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Nickel in PDB 5jsk: The 3D Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Reduced State at 0.95 Angstrom Resolution

Enzymatic activity of The 3D Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Reduced State at 0.95 Angstrom Resolution

All present enzymatic activity of The 3D Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Reduced State at 0.95 Angstrom Resolution:
1.12.7.2;

Protein crystallography data

The structure of The 3D Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Reduced State at 0.95 Angstrom Resolution, PDB code: 5jsk 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) 45.48 / 0.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 106.280, 62.770, 110.860, 90.00, 105.11, 90.00
R / Rfree (%) 11 / 12

Other elements in 5jsk:

The structure of The 3D Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Reduced State at 0.95 Angstrom Resolution also contains other interesting chemical elements:

Iron (Fe) 14 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the The 3D Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Reduced State at 0.95 Angstrom Resolution (pdb code 5jsk). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the The 3D Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Reduced State at 0.95 Angstrom Resolution, PDB code: 5jsk:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 5jsk

Go back to Nickel Binding Sites List in 5jsk
Nickel binding site 1 out of 2 in the The 3D Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Reduced State at 0.95 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 [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Reduced State at 0.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni601

b:7.2
occ:0.07
 NI B:NI603 0.9 5.8 0.8
SE B:SEC489 1.5 6.6 0.8
SE B:SEC489 2.1 10.3 0.1
SG B:CYS75 2.1 6.5 1.0
SE B:SEC489 2.2 6.7 0.1
HB2 B:SEC489 2.6 10.9 0.1
SG B:CYS492 2.7 6.6 1.0
HB2 B:CYS75 2.8 7.9 1.0
CB B:SEC489 2.9 6.5 0.1
CB B:SEC489 2.9 9.1 0.1
HB2 B:SEC489 2.9 7.8 0.1
CB B:SEC489 3.0 6.7 0.8
CB B:CYS75 3.0 6.6 1.0
HB3 B:SEC489 3.0 7.8 0.1
SG B:CYS78 3.1 6.1 1.0
HB2 B:SEC489 3.2 8.1 0.8
FE B:FCO602 3.2 5.9 1.0
HB2 B:CYS492 3.2 7.6 1.0
H B:CYS492 3.3 7.2 1.0
HB3 B:CYS75 3.3 7.9 1.0
HB3 B:SEC489 3.4 8.1 0.8
CB B:CYS492 3.5 6.3 1.0
HB3 B:SEC489 3.6 10.9 0.1
HB B:VAL77 3.7 7.9 1.0
C1 B:FCO602 3.8 6.4 1.0
H B:CYS78 3.8 6.8 1.0
HG3 B:GLU28 3.9 8.8 1.0
N B:CYS492 4.0 6.0 1.0
CA B:SEC489 4.2 7.6 0.1
HD2 B:ARG422 4.2 7.3 1.0
HB3 B:CYS78 4.2 7.2 1.0
CA B:SEC489 4.2 6.2 0.8
CA B:SEC489 4.3 6.3 0.1
CA B:CYS492 4.3 5.8 1.0
C2 B:FCO602 4.3 6.2 1.0
HB3 B:CYS492 4.3 7.6 1.0
CA B:CYS75 4.3 5.9 1.0
CB B:CYS78 4.3 6.0 1.0
HB3 B:GLU28 4.4 8.5 1.0
HA B:CYS75 4.4 7.1 1.0
HA B:SEC489 4.5 7.4 0.8
H B:VAL77 4.5 6.8 1.0
N B:CYS78 4.5 5.7 1.0
OE1 B:GLU28 4.5 8.6 1.0
N1 B:FCO602 4.6 7.1 1.0
O B:SEC489 4.6 6.9 0.1
HA B:CYS492 4.6 6.9 1.0
C B:SEC489 4.6 6.8 0.1
C B:SEC489 4.6 6.0 0.8
O B:SEC489 4.6 6.3 0.8
CG B:GLU28 4.6 7.3 1.0
C B:SEC489 4.7 6.2 0.1
O B:SEC489 4.7 6.2 0.1
CB B:VAL77 4.7 6.6 1.0
CD B:GLU28 4.8 8.0 1.0
C3 B:FCO602 4.8 7.4 1.0
HH11 B:ARG422 4.8 8.4 1.0
HG22 B:ILE74 4.9 7.5 1.0
CD B:ARG422 4.9 6.1 1.0
HD3 B:ARG422 4.9 7.3 1.0
H B:GLY491 4.9 7.6 1.0
HA3 B:GLY491 4.9 7.7 1.0
CB B:GLU28 5.0 7.0 1.0

Nickel binding site 2 out of 2 in 5jsk

Go back to Nickel Binding Sites List in 5jsk
Nickel binding site 2 out of 2 in the The 3D Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Reduced State at 0.95 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 [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Reduced State at 0.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni603

b:5.8
occ:0.81
 NI B:NI601 0.9 7.2 0.1
SG B:CYS78 2.2 6.1 1.0
SG B:CYS75 2.2 6.5 1.0
SE B:SEC489 2.3 6.6 0.8
SE B:SEC489 2.5 10.3 0.1
FE B:FCO602 2.6 5.9 1.0
SG B:CYS492 2.6 6.6 1.0
CB B:CYS75 3.1 6.6 1.0
HB2 B:CYS75 3.1 7.9 1.0
HB2 B:SEC489 3.1 10.9 0.1
SE B:SEC489 3.1 6.7 0.1
HB3 B:CYS75 3.1 7.9 1.0
H B:CYS78 3.3 6.8 1.0
HB3 B:CYS78 3.3 7.2 1.0
HB2 B:SEC489 3.3 7.8 0.1
CB B:CYS78 3.4 6.0 1.0
HB3 B:SEC489 3.4 7.8 0.1
CB B:SEC489 3.4 9.1 0.1
CB B:SEC489 3.5 6.5 0.1
CB B:SEC489 3.5 6.7 0.8
HB2 B:SEC489 3.5 8.1 0.8
C2 B:FCO602 3.5 6.2 1.0
C1 B:FCO602 3.5 6.4 1.0
HB B:VAL77 3.6 7.9 1.0
HB2 B:CYS492 3.6 7.6 1.0
HB3 B:SEC489 3.7 8.1 0.8
CB B:CYS492 3.8 6.3 1.0
HB3 B:SEC489 3.8 10.9 0.1
HD2 B:ARG422 3.8 7.3 1.0
N B:CYS78 3.9 5.7 1.0
H B:CYS492 4.0 7.2 1.0
HB2 B:CYS78 4.2 7.2 1.0
HH11 B:ARG422 4.2 8.4 1.0
C3 B:FCO602 4.2 7.4 1.0
CA B:CYS78 4.2 5.8 1.0
H B:VAL77 4.4 6.8 1.0
HB3 B:CYS492 4.4 7.6 1.0
N1 B:FCO602 4.5 7.1 1.0
N2 B:FCO602 4.5 6.6 1.0
CA B:CYS75 4.5 5.9 1.0
CB B:VAL77 4.5 6.6 1.0
NH1 B:ARG422 4.5 7.0 1.0
HG3 B:GLU28 4.6 8.8 1.0
N B:CYS492 4.6 6.0 1.0
CD B:ARG422 4.6 6.1 1.0
CA B:CYS492 4.7 5.8 1.0
HA B:CYS75 4.7 7.1 1.0
C B:VAL77 4.8 5.7 1.0
CA B:SEC489 4.8 7.6 0.1
CA B:SEC489 4.9 6.2 0.8
HD3 B:ARG422 4.9 7.3 1.0
HH12 B:ARG422 4.9 8.4 1.0
NE B:ARG422 4.9 6.4 1.0
HA B:CYS492 4.9 6.9 1.0
HD2 B:HIS82 4.9 8.1 1.0
CA B:SEC489 4.9 6.3 0.1
HG12 B:VAL77 4.9 9.0 1.0
C B:CYS78 5.0 5.6 1.0
CZ B:ARG422 5.0 6.4 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 06:33:11 2024

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