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Magnesium in PDB 5d7c: 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: 5d7c 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) 37.78 / 1.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 142.803, 55.485, 51.422, 90.00, 100.77, 90.00
R / Rfree (%) 17.1 / 19.9

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 5d7c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 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: 5d7c:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5d7c

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Magnesium binding site 1 out of 8 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
A:Mg304

b:31.1
occ:1.00
 O A:HOH532 2.0 37.2 1.0
O A:HOH477 2.2 25.9 1.0
OE1 A:GLU50 2.3 27.4 1.0
O A:HOH416 2.7 44.7 1.0
CD A:GLU50 3.4 29.2 1.0
OE2 A:GLU50 3.9 45.8 1.0
OD1 A:ASP53 4.5 29.1 1.0
CG A:GLU50 4.6 21.5 1.0
O A:GLU50 4.7 20.1 1.0
OD1 A:ASN54 4.8 33.8 1.0
CB A:GLU50 4.8 19.0 1.0
CA A:GLU50 5.0 16.8 1.0

Magnesium binding site 2 out of 8 in 5d7c

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Magnesium binding site 2 out of 8 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:Mg304

b:41.4
occ:1.00
 O B:HOH447 2.2 40.2 1.0
O B:HOH426 2.3 26.7 1.0
OD1 B:ASP53 2.4 20.9 0.5
OD2 B:ASP57 2.5 27.4 1.0
O B:HOH501 2.6 31.1 1.0
OD2 B:ASP53 2.7 20.5 0.5
O B:HOH406 2.9 45.6 1.0
CG B:ASP53 2.9 18.1 0.5
CG B:ASP57 3.3 24.4 1.0
OD1 B:ASP57 3.5 25.1 1.0
O B:ASP53 4.0 17.2 1.0
O B:HOH429 4.2 30.2 1.0
CG B:ASP53 4.3 24.8 0.5
CB B:ASP53 4.3 20.2 0.5
CB B:ASP53 4.3 16.7 0.5
OD2 B:ASP53 4.5 29.4 0.5
CB B:ASP57 4.7 17.8 1.0
OD1 B:ASP53 4.7 32.2 0.5
MG B:MG310 4.7 40.7 1.0
C B:ASP53 4.7 16.2 1.0
O B:HOH401 4.8 20.0 0.5
CA B:ASP53 4.8 18.6 0.5
CA B:ASP53 4.8 17.1 0.5
N B:ASP57 4.8 16.3 1.0
CA B:ASP57 5.0 17.7 1.0

Magnesium binding site 3 out of 8 in 5d7c

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Magnesium binding site 3 out of 8 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 3 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:28.9
occ:1.00
 O B:HOH531 2.2 33.1 1.0
OE1 B:GLU164 2.5 35.4 1.0
O B:HOH538 2.6 47.5 1.0
OE2 B:GLU164 2.6 34.3 1.0
CD B:GLU164 2.8 28.5 1.0
CG B:GLU164 4.3 23.8 1.0
O B:HOH425 4.3 35.8 1.0
O B:HOH403 4.3 43.0 1.0

Magnesium binding site 4 out of 8 in 5d7c

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Magnesium binding site 4 out of 8 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 4 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:Mg306

b:27.5
occ:1.00
 O B:HOH503 2.1 52.4 1.0
O B:HOH565 2.2 53.4 1.0
O B:LEU60 2.3 20.5 1.0
O B:HOH505 2.6 31.8 1.0
C B:LEU60 3.5 18.7 1.0
N B:ALA61 4.3 19.0 1.0
CA B:LEU60 4.4 17.0 1.0
O B:HOH551 4.4 46.8 1.0
CA B:ALA61 4.4 19.1 1.0
C B:ALA61 4.7 19.2 1.0
CB B:LEU60 4.7 17.2 1.0
O B:HOH454 4.9 37.9 1.0

Magnesium binding site 5 out of 8 in 5d7c

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Magnesium binding site 5 out of 8 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 5 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:Mg307

b:41.2
occ:1.00
 O B:HOH562 2.1 42.2 1.0
O B:HOH429 2.2 30.2 1.0
O B:HOH506 2.2 37.3 1.0
O B:HOH542 2.3 37.1 1.0
O B:HOH421 2.3 27.5 1.0
OD1 B:ASN54 2.4 24.5 1.0
MG B:MG310 2.4 40.7 1.0
CG B:ASN54 3.6 21.9 1.0
O B:HOH485 4.0 26.2 1.0
O B:HOH406 4.2 45.6 1.0
OD2 B:ASP53 4.3 20.5 0.5
O B:GLU50 4.3 19.7 1.0
N B:ASN54 4.5 16.9 1.0
ND2 B:ASN54 4.5 23.6 1.0
O B:HOH432 4.5 47.6 1.0
CA B:ASN54 4.5 17.5 1.0
OD1 B:ASP57 4.6 25.1 1.0
CB B:ASN54 4.6 19.2 1.0
O B:HOH537 4.7 40.0 1.0
OE2 B:GLU50 4.7 28.9 1.0
CB B:ASP53 4.9 20.2 0.5
C B:ASP53 4.9 16.2 1.0
C20 B:57W303 5.0 23.7 1.0
CB B:ASP53 5.0 16.7 0.5

Magnesium binding site 6 out of 8 in 5d7c

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Magnesium binding site 6 out of 8 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 6 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:Mg308

b:28.7
occ:1.00
 OG1 B:THR171 2.0 22.4 1.0
O B:ASN82 2.3 16.1 1.0
O B:HOH504 2.3 36.9 1.0
O B:HOH479 2.5 28.0 1.0
O B:GLY83 2.7 14.7 1.0
O B:THR171 2.9 18.2 1.0
O B:HOH514 3.0 36.8 1.0
C B:ASN82 3.2 13.4 1.0
CB B:THR171 3.2 21.4 1.0
C B:THR171 3.4 15.0 1.0
C B:GLY83 3.5 15.2 1.0
CA B:THR171 3.7 16.8 1.0
N B:THR171 3.9 18.0 1.0
N B:GLY83 3.9 13.3 1.0
CA B:GLY83 3.9 14.6 1.0
CA B:ASN82 4.1 13.9 1.0
N B:GLY172 4.3 13.7 1.0
CB B:ASN82 4.4 15.1 1.0
CG2 B:THR171 4.4 23.4 1.0
O B:TYR63 4.6 23.0 1.0
N B:ARG84 4.6 14.2 1.0
O B:HOH568 4.6 35.0 1.0
O B:HOH536 4.7 42.1 1.0
CA B:ARG84 4.8 14.4 1.0
CA B:GLY172 4.9 14.1 1.0
CG B:ASN82 4.9 15.7 1.0

Magnesium binding site 7 out of 8 in 5d7c

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Magnesium binding site 7 out of 8 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 7 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:Mg309

b:35.4
occ:1.00
 O B:HOH478 2.2 27.6 1.0
O B:HOH519 2.2 41.0 1.0
O B:GLY208 2.4 22.4 1.0
NE2 B:HIS228 2.8 32.6 1.0
CE1 B:HIS228 3.2 38.8 1.0
O B:HOH486 3.4 42.1 1.0
C B:GLY208 3.4 19.3 1.0
CD2 B:HIS228 3.8 31.4 1.0
CA B:GLY208 4.0 20.6 1.0
O B:HOH510 4.3 39.1 1.0
ND1 B:HIS228 4.4 34.9 1.0
N B:ILE209 4.5 16.4 1.0
CB B:ASN65 4.6 18.8 1.0
O B:ASN65 4.7 15.9 1.0
O B:HOH525 4.7 46.2 1.0
ND2 B:ASN65 4.7 26.9 1.0
CG B:HIS228 4.8 26.6 1.0
CA B:ILE209 4.8 17.4 1.0
CG B:ASN65 4.9 20.3 1.0
N B:GLN210 5.0 15.7 1.0

Magnesium binding site 8 out of 8 in 5d7c

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Magnesium binding site 8 out of 8 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 8 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:Mg310

b:40.7
occ:1.00
 O B:HOH562 2.0 42.2 1.0
O B:HOH429 2.3 30.2 1.0
MG B:MG307 2.4 41.2 1.0
O B:HOH432 2.5 47.6 1.0
O B:HOH421 2.5 27.5 1.0
OD2 B:ASP53 2.6 20.5 0.5
O B:HOH406 3.0 45.6 1.0
O B:HOH521 3.6 54.2 1.0
CG B:ASP53 3.6 18.1 0.5
CB B:ASP53 3.9 20.2 0.5
CB B:ASP53 4.0 16.7 0.5
O B:HOH542 4.0 37.1 1.0
O B:HOH447 4.1 40.2 1.0
OE2 B:GLU50 4.2 28.9 1.0
OD1 B:ASP53 4.3 32.2 0.5
O B:HOH506 4.3 37.3 1.0
OD1 B:ASN54 4.4 24.5 1.0
OD1 B:ASP57 4.5 25.1 1.0
CG B:ASP53 4.6 24.8 0.5
MG B:MG304 4.7 41.4 1.0
OD1 B:ASP53 4.7 20.9 0.5
O B:GLU50 4.8 19.7 1.0
C B:ASP53 5.0 16.2 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: Sun Sep 29 02:33:34 2024

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