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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

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