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Iron in PDB 2frv: Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase

Enzymatic activity of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase

All present enzymatic activity of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase:
1.18.99.1;

Protein crystallography data

The structure of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase, PDB code: 2frv was solved by A.Volbeda, M.Frey, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.54
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 112.780, 113.160, 133.910, 90.03, 90.02, 119.99
R / Rfree (%) 22.4 / 23.9

Other elements in 2frv:

The structure of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase also contains other interesting chemical elements:

Nickel (Ni) 6 atoms
Magnesium (Mg) 6 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 72;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase (pdb code 2frv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 72 binding sites of Iron where determined in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase, PDB code: 2frv:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 72 in 2frv

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Iron binding site 1 out of 72 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe265

b:2.0
occ:1.00
FE1 S:SF4265 0.0 2.0 1.0
S3 S:SF4265 2.2 3.1 1.0
SG S:CYS219 2.2 2.0 1.0
S4 S:SF4265 2.3 3.3 1.0
S2 S:SF4265 2.3 3.2 1.0
FE4 S:SF4265 2.7 2.0 1.0
FE2 S:SF4265 2.7 2.0 1.0
FE3 S:SF4265 2.7 3.8 1.0
CB S:CYS219 3.2 2.0 1.0
S1 S:SF4265 3.9 3.8 1.0
CA S:GLY221 4.5 2.0 1.0
CA S:CYS219 4.5 2.0 1.0
N S:GLY221 4.6 2.0 1.0
CG2 S:VAL240 4.6 2.0 1.0
ND1 S:HIS185 4.7 6.3 1.0
SG S:CYS188 4.7 2.0 1.0
CD S:PRO222 4.8 2.1 1.0
SG S:CYS213 4.8 7.0 1.0
C S:CYS219 4.8 2.0 1.0
N S:TYR215 4.9 2.0 1.0
N S:LEU214 4.9 3.3 1.0

Iron binding site 2 out of 72 in 2frv

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Iron binding site 2 out of 72 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe265

b:2.0
occ:1.00
FE2 S:SF4265 0.0 2.0 1.0
ND1 S:HIS185 2.0 6.3 1.0
S4 S:SF4265 2.2 3.3 1.0
S1 S:SF4265 2.3 3.8 1.0
S3 S:SF4265 2.3 3.1 1.0
FE3 S:SF4265 2.7 3.8 1.0
FE4 S:SF4265 2.7 2.0 1.0
FE1 S:SF4265 2.7 2.0 1.0
CE1 S:HIS185 2.9 5.9 1.0
CG S:HIS185 3.1 7.7 1.0
CB S:HIS185 3.6 5.7 1.0
CA S:HIS185 3.9 2.9 1.0
S2 S:SF4265 3.9 3.2 1.0
NE2 S:HIS185 4.0 6.2 1.0
CD2 S:HIS185 4.1 5.7 1.0
CD S:PRO222 4.4 2.1 1.0
CB S:CYS188 4.4 2.0 1.0
CG S:PRO222 4.4 2.0 1.0
O S:HIS185 4.6 4.3 1.0
SG S:CYS188 4.6 2.0 1.0
C S:HIS185 4.7 3.7 1.0
CD2 S:LEU191 4.7 10.4 1.0
SG S:CYS219 4.7 2.0 1.0
SG S:CYS213 4.7 7.0 1.0
N S:PRO222 4.8 2.7 1.0
CD1 S:PHE194 4.8 6.0 1.0
CA S:GLY221 4.9 2.0 1.0
N S:HIS185 5.0 2.9 1.0
C S:GLY221 5.0 2.7 1.0

Iron binding site 3 out of 72 in 2frv

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Iron binding site 3 out of 72 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe265

b:3.8
occ:1.00
FE3 S:SF4265 0.0 3.8 1.0
S2 S:SF4265 2.3 3.2 1.0
S1 S:SF4265 2.3 3.8 1.0
S4 S:SF4265 2.4 3.3 1.0
SG S:CYS213 2.4 7.0 1.0
FE2 S:SF4265 2.7 2.0 1.0
FE4 S:SF4265 2.7 2.0 1.0
FE1 S:SF4265 2.7 2.0 1.0
CB S:CYS213 3.4 2.0 1.0
S3 S:SF4265 3.9 3.1 1.0
CA S:CYS213 3.9 4.0 1.0
N S:LEU214 4.0 3.3 1.0
CD1 S:PHE194 4.2 6.0 1.0
ND1 S:HIS185 4.3 6.3 1.0
C S:CYS213 4.3 3.9 1.0
N S:TYR215 4.3 2.0 1.0
CE1 S:HIS185 4.6 5.9 1.0
CB S:TYR215 4.7 2.0 1.0
CB S:PHE194 4.7 2.9 1.0
CB S:ARG190 4.7 2.0 1.0
O S:ARG190 4.8 7.2 1.0
SG S:CYS219 4.8 2.0 1.0
SG S:CYS188 4.8 2.0 1.0
CG S:PHE194 4.8 4.1 1.0
CE1 S:PHE194 4.9 6.1 1.0
CA S:TYR215 4.9 2.0 1.0
CA S:LEU214 5.0 2.0 1.0

Iron binding site 4 out of 72 in 2frv

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Iron binding site 4 out of 72 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe265

b:2.0
occ:1.00
FE4 S:SF4265 0.0 2.0 1.0
S1 S:SF4265 2.2 3.8 1.0
SG S:CYS188 2.3 2.0 1.0
S2 S:SF4265 2.3 3.2 1.0
S3 S:SF4265 2.3 3.1 1.0
FE3 S:SF4265 2.7 3.8 1.0
FE1 S:SF4265 2.7 2.0 1.0
FE2 S:SF4265 2.7 2.0 1.0
CB S:CYS188 3.0 2.0 1.0
S4 S:SF4265 3.9 3.3 1.0
CB S:ARG190 4.1 2.0 1.0
ND1 S:HIS185 4.3 6.3 1.0
CG1 S:VAL240 4.4 2.0 1.0
CA S:CYS188 4.5 2.9 1.0
C S:ARG190 4.6 7.2 1.0
N S:ARG190 4.7 5.1 1.0
CA S:ARG190 4.7 4.3 1.0
N S:LEU191 4.7 9.8 1.0
SG S:CYS219 4.7 2.0 1.0
CG S:ARG190 4.9 2.0 1.0
CA S:HIS185 4.9 2.9 1.0
C S:CYS188 4.9 4.3 1.0

Iron binding site 5 out of 72 in 2frv

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Iron binding site 5 out of 72 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe266

b:2.0
occ:1.00
FE1 S:F3S266 0.0 2.0 1.0
S2 S:F3S266 2.2 2.0 1.0
SG S:CYS249 2.3 2.8 1.0
S3 S:F3S266 2.3 2.0 1.0
S1 S:F3S266 2.3 2.0 1.0
FE4 S:F3S266 2.7 2.0 1.0
FE3 S:F3S266 2.7 2.0 1.0
CB S:CYS249 3.4 2.0 1.0
N S:CYS249 3.8 2.0 1.0
S4 S:F3S266 3.9 2.0 1.0
CA S:CYS249 4.0 2.0 1.0
O S:HOH294 4.0 2.0 1.0
O L:HOH5064 4.2 7.5 1.0
C S:CYS249 4.5 2.0 1.0
ND2 S:ASN226 4.5 2.0 1.0
SG S:CYS228 4.7 2.0 1.0
N S:SER250 4.7 2.0 1.0
SG S:CYS246 4.8 2.0 1.0
CE L:LYS216 5.0 2.0 1.0

Iron binding site 6 out of 72 in 2frv

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Iron binding site 6 out of 72 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe266

b:2.0
occ:1.00
FE3 S:F3S266 0.0 2.0 1.0
S4 S:F3S266 2.2 2.0 1.0
S3 S:F3S266 2.3 2.0 1.0
S1 S:F3S266 2.3 2.0 1.0
SG S:CYS246 2.3 2.0 1.0
FE1 S:F3S266 2.7 2.0 1.0
FE4 S:F3S266 2.8 2.0 1.0
CB S:CYS246 3.3 2.0 1.0
CA S:CYS246 3.6 2.0 1.0
S2 S:F3S266 3.9 2.0 1.0
N S:ILE247 3.9 2.0 1.0
C S:CYS246 4.1 2.0 1.0
N S:ALA248 4.2 2.0 1.0
N S:CYS249 4.5 2.0 1.0
CG2 S:THR224 4.6 2.0 1.0
SG S:CYS228 4.7 2.0 1.0
NE2 L:GLN221 4.8 2.0 1.0
CA S:ALA248 4.8 2.0 1.0
SG S:CYS249 4.8 2.8 1.0
CG2 S:VAL184 4.9 2.0 1.0
C S:ILE247 4.9 2.0 1.0
CA S:ILE247 4.9 2.0 1.0
N S:CYS246 5.0 2.2 1.0
CG S:PRO239 5.0 2.0 1.0

Iron binding site 7 out of 72 in 2frv

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Iron binding site 7 out of 72 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe266

b:2.0
occ:1.00
FE4 S:F3S266 0.0 2.0 1.0
S2 S:F3S266 2.2 2.0 1.0
SG S:CYS228 2.2 2.0 1.0
S3 S:F3S266 2.3 2.0 1.0
S4 S:F3S266 2.3 2.0 1.0
FE1 S:F3S266 2.7 2.0 1.0
FE3 S:F3S266 2.8 2.0 1.0
CB S:CYS228 3.4 2.0 1.0
S1 S:F3S266 3.9 2.0 1.0
ND2 S:ASN226 4.1 2.0 1.0
CE2 S:PHE233 4.3 2.0 1.0
O S:HOH294 4.4 2.0 1.0
CZ S:PHE233 4.5 2.0 1.0
CG2 S:VAL184 4.6 2.0 1.0
CG S:ASN226 4.6 2.0 1.0
SG S:CYS249 4.7 2.8 1.0
CB S:ASN226 4.8 2.0 1.0
CA S:CYS228 4.8 2.0 1.0
CG S:PRO239 4.8 2.0 1.0
CD S:PRO239 4.8 2.4 1.0
SG S:CYS246 4.8 2.0 1.0

Iron binding site 8 out of 72 in 2frv

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Iron binding site 8 out of 72 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe267

b:2.0
occ:1.00
FE1 S:SF4267 0.0 2.0 1.0
S2 S:SF4267 2.2 2.0 1.0
SG S:CYS17 2.2 2.0 1.0
S4 S:SF4267 2.2 2.0 1.0
S3 S:SF4267 2.4 2.0 1.0
FE3 S:SF4267 2.6 2.8 1.0
FE2 S:SF4267 2.7 2.0 1.0
FE4 S:SF4267 2.7 2.0 1.0
CB S:CYS17 3.3 2.0 1.0
S1 S:SF4267 3.9 2.0 1.0
N S:CYS17 3.9 2.0 1.0
NE2 L:HIS219 4.0 2.0 1.0
CA S:CYS17 4.1 2.0 1.0
N S:GLY19 4.1 2.0 1.0
CA S:GLY19 4.5 2.0 1.0
N S:THR18 4.5 2.9 1.0
C S:CYS17 4.5 2.0 1.0
N S:CYS20 4.7 2.0 1.0
O S:HOH330 4.7 5.3 1.0
SG S:CYS112 4.7 2.0 1.0
CD2 L:HIS219 4.7 2.0 1.0
SG S:CYS148 4.8 2.0 1.0
C S:GLY19 4.9 2.0 1.0
CG L:ARG63 4.9 2.0 1.0
SG S:CYS20 4.9 2.0 1.0

Iron binding site 9 out of 72 in 2frv

Go back to Iron Binding Sites List in 2frv
Iron binding site 9 out of 72 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe267

b:2.0
occ:1.00
FE2 S:SF4267 0.0 2.0 1.0
SG S:CYS112 2.2 2.0 1.0
S3 S:SF4267 2.3 2.0 1.0
S1 S:SF4267 2.3 2.0 1.0
S4 S:SF4267 2.3 2.0 1.0
FE3 S:SF4267 2.7 2.8 1.0
FE4 S:SF4267 2.7 2.0 1.0
FE1 S:SF4267 2.7 2.0 1.0
CB S:CYS112 3.2 2.0 1.0
S2 S:SF4267 3.9 2.0 1.0
O S:HOH298 4.1 2.0 1.0
N S:CYS112 4.1 2.0 1.0
O S:HOH305 4.2 2.0 1.0
O S:HOH330 4.2 5.3 1.0
CA S:CYS112 4.3 2.0 1.0
SG S:CYS148 4.6 2.0 1.0
SG S:CYS20 4.7 2.0 1.0
SG S:CYS17 4.8 2.0 1.0
N S:CYS17 4.9 2.0 1.0

Iron binding site 10 out of 72 in 2frv

Go back to Iron Binding Sites List in 2frv
Iron binding site 10 out of 72 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe267

b:2.8
occ:1.00
FE3 S:SF4267 0.0 2.8 1.0
S4 S:SF4267 2.2 2.0 1.0
S2 S:SF4267 2.3 2.0 1.0
S1 S:SF4267 2.3 2.0 1.0
SG S:CYS148 2.4 2.0 1.0
FE1 S:SF4267 2.6 2.0 1.0
FE2 S:SF4267 2.7 2.0 1.0
FE4 S:SF4267 2.8 2.0 1.0
CB S:CYS148 3.5 2.0 1.0
CA S:CYS148 3.5 2.0 1.0
S3 S:SF4267 3.9 2.0 1.0
C S:CYS148 3.9 3.1 1.0
O S:HOH305 3.9 2.0 1.0
O S:CYS148 4.2 3.0 1.0
SG S:CYS112 4.4 2.0 1.0
CG L:ARG63 4.4 2.0 1.0
N S:PRO149 4.4 3.4 1.0
NE2 L:HIS219 4.5 2.0 1.0
CD2 L:HIS219 4.5 2.0 1.0
SG S:CYS17 4.6 2.0 1.0
NE L:ARG63 4.7 2.0 1.0
O S:GLY147 4.8 2.0 1.0
CA S:PRO149 4.8 2.5 1.0
SG S:CYS20 4.8 2.0 1.0
N S:CYS148 4.9 2.6 1.0

Reference:

A.Volbeda, E.Garcin, C.Piras, A.L.De Lacey, V.M.Fernandez, E.C.Hatchikian, M.Frey, J.C.Fontecilla-Camps. Structure of the [Nife] Hydrogenase Active Site: Evidence For Biologically Uncommon Fe Ligands J.Am.Chem.Soc. V. 118 12989 1996.
ISSN: ISSN 0002-7863
Page generated: Sun Dec 13 14:44:31 2020

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