Sodium in PDB 4azj: Structural Basis of L-Phosphoserine Binding to Bacillus Alcalophilus Phosphoserine Aminotransferase

Enzymatic activity of Structural Basis of L-Phosphoserine Binding to Bacillus Alcalophilus Phosphoserine Aminotransferase

All present enzymatic activity of Structural Basis of L-Phosphoserine Binding to Bacillus Alcalophilus Phosphoserine Aminotransferase:
2.6.1.52;

Protein crystallography data

The structure of Structural Basis of L-Phosphoserine Binding to Bacillus Alcalophilus Phosphoserine Aminotransferase, PDB code: 4azj was solved by P.Battula, A.P.Dubnovitsky, A.C.Papageorgiou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	19.88 / 1.50
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	104.692, 136.194, 151.283, 90.00, 90.00, 90.00
*R / R_free (%)*	14.6 / 16.5

Other elements in 4azj:

The structure of Structural Basis of L-Phosphoserine Binding to Bacillus Alcalophilus Phosphoserine Aminotransferase also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structural Basis of L-Phosphoserine Binding to Bacillus Alcalophilus Phosphoserine Aminotransferase (pdb code 4azj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structural Basis of L-Phosphoserine Binding to Bacillus Alcalophilus Phosphoserine Aminotransferase, PDB code: 4azj:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4azj

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Sodium Binding Sites List in 4azj

Sodium binding site 1 out of 3 in the Structural Basis of L-Phosphoserine Binding to Bacillus Alcalophilus Phosphoserine Aminotransferase

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Basis of L-Phosphoserine Binding to Bacillus Alcalophilus Phosphoserine Aminotransferase within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na1362 b:29.7 occ:1.00	O3P	A:SEP500	2.7	11.8	1.0
	O	A:HOH2260	2.7	43.6	1.0
	O	A:HOH2567	2.8	13.7	1.0
	CH2	A:TRP102	3.5	12.6	1.0
	NH2	A:ARG328	3.6	13.5	1.0
	O	A:HOH2540	3.6	22.8	1.0
	O	A:HOH2111	3.8	40.8	1.0
	P	A:SEP500	4.0	11.0	1.0
	O	A:HOH2565	4.0	10.8	1.0
	CE	A:LYS105	4.1	35.5	1.0
	O	A:HOH2247	4.1	22.2	1.0
	O	B:TYR236	4.1	11.7	1.0
	NZ	A:LYS105	4.2	46.1	1.0
	CZ2	A:TRP102	4.2	11.6	1.0
	O2P	A:SEP500	4.2	11.5	1.0
	CZ3	A:TRP102	4.3	9.9	1.0
	NE2	A:HIS327	4.5	12.6	1.0
	OG	A:SEP500	4.7	11.0	1.0
	CZ	A:ARG328	4.8	17.4	1.0
	NH2	B:ARG42	4.8	10.8	1.0
	CE1	A:HIS327	4.8	13.3	1.0
	O	A:HOH2202	4.8	13.1	1.0

Sodium binding site 2 out of 3 in 4azj

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Sodium Binding Sites List in 4azj

Sodium binding site 2 out of 3 in the Structural Basis of L-Phosphoserine Binding to Bacillus Alcalophilus Phosphoserine Aminotransferase

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Basis of L-Phosphoserine Binding to Bacillus Alcalophilus Phosphoserine Aminotransferase within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na1363 b:34.9 occ:1.00	OD1	A:ASP276	2.6	18.5	1.0
	OD2	A:ASP279	2.8	15.5	1.0
	O	A:HOH2569	2.8	27.8	1.0
	O	A:HOH2568	3.3	54.0	1.0
	N	A:ASP276	3.5	11.9	1.0
	C	A:TYR275	3.5	12.7	1.0
	O	A:TYR275	3.6	12.3	1.0
	CB	A:TYR275	3.7	12.0	1.0
	CA	A:ASP276	3.7	12.2	1.0
	O	A:HOH2476	3.7	46.2	1.0
	CG	A:ASP276	3.8	14.6	1.0
	CG	A:ASP279	3.8	12.4	1.0
	NH1	A:ARG294	3.8	12.7	1.0
	O	A:HOH2497	4.0	22.0	1.0
	CA	A:TYR275	4.2	10.1	1.0
	O	A:HOH2240	4.3	41.6	1.0
	CB	A:ASP279	4.3	11.4	1.0
	CB	A:ASP276	4.3	12.5	1.0
	O	A:HOH2467	4.3	41.7	1.0
	OD2	A:ASP276	4.8	23.3	1.0
	OD1	A:ASP279	4.8	15.3	1.0
	O	A:LYS272	4.9	12.7	1.0
	CG	A:TYR275	4.9	12.2	1.0
	C	A:ASP276	5.0	13.6	1.0

Sodium binding site 3 out of 3 in 4azj

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Sodium Binding Sites List in 4azj

Sodium binding site 3 out of 3 in the Structural Basis of L-Phosphoserine Binding to Bacillus Alcalophilus Phosphoserine Aminotransferase

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structural Basis of L-Phosphoserine Binding to Bacillus Alcalophilus Phosphoserine Aminotransferase within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Na1362 b:33.1 occ:1.00	O3P	B:SEP500	2.7	10.6	1.0
	O	A:HOH2422	2.9	11.3	1.0
	O	B:HOH2227	3.3	44.2	1.0
	CH2	B:TRP102	3.4	10.3	1.0
	NH2	B:ARG328	3.6	14.1	1.0
	O	A:HOH2421	3.7	19.8	1.0
	O	B:HOH2250	3.8	34.2	1.0
	O	B:HOH2217	3.8	20.3	1.0
	NZ	B:LYS105	3.9	58.1	1.0
	P	B:SEP500	4.0	9.7	1.0
	CE	B:LYS105	4.0	43.9	1.0
	CZ2	B:TRP102	4.1	9.8	1.0
	CZ3	B:TRP102	4.1	10.8	1.0
	O	B:HOH2557	4.1	9.6	1.0
	O	A:TYR236	4.3	9.2	1.0
	O1P	B:SEP500	4.3	9.3	1.0
	NE2	B:HIS327	4.5	9.9	1.0
	CZ	B:ARG328	4.7	14.6	1.0
	OG	B:SEP500	4.7	10.4	1.0
	CE1	B:HIS327	4.7	10.2	1.0
	O	B:HOH2174	4.8	11.4	1.0
	NH2	A:ARG42	4.8	9.4	1.0
	O	B:HOH2520	4.9	53.0	1.0

Reference:

P.Battula, A.P.Dubnovitsky, A.C.Papageorgiou. Structural Basis of L-Phosphoserine Binding to Bacillus Alcalophilus Phosphoserine Aminotransferase Acta Crystallogr.,Sect.D V. 69 804 2013.
ISSN: ISSN 0907-4449
PubMed: 23633589
DOI: 10.1107/S0907444913002096

Page generated: Mon Oct 7 14:26:19 2024

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