Atomistry » Nickel » PDB 1xu1-2c0n » 1yrq
Atomistry »
  Nickel »
    PDB 1xu1-2c0n »
      1yrq »

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

Other elements in 1yrq:

The structure of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase also contains other interesting chemical elements:

Magnesium (Mg) 12 atoms
Iron (Fe) 144 atoms

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

Go back to Nickel Binding Sites List in 1yrq
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

Go back to Nickel Binding Sites List in 1yrq
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

Go back to Nickel Binding Sites List in 1yrq
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

Go back to Nickel Binding Sites List in 1yrq
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

Go back to Nickel Binding Sites List in 1yrq
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

Go back to Nickel Binding Sites List in 1yrq
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: Wed Dec 16 01:16:51 2020

Last articles

Zn in 7L3L
Zn in 7KSO
Zn in 7KSR
Zn in 7KTP
Zn in 7LMM
Zn in 7LMK
Zn in 7LLZ
Zn in 7LLF
Zn in 7L0N
Zn in 7LBR
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy