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Magnesium in PDB 5d6q: Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand

Enzymatic activity of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand

All present enzymatic activity of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand:
5.99.1.3;

Protein crystallography data

The structure of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand, PDB code: 5d6q was solved by J.Zhang, Q.Yang, J.B.Cross, J.A.C.Romero, M.D.Ryan, B.Lippa, R.E.Dolle, O.A.Andersen, J.Barker, R.K.Cheng, J.Kahmann, B.Felicetti, M.Wood, C.Scheich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.64 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 142.910, 55.860, 51.460, 90.00, 100.62, 90.00
R / Rfree (%) 16.7 / 19.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand (pdb code 5d6q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand, PDB code: 5d6q:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5d6q

Go back to Magnesium Binding Sites List in 5d6q
Magnesium binding site 1 out of 2 in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:22.2
occ:1.00
O B:HOH525 2.3 37.7 1.0
O B:HOH421 2.3 28.8 1.0
O B:HOH530 2.3 37.2 1.0
OE1 B:GLU219 2.4 29.2 1.0
OE2 B:GLU219 2.5 29.4 1.0
CD B:GLU219 2.7 30.3 1.0
OE1 B:GLU220 4.0 24.3 1.0
NZ B:LYS73 4.1 30.0 1.0
CG B:GLU219 4.2 26.8 1.0
CD B:GLU220 4.5 23.4 1.0
N B:GLU219 4.6 19.4 1.0
OD1 B:ASP218 4.7 16.1 1.0
CG B:GLU220 4.7 19.6 1.0
O B:HOH430 5.0 35.7 1.0

Magnesium binding site 2 out of 2 in 5d6q

Go back to Magnesium Binding Sites List in 5d6q
Magnesium binding site 2 out of 2 in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:31.6
occ:1.00
OG1 B:THR171 1.9 17.1 1.0
O B:HOH536 2.3 33.2 1.0
O B:ASN82 2.3 10.8 1.0
O B:GLY83 2.5 10.6 1.0
O B:HOH443 2.5 22.4 1.0
O B:THR171 2.9 14.7 1.0
CB B:THR171 3.2 15.5 1.0
C B:ASN82 3.2 10.3 1.0
C B:GLY83 3.3 10.6 1.0
C B:THR171 3.3 10.9 1.0
O B:HOH524 3.5 38.7 1.0
CA B:THR171 3.7 11.6 1.0
CA B:GLY83 3.8 11.3 1.0
N B:GLY83 3.8 9.9 1.0
N B:THR171 4.0 13.8 1.0
CA B:ASN82 4.0 9.5 1.0
N B:GLY172 4.2 10.1 1.0
N B:ARG84 4.3 9.7 1.0
CG2 B:THR171 4.3 17.5 1.0
CB B:ASN82 4.4 11.3 1.0
O B:TYR63 4.4 17.0 1.0
CA B:ARG84 4.6 9.6 1.0
CA B:GLY172 4.7 9.3 1.0
O B:HOH547 4.9 40.4 1.0
CG B:ASN82 5.0 13.4 1.0

Reference:

J.Zhang, Q.Yang, J.B.Cross, J.A.Romero, K.M.Poutsiaka, F.Epie, D.Bevan, B.Wang, Y.Zhang, A.Chavan, X.Zhang, T.Moy, A.Daniel, K.Nguyen, B.Chamberlain, N.Carter, J.Shotwell, J.Silverman, C.A.Metcalf, D.Ryan, B.Lippa, R.E.Dolle. Discovery of Azaindole Ureas As A Novel Class of Bacterial Gyrase B Inhibitors. J.Med.Chem. V. 58 8503 2015.
ISSN: ISSN 0022-2623
PubMed: 26460684
DOI: 10.1021/ACS.JMEDCHEM.5B00961
Page generated: Mon Dec 14 20:10:15 2020

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