Sodium in PDB 6p5o: The Structure of Rat Cytosolic Pepck in Complex with 3- (Carboxymethylthiol)-Picolinic Acid

Enzymatic activity of The Structure of Rat Cytosolic Pepck in Complex with 3- (Carboxymethylthiol)-Picolinic Acid

All present enzymatic activity of The Structure of Rat Cytosolic Pepck in Complex with 3- (Carboxymethylthiol)-Picolinic Acid:
4.1.1.32;

Protein crystallography data

The structure of The Structure of Rat Cytosolic Pepck in Complex with 3- (Carboxymethylthiol)-Picolinic Acid, PDB code: 6p5o was solved by M.J.Mcleod, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	59.35 / 1.49
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	44.409, 118.707, 60.863, 90.00, 109.61, 90.00
*R / R_free (%)*	15.9 / 17.9

Other elements in 6p5o:

The structure of The Structure of Rat Cytosolic Pepck in Complex with 3- (Carboxymethylthiol)-Picolinic Acid 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 3- (Carboxymethylthiol)-Picolinic Acid (pdb code 6p5o). 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 3- (Carboxymethylthiol)-Picolinic Acid, PDB code: 6p5o:

Sodium binding site 1 out of 1 in 6p5o

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Sodium Binding Sites List in 6p5o

Sodium binding site 1 out of 1 in the The Structure of Rat Cytosolic Pepck in Complex with 3- (Carboxymethylthiol)-Picolinic Acid

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 3- (Carboxymethylthiol)-Picolinic Acid within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na704 b:23.0 occ:1.00	O	A:ASN208	2.1	21.9	1.0
	O	A:LEU79	2.3	20.7	1.0
	O	A:HOH1294	2.3	35.7	1.0
	O	A:HOH1075	2.4	22.0	1.0
	O	A:HOH1050	2.5	24.0	1.0
	C	A:ASN208	3.3	22.6	1.0
	C	A:LEU79	3.5	20.0	1.0
	CB	A:ASN208	3.9	25.9	1.0
	N	A:LEU79	3.9	19.7	1.0
	O	A:VAL65	4.0	22.1	1.0
	CA	A:LEU79	4.0	19.8	1.0
	CA	A:ASN208	4.1	24.3	1.0
	CB	A:LEU79	4.1	20.8	1.0
	O	A:HOH1403	4.2	44.9	1.0
	C	A:ASN209	4.3	21.2	1.0
	CB	A:ASN209	4.3	24.5	1.0
	N	A:ASN209	4.3	22.7	1.0
	O	A:ASN209	4.3	20.2	1.0
	O	A:GLY64	4.3	30.1	1.0
	CA	A:ASN209	4.5	22.9	1.0
	N	A:THR80	4.6	19.9	1.0
	CB	A:TRP210	4.6	18.9	1.0
	N	A:TRP210	4.7	20.3	1.0
	C	A:VAL65	4.7	22.3	1.0
	CA	A:THR80	4.9	19.7	1.0
	CA	A:VAL65	4.9	24.1	1.0
	C	A:ALA78	5.0	19.5	1.0

Reference:

M.J.Mcleod, A.P.Krismanich, A.Assoud, G.I.Dmitrienko, T.Holyoak. Characterization of 3-[(Carboxymethyl)Thio]Picolinic Acid: A Novel Inhibitor of Phosphoenolpyruvate Carboxykinase. Biochemistry V. 58 3918 2019.
ISSN: ISSN 0006-2960
PubMed: 31461616
DOI: 10.1021/ACS.BIOCHEM.9B00583

Page generated: Tue Oct 8 12:40:43 2024

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