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Nickel in PDB 1yrq: Structure of the Ready Oxidized Form of [Nife]-Hydrogenase

Enzymatic activity of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase

All present enzymatic activity of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase:
1.12.2.1;

Protein crystallography data

The structure of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase, PDB code: 1yrq was solved by A.Volbeda, L.Martin, C.Cavazza, M.Matho, B.W.Faber, W.Roseboom, S.P.Albracht, E.Garcin, M.Rousset, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 127.500, 99.700, 183.200, 90.00, 91.80, 90.00
R / Rfree (%) 17.1 / 22

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase (pdb code 1yrq). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase, PDB code: 1yrq:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 1yrq

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Nickel binding site 1 out of 6 in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ni551

b:10.0
occ:1.00
O H:HOH557 1.9 8.0 1.0
SG H:CYS72 2.2 10.8 1.0
SG H:CYS543 2.2 14.0 1.0
SG H:CYS75 2.3 6.9 1.0
SG H:CYS546 2.5 8.1 1.0
FE H:FCO550 2.8 9.1 1.0
CB H:CYS72 3.0 6.6 1.0
CB H:CYS543 3.2 6.9 1.0
CB H:CYS75 3.5 9.7 1.0
N H:CYS75 3.5 7.2 1.0
CB H:CYS546 3.5 5.6 1.0
C1 H:FCO550 3.9 9.1 1.0
C2 H:FCO550 4.0 10.4 1.0
CA H:CYS75 4.0 9.6 1.0
NH1 H:ARG476 4.3 14.8 1.0
C3 H:FCO550 4.4 11.9 1.0
CA H:CYS72 4.5 5.9 1.0
CB H:VAL74 4.5 10.5 1.0
CA H:CYS546 4.6 5.1 1.0
N H:CYS546 4.6 5.5 1.0
C H:VAL74 4.6 10.6 1.0
CA H:CYS543 4.7 8.2 1.0
CZ H:ARG476 4.7 11.4 1.0
CD H:ARG476 4.7 10.2 1.0
N1 H:FCO550 4.8 13.7 1.0
C H:CYS75 4.8 11.0 1.0
N H:VAL74 4.9 9.4 1.0
NE H:ARG476 4.9 11.7 1.0
O H:CYS75 4.9 12.9 1.0
CA H:VAL74 4.9 9.1 1.0

Nickel binding site 2 out of 6 in 1yrq

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Nickel binding site 2 out of 6 in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ni551

b:10.7
occ:1.00
O I:HOH557 1.9 9.1 1.0
SG I:CYS72 2.1 12.2 1.0
SG I:CYS543 2.1 14.2 1.0
SG I:CYS75 2.3 7.0 1.0
SG I:CYS546 2.5 6.3 1.0
FE I:FCO550 2.8 7.4 1.0
CB I:CYS72 3.0 9.6 1.0
CB I:CYS543 3.2 10.9 1.0
CB I:CYS75 3.4 8.8 1.0
CB I:CYS546 3.5 8.9 1.0
N I:CYS75 3.6 8.9 1.0
C1 I:FCO550 3.9 3.3 1.0
CA I:CYS75 4.1 8.8 1.0
C2 I:FCO550 4.1 5.2 1.0
C3 I:FCO550 4.3 9.1 1.0
NH1 I:ARG476 4.5 17.1 1.0
CA I:CYS72 4.5 8.4 1.0
CA I:CYS546 4.6 7.3 1.0
CB I:VAL74 4.6 11.2 1.0
CA I:CYS543 4.6 11.6 1.0
N I:CYS546 4.6 9.5 1.0
CZ I:ARG476 4.7 16.3 1.0
CD I:ARG476 4.7 11.3 1.0
C I:VAL74 4.8 10.5 1.0
NE I:ARG476 4.8 13.0 1.0
C I:CYS75 4.8 10.7 1.0
N1 I:FCO550 4.8 4.9 1.0
O I:CYS75 4.9 10.3 1.0
N I:VAL74 5.0 7.7 1.0

Nickel binding site 3 out of 6 in 1yrq

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Nickel binding site 3 out of 6 in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ni551

b:9.9
occ:1.00
O J:HOH557 1.9 9.3 1.0
SG J:CYS72 2.1 8.0 1.0
SG J:CYS543 2.2 10.7 1.0
SG J:CYS75 2.3 7.2 1.0
SG J:CYS546 2.4 8.9 1.0
FE J:FCO550 2.8 8.4 1.0
CB J:CYS72 2.9 5.8 1.0
CB J:CYS543 3.2 9.8 1.0
CB J:CYS75 3.4 7.8 1.0
CB J:CYS546 3.5 7.7 1.0
N J:CYS75 3.6 7.9 1.0
C1 J:FCO550 3.9 9.9 1.0
C2 J:FCO550 4.0 7.8 1.0
CA J:CYS75 4.0 5.4 1.0
C3 J:FCO550 4.4 11.4 1.0
CA J:CYS72 4.4 8.5 1.0
NH1 J:ARG476 4.4 13.9 1.0
CA J:CYS546 4.5 9.6 1.0
N J:CYS546 4.5 9.3 1.0
CB J:VAL74 4.6 8.5 1.0
CA J:CYS543 4.7 8.5 1.0
CD J:ARG476 4.7 7.0 1.0
C J:VAL74 4.7 7.9 1.0
CZ J:ARG476 4.8 9.4 1.0
C J:CYS75 4.8 9.7 1.0
N1 J:FCO550 4.8 12.4 1.0
NE J:ARG476 4.9 12.0 1.0
O J:CYS75 4.9 8.6 1.0
N J:VAL74 4.9 9.2 1.0
N2 J:FCO550 4.9 7.4 1.0
C J:CYS72 5.0 6.9 1.0

Nickel binding site 4 out of 6 in 1yrq

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Nickel binding site 4 out of 6 in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ni551

b:11.4
occ:1.00
O K:HOH557 1.9 10.7 1.0
SG K:CYS72 2.2 9.7 1.0
SG K:CYS543 2.2 12.0 1.0
SG K:CYS75 2.3 7.3 1.0
SG K:CYS546 2.5 7.5 1.0
FE K:FCO550 2.7 9.1 1.0
CB K:CYS72 3.1 8.6 1.0
CB K:CYS543 3.2 8.3 1.0
CB K:CYS75 3.3 6.0 1.0
N K:CYS75 3.6 9.1 1.0
CB K:CYS546 3.6 4.3 1.0
C1 K:FCO550 3.8 8.4 1.0
C2 K:FCO550 4.0 6.5 1.0
CA K:CYS75 4.0 8.3 1.0
NH1 K:ARG476 4.1 11.5 1.0
C3 K:FCO550 4.3 10.3 1.0
CA K:CYS72 4.5 7.8 1.0
CB K:VAL74 4.6 5.2 1.0
CA K:CYS543 4.6 8.7 1.0
CA K:CYS546 4.7 6.3 1.0
N1 K:FCO550 4.7 8.5 1.0
N K:CYS546 4.7 4.8 1.0
CZ K:ARG476 4.7 7.8 1.0
C K:VAL74 4.7 9.4 1.0
CD K:ARG476 4.7 9.0 1.0
C K:CYS75 4.8 9.5 1.0
NE K:ARG476 4.9 9.5 1.0
O K:CYS75 4.9 9.1 1.0
N K:VAL74 4.9 6.7 1.0
N2 K:FCO550 4.9 12.4 1.0

Nickel binding site 5 out of 6 in 1yrq

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Nickel binding site 5 out of 6 in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ni551

b:8.7
occ:1.00
O M:HOH557 1.9 10.6 1.0
SG M:CYS543 2.1 9.3 1.0
SG M:CYS72 2.1 12.1 1.0
SG M:CYS75 2.3 7.1 1.0
SG M:CYS546 2.5 7.5 1.0
FE M:FCO550 2.9 6.7 1.0
CB M:CYS72 3.0 7.2 1.0
CB M:CYS543 3.1 5.7 1.0
CB M:CYS75 3.5 9.2 1.0
CB M:CYS546 3.5 5.1 1.0
N M:CYS75 3.6 7.0 1.0
C1 M:FCO550 4.0 6.8 1.0
C2 M:FCO550 4.0 4.4 1.0
CA M:CYS75 4.1 7.0 1.0
NH1 M:ARG476 4.3 6.7 1.0
C3 M:FCO550 4.4 6.0 1.0
CA M:CYS72 4.5 8.3 1.0
CA M:CYS543 4.6 7.3 1.0
CA M:CYS546 4.6 6.9 1.0
CB M:VAL74 4.6 10.3 1.0
N M:CYS546 4.6 5.6 1.0
CD M:ARG476 4.6 7.5 1.0
CZ M:ARG476 4.7 9.2 1.0
C M:VAL74 4.7 7.4 1.0
NE M:ARG476 4.8 5.0 1.0
C M:CYS75 4.9 8.7 1.0
N1 M:FCO550 4.9 7.9 1.0
N2 M:FCO550 5.0 7.7 1.0
N M:VAL74 5.0 8.8 1.0

Nickel binding site 6 out of 6 in 1yrq

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Nickel binding site 6 out of 6 in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Ni551

b:13.0
occ:0.59
O N:HOH557 1.9 9.9 0.6
SG N:CYS543 2.2 11.3 0.6
SG N:CYS72 2.2 10.2 0.6
SG N:CYS75 2.5 5.6 0.6
SG N:CYS546 2.7 5.4 0.6
FE N:FCO550 2.8 7.1 0.6
CB N:CYS72 3.0 8.5 0.6
CB N:CYS543 3.0 9.5 0.6
CB N:CYS75 3.2 7.9 0.6
CB N:CYS546 3.3 8.2 0.6
N N:CYS75 3.7 9.3 0.6
C1 N:FCO550 3.9 7.5 0.6
CA N:CYS75 4.0 8.5 0.6
C2 N:FCO550 4.1 5.3 0.6
C3 N:FCO550 4.3 6.7 0.6
CA N:CYS72 4.4 9.5 0.6
CA N:CYS543 4.5 9.5 0.6
CB N:VAL74 4.5 10.4 0.6
CA N:CYS546 4.6 8.4 0.6
CD N:ARG476 4.7 9.6 0.6
NH1 N:ARG476 4.7 11.0 0.6
OE1 N:GLU25 4.7 11.1 0.6
NE N:ARG476 4.8 10.3 0.6
N N:CYS546 4.8 9.2 0.6
N1 N:FCO550 4.8 9.6 0.6
CZ N:ARG476 4.8 11.2 0.6
C N:VAL74 4.8 10.0 0.6
C N:CYS75 4.9 8.5 0.6
N N:VAL74 4.9 9.8 0.6
C N:CYS72 4.9 8.8 0.6
CG N:GLU25 5.0 9.8 0.6

Reference:

A.Volbeda, L.Martin, C.Cavazza, M.Matho, B.W.Faber, W.Roseboom, S.P.Albracht, E.Garcin, M.Rousset, J.C.Fontecilla-Camps. Structural Differences Between the Ready and Unready Oxidized States of [Nife] Hydrogenases. J.Biol.Inorg.Chem. V. 10 239 2005.
ISSN: ISSN 0949-8257
PubMed: 15803334
DOI: 10.1007/S00775-005-0632-X
Page generated: Fri Sep 25 08:04:39 2020
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