Atomistry » Sodium » PDB 6g3r-6gn7 » 6g59
Atomistry »
  Sodium »
    PDB 6g3r-6gn7 »
      6g59 »

Sodium in PDB 6g59: Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with An Pyridoxal-6- Phosphate Derivative

Enzymatic activity of Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with An Pyridoxal-6- Phosphate Derivative

All present enzymatic activity of Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with An Pyridoxal-6- Phosphate Derivative:
5.1.1.1;

Protein crystallography data

The structure of Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with An Pyridoxal-6- Phosphate Derivative, PDB code: 6g59 was solved by A.Hoegl, S.A.Sieber, S.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.50 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.924, 106.855, 131.023, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 21.5

Other elements in 6g59:

The structure of Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with An Pyridoxal-6- Phosphate Derivative also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with An Pyridoxal-6- Phosphate Derivative (pdb code 6g59). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with An Pyridoxal-6- Phosphate Derivative, PDB code: 6g59:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6g59

Go back to Sodium Binding Sites List in 6g59
Sodium binding site 1 out of 4 in the Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with An Pyridoxal-6- Phosphate Derivative


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with An Pyridoxal-6- Phosphate Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:47.9
occ:1.00
 O A:LEU160 2.5 34.6 1.0
O A:ILE154 2.8 38.6 1.0
O A:TYR157 2.9 40.9 1.0
C A:ILE154 3.7 37.2 1.0
C A:LEU160 3.7 31.8 1.0
CA A:GLN155 3.9 41.6 1.0
C A:TYR157 3.9 43.1 1.0
CG2 A:ILE154 4.2 34.4 1.0
N A:GLN155 4.2 38.6 1.0
C A:GLN155 4.3 42.8 1.0
O A:GLN155 4.3 45.8 1.0
CA A:GLU158 4.4 45.0 1.0
N A:GLU158 4.6 43.8 1.0
O A:GLU158 4.6 38.1 1.0
N A:VAL161 4.6 30.8 1.0
CA A:VAL161 4.6 30.1 1.0
C A:GLU158 4.7 40.9 1.0
CA A:LEU160 4.7 32.6 1.0
N A:LEU160 4.7 34.8 1.0
N A:TYR157 4.8 46.1 1.0
CB A:LEU160 4.9 32.9 1.0
CA A:ILE154 4.9 35.5 1.0
CA A:TYR157 5.0 44.7 1.0

Sodium binding site 2 out of 4 in 6g59

Go back to Sodium Binding Sites List in 6g59
Sodium binding site 2 out of 4 in the Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with An Pyridoxal-6- Phosphate Derivative


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with An Pyridoxal-6- Phosphate Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:42.4
occ:1.00
 O A:VAL245 2.6 28.3 1.0
O A:ASP333 2.8 28.9 1.0
OH A:TYR227 2.8 25.9 1.0
O A:HOH574 3.0 30.7 1.0
CG2 A:VAL342 3.4 26.8 1.0
C A:ASP333 3.5 30.1 1.0
CE1 A:TYR227 3.6 26.8 1.0
CZ A:TYR227 3.7 26.8 1.0
C A:VAL245 3.7 26.7 1.0
CA A:ASN334 3.7 29.8 1.0
CG2 A:ILE332 3.8 26.2 1.0
N A:ASN334 4.0 30.0 1.0
CB A:PRO243 4.0 28.5 1.0
N A:VAL245 4.0 26.3 1.0
CB A:VAL245 4.1 26.1 1.0
CA A:VAL245 4.1 26.2 1.0
CB A:ASN334 4.5 28.8 1.0
C A:ASN334 4.6 31.5 1.0
N A:ASP333 4.6 30.2 1.0
CA A:ASP333 4.7 31.3 1.0
CB A:VAL342 4.7 25.9 1.0
N A:HIS335 4.7 31.7 1.0
CG1 A:VAL245 4.8 25.8 1.0
N A:GLN246 4.8 26.3 1.0
N A:VAL342 4.9 24.7 1.0
CD1 A:TYR227 4.9 26.8 1.0
CA A:PRO243 4.9 28.0 1.0
N A:SER244 4.9 26.2 1.0
CE2 A:TYR227 5.0 26.2 1.0

Sodium binding site 3 out of 4 in 6g59

Go back to Sodium Binding Sites List in 6g59
Sodium binding site 3 out of 4 in the Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with An Pyridoxal-6- Phosphate Derivative


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with An Pyridoxal-6- Phosphate Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:50.9
occ:1.00
 O A:SER264 2.9 42.7 1.0
O B:GLY135 3.5 38.3 1.0
O B:MET136 3.5 48.4 1.0
CB B:ALA170 3.6 37.0 1.0
CB A:SER262 3.6 61.6 1.0
C A:SER262 3.7 58.0 1.0
N A:SER264 3.8 46.5 1.0
O A:SER262 3.8 58.5 1.0
N A:VAL263 3.8 54.3 1.0
C A:VAL263 3.8 49.4 1.0
CA B:MET136 3.9 48.1 1.0
CE B:MET178 3.9 42.6 1.0
C B:MET136 3.9 50.7 1.0
CA A:ALA267 3.9 49.2 1.0
C A:SER264 3.9 43.6 1.0
CA A:VAL263 4.0 52.0 1.0
N A:ALA267 4.1 48.2 1.0
O A:VAL263 4.2 50.3 1.0
CA A:SER262 4.3 60.0 1.0
CB A:ALA267 4.3 49.1 1.0
C B:GLY135 4.3 38.8 1.0
CA A:SER264 4.4 43.4 1.0
O B:HOH541 4.4 26.1 1.0
N B:MET136 4.5 44.2 1.0
SD B:MET178 4.6 45.0 1.0
OG A:SER262 4.9 66.2 1.0
SD B:MET136 4.9 58.0 1.0
N B:GLY137 4.9 51.2 1.0

Sodium binding site 4 out of 4 in 6g59

Go back to Sodium Binding Sites List in 6g59
Sodium binding site 4 out of 4 in the Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with An Pyridoxal-6- Phosphate Derivative


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with An Pyridoxal-6- Phosphate Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:45.9
occ:1.00
 O B:HOH547 2.3 39.6 1.0
O B:LEU160 2.4 28.7 1.0
O B:TYR157 2.7 35.1 1.0
O B:ILE154 2.8 30.1 1.0
C B:LEU160 3.6 28.5 1.0
C B:TYR157 3.8 35.0 1.0
O B:HOH554 3.8 24.6 1.0
C B:ILE154 3.8 29.9 1.0
CA B:GLN155 4.0 33.1 1.0
CG2 B:ILE154 4.2 27.2 1.0
CA B:GLU158 4.3 39.1 1.0
N B:GLN155 4.3 31.6 1.0
O B:GLN155 4.4 33.1 1.0
C B:GLN155 4.4 33.2 1.0
O B:GLU158 4.4 36.5 1.0
N B:GLU158 4.4 37.2 1.0
C B:GLU158 4.5 36.6 1.0
N B:LEU160 4.5 30.5 1.0
CA B:LEU160 4.5 28.9 1.0
N B:VAL161 4.6 27.3 1.0
CA B:VAL161 4.7 27.3 1.0
N B:TYR157 4.7 35.5 1.0
CB B:LEU160 4.8 28.9 1.0
CA B:TYR157 4.8 35.4 1.0
CA B:ILE154 4.9 28.8 1.0

Reference:

A.Hoegl, M.B.Nodwell, V.C.Kirsch, N.C.Bach, M.Pfanzelt, M.Stahl, S.Schneider, S.A.Sieber. Mining the Cellular Inventory of Pyridoxal Phosphate-Dependent Enzymes with Functionalized Cofactor Mimics. Nat Chem V. 10 1234 2018.
ISSN: ESSN 1755-4349
PubMed: 30297752
DOI: 10.1038/S41557-018-0144-2
Page generated: Tue Oct 8 08:56:47 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy