Sodium in PDB 2xvz: Cobalt Chelatase Cbik (Periplasmatic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallized with Cobalt)

Enzymatic activity of Cobalt Chelatase Cbik (Periplasmatic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallized with Cobalt)

All present enzymatic activity of Cobalt Chelatase Cbik (Periplasmatic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallized with Cobalt):
4.99.1.3;

Protein crystallography data

The structure of Cobalt Chelatase Cbik (Periplasmatic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallized with Cobalt), PDB code: 2xvz was solved by C.V.Romao, S.A.L.Lobo, M.A.Carrondo, L.M.Saraiva, P.M.Matias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	85.75 / 2.40
*Space group*	I 4 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	121.441, 121.441, 121.100, 90.00, 90.00, 90.00
*R / R_free (%)*	16.96 / 22.022

Other elements in 2xvz:

The structure of Cobalt Chelatase Cbik (Periplasmatic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallized with Cobalt) also contains other interesting chemical elements:

Cobalt	(Co)	1 atom
Iron	(Fe)	1 atom
Chlorine	(Cl)	1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Cobalt Chelatase Cbik (Periplasmatic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallized with Cobalt) (pdb code 2xvz). 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 Cobalt Chelatase Cbik (Periplasmatic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallized with Cobalt), PDB code: 2xvz:

Sodium binding site 1 out of 1 in 2xvz

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Sodium Binding Sites List in 2xvz

Sodium binding site 1 out of 1 in the Cobalt Chelatase Cbik (Periplasmatic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallized with Cobalt)

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cobalt Chelatase Cbik (Periplasmatic) From Desulvobrio Vulgaris Hildenborough (Co-Crystallized with Cobalt) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na1283 b:15.9 occ:1.00	OH	A:TYR164	2.8	21.1	1.0
	N	A:HIS154	3.1	21.6	1.0
	O2	A:SO41273	3.2	80.7	1.0
	CA	A:GLY153	3.6	18.7	1.0
	CB	A:THR89	3.8	23.6	1.0
	CZ	A:TYR164	3.8	18.2	1.0
	C	A:GLY153	3.8	20.1	1.0
	OG1	A:THR89	3.9	27.1	1.0
	CE1	A:TYR164	3.9	16.7	1.0
	CB	A:HIS154	4.0	22.6	1.0
	CG2	A:THR89	4.0	22.7	1.0
	CA	A:HIS154	4.1	22.4	1.0
	S	A:SO41273	4.3	81.7	1.0
	CB	A:MET210	4.4	25.0	1.0
	O4	A:SO41273	4.4	81.3	1.0
	CA	A:MET210	4.5	25.1	1.0
	N	A:MET210	4.5	24.3	1.0
	CE	A:MET210	4.5	36.6	1.0
	C	A:LEU209	4.6	25.2	1.0
	CB	A:LEU209	4.6	23.4	1.0
	O1	A:SO41273	4.7	79.9	1.0
	CG	A:LEU209	4.8	26.2	1.0
	O	A:LEU209	4.9	27.6	1.0
	SD	A:MET210	4.9	41.6	1.0
	N	A:GLY153	4.9	16.7	1.0
	O	A:HOH2108	4.9	25.5	1.0
	O	A:MET152	5.0	16.0	1.0

Reference:

C.V.Romao, D.Ladakis, S.A.L.Lobo, M.A.Carrondo, A.A.Brindley, E.Deery, P.M.Matias, R.W.Pickersgill, L.M.Saraiva, M.J.Warren. Evolution in A Family of Chelatases Facilitated By the Introduction of Active Site Asymmetry and Protein Oligomerization. Proc.Natl.Acad.Sci.Usa V. 108 97 2011.
ISSN: ISSN 0027-8424
PubMed: 21173279
DOI: 10.1073/PNAS.1014298108

Page generated: Mon Oct 7 05:16:09 2024

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