Sodium in PDB 1zc9: The Crystal Structure of Dialkylglycine Decarboxylase Complex with Pyridoxamine 5-Phosphate

Enzymatic activity of The Crystal Structure of Dialkylglycine Decarboxylase Complex with Pyridoxamine 5-Phosphate

All present enzymatic activity of The Crystal Structure of Dialkylglycine Decarboxylase Complex with Pyridoxamine 5-Phosphate:
4.1.1.64;

Protein crystallography data

The structure of The Crystal Structure of Dialkylglycine Decarboxylase Complex with Pyridoxamine 5-Phosphate, PDB code: 1zc9 was solved by E.J.Fogle, W.Liu, M.D.Toney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	50.00 / 2.00
*Space group*	P 6₄ 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	151.652, 151.652, 85.044, 90.00, 90.00, 120.00
*R / R_free (%)*	19.9 / 23.7

Other elements in 1zc9:

The structure of The Crystal Structure of Dialkylglycine Decarboxylase Complex with Pyridoxamine 5-Phosphate also contains other interesting chemical elements:

Potassium

(K)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of Dialkylglycine Decarboxylase Complex with Pyridoxamine 5-Phosphate (pdb code 1zc9). 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 Crystal Structure of Dialkylglycine Decarboxylase Complex with Pyridoxamine 5-Phosphate, PDB code: 1zc9:

Sodium binding site 1 out of 1 in 1zc9

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Sodium Binding Sites List in 1zc9

Sodium binding site 1 out of 1 in the The Crystal Structure of Dialkylglycine Decarboxylase Complex with Pyridoxamine 5-Phosphate

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Dialkylglycine Decarboxylase Complex with Pyridoxamine 5-Phosphate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na501 b:14.1 occ:1.00	O	A:HOH791	2.1	36.3	1.0
	O	A:ALA95	2.5	20.6	1.0
	O	A:THR98	2.5	19.1	1.0
	O	A:PRO99	2.6	22.3	1.0
	O	A:LEU102	2.6	16.8	1.0
	OG1	A:THR98	2.7	13.9	1.0
	C	A:THR98	3.2	16.2	1.0
	C	A:PRO99	3.3	23.4	1.0
	C	A:ALA95	3.6	16.4	1.0
	C	A:LEU102	3.7	19.7	1.0
	CB	A:THR98	3.8	14.4	1.0
	CA	A:THR98	3.9	15.9	1.0
	N	A:PRO99	3.9	18.3	1.0
	N	A:THR98	4.0	13.9	1.0
	CB	A:LEU102	4.0	19.4	1.0
	N	A:PRO100	4.0	21.6	1.0
	N	A:LEU102	4.1	19.5	1.0
	CA	A:PRO99	4.1	20.2	1.0
	CA	A:ALA95	4.2	17.0	1.0
	CA	A:LEU102	4.2	17.9	1.0
	CA	A:PRO100	4.2	21.8	1.0
	O	A:HOH638	4.4	24.8	1.0
	O	A:HOH632	4.4	39.4	1.0
	O	A:LEU94	4.5	19.1	1.0
	N	A:ASN96	4.7	18.4	1.0
	C	A:PRO100	4.7	22.1	1.0
	N	A:GLY101	4.8	22.1	1.0
	O	A:HOH653	4.8	41.8	1.0
	N	A:ASP103	4.9	18.4	1.0
	C	A:ASN96	4.9	21.1	1.0
	CA	A:ASN96	4.9	22.3	1.0

Reference:

E.J.Fogle, W.Liu, S.T.Woon, J.W.Keller, M.D.Toney. Role of Q52 in Catalysis of Decarboxylation and Transamination in Dialkylglycine Decarboxylase. Biochemistry V. 44 16392 2005.
ISSN: ISSN 0006-2960
PubMed: 16342932
DOI: 10.1021/BI051475B

Page generated: Sun Aug 17 09:58:14 2025

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