Sodium in PDB 3gvf: 1.7 Angstrom Crystal Structure of Inorganic Pyrophosphatase From Burkholderia Pseudomallei Bound with Phosphate

Enzymatic activity of 1.7 Angstrom Crystal Structure of Inorganic Pyrophosphatase From Burkholderia Pseudomallei Bound with Phosphate

All present enzymatic activity of 1.7 Angstrom Crystal Structure of Inorganic Pyrophosphatase From Burkholderia Pseudomallei Bound with Phosphate:
3.6.1.1;

Protein crystallography data

The structure of 1.7 Angstrom Crystal Structure of Inorganic Pyrophosphatase From Burkholderia Pseudomallei Bound with Phosphate, PDB code: 3gvf was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	50.00 / 1.75
*Space group*	P 6₃ 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	100.212, 100.212, 110.667, 90.00, 90.00, 120.00
*R / R_free (%)*	17.5 / 18.5

Other elements in 3gvf:

The structure of 1.7 Angstrom Crystal Structure of Inorganic Pyrophosphatase From Burkholderia Pseudomallei Bound with Phosphate also contains other interesting chemical elements:

Potassium

(K)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.7 Angstrom Crystal Structure of Inorganic Pyrophosphatase From Burkholderia Pseudomallei Bound with Phosphate (pdb code 3gvf). 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 1.7 Angstrom Crystal Structure of Inorganic Pyrophosphatase From Burkholderia Pseudomallei Bound with Phosphate, PDB code: 3gvf:

Sodium binding site 1 out of 1 in 3gvf

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Sodium Binding Sites List in 3gvf

Sodium binding site 1 out of 1 in the 1.7 Angstrom Crystal Structure of Inorganic Pyrophosphatase From Burkholderia Pseudomallei Bound with Phosphate

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.7 Angstrom Crystal Structure of Inorganic Pyrophosphatase From Burkholderia Pseudomallei Bound with Phosphate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na178 b:44.2 occ:1.00	OD2	A:ASP71	2.3	26.7	1.0
	O	A:HOH308	2.3	50.1	1.0
	OD2	A:ASP66	2.5	24.1	1.0
	O	A:HOH305	2.6	21.3	1.0
	CG	A:ASP71	3.2	22.1	1.0
	OD2	A:ASP103	3.3	18.4	1.0
	OD1	A:ASP71	3.4	27.9	1.0
	O	A:HOH298	3.4	28.2	1.0
	OD1	A:ASP103	3.5	18.1	1.0
	CG	A:ASP66	3.6	22.5	1.0
	CG	A:ASP103	3.8	18.0	1.0
	NZ	A:LYS105	3.9	17.9	1.0
	OD1	A:ASP66	4.0	22.9	1.0
	O	A:HOH306	4.0	39.1	1.0
	O	A:HOH264	4.1	35.2	1.0
	CB	A:ASP68	4.3	20.4	1.0
	O	A:HOH304	4.5	36.3	1.0
	OD2	A:ASP68	4.5	24.9	1.0
	O	A:PRO69	4.5	16.3	1.0
	CB	A:ASP71	4.5	18.0	1.0
	O	A:HOH266	4.5	30.7	1.0
	OH	A:TYR56	4.7	21.0	1.0
	O2	A:PO4176	4.8	60.1	1.0
	CB	A:ASP66	4.9	21.5	1.0
	CG	A:ASP68	5.0	22.4	1.0

Reference:

L.Baugh, L.A.Gallagher, R.Patrapuvich, M.C.Clifton, A.S.Gardberg, T.E.Edwards, B.Armour, D.W.Begley, S.H.Dieterich, D.M.Dranow, J.Abendroth, J.W.Fairman, D.Fox, B.L.Staker, I.Phan, A.Gillespie, R.Choi, S.Nakazawa-Hewitt, M.T.Nguyen, A.Napuli, L.Barrett, G.W.Buchko, R.Stacy, P.J.Myler, L.J.Stewart, C.Manoil, W.C.Van Voorhis. Combining Functional and Structural Genomics to Sample the Essential Burkholderia Structome. Plos One V. 8 53851 2013.
ISSN: ESSN 1932-6203
PubMed: 23382856
DOI: 10.1371/JOURNAL.PONE.0053851

Page generated: Mon Oct 7 10:17:57 2024

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