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Nickel 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

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 6 binding sites of Nickel where determined in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase, PDB code: 2frv:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 2frv

Go back to Nickel Binding Sites List in 2frv
Nickel binding site 1 out of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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
L:Ni538

b:7.6
occ:1.00
O L:O539 1.7 7.6 1.0
SG L:CYS65 2.2 4.0 1.0
SG L:CYS530 2.3 10.1 1.0
SG L:CYS68 2.6 2.0 1.0
SG L:CYS533 2.6 2.0 1.0
FE L:FCO537 2.9 2.0 1.0
CB L:CYS65 3.0 2.0 1.0
CB L:CYS530 3.3 2.0 1.0
CB L:CYS68 3.6 2.0 1.0
CB L:CYS533 3.7 2.0 1.0
N L:CYS68 3.8 2.5 1.0
C2 L:FCO537 3.9 2.7 1.0
C1 L:FCO537 4.0 2.3 1.0
CA L:CYS68 4.3 3.6 1.0
CA L:CYS65 4.4 2.0 1.0
CB L:VAL67 4.5 4.7 1.0
N L:CYS533 4.6 2.0 1.0
C3 L:FCO537 4.6 2.6 1.0
CA L:CYS530 4.6 2.6 1.0
CA L:CYS533 4.6 2.0 1.0
N2 L:FCO537 4.8 7.5 1.0
NH1 L:ARG463 4.8 5.7 1.0
C L:VAL67 4.8 3.4 1.0
N1 L:FCO537 4.9 3.8 1.0
C L:CYS65 4.9 2.0 1.0
CZ L:ARG463 4.9 6.3 1.0
N L:VAL67 4.9 2.0 1.0
CG L:GLU18 4.9 5.5 1.0
C L:CYS68 5.0 5.3 1.0
NE L:ARG463 5.0 4.0 1.0

Nickel binding site 2 out of 6 in 2frv

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Nickel binding site 2 out of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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
B:Ni538

b:7.6
occ:1.00
O B:O539 1.7 7.6 1.0
SG B:CYS65 2.2 4.0 1.0
SG B:CYS530 2.3 10.1 1.0
SG B:CYS68 2.6 2.0 1.0
SG B:CYS533 2.6 2.0 1.0
FE B:FCO537 2.9 2.0 1.0
CB B:CYS65 3.0 2.0 1.0
CB B:CYS530 3.3 2.0 1.0
CB B:CYS68 3.6 2.0 1.0
CB B:CYS533 3.7 2.0 1.0
N B:CYS68 3.8 2.5 1.0
C2 B:FCO537 3.9 2.7 1.0
C1 B:FCO537 4.0 2.3 1.0
CA B:CYS68 4.3 3.6 1.0
CA B:CYS65 4.4 2.0 1.0
CB B:VAL67 4.5 4.7 1.0
N B:CYS533 4.6 2.0 1.0
C3 B:FCO537 4.6 2.6 1.0
CA B:CYS530 4.6 2.6 1.0
CA B:CYS533 4.6 2.0 1.0
N2 B:FCO537 4.8 7.5 1.0
NH1 B:ARG463 4.8 5.7 1.0
C B:VAL67 4.8 3.4 1.0
N1 B:FCO537 4.9 3.8 1.0
C B:CYS65 4.9 2.0 1.0
CZ B:ARG463 4.9 6.3 1.0
N B:VAL67 4.9 2.0 1.0
CG B:GLU18 4.9 5.5 1.0
C B:CYS68 5.0 5.3 1.0
NE B:ARG463 5.0 4.0 1.0

Nickel binding site 3 out of 6 in 2frv

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Nickel binding site 3 out of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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
D:Ni538

b:7.6
occ:1.00
O D:O539 1.7 7.6 1.0
SG D:CYS65 2.2 4.0 1.0
SG D:CYS530 2.3 10.1 1.0
SG D:CYS68 2.6 2.0 1.0
SG D:CYS533 2.6 2.0 1.0
FE D:FCO537 2.9 2.0 1.0
CB D:CYS65 3.0 2.0 1.0
CB D:CYS530 3.3 2.0 1.0
CB D:CYS68 3.6 2.0 1.0
CB D:CYS533 3.7 2.0 1.0
N D:CYS68 3.8 2.5 1.0
C2 D:FCO537 3.9 2.7 1.0
C1 D:FCO537 4.0 2.3 1.0
CA D:CYS68 4.3 3.6 1.0
CA D:CYS65 4.4 2.0 1.0
CB D:VAL67 4.5 4.7 1.0
N D:CYS533 4.6 2.0 1.0
CA D:CYS530 4.6 2.6 1.0
C3 D:FCO537 4.6 2.6 1.0
CA D:CYS533 4.6 2.0 1.0
N2 D:FCO537 4.8 7.5 1.0
NH1 D:ARG463 4.8 5.7 1.0
C D:VAL67 4.8 3.4 1.0
N1 D:FCO537 4.9 3.8 1.0
C D:CYS65 4.9 2.0 1.0
CZ D:ARG463 4.9 6.3 1.0
N D:VAL67 4.9 2.0 1.0
CG D:GLU18 4.9 5.5 1.0
C D:CYS68 5.0 5.3 1.0
NE D:ARG463 5.0 4.0 1.0

Nickel binding site 4 out of 6 in 2frv

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Nickel binding site 4 out of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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
F:Ni538

b:7.6
occ:1.00
O F:O539 1.7 7.6 1.0
SG F:CYS65 2.2 4.0 1.0
SG F:CYS530 2.3 10.1 1.0
SG F:CYS68 2.6 2.0 1.0
SG F:CYS533 2.6 2.0 1.0
FE F:FCO537 2.9 2.0 1.0
CB F:CYS65 3.0 2.0 1.0
CB F:CYS530 3.3 2.0 1.0
CB F:CYS68 3.6 2.0 1.0
CB F:CYS533 3.7 2.0 1.0
N F:CYS68 3.8 2.5 1.0
C2 F:FCO537 3.9 2.7 1.0
C1 F:FCO537 4.0 2.3 1.0
CA F:CYS68 4.3 3.6 1.0
CA F:CYS65 4.4 2.0 1.0
CB F:VAL67 4.5 4.7 1.0
N F:CYS533 4.6 2.0 1.0
C3 F:FCO537 4.6 2.6 1.0
CA F:CYS530 4.6 2.6 1.0
CA F:CYS533 4.6 2.0 1.0
N2 F:FCO537 4.8 7.5 1.0
NH1 F:ARG463 4.8 5.7 1.0
C F:VAL67 4.8 3.4 1.0
N1 F:FCO537 4.9 3.8 1.0
C F:CYS65 4.9 2.0 1.0
CZ F:ARG463 4.9 6.3 1.0
N F:VAL67 4.9 2.0 1.0
CG F:GLU18 4.9 5.5 1.0
C F:CYS68 5.0 5.3 1.0
NE F:ARG463 5.0 4.0 1.0

Nickel binding site 5 out of 6 in 2frv

Go back to Nickel Binding Sites List in 2frv
Nickel binding site 5 out of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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
H:Ni538

b:7.6
occ:1.00
O H:O539 1.7 7.6 1.0
SG H:CYS65 2.2 4.0 1.0
SG H:CYS530 2.3 10.1 1.0
SG H:CYS68 2.6 2.0 1.0
SG H:CYS533 2.6 2.0 1.0
FE H:FCO537 2.9 2.0 1.0
CB H:CYS65 3.0 2.0 1.0
CB H:CYS530 3.3 2.0 1.0
CB H:CYS68 3.6 2.0 1.0
CB H:CYS533 3.7 2.0 1.0
N H:CYS68 3.8 2.5 1.0
C2 H:FCO537 3.9 2.7 1.0
C1 H:FCO537 4.0 2.3 1.0
CA H:CYS68 4.3 3.6 1.0
CA H:CYS65 4.4 2.0 1.0
CB H:VAL67 4.5 4.7 1.0
N H:CYS533 4.6 2.0 1.0
C3 H:FCO537 4.6 2.6 1.0
CA H:CYS530 4.6 2.6 1.0
CA H:CYS533 4.6 2.0 1.0
N2 H:FCO537 4.8 7.5 1.0
NH1 H:ARG463 4.8 5.7 1.0
C H:VAL67 4.8 3.4 1.0
N1 H:FCO537 4.9 3.8 1.0
C H:CYS65 4.9 2.0 1.0
CZ H:ARG463 4.9 6.3 1.0
N H:VAL67 4.9 2.0 1.0
CG H:GLU18 4.9 5.5 1.0
C H:CYS68 5.0 5.3 1.0
NE H:ARG463 5.0 4.0 1.0

Nickel binding site 6 out of 6 in 2frv

Go back to Nickel Binding Sites List in 2frv
Nickel binding site 6 out of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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
J:Ni538

b:7.6
occ:1.00
O J:O539 1.7 7.6 1.0
SG J:CYS65 2.2 4.0 1.0
SG J:CYS530 2.3 10.1 1.0
SG J:CYS68 2.6 2.0 1.0
SG J:CYS533 2.6 2.0 1.0
FE J:FCO537 2.9 2.0 1.0
CB J:CYS65 3.0 2.0 1.0
CB J:CYS530 3.3 2.0 1.0
CB J:CYS68 3.6 2.0 1.0
CB J:CYS533 3.7 2.0 1.0
N J:CYS68 3.8 2.5 1.0
C2 J:FCO537 3.9 2.7 1.0
C1 J:FCO537 4.0 2.3 1.0
CA J:CYS68 4.3 3.6 1.0
CA J:CYS65 4.4 2.0 1.0
CB J:VAL67 4.5 4.7 1.0
N J:CYS533 4.6 2.0 1.0
C3 J:FCO537 4.6 2.6 1.0
CA J:CYS530 4.6 2.6 1.0
CA J:CYS533 4.6 2.0 1.0
N2 J:FCO537 4.8 7.5 1.0
NH1 J:ARG463 4.8 5.7 1.0
C J:VAL67 4.8 3.4 1.0
N1 J:FCO537 4.9 3.8 1.0
C J:CYS65 4.9 2.0 1.0
CZ J:ARG463 4.9 6.3 1.0
N J:VAL67 4.9 2.0 1.0
CG J:GLU18 4.9 5.5 1.0
C J:CYS68 5.0 5.3 1.0
NE J:ARG463 5.0 4.0 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
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