Sodium in PDB 5fh1: The Structure of Rat Cytosolic Pepck Variant E89D in Complex with Gtp

Enzymatic activity of The Structure of Rat Cytosolic Pepck Variant E89D in Complex with Gtp

All present enzymatic activity of The Structure of Rat Cytosolic Pepck Variant E89D in Complex with Gtp:
4.1.1.32;

Protein crystallography data

The structure of The Structure of Rat Cytosolic Pepck Variant E89D in Complex with Gtp, PDB code: 5fh1 was solved by T.A.Johnson, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	59.56 / 1.55
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	45.523, 119.119, 60.894, 90.00, 107.66, 90.00
*R / R_free (%)*	18.4 / 21.8

Other elements in 5fh1:

The structure of The Structure of Rat Cytosolic Pepck Variant E89D in Complex with Gtp also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Structure of Rat Cytosolic Pepck Variant E89D in Complex with Gtp (pdb code 5fh1). 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 The Structure of Rat Cytosolic Pepck Variant E89D in Complex with Gtp, PDB code: 5fh1:

Sodium binding site 1 out of 1 in 5fh1

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Sodium Binding Sites List in 5fh1

Sodium binding site 1 out of 1 in the The Structure of Rat Cytosolic Pepck Variant E89D in Complex with Gtp

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Rat Cytosolic Pepck Variant E89D in Complex with Gtp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na705 b:34.0 occ:1.00	O	A:HOH952	2.3	33.0	1.0
	O	A:LEU79	2.3	30.8	1.0
	O	A:HOH1016	2.4	38.0	1.0
	O	A:ASN208	2.4	36.6	1.0
	O	A:HOH1226	2.4	46.8	1.0
	C	A:LEU79	3.4	29.6	1.0
	C	A:ASN208	3.5	34.7	1.0
	O	A:VAL65	3.9	34.6	1.0
	N	A:LEU79	3.9	29.7	1.0
	CA	A:LEU79	4.0	28.6	1.0
	CB	A:ASN208	4.0	38.4	1.0
	CB	A:LEU79	4.1	30.9	1.0
	O	A:HOH1350	4.3	51.5	1.0
	CA	A:ASN208	4.3	37.1	1.0
	CB	A:ASN209	4.3	40.4	1.0
	O	A:ASN209	4.4	32.4	1.0
	O	A:GLY64	4.4	41.8	1.0
	C	A:ASN209	4.4	32.8	1.0
	N	A:ASN209	4.5	35.8	1.0
	N	A:THR80	4.6	31.1	1.0
	CB	A:TRP210	4.6	28.4	1.0
	O	A:HOH1223	4.6	52.2	1.0
	CA	A:ASN209	4.6	37.1	1.0
	C	A:VAL65	4.7	33.4	1.0
	N	A:TRP210	4.8	30.3	1.0
	CE3	A:TRP210	4.9	27.6	1.0
	CA	A:THR80	4.9	30.3	1.0

Reference:

T.A.Johnson, M.J.Mcleod, T.Holyoak. Utilization of Substrate Intrinsic Binding Energy For Conformational Change and Catalytic Function in Phosphoenolpyruvate Carboxykinase. Biochemistry V. 55 575 2016.
ISSN: ISSN 1520-4995
PubMed: 26709450
DOI: 10.1021/ACS.BIOCHEM.5B01215

Page generated: Sun Aug 17 23:49:20 2025

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