Sodium in PDB 6zje: Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor AP5A

Enzymatic activity of Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor AP5A

All present enzymatic activity of Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor AP5A:
2.7.4.10;

Protein crystallography data

The structure of Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor AP5A, PDB code: 6zje was solved by C.Grundstrom, P.Rogne, M.Wolf-Watz, A.E.Sauer-Eriksson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	40.62 / 1.48
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	42.716, 62.639, 50.162, 90.00, 108.01, 90.00
*R / R_free (%)*	14.3 / 18.4

Other elements in 6zje:

The structure of Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor AP5A also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor AP5A (pdb code 6zje). 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 Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor AP5A, PDB code: 6zje:

Sodium binding site 1 out of 1 in 6zje

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Sodium Binding Sites List in 6zje

Sodium binding site 1 out of 1 in the Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor AP5A

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor AP5A within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na404 b:58.3 occ:1.00	O	A:HOH547	2.4	47.2	1.0
	O	A:HOH643	2.4	63.3	1.0
	OD1	A:ASN143	2.5	33.0	0.6
	O	A:HOH552	3.1	38.0	1.0
	O	A:HOH604	3.4	41.8	1.0
	CG	A:ASN143	3.7	32.4	0.6
	O	A:HOH602	4.0	52.5	1.0
	O	A:HOH550	4.1	43.8	1.0
	ND2	A:ASN143	4.2	33.6	0.6
	O	A:HOH735	4.3	52.0	1.0
	CB	A:ASN143	4.4	27.8	0.5
	OD2	A:ASP152	4.6	28.0	1.0
	O	A:PRO144	4.7	25.7	1.0
	ND2	A:ASN143	4.8	26.1	0.5
	CB	A:ASN143	4.9	31.6	0.6
	O	A:HOH693	4.9	41.5	1.0
	O	A:HOH554	4.9	53.3	1.0

Reference:

P.Rogne, B.Dulko-Smith, J.Goodman, M.Rosselin, C.Grundstrom, C.Hedberg, K.Nam, A.E.Sauer-Eriksson, M.Wolf-Watz. Structural Basis For Gtp Versus Atp Selectivity in the Nmp Kinase AK3. Biochemistry V. 59 3570 2020.
ISSN: ISSN 0006-2960
PubMed: 32822537
DOI: 10.1021/ACS.BIOCHEM.0C00549

Page generated: Mon Aug 18 08:51:06 2025

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