Sodium in PDB 5v9f: Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Beta Sulfopyruvate and Gtp.

Enzymatic activity of Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Beta Sulfopyruvate and Gtp.

All present enzymatic activity of Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Beta Sulfopyruvate and Gtp.:
4.1.1.32;

Protein crystallography data

The structure of Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Beta Sulfopyruvate and Gtp., PDB code: 5v9f was solved by T.Holyoak, D.S.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	59.75 / 2.05
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	46.285, 119.506, 60.707, 90.00, 107.81, 90.00
*R / R_free (%)*	19.5 / 23.4

Other elements in 5v9f:

The structure of Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Beta Sulfopyruvate and Gtp. also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Beta Sulfopyruvate and Gtp. (pdb code 5v9f). 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 Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Beta Sulfopyruvate and Gtp., PDB code: 5v9f:

Sodium binding site 1 out of 1 in 5v9f

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Sodium Binding Sites List in 5v9f

Sodium binding site 1 out of 1 in the Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Beta Sulfopyruvate and Gtp.

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Beta Sulfopyruvate and Gtp. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na703 b:77.7 occ:1.00	O	A:HOH895	2.1	42.4	1.0
	O	A:ASN208	2.5	52.1	1.0
	O	A:HOH940	3.0	43.0	1.0
	O	A:LEU79	3.2	42.7	1.0
	C	A:ASN208	3.5	53.4	1.0
	O	A:GLY64	3.5	61.0	1.0
	O	A:VAL65	3.8	51.2	1.0
	CB	A:ASN208	4.1	59.5	1.0
	N	A:LEU79	4.1	41.3	1.0
	CB	A:LEU79	4.2	42.7	1.0
	C	A:LEU79	4.2	41.5	1.0
	CB	A:ASN209	4.2	52.7	1.0
	CA	A:ASN208	4.2	55.5	1.0
	N	A:ASN209	4.4	50.9	1.0
	CA	A:LEU79	4.4	41.5	1.0
	C	A:VAL65	4.5	50.3	1.0
	ND2	A:ASN209	4.6	56.2	1.0
	CA	A:ASN209	4.6	50.3	1.0
	C	A:GLY64	4.7	57.1	1.0
	CA	A:VAL65	4.7	52.4	1.0
	C	A:ASN209	4.7	45.9	1.0
	O	A:ASN209	4.8	45.3	1.0
	CG	A:LEU79	5.0	43.4	1.0
	CG	A:ASN209	5.0	55.7	1.0

Reference:

D.S.Cui, A.Broom, M.J.Mcleod, E.M.Meiering, T.Holyoak. Asymmetric Anchoring Is Required For Efficient Omega-Loop Opening and Closing in Cytosolic Phosphoenolpyruvate Carboxykinase. Biochemistry V. 56 2106 2017.
ISSN: ISSN 1520-4995
PubMed: 28345895
DOI: 10.1021/ACS.BIOCHEM.7B00178

Page generated: Tue Oct 8 00:46:19 2024

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