Sodium in PDB 3f7l: X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase

Enzymatic activity of X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase

All present enzymatic activity of X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase, PDB code: 3f7l was solved by D.S.Shin, M.Didonato, D.P.Barondeau, E.D.Getzoff, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	45.00 / 0.99
*Space group*	P 6₁ 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	62.493, 62.493, 163.191, 90.00, 90.00, 120.00
*R / R_free (%)*	11.2 / 13.8

Other elements in 3f7l:

The structure of X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase also contains other interesting chemical elements:

Copper	(Cu)	2 atoms
Zinc	(Zn)	1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase (pdb code 3f7l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase, PDB code: 3f7l:

Sodium binding site 1 out of 1 in 3f7l

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Sodium Binding Sites List in 3f7l

Sodium binding site 1 out of 1 in the X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of Alvinella Pompejana Cu,Zn Superoxide Dismutase within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na204 b:9.2 occ:0.44	OD1	A:ASP90	1.5	13.3	1.0
	O	A:HOH397	2.1	14.3	0.6
	CG	A:ASP90	2.4	12.4	1.0
	CA	A:GLY88	3.0	10.1	1.0
	N	A:ASP90	3.1	10.7	1.0
	C	A:GLY88	3.2	9.8	1.0
	OD2	A:ASP90	3.3	14.2	1.0
	N	A:GLY88	3.4	9.5	1.0
	CB	A:ASP90	3.4	13.4	1.0
	O	A:LYS92	3.5	10.5	1.0
	CA	A:ASP90	3.6	11.1	1.0
	N	A:GLU89	3.6	10.8	1.0
	N	A:LYS92	3.6	9.5	1.0
	O	A:GLY88	3.7	9.9	1.0
	N	A:GLY91	3.8	9.4	1.0
	C	A:ASP90	3.9	10.8	1.0
	O	A:HOH332	4.0	10.5	0.5
	CB	A:LYS92	4.2	10.9	1.0
	CA	A:LYS92	4.2	9.4	1.0
	C	A:GLU89	4.2	10.8	1.0
	C	A:LYS92	4.3	9.2	1.0
	O	A:HOH412	4.5	11.9	1.0
	CA	A:GLU89	4.5	10.4	1.0
	O	A:ASP90	4.6	12.1	1.0
	C	A:ALA87	4.7	9.2	1.0
	C	A:GLY91	4.7	9.2	1.0
	CA	A:GLY91	4.8	9.6	1.0
	CG	A:LYS92	4.9	12.2	1.0
	O	A:HOH595	4.9	23.6	0.5

Reference:

D.S.Shin, M.Didonato, D.P.Barondeau, G.L.Hura, C.Hitomi, J.A.Berglund, E.D.Getzoff, S.C.Cary, J.A.Tainer. Superoxide Dismutase From the Eukaryotic Thermophile Alvinella Pompejana: Structures, Stability, Mechanism, and Insights Into Amyotrophic Lateral Sclerosis. J.Mol.Biol. V. 385 1534 2009.
ISSN: ISSN 0022-2836
PubMed: 19063897
DOI: 10.1016/J.JMB.2008.11.031

Page generated: Mon Oct 7 08:59:08 2024

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