Sodium in PDB 1d7u: Crystal Structure of the Complex of 2,2-Dialkylglycine Decarboxylase with Lcs

Enzymatic activity of Crystal Structure of the Complex of 2,2-Dialkylglycine Decarboxylase with Lcs

All present enzymatic activity of Crystal Structure of the Complex of 2,2-Dialkylglycine Decarboxylase with Lcs:
4.1.1.64;

Protein crystallography data

The structure of Crystal Structure of the Complex of 2,2-Dialkylglycine Decarboxylase with Lcs, PDB code: 1d7u was solved by V.N.Malashkevich, M.D.Toney, P.Strop, J.Keller, J.N.Jansonius, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	10.00 / 1.95
*Space group*	P 6₄ 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	153.230, 153.230, 86.480, 90.00, 90.00, 120.00
*R / R_free (%)*	n/a / n/a

Other elements in 1d7u:

The structure of Crystal Structure of the Complex of 2,2-Dialkylglycine Decarboxylase with Lcs also contains other interesting chemical elements:

Potassium

(K)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Complex of 2,2-Dialkylglycine Decarboxylase with Lcs (pdb code 1d7u). 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 Complex of 2,2-Dialkylglycine Decarboxylase with Lcs, PDB code: 1d7u:

Sodium binding site 1 out of 1 in 1d7u

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Sodium Binding Sites List in 1d7u

Sodium binding site 1 out of 1 in the Crystal Structure of the Complex of 2,2-Dialkylglycine Decarboxylase with Lcs

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 Complex of 2,2-Dialkylglycine Decarboxylase with Lcs within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na435 b:16.6 occ:1.00	O	A:ALA95	2.4	41.5	1.0
	O	A:PRO99	2.5	26.7	1.0
	O	A:THR98	2.6	31.2	1.0
	O	A:LEU102	2.7	28.7	1.0
	OG1	A:THR98	2.9	20.7	1.0
	C	A:PRO99	3.3	26.1	1.0
	C	A:THR98	3.3	39.0	1.0
	C	A:ALA95	3.6	28.5	1.0
	C	A:LEU102	3.8	27.1	1.0
	CB	A:THR98	4.0	22.4	1.0
	N	A:PRO100	4.0	30.1	1.0
	N	A:PRO99	4.0	27.0	1.0
	CA	A:THR98	4.1	23.8	1.0
	CA	A:PRO100	4.1	23.2	1.0
	N	A:LEU102	4.1	22.8	1.0
	CA	A:PRO99	4.1	23.4	1.0
	N	A:THR98	4.2	20.4	1.0
	CB	A:LEU102	4.2	21.7	1.0
	CA	A:ALA95	4.2	25.4	1.0
	CA	A:LEU102	4.3	23.7	1.0
	O	A:HOH547	4.6	37.8	1.0
	N	A:GLY101	4.6	24.6	1.0
	C	A:PRO100	4.7	22.4	1.0
	N	A:ASN96	4.7	25.0	1.0
	O	A:LEU94	4.8	24.4	1.0
	N	A:ASP103	4.9	18.9	1.0
	CB	A:ALA95	5.0	25.3	1.0
	C	A:ASN96	5.0	38.0	1.0
	CA	A:ASN96	5.0	23.3	1.0

Reference:

V.N.Malashkevich, P.Strop, J.W.Keller, J.N.Jansonius, M.D.Toney. Crystal Structures of Dialkylglycine Decarboxylase Inhibitor Complexes. J.Mol.Biol. V. 294 193 1999.
ISSN: ISSN 0022-2836
PubMed: 10556038
DOI: 10.1006/JMBI.1999.3254

Page generated: Sun Oct 6 18:03:08 2024

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