Sodium in PDB 4gmz: Structure of Rat Cytosolic Pepck LD_2G in Complex with Beta- Sulfopyruvate and Gtp

Enzymatic activity of Structure of Rat Cytosolic Pepck LD_2G in Complex with Beta- Sulfopyruvate and Gtp

All present enzymatic activity of Structure of Rat Cytosolic Pepck LD_2G in Complex with Beta- Sulfopyruvate and Gtp:
4.1.1.32;

Protein crystallography data

The structure of Structure of Rat Cytosolic Pepck LD_2G in Complex with Beta- Sulfopyruvate and Gtp, PDB code: 4gmz 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)*	30.80 / 2.05
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	60.624, 83.908, 118.583, 90.00, 90.00, 90.00
*R / R_free (%)*	18.3 / 23.2

Other elements in 4gmz:

The structure of Structure of Rat Cytosolic Pepck LD_2G 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 Rat Cytosolic Pepck LD_2G in Complex with Beta- Sulfopyruvate and Gtp (pdb code 4gmz). 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 Rat Cytosolic Pepck LD_2G in Complex with Beta- Sulfopyruvate and Gtp, PDB code: 4gmz:

Sodium binding site 1 out of 1 in 4gmz

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Sodium Binding Sites List in 4gmz

Sodium binding site 1 out of 1 in the Structure of Rat Cytosolic Pepck LD_2G 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 Rat Cytosolic Pepck LD_2G in Complex with Beta- Sulfopyruvate and Gtp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na701 b:43.4 occ:1.00	O	A:HOH1101	2.0	32.9	1.0
	O	A:ASN208	2.3	33.0	1.0
	O	A:HOH979	2.5	32.4	1.0
	O	A:HOH1163	2.6	31.8	1.0
	O	A:LEU79	2.7	18.5	1.0
	C	A:ASN208	3.4	34.0	1.0
	N	A:LEU79	3.6	20.1	1.0
	C	A:LEU79	3.7	19.3	1.0
	O	A:VAL65	3.9	29.8	1.0
	CA	A:LEU79	4.0	19.3	1.0
	CB	A:ASN209	4.0	33.7	1.0
	CB	A:LEU79	4.0	19.6	1.0
	CB	A:ASN208	4.2	37.3	1.0
	O	A:GLY64	4.2	32.0	1.0
	C	A:ASN209	4.3	29.1	1.0
	N	A:ASN209	4.3	32.9	1.0
	O	A:ASN209	4.3	30.1	1.0
	CA	A:ASN208	4.3	35.6	1.0
	CA	A:ASN209	4.4	31.6	1.0
	C	A:VAL65	4.5	29.0	1.0
	N	A:TRP210	4.7	26.1	1.0
	C	A:ALA78	4.7	20.0	1.0
	CA	A:VAL65	4.8	29.6	1.0
	OD1	A:ASN208	4.8	40.8	1.0
	CB	A:TRP210	4.8	23.2	1.0
	CG	A:ASN209	4.9	35.5	1.0
	N	A:THR80	4.9	19.0	1.0
	CA	A:ALA78	5.0	20.2	1.0
	CG	A:LEU79	5.0	19.7	1.0
	CG	A:ASN208	5.0	39.3	1.0

Reference:

T.A.Johnson, T.Holyoak. The {Omega}-Loop Lid Domain of Phosphoenolpyruvate Carboxykinase Is Essential For Catalytic Function. Biochemistry V. 51 9547 2012.
ISSN: ISSN 0006-2960
PubMed: 23127136
DOI: 10.1021/BI301278T

Page generated: Sun Aug 17 19:30:49 2025

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