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Magnesium in PDB 5d7r: 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: 5d7r 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) 31.34 / 1.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 143.192, 55.514, 51.114, 90.00, 100.65, 90.00
R / Rfree (%) 18.1 / 22

Other elements in 5d7r:

The structure of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with A Ligand also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

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 5d7r). 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: 5d7r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5d7r

Go back to Magnesium Binding Sites List in 5d7r
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:Mg301

b:67.6
occ:1.00
 O A:HOH409 2.0 39.6 1.0
O A:HOH470 2.1 26.4 1.0
O A:HOH521 2.1 45.1 1.0
OD1 A:ASN54 2.4 29.5 1.0
MG A:MG302 2.5 30.9 1.0
OD1 A:ASP53 3.4 29.4 1.0
CG A:ASN54 3.4 28.4 1.0
MG A:MG303 3.9 45.2 0.5
ND2 A:ASN54 4.0 31.4 1.0
O A:HOH524 4.2 39.1 1.0
O A:GLU50 4.3 20.6 1.0
CG A:ASP53 4.4 27.8 1.0
N A:ASN54 4.5 20.9 1.0
OE1 A:GLU50 4.5 29.1 1.0
CA A:ASN54 4.6 23.6 1.0
CB A:ASN54 4.6 25.4 1.0
CB A:ASP53 4.7 23.4 1.0
OD1 A:ASP57 4.8 34.7 1.0
C A:ASP53 4.9 20.4 1.0

Magnesium binding site 2 out of 8 in 5d7r

Go back to Magnesium Binding Sites List in 5d7r
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
A:Mg302

b:30.9
occ:1.00
 O A:HOH521 2.2 45.1 1.0
O A:HOH470 2.3 26.4 1.0
MG A:MG301 2.5 67.6 1.0
OE1 A:GLU50 2.6 29.1 1.0
CD A:GLU50 3.8 33.6 1.0
O A:HOH409 4.4 39.6 1.0
OD1 A:ASN54 4.4 29.5 1.0
OE2 A:GLU50 4.4 42.6 1.0
OD1 A:ASP53 4.6 29.4 1.0
O A:HOH542 4.8 38.8 1.0
O A:GLU50 4.8 20.6 1.0
O A:HOH512 4.9 34.8 1.0
CG A:GLU50 4.9 28.4 1.0

Magnesium binding site 3 out of 8 in 5d7r

Go back to Magnesium Binding Sites List in 5d7r
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
A:Mg303

b:45.2
occ:0.50
 O A:HOH524 2.3 39.1 1.0
OD1 A:ASP57 2.4 34.7 1.0
O A:HOH409 2.7 39.6 1.0
CG A:ASP57 3.5 28.1 1.0
MG A:MG301 3.9 67.6 1.0
CB A:ASP57 4.0 26.3 1.0
O A:HOH503 4.2 34.8 1.0
O A:HOH538 4.3 51.0 1.0
OD1 A:ASN54 4.4 29.5 1.0
OD2 A:ASP57 4.5 33.8 1.0
OD1 A:ASP53 4.8 29.4 1.0
O A:HOH458 4.9 33.1 1.0

Magnesium binding site 4 out of 8 in 5d7r

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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
A:Mg304

b:44.3
occ:1.00
 O A:HOH506 2.1 36.6 1.0
O A:GLY208 2.2 25.9 1.0
O A:HOH505 2.3 40.1 1.0
NE2 A:HIS228 2.5 31.1 1.0
C A:GLY208 3.1 22.7 1.0
CE1 A:HIS228 3.2 31.8 1.0
CD2 A:HIS228 3.5 29.6 1.0
CA A:GLY208 3.5 23.5 1.0
ND1 A:HIS228 4.3 31.7 1.0
N A:ILE209 4.3 19.9 1.0
ND2 A:ASN65 4.3 31.9 1.0
CG A:HIS228 4.5 26.8 1.0
CB A:ASN65 4.5 19.2 1.0
O A:HOH529 4.5 44.0 1.0
CA A:ILE209 4.6 19.4 1.0
O A:ASN65 4.7 17.8 1.0
N A:GLN210 4.8 18.7 1.0
CG A:ASN65 4.8 25.1 1.0
N A:GLY208 4.8 24.4 1.0
O A:GLU230 4.9 57.5 1.0
C A:ILE209 4.9 20.9 1.0

Magnesium binding site 5 out of 8 in 5d7r

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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:Mg301

b:36.3
occ:1.00
 O B:HOH506 1.8 42.3 1.0
O B:HOH533 2.2 48.2 1.0
O B:HOH409 2.3 40.6 1.0
OD1 B:ASN54 2.3 28.6 1.0
O B:HOH429 2.3 28.1 1.0
CG B:ASN54 3.3 25.3 1.0
ND2 B:ASN54 3.7 30.3 1.0
OD2 B:ASP53 4.1 26.5 0.5
O B:HOH426 4.4 45.7 1.0
O B:GLU50 4.5 19.9 1.0
O B:HOH515 4.5 46.3 1.0
CB B:ASN54 4.6 23.1 1.0
OE2 B:GLU50 4.6 30.1 1.0
OD1 B:ASP57 4.7 30.2 1.0
N B:ASN54 4.7 19.4 1.0
CA B:ASN54 4.8 22.4 1.0
CB B:ASP53 4.9 21.1 0.5
CB B:ASP53 5.0 21.8 0.5
CG B:ASP53 5.0 22.7 0.5

Magnesium binding site 6 out of 8 in 5d7r

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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:Mg302

b:40.2
occ:1.00
 O B:HOH534 1.9 60.0 1.0
O B:HOH490 2.1 29.7 1.0
O B:HOH496 2.2 46.9 1.0
O B:GLY208 2.5 24.9 1.0
NE2 B:HIS228 2.6 26.5 0.5
NE2 B:HIS228 2.9 25.1 0.5
CE1 B:HIS228 3.2 25.7 0.5
C B:GLY208 3.5 22.0 1.0
CE1 B:HIS228 3.6 27.0 0.5
CD2 B:HIS228 3.6 24.4 0.5
CA B:GLY208 4.0 23.7 1.0
CD2 B:HIS228 4.1 23.1 0.5
O B:HOH519 4.3 41.6 1.0
ND1 B:HIS228 4.3 24.6 0.5
N B:ILE209 4.6 19.0 1.0
ND2 B:ASN65 4.6 32.2 1.0
CB B:ASN65 4.7 20.6 1.0
O B:ASN65 4.7 17.8 1.0
ND1 B:HIS228 4.7 26.7 0.5
CG B:HIS228 4.7 25.3 0.5
CG B:HIS228 4.8 24.4 0.5
CA B:ILE209 4.9 19.8 1.0
CG B:ASN65 4.9 24.8 1.0

Magnesium binding site 7 out of 8 in 5d7r

Go back to Magnesium Binding Sites List in 5d7r
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:Mg303

b:30.4
occ:1.00
 O B:HOH461 2.1 35.5 1.0
OE1 B:GLU219 2.3 38.5 1.0
O B:HOH487 2.3 41.2 1.0
OE2 B:GLU219 2.4 37.1 1.0
CD B:GLU219 2.6 39.2 1.0
NZ B:LYS73 4.0 27.9 1.0
CG B:GLU219 4.1 35.0 1.0
OE1 B:GLU220 4.1 30.1 1.0
CD B:GLU220 4.5 29.0 1.0
OD1 B:ASP218 4.6 26.3 1.0
CG B:GLU220 4.6 27.8 1.0
N B:GLU219 4.7 26.0 1.0

Magnesium binding site 8 out of 8 in 5d7r

Go back to Magnesium Binding Sites List in 5d7r
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:Mg304

b:28.3
occ:1.00
 OG1 B:THR171 2.1 21.9 1.0
O B:ASN82 2.3 16.2 1.0
O B:HOH520 2.5 40.4 1.0
O B:HOH467 2.5 30.6 1.0
O B:GLY83 2.6 16.1 1.0
O B:THR171 2.7 18.9 1.0
O B:HOH512 3.1 34.5 1.0
C B:ASN82 3.2 14.2 1.0
CB B:THR171 3.3 21.0 1.0
C B:THR171 3.3 15.5 1.0
C B:GLY83 3.4 16.0 1.0
O B:HOH511 3.5 41.6 1.0
CA B:THR171 3.6 16.6 1.0
N B:GLY83 3.9 15.2 1.0
N B:THR171 3.9 15.4 1.0
CA B:GLY83 3.9 16.3 1.0
CA B:ASN82 4.1 15.1 1.0
N B:GLY172 4.2 15.2 1.0
CB B:ASN82 4.3 17.2 1.0
CG2 B:THR171 4.4 20.4 1.0
O B:TYR63 4.5 22.7 1.0
N B:ARG84 4.5 16.0 1.0
CA B:GLY172 4.8 15.7 1.0
CA B:ARG84 4.8 16.3 1.0
CG B:ASN82 4.9 18.6 1.0

Reference:

J.Zhang, Q.Yang, J.A.Romero, J.Cross, B.Wang, K.M.Poutsiaka, F.Epie, D.Bevan, Y.Wu, T.Moy, A.Daniel, B.Chamberlain, N.Carter, J.Shotwell, A.Arya, V.Kumar, J.Silverman, K.Nguyen, C.A.Metcalf, D.Ryan, B.Lippa, R.E.Dolle. Discovery of Indazole Derivatives As A Novel Class of Bacterial Gyrase B Inhibitors. Acs Med.Chem.Lett. V. 6 1080 2015.
ISSN: ISSN 1948-5875
PubMed: 26487916
DOI: 10.1021/ACSMEDCHEMLETT.5B00266
Page generated: Sun Sep 29 02:35:24 2024

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