Sodium in PDB 3dt2: The Structure of Rat Cytosolic Pepck in Complex with Oxalate and Gtp

Enzymatic activity of The Structure of Rat Cytosolic Pepck in Complex with Oxalate and Gtp

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

Protein crystallography data

The structure of The Structure of Rat Cytosolic Pepck in Complex with Oxalate and Gtp, PDB code: 3dt2 was solved by S.M.Sullivan, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	33.17 / 1.50
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	60.423, 84.906, 119.027, 90.00, 90.00, 90.00
*R / R_free (%)*	15.9 / 18.5

Other elements in 3dt2:

The structure of The Structure of Rat Cytosolic Pepck in Complex with Oxalate and 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 in Complex with Oxalate and Gtp (pdb code 3dt2). 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 in Complex with Oxalate and Gtp, PDB code: 3dt2:

Sodium binding site 1 out of 1 in 3dt2

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Sodium Binding Sites List in 3dt2

Sodium binding site 1 out of 1 in the The Structure of Rat Cytosolic Pepck in Complex with Oxalate and 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 in Complex with Oxalate and Gtp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na1000 b:15.5 occ:1.00	O	A:ASN208	2.3	10.6	1.0
	O	A:HOH1422	2.3	23.2	1.0
	O	A:LEU79	2.3	7.8	1.0
	O	A:HOH1217	2.4	15.6	1.0
	O	A:HOH1261	2.4	16.2	1.0
	C	A:LEU79	3.4	6.9	1.0
	C	A:ASN208	3.5	10.6	1.0
	N	A:LEU79	3.8	6.0	1.0
	CA	A:LEU79	3.9	6.3	1.0
	CB	A:LEU79	4.0	7.2	1.0
	CB	A:ASN208	4.0	11.6	1.0
	O	A:VAL65	4.1	12.1	1.0
	O	A:HOH1774	4.2	38.6	1.0
	CA	A:ASN208	4.3	11.4	1.0
	CB	A:ASN209	4.3	10.6	0.5
	C	A:ASN209	4.3	9.6	1.0
	O	A:ASN209	4.4	9.0	1.0
	O	A:HOH1834	4.4	32.8	1.0
	N	A:ASN209	4.5	10.8	1.0
	CB	A:ASN209	4.5	11.2	0.5
	N	A:THR80	4.6	6.3	1.0
	CB	A:TRP210	4.6	7.1	1.0
	CA	A:ASN209	4.6	10.4	0.5
	O	A:HOH1686	4.6	35.6	1.0
	CA	A:ASN209	4.6	10.7	0.5
	N	A:TRP210	4.7	8.5	1.0
	O	A:GLY64	4.7	16.1	1.0
	C	A:VAL65	4.9	11.8	1.0
	CE3	A:TRP210	4.9	9.3	1.0
	CA	A:THR80	4.9	7.2	1.0
	C	A:ALA78	5.0	6.1	1.0

Reference:

S.M.Sullivan, T.Holyoak. Enzymes with Lid-Gated Active Sites Must Operate By An Induced Fit Mechanism Instead of Conformational Selection. Proc.Natl.Acad.Sci.Usa V. 105 13829 2008.
ISSN: ISSN 0027-8424
PubMed: 18772387
DOI: 10.1073/PNAS.0805364105

Page generated: Sun Aug 17 14:33:39 2025

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