Sodium in PDB 5fh5: The Structure of Rat Cytosolic Pepck Variant E89Q in Complex with Phosphoglycolate and Gdp

Enzymatic activity of The Structure of Rat Cytosolic Pepck Variant E89Q in Complex with Phosphoglycolate and Gdp

All present enzymatic activity of The Structure of Rat Cytosolic Pepck Variant E89Q in Complex with Phosphoglycolate and Gdp:
4.1.1.32;

Protein crystallography data

The structure of The Structure of Rat Cytosolic Pepck Variant E89Q in Complex with Phosphoglycolate and Gdp, PDB code: 5fh5 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)*	35.50 / 1.55
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	46.176, 119.717, 60.897, 90.00, 107.29, 90.00
*R / R_free (%)*	20.8 / 23.7

Other elements in 5fh5:

The structure of The Structure of Rat Cytosolic Pepck Variant E89Q in Complex with Phosphoglycolate and Gdp 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 E89Q in Complex with Phosphoglycolate and Gdp (pdb code 5fh5). 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 E89Q in Complex with Phosphoglycolate and Gdp, PDB code: 5fh5:

Sodium binding site 1 out of 1 in 5fh5

Go back to

Sodium Binding Sites List in 5fh5

Sodium binding site 1 out of 1 in the The Structure of Rat Cytosolic Pepck Variant E89Q in Complex with Phosphoglycolate and Gdp

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 E89Q in Complex with Phosphoglycolate and Gdp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na705 b:28.4 occ:1.00	O	A:HOH965	2.3	26.6	1.0
	O	A:LEU79	2.4	29.4	1.0
	O	A:HOH869	2.4	29.3	1.0
	O	A:ASN208	2.4	29.6	1.0
	O	A:HOH1199	2.5	49.5	1.0
	C	A:LEU79	3.5	29.0	1.0
	C	A:ASN208	3.6	30.0	1.0
	O	A:VAL65	3.7	31.3	1.0
	N	A:LEU79	3.8	29.0	1.0
	CA	A:LEU79	4.0	29.4	1.0
	CB	A:LEU79	4.1	31.2	1.0
	O	A:HOH1305	4.1	41.7	1.0
	CB	A:ASN208	4.2	31.1	1.0
	O	A:GLY64	4.2	35.2	1.0
	CB	A:ASN209	4.3	30.6	1.0
	O	A:ASN209	4.3	26.2	1.0
	C	A:ASN209	4.4	26.8	1.0
	CA	A:ASN208	4.4	31.0	1.0
	C	A:VAL65	4.5	32.0	1.0
	N	A:ASN209	4.5	29.6	1.0
	N	A:THR80	4.6	28.1	1.0
	CA	A:ASN209	4.6	29.0	1.0
	CB	A:TRP210	4.7	22.8	1.0
	CA	A:VAL65	4.7	31.3	1.0
	N	A:TRP210	4.9	24.8	1.0
	C	A:ALA78	4.9	28.6	1.0
	CA	A:THR80	4.9	27.0	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 0006-2960
PubMed: 26709450
DOI: 10.1021/ACS.BIOCHEM.5B01215

Page generated: Mon Oct 7 21:02:34 2024

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