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Magnesium in PDB 5d7d: 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: 5d7d 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) 50.10 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 143.300, 55.446, 51.029, 90.00, 100.95, 90.00
R / Rfree (%) 16.5 / 19.5

Other elements in 5d7d:

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 5d7d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 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: 5d7d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5d7d

Go back to Magnesium Binding Sites List in 5d7d
Magnesium binding site 1 out of 7 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:36.9
occ:0.50
OD1 A:ASP57 2.2 36.5 1.0
O A:HOH446 2.7 41.0 1.0
O A:HOH516 2.8 42.6 1.0
CG A:ASP57 3.3 30.4 1.0
CB A:ASP57 4.0 26.3 1.0
MG A:MG305 4.1 48.7 1.0
O A:HOH531 4.2 31.6 1.0
OD2 A:ASP57 4.2 32.8 1.0
O A:HOH537 4.6 46.9 1.0
OD1 A:ASP53 4.8 31.8 1.0
OD1 A:ASN54 4.8 30.8 1.0

Magnesium binding site 2 out of 7 in 5d7d

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Magnesium binding site 2 out of 7 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:Mg305

b:48.7
occ:1.00
O A:HOH446 2.0 41.0 1.0
O A:HOH499 2.1 42.5 1.0
O A:HOH469 2.1 33.9 1.0
O A:HOH531 2.2 31.6 1.0
OD1 A:ASN54 2.2 30.8 1.0
MG A:MG306 2.5 35.8 1.0
CG A:ASN54 3.4 26.2 1.0
OD1 A:ASP53 3.6 31.8 1.0
ND2 A:ASN54 4.0 28.1 1.0
O A:HOH516 4.0 42.6 1.0
MG A:MG304 4.1 36.9 0.5
O A:HOH521 4.3 51.8 1.0
OE1 A:GLU50 4.3 35.3 1.0
O A:GLU50 4.4 23.5 1.0
N A:ASN54 4.6 21.3 1.0
CB A:ASN54 4.6 22.5 1.0
CG A:ASP53 4.6 30.9 1.0
CA A:ASN54 4.6 22.4 1.0
OD1 A:ASP57 4.7 36.5 1.0
CB A:ASP53 4.8 24.2 1.0
C A:ASP53 5.0 22.4 1.0

Magnesium binding site 3 out of 7 in 5d7d

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Magnesium binding site 3 out of 7 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:Mg306

b:35.8
occ:1.00
O A:HOH521 2.2 51.8 1.0
O A:HOH531 2.2 31.6 1.0
O A:HOH469 2.4 33.9 1.0
OE1 A:GLU50 2.4 35.3 1.0
O A:HOH499 2.5 42.5 1.0
MG A:MG305 2.5 48.7 1.0
CD A:GLU50 3.6 38.4 1.0
OE2 A:GLU50 4.0 58.0 1.0
O A:HOH446 4.3 41.0 1.0
OD1 A:ASN54 4.3 30.8 1.0
OD1 A:ASP53 4.7 31.8 1.0
O A:HOH528 4.7 45.4 1.0
O A:HOH501 4.7 36.0 1.0
CG A:GLU50 4.8 31.4 1.0
O A:GLU50 4.9 23.5 1.0

Magnesium binding site 4 out of 7 in 5d7d

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Magnesium binding site 4 out of 7 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:Mg300

b:55.6
occ:1.00
O A:HOH475 2.2 35.9 1.0
O A:HOH450 2.6 38.8 1.0
NZ A:LYS163 2.7 54.9 1.0
O A:GLU164 3.8 23.8 1.0
CE A:LYS163 3.9 52.7 1.0
CD A:LYS163 4.9 46.3 1.0
O A:HOH476 4.9 33.4 1.0

Magnesium binding site 5 out of 7 in 5d7d

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Magnesium binding site 5 out of 7 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:Mg305

b:33.7
occ:1.00
O B:HOH408 2.0 37.6 1.0
O B:HOH492 2.1 45.0 1.0
O B:HOH540 2.1 43.0 1.0
O B:HOH449 2.2 26.4 1.0
OD1 B:ASN54 2.3 28.3 1.0
O B:HOH493 2.3 46.6 1.0
CG B:ASN54 3.4 23.5 1.0
ND2 B:ASN54 4.0 25.2 1.0
OD2 B:ASP53 4.0 27.3 0.5
O B:HOH466 4.1 42.6 1.0
O B:GLU50 4.5 21.8 1.0
OE2 B:GLU50 4.5 33.3 1.0
OD1 B:ASP57 4.5 35.4 1.0
CB B:ASN54 4.6 21.0 1.0
N B:ASN54 4.7 19.6 1.0
CA B:ASN54 4.7 19.8 1.0
CG B:ASP53 5.0 24.2 0.5
CB B:ASP53 5.0 23.9 0.5

Magnesium binding site 6 out of 7 in 5d7d

Go back to Magnesium Binding Sites List in 5d7d
Magnesium binding site 6 out of 7 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:Mg306

b:20.4
occ:1.00
OG1 B:THR171 2.3 21.9 1.0
O B:ASN82 2.4 19.1 1.0
O B:HOH508 2.4 41.0 1.0
O B:HOH467 2.4 25.3 1.0
O B:THR171 2.5 20.4 1.0
O B:GLY83 2.6 18.7 1.0
O B:HOH479 2.7 39.5 1.0
O B:HOH510 2.9 36.5 1.0
C B:ASN82 3.2 17.2 1.0
C B:THR171 3.2 18.9 1.0
CB B:THR171 3.4 23.4 1.0
C B:GLY83 3.4 18.4 1.0
CA B:THR171 3.7 18.6 1.0
N B:GLY83 3.9 17.6 1.0
CA B:GLY83 3.9 17.6 1.0
N B:THR171 4.0 20.3 1.0
O B:HOH426 4.1 32.0 1.0
CA B:ASN82 4.2 17.0 1.0
N B:GLY172 4.2 17.8 1.0
O B:HOH514 4.3 45.3 1.0
CB B:ASN82 4.4 18.6 1.0
O B:TYR63 4.4 23.6 1.0
O B:HOH416 4.4 46.2 1.0
N B:ARG84 4.5 17.5 1.0
CG2 B:THR171 4.7 25.3 1.0
O B:HOH547 4.7 26.2 1.0
CA B:ARG84 4.7 17.3 1.0
CA B:GLY172 4.7 17.0 1.0
CG B:ASN82 4.9 20.0 1.0

Magnesium binding site 7 out of 7 in 5d7d

Go back to Magnesium Binding Sites List in 5d7d
Magnesium binding site 7 out of 7 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:Mg307

b:44.2
occ:1.00
O B:HOH521 2.0 40.5 0.5
O B:HOH524 2.1 63.0 1.0
O B:HOH462 2.2 34.4 1.0
O B:HOH483 2.3 48.5 1.0
O B:GLY208 2.5 29.8 1.0
NE2 B:HIS228 2.6 33.1 0.5
NE2 B:HIS228 2.7 35.5 0.5
CE1 B:HIS228 3.1 35.0 0.5
C B:GLY208 3.5 27.0 1.0
CD2 B:HIS228 3.5 28.1 0.5
CE1 B:HIS228 3.5 30.5 0.5
CD2 B:HIS228 3.8 31.9 0.5
CA B:GLY208 4.0 27.5 1.0
O B:HOH523 4.0 47.3 1.0
ND1 B:HIS228 4.3 32.1 0.5
O B:HOH487 4.4 48.1 1.0
N B:ILE209 4.5 23.4 1.0
ND1 B:HIS228 4.7 30.5 0.5
CG B:HIS228 4.7 30.6 0.5
CG B:HIS228 4.7 28.4 0.5
CB B:ASN65 4.7 23.0 1.0
O B:ASN65 4.7 20.4 1.0
ND2 B:ASN65 4.8 37.5 1.0
CA B:ILE209 4.9 23.7 1.0
CG B:ASN65 5.0 26.2 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: Mon Dec 14 20:10:22 2020

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