Sodium in PDB 2dea: Crystal Structure of the Aminopeptidase of Aeromonas Proteolytica at pH 4.7

Enzymatic activity of Crystal Structure of the Aminopeptidase of Aeromonas Proteolytica at pH 4.7

All present enzymatic activity of Crystal Structure of the Aminopeptidase of Aeromonas Proteolytica at pH 4.7:
3.4.11.10;

Protein crystallography data

The structure of Crystal Structure of the Aminopeptidase of Aeromonas Proteolytica at pH 4.7, PDB code: 2dea was solved by G.A.Petsko, D.Ringe, W.Desmarais, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	30.00 / 1.24
*Space group*	P 6₁ 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	109.605, 109.605, 90.816, 90.00, 90.00, 120.00
*R / R_free (%)*	15.3 / 16.3

Other elements in 2dea:

The structure of Crystal Structure of the Aminopeptidase of Aeromonas Proteolytica at pH 4.7 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Aminopeptidase of Aeromonas Proteolytica at pH 4.7 (pdb code 2dea). 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 the Aminopeptidase of Aeromonas Proteolytica at pH 4.7, PDB code: 2dea:

Sodium binding site 1 out of 1 in 2dea

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Sodium Binding Sites List in 2dea

Sodium binding site 1 out of 1 in the Crystal Structure of the Aminopeptidase of Aeromonas Proteolytica at pH 4.7

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 the Aminopeptidase of Aeromonas Proteolytica at pH 4.7 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na403 b:12.1 occ:1.00	O	A:HOH550	2.3	14.3	1.0
	O	A:HOH545	2.4	13.5	1.0
	OH	A:TYR218	2.4	11.5	1.0
	O	A:HOH534	2.4	12.4	1.0
	O	A:HOH548	2.4	15.1	1.0
	O	A:HOH538	2.5	12.3	1.0
	CZ	A:TYR218	3.5	9.7	1.0
	CE1	A:TYR218	3.7	11.2	1.0
	OG1	A:THR206	4.0	10.5	1.0
	OD2	A:ASP210	4.1	13.8	1.0
	CB	A:THR206	4.3	10.4	1.0
	OD1	A:ASP210	4.4	11.7	1.0
	O	A:HOH728	4.5	33.0	1.0
	CG	A:ASP210	4.7	12.2	1.0
	CE2	A:TYR218	4.7	10.8	1.0
	NE2	A:GLN203	4.8	10.6	1.0
	O	A:HOH559	4.9	16.5	1.0

Reference:

W.Desmarais, D.L.Bienvenue, K.P.Bzymek, G.A.Petsko, D.Ringe, R.C.Holz. The High-Resolution Structures of the Neutral and the Low pH Crystals of Aminopeptidase From Aeromonas Proteolytica. J.Biol.Inorg.Chem. V. 11 398 2006.
ISSN: ISSN 0949-8257
PubMed: 16596389
DOI: 10.1007/S00775-006-0093-X

Page generated: Mon Oct 7 02:13:30 2024

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