Sodium in PDB 4gnl: Structure of Rat Cytosolic Pepck LD_2G in Complex with Pep and Gdp

Enzymatic activity of Structure of Rat Cytosolic Pepck LD_2G in Complex with Pep and Gdp

All present enzymatic activity of Structure of Rat Cytosolic Pepck LD_2G in Complex with Pep and Gdp:
4.1.1.32;

Protein crystallography data

The structure of Structure of Rat Cytosolic Pepck LD_2G in Complex with Pep and Gdp, PDB code: 4gnl 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)*	38.11 / 1.70
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	61.255, 84.752, 118.962, 90.00, 90.00, 90.00
*R / R_free (%)*	19.2 / 23.3

Other elements in 4gnl:

The structure of Structure of Rat Cytosolic Pepck LD_2G in Complex with Pep and Gdp also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Rat Cytosolic Pepck LD_2G in Complex with Pep and Gdp (pdb code 4gnl). 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 Pep and Gdp, PDB code: 4gnl:

Sodium binding site 1 out of 1 in 4gnl

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Sodium Binding Sites List in 4gnl

Sodium binding site 1 out of 1 in the Structure of Rat Cytosolic Pepck LD_2G in Complex with Pep and Gdp

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 Pep and Gdp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na703 b:37.8 occ:1.00	O	A:ASN208	2.2	33.0	1.0
	O	A:LEU79	2.3	34.5	1.0
	O	A:HOH880	2.3	28.4	1.0
	O	A:HOH1082	2.4	46.4	1.0
	O	A:HOH886	2.5	34.0	1.0
	C	A:ASN208	3.4	34.2	1.0
	C	A:LEU79	3.4	31.3	1.0
	N	A:LEU79	3.8	31.2	1.0
	CB	A:ASN208	3.9	36.0	1.0
	O	A:VAL65	3.9	33.6	1.0
	CA	A:LEU79	3.9	32.6	1.0
	CB	A:LEU79	4.1	31.9	1.0
	CA	A:ASN208	4.2	34.7	1.0
	O	A:ASN209	4.2	33.3	1.0
	CB	A:ASN209	4.2	35.1	1.0
	C	A:ASN209	4.2	33.2	1.0
	O	A:GLY64	4.3	38.2	1.0
	N	A:ASN209	4.3	35.6	1.0
	N	A:THR80	4.5	30.2	1.0
	CA	A:ASN209	4.5	32.5	1.0
	CB	A:TRP210	4.5	30.0	1.0
	N	A:TRP210	4.6	28.9	1.0
	C	A:VAL65	4.6	33.9	1.0
	CA	A:THR80	4.8	28.2	1.0
	CA	A:VAL65	4.9	34.5	1.0
	C	A:ALA78	4.9	29.9	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: Mon Oct 7 15:36:59 2024

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