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Nickel in PDB 5jsy: The 3D Structure of the Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough at 1.04 Angstrom Resolution

Enzymatic activity of The 3D Structure of the Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough at 1.04 Angstrom Resolution

All present enzymatic activity of The 3D Structure of the Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough at 1.04 Angstrom Resolution:
1.12.7.2;

Protein crystallography data

The structure of The 3D Structure of the Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough at 1.04 Angstrom Resolution, PDB code: 5jsy was solved by M.C.Marques, 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) 29.20 / 1.04
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 106.324, 62.857, 110.823, 90.00, 105.18, 90.00
R / Rfree (%) 11.2 / 12.8

Other elements in 5jsy:

The structure of The 3D Structure of the Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough at 1.04 Angstrom Resolution also contains other interesting chemical elements:

Iron (Fe) 14 atoms
Chlorine (Cl) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the The 3D Structure of the Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough at 1.04 Angstrom Resolution (pdb code 5jsy). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the The 3D Structure of the Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough at 1.04 Angstrom Resolution, PDB code: 5jsy:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 5jsy

Go back to Nickel Binding Sites List in 5jsy
Nickel binding site 1 out of 3 in the The 3D Structure of the Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough at 1.04 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The 3D Structure of the Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough at 1.04 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni602

b:9.0
occ:0.17
 NI B:NI602 0.0 9.0 0.2
NI B:NI602 0.9 10.2 0.3
NI B:NI602 1.2 9.5 0.1
S B:H2S604 1.3 17.1 0.5
SG B:CYS75 1.7 12.2 0.4
SG B:CYS78 2.1 10.3 1.0
SG B:CYS489 2.2 11.5 0.6
FE B:FCO601 2.3 9.0 1.0
SG B:CYS75 2.3 8.9 0.3
SG B:CYS492 2.5 9.7 1.0
HB3 B:CYS75 2.8 11.3 0.3
SG B:CYS75 2.9 10.3 0.3
HB3 B:CYS75 3.0 10.0 0.3
OD1 B:CYS489 3.0 12.0 0.6
SG B:CYS489 3.1 11.3 0.4
CB B:CYS75 3.1 8.3 0.3
HB3 B:CYS78 3.1 10.9 1.0
CB B:CYS75 3.1 9.4 0.3
HB2 B:CYS75 3.1 10.0 0.3
OD3 B:CYS489 3.2 13.0 0.6
CB B:CYS75 3.2 10.9 0.4
HB2 B:CYS75 3.2 11.3 0.3
HB2 B:CYS75 3.2 13.1 0.4
CB B:CYS78 3.3 9.1 1.0
HB3 B:CYS489 3.3 11.9 0.4
C2 B:FCO601 3.3 8.4 1.0
C1 B:FCO601 3.4 9.4 1.0
H B:CYS78 3.4 9.4 1.0
CB B:CYS489 3.6 9.4 0.6
CB B:CYS489 3.6 10.0 0.4
HB3 B:CYS489 3.6 11.3 0.6
O B:HOH1024 3.6 10.7 0.4
HB2 B:CYS489 3.6 11.9 0.4
HB3 B:CYS75 3.7 13.1 0.4
HB2 B:CYS492 3.7 10.1 1.0
HB B:VAL77 3.8 10.6 1.0
CB B:CYS492 3.8 8.4 1.0
HD2 B:ARG422 3.8 9.2 1.0
C3 B:FCO601 3.9 12.0 1.0
HB2 B:CYS489 3.9 11.3 0.6
N B:CYS78 3.9 7.8 1.0
HB2 B:CYS78 4.0 10.9 1.0
H B:CYS492 4.1 9.1 1.0
CA B:CYS78 4.2 8.2 1.0
HH11 B:ARG422 4.2 10.6 1.0
HA B:CYS75 4.3 11.6 0.4
N2 B:FCO601 4.3 8.7 1.0
CA B:CYS75 4.4 9.7 0.4
N1 B:FCO601 4.4 9.9 1.0
HB3 B:CYS492 4.4 10.1 1.0
H B:VAL77 4.5 9.4 1.0
CA B:CYS75 4.5 8.4 0.3
CA B:CYS75 4.6 9.0 0.3
NH1 B:ARG422 4.6 8.9 1.0
CB B:VAL77 4.7 8.8 1.0
CD B:ARG422 4.7 7.7 1.0
N B:CYS492 4.7 7.5 1.0
CA B:CYS492 4.8 7.7 1.0
HD2 B:HIS82 4.8 11.0 1.0
C B:CYS78 4.9 7.7 1.0
HA B:CYS75 4.9 10.1 0.3
C B:VAL77 4.9 7.8 1.0
HD3 B:ARG422 4.9 9.2 1.0
O3 B:FCO601 4.9 13.5 1.0
CA B:CYS489 4.9 8.1 0.6
HH12 B:ARG422 5.0 10.6 1.0
HA B:CYS78 5.0 9.9 1.0
C B:CYS75 5.0 8.3 0.3
HA B:CYS492 5.0 9.2 1.0
NE2 B:HIS82 5.0 9.5 1.0

Nickel binding site 2 out of 3 in 5jsy

Go back to Nickel Binding Sites List in 5jsy
Nickel binding site 2 out of 3 in the The 3D Structure of the Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough at 1.04 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The 3D Structure of the Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough at 1.04 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni602

b:10.2
occ:0.35
 NI B:NI602 0.0 10.2 0.3
NI B:NI602 0.9 9.0 0.2
NI B:NI602 1.3 9.5 0.1
S B:H2S604 1.5 17.1 0.5
SG B:CYS489 1.6 11.5 0.6
SG B:CYS75 1.9 12.2 0.4
SG B:CYS75 1.9 8.9 0.3
SG B:CYS75 2.2 10.3 0.3
SG B:CYS489 2.3 11.3 0.4
OD1 B:CYS489 2.3 12.0 0.6
OD3 B:CYS489 2.4 13.0 0.6
HB3 B:CYS75 2.8 11.3 0.3
SG B:CYS492 2.9 9.7 1.0
HB2 B:CYS75 2.9 10.0 0.3
CB B:CYS75 2.9 8.3 0.3
SG B:CYS78 2.9 10.3 1.0
CB B:CYS75 2.9 9.4 0.3
O B:HOH1024 3.0 10.7 0.4
FE B:FCO601 3.1 9.0 1.0
HB3 B:CYS489 3.1 11.9 0.4
CB B:CYS489 3.1 10.0 0.4
HB2 B:CYS75 3.1 11.3 0.3
HB3 B:CYS75 3.1 10.0 0.3
CB B:CYS489 3.2 9.4 0.6
HB2 B:CYS489 3.2 11.9 0.4
CB B:CYS75 3.3 10.9 0.4
HB2 B:CYS75 3.3 13.1 0.4
HB B:VAL77 3.4 10.6 1.0
HB3 B:CYS489 3.5 11.3 0.6
HB2 B:CYS489 3.6 11.3 0.6
H B:CYS78 3.6 9.4 1.0
HB3 B:CYS78 3.7 10.9 1.0
H B:CYS492 3.8 9.1 1.0
HB2 B:CYS492 3.8 10.1 1.0
C1 B:FCO601 3.9 9.4 1.0
HA B:CYS75 3.9 11.6 0.4
CB B:CYS78 4.0 9.1 1.0
HB3 B:CYS75 4.0 13.1 0.4
CB B:CYS492 4.0 8.4 1.0
HD2 B:ARG422 4.1 9.2 1.0
C2 B:FCO601 4.1 8.4 1.0
H B:VAL77 4.1 9.4 1.0
N B:CYS78 4.2 7.8 1.0
CA B:CYS75 4.2 9.7 0.4
HG3 B:GLU28 4.2 13.2 1.0
CA B:CYS75 4.3 8.4 0.3
CB B:VAL77 4.4 8.8 1.0
CA B:CYS75 4.4 9.0 0.3
CA B:CYS489 4.4 8.1 0.6
N B:CYS492 4.5 7.5 1.0
HA B:CYS75 4.5 10.1 0.3
CA B:CYS489 4.5 8.8 0.4
HH11 B:ARG422 4.5 10.6 1.0
OE1 B:GLU28 4.5 12.2 0.7
HA B:CYS75 4.6 10.8 0.3
HB3 B:GLU28 4.6 12.4 1.0
HA B:CYS489 4.6 9.8 0.6
CA B:CYS78 4.7 8.2 1.0
C3 B:FCO601 4.7 12.0 1.0
N1 B:FCO601 4.7 9.9 1.0
HB2 B:CYS78 4.7 10.9 1.0
HB3 B:CYS492 4.7 10.1 1.0
HA B:CYS489 4.8 10.5 0.4
CD B:GLU28 4.8 11.2 0.7
CD B:ARG422 4.8 7.7 1.0
NH1 B:ARG422 4.8 8.9 1.0
CA B:CYS492 4.8 7.7 1.0
C B:CYS75 4.8 8.3 0.3
N B:VAL77 4.8 7.8 1.0
C B:CYS75 4.9 8.9 0.4
CG B:GLU28 4.9 11.0 0.7
C B:CYS75 4.9 8.6 0.3
C B:CYS489 4.9 7.8 0.6
O B:CYS489 4.9 7.8 0.6
HD3 B:ARG422 4.9 9.2 1.0
HG23 B:VAL77 4.9 13.2 1.0
CA B:VAL77 5.0 7.7 1.0
C B:VAL77 5.0 7.8 1.0
NE B:ARG422 5.0 8.4 1.0
C B:CYS489 5.0 8.3 0.4
HG12 B:VAL77 5.0 12.5 1.0
N2 B:FCO601 5.0 8.7 1.0

Nickel binding site 3 out of 3 in 5jsy

Go back to Nickel Binding Sites List in 5jsy
Nickel binding site 3 out of 3 in the The 3D Structure of the Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough at 1.04 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of The 3D Structure of the Ni-Reconstituted U489C Variant of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough at 1.04 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni602

b:9.5
occ:0.06
 NI B:NI602 0.0 9.5 0.1
NI B:NI602 1.2 9.0 0.2
NI B:NI602 1.3 10.2 0.3
SG B:CYS75 1.4 12.2 0.4
SG B:CYS75 1.9 8.9 0.3
HB3 B:CYS75 2.0 11.3 0.3
SG B:CYS492 2.0 9.7 1.0
HB2 B:CYS75 2.0 10.0 0.3
CB B:CYS75 2.1 8.3 0.3
HB2 B:CYS75 2.1 11.3 0.3
HB3 B:CYS75 2.1 10.0 0.3
CB B:CYS75 2.2 9.4 0.3
HB2 B:CYS75 2.2 13.1 0.4
SG B:CYS75 2.3 10.3 0.3
CB B:CYS75 2.3 10.9 0.4
S B:H2S604 2.4 17.1 0.5
SG B:CYS78 2.4 10.3 1.0
SG B:CYS489 2.5 11.5 0.6
OD1 B:CYS489 2.7 12.0 0.6
FE B:FCO601 2.9 9.0 1.0
HB3 B:CYS75 3.0 13.1 0.4
SG B:CYS489 3.1 11.3 0.4
O B:HOH1024 3.3 10.7 0.4
HA B:CYS75 3.3 11.6 0.4
CA B:CYS75 3.4 9.7 0.4
CB B:CYS492 3.5 8.4 1.0
OD3 B:CYS489 3.5 13.0 0.6
H B:CYS492 3.5 9.1 1.0
HB2 B:CYS492 3.5 10.1 1.0
CA B:CYS75 3.6 8.4 0.3
H B:CYS78 3.6 9.4 1.0
CA B:CYS75 3.7 9.0 0.3
HB3 B:CYS489 3.8 11.9 0.4
CB B:CYS78 3.9 9.1 1.0
HA B:CYS75 4.0 10.1 0.3
N B:CYS492 4.0 7.5 1.0
C1 B:FCO601 4.0 9.4 1.0
HB3 B:CYS78 4.0 10.9 1.0
HG22 B:ILE74 4.0 9.4 1.0
CB B:CYS489 4.0 10.0 0.4
CB B:CYS489 4.1 9.4 0.6
HA B:CYS75 4.1 10.8 0.3
CA B:CYS492 4.1 7.7 1.0
HB3 B:CYS489 4.1 11.3 0.6
HB3 B:CYS492 4.2 10.1 1.0
HA B:CYS492 4.2 9.2 1.0
C3 B:FCO601 4.2 12.0 1.0
HB B:VAL77 4.3 10.6 1.0
HB2 B:CYS489 4.3 11.9 0.4
C2 B:FCO601 4.3 8.4 1.0
C B:CYS75 4.3 8.3 0.3
HD2 B:HIS82 4.3 11.0 1.0
N B:CYS78 4.3 7.8 1.0
C B:CYS75 4.3 8.9 0.4
C B:CYS75 4.4 8.6 0.3
N B:CYS75 4.4 8.5 0.3
N B:CYS75 4.4 8.2 0.3
NE2 B:HIS82 4.4 9.5 1.0
H B:VAL77 4.4 9.4 1.0
N B:CYS75 4.4 8.8 0.4
O B:CYS75 4.5 8.8 0.3
O B:ILE74 4.6 8.7 1.0
CA B:CYS78 4.6 8.2 1.0
HB2 B:CYS78 4.6 10.9 1.0
HB2 B:CYS489 4.6 11.3 0.6
O B:CYS75 4.6 9.0 0.3
CD2 B:HIS82 4.7 9.2 1.0
C B:ILE74 4.8 8.0 1.0
O B:CYS75 4.8 9.3 0.4
H B:CYS75 4.8 10.2 0.3
H B:CYS75 4.8 9.9 0.3
N1 B:FCO601 4.9 9.9 1.0
HD2 B:ARG422 4.9 9.2 1.0
HA3 B:GLY491 4.9 9.7 1.0
CG2 B:ILE74 4.9 7.8 1.0
C B:GLY491 4.9 7.7 1.0

Reference:

M.C.Marques, C.Tapia, O.Gutierrez-Sanz, A.R.Ramos, K.L.Keller, J.D.Wall, A.L.De Lacey, P.M.Matias, I.A.C.Pereira. The Direct Role of Selenocysteine in [Nifese] Hydrogenase Maturation and Catalysis. Nat. Chem. Biol. V. 13 544 2017.
ISSN: ESSN 1552-4469
PubMed: 28319099
DOI: 10.1038/NCHEMBIO.2335
Page generated: Thu Oct 10 06:34:08 2024

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