.0 16.1 1.0

Iron binding site 2 out of 14 in 3ze7

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Iron binding site 2 out of 14 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe284

b:14.2
occ:1.00
 FE2 A:SF4284 0.0 14.2 1.0
S1 A:SF4284 2.3 13.4 1.0
SG A:CYS232 2.3 12.4 1.0
S4 A:SF4284 2.3 13.9 1.0
S3 A:SF4284 2.3 13.2 1.0
FE4 A:SF4284 2.7 13.5 1.0
FE3 A:SF4284 2.7 14.1 1.0
FE1 A:SF4284 2.8 13.9 1.0
CB A:CYS232 3.5 9.6 1.0
N A:ARG233 3.7 8.4 1.0
CA A:CYS232 3.9 10.8 1.0
S2 A:SF4284 4.0 14.5 1.0
N A:TYR234 4.1 14.6 1.0
C A:CYS232 4.2 11.6 1.0
CD2 A:TYR217 4.3 16.5 1.0
CB A:TYR217 4.3 17.5 1.0
ND1 A:HIS208 4.5 12.8 1.0
CB A:TYR234 4.6 12.3 1.0
CB A:TYR213 4.6 14.8 1.0
CG A:TYR217 4.7 19.8 1.0
CA A:ARG233 4.7 9.8 1.0
CE1 A:HIS208 4.7 13.0 1.0
O A:TYR213 4.7 10.7 1.0
CA A:TYR234 4.8 12.4 1.0
C A:ARG233 4.8 16.1 1.0
SG A:CYS211 4.8 15.4 1.0
SG A:CYS238 4.9 13.7 1.0
C A:TYR213 5.0 15.2 1.0

Iron binding site 3 out of 14 in 3ze7

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Iron binding site 3 out of 14 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe284

b:14.1
occ:1.00
 FE3 A:SF4284 0.0 14.1 1.0
SG A:CYS211 2.3 15.4 1.0
S4 A:SF4284 2.3 13.9 1.0
S1 A:SF4284 2.3 13.4 1.0
S2 A:SF4284 2.3 14.5 1.0
FE4 A:SF4284 2.7 13.5 1.0
FE1 A:SF4284 2.7 13.9 1.0
FE2 A:SF4284 2.7 14.2 1.0
CB A:CYS211 3.1 17.9 1.0
S3 A:SF4284 3.9 13.2 1.0
CB A:TYR213 4.0 14.8 1.0
CG1 A:VAL260 4.3 8.8 1.0
ND1 A:HIS208 4.4 12.8 1.0
CD2 A:TYR213 4.5 13.4 1.0
CA A:CYS211 4.6 13.4 1.0
C A:TYR213 4.6 15.2 1.0
CA A:TYR213 4.6 17.9 1.0
N A:TYR213 4.6 17.2 1.0
N A:LEU214 4.7 14.6 1.0
CG A:TYR213 4.8 14.8 1.0
SG A:CYS238 4.8 13.7 1.0
SG A:CYS232 4.9 12.4 1.0
CA A:HIS208 5.0 14.2 1.0

Iron binding site 4 out of 14 in 3ze7

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Iron binding site 4 out of 14 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe284

b:13.5
occ:1.00
 FE4 A:SF4284 0.0 13.5 1.0
ND1 A:HIS208 2.1 12.8 1.0
S3 A:SF4284 2.3 13.2 1.0
S2 A:SF4284 2.3 14.5 1.0
S1 A:SF4284 2.3 13.4 1.0
FE3 A:SF4284 2.7 14.1 1.0
FE1 A:SF4284 2.7 13.9 1.0
FE2 A:SF4284 2.7 14.2 1.0
CE1 A:HIS208 2.9 13.0 1.0
CG A:HIS208 3.2 13.4 1.0
CB A:HIS208 3.7 14.0 1.0
S4 A:SF4284 3.9 13.9 1.0
CA A:HIS208 4.0 14.2 1.0
CD A:PRO241 4.0 11.9 1.0
NE2 A:HIS208 4.1 13.2 1.0
CG A:PRO241 4.2 13.5 1.0
CD2 A:HIS208 4.3 14.4 1.0
CD2 A:TYR217 4.5 16.5 1.0
CB A:CYS211 4.6 17.9 1.0
O A:HIS208 4.6 18.8 1.0
SG A:CYS232 4.6 12.4 1.0
SG A:CYS211 4.6 15.4 1.0
N A:PRO241 4.7 10.0 1.0
C A:HIS208 4.8 18.5 1.0
SG A:CYS238 4.8 13.7 1.0
CG A:TYR217 4.9 19.8 1.0
CA A:GLY240 5.0 9.1 1.0

Iron binding site 5 out of 14 in 3ze7

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Iron binding site 5 out of 14 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe285

b:11.9
occ:1.00
 FE1 A:SF4285 0.0 11.9 1.0
S3 A:SF4285 2.3 12.9 1.0
S4 A:SF4285 2.3 11.6 1.0
S2 A:SF4285 2.3 11.9 1.0
SG A:CYS268 2.3 11.5 1.0
FE4 A:SF4285 2.7 11.7 1.0
FE2 A:SF4285 2.7 11.9 1.0
FE3 A:SF4285 2.8 11.7 1.0
CB A:CYS268 3.4 8.9 1.0
N A:CYS268 3.7 10.8 1.0
S1 A:SF4285 3.9 12.8 1.0
CA A:CYS268 4.0 11.3 1.0
NH2 B:ARG182 4.0 15.9 1.0
NH1 B:ARG182 4.1 10.2 1.0
CZ B:ARG182 4.3 12.6 1.0
N A:VAL269 4.5 9.1 1.0
CG1 A:VAL269 4.6 7.1 1.0
C A:CYS268 4.6 13.7 1.0
SG A:CYS247 4.8 13.0 1.0
SG A:CYS259 4.8 11.2 1.0
SG A:CYS265 4.8 11.1 1.0
C A:GLY267 4.8 13.7 1.0
N A:GLY267 4.9 8.1 1.0

Iron binding site 6 out of 14 in 3ze7

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Iron binding site 6 out of 14 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe285

b:11.9
occ:1.00
 FE2 A:SF4285 0.0 11.9 1.0
SG A:CYS259 2.3 11.2 1.0
S3 A:SF4285 2.3 12.9 1.0
S1 A:SF4285 2.3 12.8 1.0
S4 A:SF4285 2.3 11.6 1.0
FE4 A:SF4285 2.7 11.7 1.0
FE1 A:SF4285 2.7 11.9 1.0
FE3 A:SF4285 2.7 11.7 1.0
CB A:CYS259 3.1 5.7 1.0
S2 A:SF4285 3.9 11.9 1.0
NE2 B:GLN187 4.2 12.6 1.0
CZ B:ARG182 4.2 12.6 1.0
NH2 B:ARG182 4.3 15.9 1.0
NE B:ARG182 4.3 12.0 1.0
CA A:CYS259 4.5 5.9 1.0
SG A:CYS247 4.5 13.0 1.0
NH1 B:ARG182 4.6 10.2 1.0
N A:CYS259 4.6 11.9 1.0
NE1 A:TRP252 4.7 10.6 1.0
SG A:CYS265 4.7 11.1 1.0
SG A:CYS268 4.7 11.5 1.0
CA A:CYS265 4.8 10.3 1.0
CD B:ARG182 4.9 15.1 1.0

Iron binding site 7 out of 14 in 3ze7

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Iron binding site 7 out of 14 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe285

b:11.7
occ:1.00
 FE3 A:SF4285 0.0 11.7 1.0
SG A:CYS247 2.2 13.0 1.0
S4 A:SF4285 2.3 11.6 1.0
S2 A:SF4285 2.3 11.9 1.0
S1 A:SF4285 2.3 12.8 1.0
FE2 A:SF4285 2.7 11.9 1.0
FE4 A:SF4285 2.8 11.7 1.0
FE1 A:SF4285 2.8 11.9 1.0
CB A:CYS247 3.4 13.7 1.0
S3 A:SF4285 4.0 12.9 1.0
NE1 A:TRP252 4.3 10.6 1.0
CH2 A:TRP165 4.5 6.5 1.0
CB A:ALA245 4.6 10.9 1.0
SG A:CYS259 4.6 11.2 1.0
CA A:CYS247 4.7 14.4 1.0
SG A:CYS265 4.8 11.1 1.0
SG A:CYS268 4.8 11.5 1.0
CD1 A:ILE207 5.0 27.1 1.0
N A:CYS247 5.0 15.4 1.0

Iron binding site 8 out of 14 in 3ze7

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Iron binding site 8 out of 14 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe285

b:11.7
occ:1.00
 FE4 A:SF4285 0.0 11.7 1.0
S2 A:SF4285 2.3 11.9 1.0
S3 A:SF4285 2.3 12.9 1.0
S1 A:SF4285 2.3 12.8 1.0
SG A:CYS265 2.3 11.1 1.0
FE2 A:SF4285 2.7 11.9 1.0
FE1 A:SF4285 2.7 11.9 1.0
FE3 A:SF4285 2.8 11.7 1.0
CB A:CYS265 3.3 6.3 1.0
CA A:CYS265 3.8 10.3 1.0
S4 A:SF4285 3.9 11.6 1.0
N A:ILE266 4.0 9.3 1.0
N A:GLY267 4.1 8.1 1.0
C A:CYS265 4.3 10.1 1.0
CG2 A:THR243 4.4 10.5 1.0
N A:CYS268 4.5 10.8 1.0
CA A:GLY267 4.7 9.4 1.0
SG A:CYS259 4.7 11.2 1.0
CB A:CYS259 4.7 5.7 1.0
SG A:CYS247 4.9 13.0 1.0
SG A:CYS268 4.9 11.5 1.0

Iron binding site 9 out of 14 in 3ze7

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Iron binding site 9 out of 14 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe286

b:10.1
occ:1.00
 FE1 A:SF4286 0.0 10.1 1.0
SG A:CYS18 2.3 9.9 1.0
S3 A:SF4286 2.3 10.5 1.0
S4 A:SF4286 2.3 10.5 1.0
S2 A:SF4286 2.3 10.7 1.0
FE3 A:SF4286 2.6 10.6 1.0
FE2 A:SF4286 2.7 10.5 1.0
FE4 A:SF4286 2.7 10.6 1.0
CB A:CYS18 3.4 8.9 1.0
N A:CYS18 3.7 9.3 1.0
S1 A:SF4286 3.8 11.3 1.0
CA A:CYS18 4.1 9.0 1.0
NE2 B:HIS185 4.1 11.3 1.0
N A:GLY20 4.3 9.0 1.0
CA A:GLY20 4.5 10.4 1.0
O A:HOH2010 4.5 8.4 1.0
C A:CYS18 4.6 9.1 1.0
N A:CYS21 4.6 8.9 1.0
SG A:CYS159 4.7 8.0 1.0
SG A:CYS121 4.7 10.9 1.0
SG A:CYS21 4.8 10.1 1.0
N A:THR19 4.8 9.8 1.0
O B:ARG73 4.8 9.5 1.0
C A:GLY17 4.8 11.1 1.0
CG B:ARG73 4.9 8.2 1.0
C A:GLY20 5.0 10.2 1.0
CD2 B:HIS185 5.0 6.2 1.0

Iron binding site 10 out of 14 in 3ze7

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Iron binding site 10 out of 14 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the Reduced State at 1.95 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe286

b:10.5
occ:1.00
 FE2 A:SF4286 0.0 10.5 1.0
SG A:CYS159 2.3 8.0 1.0
S3 A:SF4286 2.3 10.5 1.0
S1 A:SF4286 2.3 11.3 1.0
S4 A:SF4286 2.3 10.5 1.0
FE4 A:SF4286 2.7 10.6 1.0
FE1 A:SF4286 2.7 10.1 1.0
FE3 A:SF4286 2.8 10.6 1.0
CB A:CYS159 3.4 8.3 1.0
CA A:CYS159 3.5 4.3 1.0
S2 A:SF4286 3.9 10.7 1.0
C A:CYS159 4.0 9.9 1.0
CG B:ARG73 4.1 8.2 1.0
O A:HOH2149 4.2 9.4 1.0
NE2 B:HIS185 4.3 11.3 1.0
SG A:CYS121 4.4 10.9 1.0
N A:PRO160 4.5 11.0 1.0
O A:CYS159 4.5 8.4 1.0
CD2 B:HIS185 4.5 6.2 1.0
O A:GLY158 4.6 9.1 1.0
SG A:CYS18 4.6 9.9 1.0
CA A:PRO160 4.7 7.3 1.0
N A:CYS159 4.8 8.9 1.0
SG A:CYS21 4.8 10.1 1.0
NE B:ARG73 4.9 7.0 1.0

Reference:

M.C.Marques, R.Coelho, I.A.C.Pereira, P.M.Matias. Redox State-Dependent Changes in the Crystal Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Int.J.Hydrogen Energy V. 38 8664 2013.
ISSN: ISSN 0360-3199
DOI: 10.1016/J.IJHYDENE.2013.04.132
Page generated: Tue Aug 5 08:34:50 2025

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