Sodium in PDB 4x8o: Crystal Structure of E. Coli Adenylate Kinase Y171W Mutant in Complex with Inhibitor AP5A

Enzymatic activity of Crystal Structure of E. Coli Adenylate Kinase Y171W Mutant in Complex with Inhibitor AP5A

All present enzymatic activity of Crystal Structure of E. Coli Adenylate Kinase Y171W Mutant in Complex with Inhibitor AP5A:
2.7.4.3;

Protein crystallography data

The structure of Crystal Structure of E. Coli Adenylate Kinase Y171W Mutant in Complex with Inhibitor AP5A, PDB code: 4x8o was solved by A.E.Sauer-Eriksson, M.Kovermann, J.Aden, C.Grundstrom, M.Wolf-Watz, U.H.Sauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	41.13 / 2.10
*Space group*	P 2₁ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	82.257, 72.654, 79.480, 90.00, 90.00, 90.00
*R / R_free (%)*	17.7 / 24

Other elements in 4x8o:

The structure of Crystal Structure of E. Coli Adenylate Kinase Y171W Mutant in Complex with Inhibitor AP5A also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of E. Coli Adenylate Kinase Y171W Mutant in Complex with Inhibitor AP5A (pdb code 4x8o). 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 E. Coli Adenylate Kinase Y171W Mutant in Complex with Inhibitor AP5A, PDB code: 4x8o:

Sodium binding site 1 out of 1 in 4x8o

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Sodium Binding Sites List in 4x8o

Sodium binding site 1 out of 1 in the Crystal Structure of E. Coli Adenylate Kinase Y171W Mutant 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 E. Coli Adenylate Kinase Y171W Mutant in Complex with Inhibitor AP5A within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na303 b:16.7 occ:1.00	O	A:ASN190	2.4	9.1	1.0
	O	A:HOH452	2.4	16.3	1.0
	O	A:HOH444	2.5	19.5	1.0
	O	A:VAL103	2.6	7.1	1.0
	C	A:ASN190	3.3	6.9	1.0
	O	A:HOH474	3.6	18.4	1.0
	C	A:VAL103	3.6	9.3	1.0
	N	A:VAL103	4.0	15.3	1.0
	O	A:HOH409	4.1	10.3	1.0
	N	A:THR191	4.1	7.7	1.0
	CA	A:THR191	4.1	6.7	1.0
	CB	A:ASN102	4.2	21.7	1.0
	CA	A:ASN190	4.3	8.3	1.0
	N	A:ASP104	4.4	6.7	1.0
	CA	A:ASP104	4.4	8.3	1.0
	CA	A:VAL103	4.5	8.7	1.0
	OD1	A:ASP104	4.5	11.3	1.0
	CB	A:THR191	4.6	10.6	1.0
	C	A:ASN102	4.7	25.3	1.0
	CA	A:ASN102	4.8	28.8	1.0
	CG	A:ASN102	5.0	47.3	1.0

Reference:

M.Kovermann, J.Aden, C.Grundstrom, A.Elisabeth Sauer-Eriksson, U.H.Sauer, M.Wolf-Watz. Structural Basis For Catalytically Restrictive Dynamics of A High-Energy Enzyme State. Nat Commun V. 6 7644 2015.
ISSN: ESSN 2041-1723
PubMed: 26138143
DOI: 10.1038/NCOMMS8644

Page generated: Mon Oct 7 18:59:36 2024

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