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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 / Rfree (%) 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

Go back to 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

Go back to 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

Go back to 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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