Nickel in PDB 2wpn: Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough

Enzymatic activity of Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough

All present enzymatic activity of Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough:
1.18.99.1;

Protein crystallography data

The structure of Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough, PDB code: 2wpn was solved by M.C.Marques, R.Coelho, A.L.De Lacey, 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)*	65.36 / 2.04
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	60.596, 91.223, 66.751, 90.00, 101.73, 90.00
*R / R_free (%)*	14.4 / 20.1

Other elements in 2wpn:

The structure of Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough also contains other interesting chemical elements:

Iron	(Fe)	18 atoms
Chlorine	(Cl)	1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough (pdb code 2wpn). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough, PDB code: 2wpn:

Nickel binding site 1 out of 1 in 2wpn

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Nickel Binding Sites List in 2wpn

Nickel binding site 1 out of 1 in the Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough

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 Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Ni1498 b:24.9 occ:1.00	SD	B:SEC489	2.1	19.3	0.7
	SD	B:SEC489	2.1	15.4	0.1
	SE	B:SEC489	2.2	16.8	0.1
	SG	B:CYS78	2.3	19.7	1.0
	SG	B:OCS75	2.3	23.3	1.0
	SG	B:CYS492	2.3	20.5	1.0
	SE	B:SEC489	2.3	24.9	0.7
	FE	B:FCO1497	2.5	23.8	1.0
	SE	B:SEC489	3.0	22.1	0.1
	CB	B:OCS75	3.1	21.8	1.0
	OD2	B:OCS75	3.1	21.7	1.0
	OD1	B:OCS75	3.2	23.1	1.0
	C1	B:FCO1497	3.3	19.5	1.0
	CB	B:SEC489	3.3	82.7	0.1
	CB	B:CYS492	3.4	21.3	1.0
	C2	B:FCO1497	3.5	15.6	1.0
	CB	B:CYS78	3.5	21.2	1.0
	CB	B:SEC489	3.6	15.9	0.7
	CB	B:SEC489	3.7	10.5	0.1
	N1	B:FCO1497	4.1	21.4	1.0
	C3	B:FCO1497	4.2	19.4	1.0
	N	B:CYS78	4.2	19.7	1.0
	N	B:CYS492	4.4	16.1	1.0
	N2	B:FCO1497	4.4	17.8	1.0
	CA	B:CYS492	4.4	19.1	1.0
	CA	B:CYS78	4.4	14.8	1.0
	CA	B:OCS75	4.5	16.7	1.0
	CD	B:ARG422	4.8	20.2	1.0
	CA	B:SEC489	4.8	23.4	0.1
	NE2	B:HIS82	4.8	19.9	1.0
	CA	B:SEC489	4.9	20.4	0.7
	CA	B:SEC489	4.9	18.9	0.1
	O	B:SEC489	4.9	22.4	0.2
	O	B:SEC489	4.9	22.4	0.2
	O	B:SEC489	4.9	22.4	0.5

Reference:

M.C.Marques, R.Coelho, A.L.De Lacey, I.A.Pereira, P.M.Matias. The Three-Dimensional Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough: A Hydrogenase Without A Bridging Ligand in the Active Site in Its Oxidised, "As-Isolated" State. J.Mol.Biol. V. 396 893 2010.
ISSN: ESSN 1089-8638
PubMed: 20026074
DOI: 10.1016/J.JMB.2009.12.013

Page generated: Wed Oct 9 17:03:13 2024

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