Atomistry » Sodium » PDB 4adn-4b16 » 4azj
Atomistry »
  Sodium »
    PDB 4adn-4b16 »
      4azj »

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: Tue Dec 15 06:33:20 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy