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Sodium in PDB 6g58: Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with A Pyridoxal 5' Phosphate-Derivative

Enzymatic activity of Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with A Pyridoxal 5' Phosphate-Derivative

All present enzymatic activity of Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with A Pyridoxal 5' Phosphate-Derivative:
5.1.1.1;

Protein crystallography data

The structure of Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with A Pyridoxal 5' Phosphate-Derivative, PDB code: 6g58 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) 49.40 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.543, 106.767, 130.835, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 17

Other elements in 6g58:

The structure of Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with A Pyridoxal 5' Phosphate-Derivative also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with A Pyridoxal 5' Phosphate-Derivative (pdb code 6g58). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with A Pyridoxal 5' Phosphate-Derivative, PDB code: 6g58:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6g58

Go back to Sodium Binding Sites List in 6g58
Sodium binding site 1 out of 6 in the Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with A Pyridoxal 5' 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 A Pyridoxal 5' Phosphate-Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:35.5
occ:1.00
 O B:HOH706 2.1 42.0 1.0
O B:HOH502 2.5 26.5 1.0
O A:ASN359 2.5 18.3 1.0
O B:HOH680 2.6 27.5 1.0
O B:HOH629 2.7 31.4 1.0
O A:HOH676 3.1 28.8 1.0
C A:ASN359 3.4 19.7 1.0
O A:HOH546 3.8 37.2 1.0
CA A:ASN359 3.8 21.1 1.0
CB A:SER361 3.9 23.9 1.0
O B:ASN359 3.9 21.9 1.0
CA B:ASN359 4.1 22.6 1.0
O B:CYS358 4.1 21.0 1.0
CA A:SER361 4.3 22.1 1.0
C B:ASN359 4.3 21.8 1.0
CA A:GLY287 4.4 25.3 1.0
N A:SER361 4.4 20.7 1.0
OD1 B:ASN359 4.4 24.3 1.0
CB A:ASN359 4.5 20.4 1.0
N A:LEU360 4.6 21.8 1.0
N A:GLY287 4.7 20.3 1.0
C A:LEU360 4.7 21.0 1.0
O A:CYS358 4.8 21.8 1.0
C B:CYS358 4.8 22.4 1.0
OD1 A:ASN359 4.9 24.1 1.0
N B:ASN359 4.9 20.3 1.0
O A:HOH698 4.9 25.6 1.0
O A:HOH549 5.0 23.2 1.0
CB B:ASN359 5.0 22.6 1.0
O B:HOH597 5.0 41.6 1.0

Sodium binding site 2 out of 6 in 6g58

Go back to Sodium Binding Sites List in 6g58
Sodium binding site 2 out of 6 in the Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with A Pyridoxal 5' 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 A Pyridoxal 5' Phosphate-Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:36.9
occ:1.00
 O A:HOH709 2.3 38.4 1.0
O A:LEU160 2.3 34.6 1.0
O A:ILE154 2.4 40.9 1.0
O A:TYR157 2.5 40.9 1.0
O A:HOH629 2.6 36.7 1.0
O A:HOH607 2.6 52.5 1.0
C A:ILE154 3.4 39.5 1.0
C A:LEU160 3.5 34.1 1.0
C A:TYR157 3.5 44.5 1.0
CG2 A:ILE154 3.8 33.4 1.0
CA A:GLN155 3.9 42.9 1.0
N A:GLN155 4.1 39.6 1.0
CA A:LEU160 4.2 34.9 1.0
N A:LEU160 4.2 36.4 1.0
CB A:LEU160 4.2 35.7 1.0
N A:TYR157 4.2 44.5 1.0
N A:GLU158 4.2 45.0 1.0
C A:GLN155 4.2 46.1 1.0
CA A:GLU158 4.3 47.4 1.0
O A:GLU158 4.3 40.9 1.0
C A:GLU158 4.4 43.0 1.0
O A:HOH637 4.4 30.3 1.0
O A:GLN155 4.4 49.2 1.0
O A:HOH737 4.4 42.5 1.0
CA A:TYR157 4.4 45.2 1.0
O A:HOH724 4.5 46.2 1.0
N A:VAL161 4.5 31.9 1.0
CA A:ILE154 4.5 37.1 1.0
CA A:VAL161 4.7 32.1 1.0
CB A:ILE154 4.8 34.4 1.0
N A:GLN156 4.9 47.1 1.0

Sodium binding site 3 out of 6 in 6g58

Go back to Sodium Binding Sites List in 6g58
Sodium binding site 3 out of 6 in the Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with A Pyridoxal 5' 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 A Pyridoxal 5' Phosphate-Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:33.8
occ:1.00
 O A:HOH726 2.4 36.9 1.0
O A:ACT408 2.5 28.5 1.0
OH A:TYR284 2.9 24.2 1.0
O A:HOH554 2.9 21.9 1.0
C A:ACT408 3.4 35.3 1.0
CE2 A:TYR284 3.5 20.9 1.0
CH3 A:ACT408 3.6 30.0 1.0
CZ A:TYR284 3.6 22.7 1.0
CE2 A:TYR265 3.7 26.5 1.0
CD2 A:TYR265 3.7 27.1 1.0
CD1 B:ILE352 3.8 26.8 1.0
O B:HOH724 4.2 41.7 1.0
O A:HOH682 4.3 27.1 1.0
CA A:CYS311 4.6 22.4 1.0
N A:MET312 4.6 19.4 1.0
CZ A:TYR265 4.6 27.2 1.0
O A:VAL310 4.6 22.7 1.0
OXT A:ACT408 4.6 37.2 1.0
CG A:TYR265 4.6 27.4 1.0
CG B:TYR354 4.7 20.7 1.0
CD1 B:TYR354 4.8 21.6 1.0
O B:HOH703 4.8 43.1 1.0
CD2 A:TYR284 4.8 21.6 1.0
NE A:ARG290 4.9 25.1 1.0
CD2 B:TYR354 4.9 21.9 1.0
C A:CYS311 5.0 19.8 1.0
CE1 A:TYR284 5.0 23.9 1.0

Sodium binding site 4 out of 6 in 6g58

Go back to Sodium Binding Sites List in 6g58
Sodium binding site 4 out of 6 in the Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with A Pyridoxal 5' 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 A Pyridoxal 5' Phosphate-Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:29.1
occ:1.00
 O B:HOH711 2.3 31.8 1.0
O B:TYR157 2.4 27.1 1.0
O B:LEU160 2.4 25.8 1.0
O B:ILE154 2.4 28.2 1.0
O B:HOH610 2.5 32.0 1.0
O B:HOH566 2.6 44.1 1.0
C B:TYR157 3.4 30.0 1.0
C B:ILE154 3.5 27.2 1.0
C B:LEU160 3.5 26.3 1.0
CG2 B:ILE154 4.0 27.0 1.0
CA B:GLN155 4.0 31.6 1.0
CA B:GLU158 4.1 33.9 1.0
N B:GLU158 4.1 30.8 1.0
N B:LEU160 4.1 27.3 1.0
O B:GLU158 4.2 30.4 1.0
N B:GLN155 4.2 29.4 1.0
CA B:LEU160 4.2 26.6 0.7
CA B:LEU160 4.2 25.3 0.3
N B:TYR157 4.2 29.0 1.0
C B:GLU158 4.2 32.8 1.0
C B:GLN155 4.2 31.6 1.0
CB B:LEU160 4.3 25.8 0.7
CB B:LEU160 4.3 23.6 0.3
O B:HOH656 4.3 25.2 1.0
O B:GLN155 4.3 32.2 1.0
CA B:TYR157 4.4 30.1 1.0
O B:HOH733 4.5 44.2 1.0
N B:VAL161 4.6 24.6 1.0
CA B:ILE154 4.6 26.0 1.0
CA B:VAL161 4.8 25.3 1.0
N B:GLN156 4.9 31.5 1.0
CB B:ILE154 4.9 26.0 1.0
CB B:TYR157 5.0 29.2 1.0
N B:GLN159 5.0 30.4 1.0

Sodium binding site 5 out of 6 in 6g58

Go back to Sodium Binding Sites List in 6g58
Sodium binding site 5 out of 6 in the Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with A Pyridoxal 5' Phosphate-Derivative


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with A Pyridoxal 5' Phosphate-Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:34.5
occ:1.00
 OXT B:ACT412 2.5 32.4 1.0
O B:HOH726 2.5 45.6 1.0
OH B:TYR284 2.7 28.2 1.0
O B:HOH585 2.8 25.2 1.0
CE2 B:TYR284 3.4 25.4 1.0
C B:ACT412 3.5 38.3 1.0
CZ B:TYR284 3.5 26.1 1.0
CE2 B:TYR265 3.7 33.7 1.0
CH3 B:ACT412 3.7 35.5 1.0
CD2 B:TYR265 3.7 33.9 1.0
CD1 A:ILE352 3.8 28.2 1.0
O A:HOH720 4.3 46.9 1.0
O B:HOH675 4.4 28.8 1.0
CA B:CYS311 4.5 27.2 1.0
N B:MET312 4.5 25.6 1.0
O B:VAL310 4.6 27.3 1.0
CZ B:TYR265 4.6 36.0 1.0
O B:ACT412 4.6 39.0 1.0
CG B:TYR265 4.7 36.3 1.0
CD2 B:TYR284 4.7 23.6 1.0
CG A:TYR354 4.8 22.5 1.0
CG B:MET312 4.8 27.5 0.5
CD1 A:TYR354 4.9 22.8 1.0
C B:CYS311 4.9 25.3 1.0
NE B:ARG290 4.9 27.3 1.0
CE1 B:TYR284 4.9 25.1 1.0
CD2 A:TYR354 4.9 22.2 1.0

Sodium binding site 6 out of 6 in 6g58

Go back to Sodium Binding Sites List in 6g58
Sodium binding site 6 out of 6 in the Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with A Pyridoxal 5' Phosphate-Derivative


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of the Alanine Racemase From Staphylococcus Aureus in Complex with A Pyridoxal 5' Phosphate-Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:45.7
occ:1.00
 O B:HOH697 2.3 39.0 1.0
O B:HOH569 2.3 35.0 1.0
O B:CYS215 2.5 29.0 1.0
O B:GLN213 2.7 29.1 1.0
O B:HOH698 2.7 53.3 1.0
C B:CYS215 3.6 27.3 1.0
C B:GLN213 3.6 28.8 1.0
CA B:ASN216 4.1 25.2 1.0
CA B:GLN213 4.1 31.6 1.0
CE B:LYS32 4.3 33.3 1.0
N B:ASN216 4.3 24.4 1.0
CB B:ASN216 4.4 25.1 1.0
N B:CYS215 4.4 28.8 1.0
CG B:LYS32 4.5 27.8 1.0
C B:PHE214 4.5 28.3 1.0
NZ B:LYS32 4.6 36.8 1.0
CA B:CYS215 4.6 27.7 1.0
N B:PHE214 4.7 27.5 1.0
O B:CYS212 4.7 28.9 1.0
O B:PHE214 4.8 27.9 1.0
O B:ASN31 4.8 32.5 1.0
CB B:GLN213 4.9 36.4 1.0
CD B:LYS32 4.9 29.0 1.0
O B:HOH701 4.9 55.6 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 08:56:48 2024

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