Atomistry » Manganese » PDB 6f4q-6fxr » 6fqm
Atomistry »
  Manganese »
    PDB 6f4q-6fxr »
      6fqm »

Manganese in PDB 6fqm: 3.06A Complex of S.Aureus Gyrase with Imidazopyrazinone T1 and Dna

Enzymatic activity of 3.06A Complex of S.Aureus Gyrase with Imidazopyrazinone T1 and Dna

All present enzymatic activity of 3.06A Complex of S.Aureus Gyrase with Imidazopyrazinone T1 and Dna:
5.99.1.3;

Protein crystallography data

The structure of 3.06A Complex of S.Aureus Gyrase with Imidazopyrazinone T1 and Dna, PDB code: 6fqm was solved by B.D.Bax, T.Germe, E.Basque, A.Maxwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.90 / 3.06
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 88.340, 171.710, 124.870, 90.00, 102.86, 90.00
R / Rfree (%) 19.5 / 23.4

Other elements in 6fqm:

The structure of 3.06A Complex of S.Aureus Gyrase with Imidazopyrazinone T1 and Dna also contains other interesting chemical elements:

Fluorine (F) 7 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the 3.06A Complex of S.Aureus Gyrase with Imidazopyrazinone T1 and Dna (pdb code 6fqm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the 3.06A Complex of S.Aureus Gyrase with Imidazopyrazinone T1 and Dna, PDB code: 6fqm:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6fqm

Go back to Manganese Binding Sites List in 6fqm
Manganese binding site 1 out of 4 in the 3.06A Complex of S.Aureus Gyrase with Imidazopyrazinone T1 and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 3.06A Complex of S.Aureus Gyrase with Imidazopyrazinone T1 and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn901

b:0.2
occ:1.00
 OD2 B:ASP510 2.1 0.2 1.0
O B:HOH1003 2.1 0.9 1.0
O B:HOH1004 2.1 0.1 1.0
O B:HOH1005 2.1 0.7 1.0
O F:HOH201 2.1 0.9 1.0
OD2 B:ASP508 2.1 0.7 1.0
CG B:ASP510 3.0 98.2 1.0
CG B:ASP508 3.2 0.3 1.0
OD1 B:ASP510 3.3 97.5 1.0
CB B:ASP508 3.6 99.8 1.0
OD1 B:ASP508 4.3 0.9 1.0
CB B:ASP510 4.4 92.2 1.0
OE2 B:GLU435 4.5 0.4 1.0
OE1 B:GLU435 4.6 0.3 1.0
OP1 F:DT-1 4.8 68.7 1.0
C5' F:DT-1 4.8 72.7 1.0
CD B:GLU435 4.8 0.8 1.0

Manganese binding site 2 out of 4 in 6fqm

Go back to Manganese Binding Sites List in 6fqm
Manganese binding site 2 out of 4 in the 3.06A Complex of S.Aureus Gyrase with Imidazopyrazinone T1 and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 3.06A Complex of S.Aureus Gyrase with Imidazopyrazinone T1 and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn901

b:0.8
occ:1.00
 O D:HOH1005 2.1 0.3 1.0
O D:HOH1003 2.1 0.9 1.0
O D:HOH1004 2.1 0.5 1.0
O D:HOH1001 2.1 0.6 1.0
OD2 D:ASP510 2.1 0.2 1.0
OD2 D:ASP508 2.2 0.8 1.0
CG D:ASP508 3.1 0.5 1.0
CG D:ASP510 3.2 0.7 1.0
CB D:ASP508 3.5 0.9 1.0
OD1 D:ASP510 3.5 0.6 1.0
OE2 D:GLU435 4.1 92.4 1.0
OD1 D:ASP508 4.2 1.0 1.0
CB D:ASP510 4.5 98.9 1.0
CD D:GLU435 4.8 86.1 1.0
OE1 D:GLU435 4.8 88.8 1.0
OP1 E:DT-1 4.9 71.4 1.0
C5' E:DT-1 5.0 71.8 1.0
CA D:ASP508 5.0 0.9 1.0

Manganese binding site 3 out of 4 in 6fqm

Go back to Manganese Binding Sites List in 6fqm
Manganese binding site 3 out of 4 in the 3.06A Complex of S.Aureus Gyrase with Imidazopyrazinone T1 and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 3.06A Complex of S.Aureus Gyrase with Imidazopyrazinone T1 and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Mn901

b:0.2
occ:1.00
 O f:HOH1102 2.1 0.3 1.0
O b:HOH1005 2.1 0.7 1.0
O b:HOH1003 2.1 0.8 1.0
OD2 b:ASP510 2.1 0.4 1.0
OD2 b:ASP508 2.2 0.7 1.0
O b:HOH1002 2.2 0.4 1.0
CG b:ASP510 3.0 0.6 1.0
CG b:ASP508 3.1 0.7 1.0
OD1 b:ASP510 3.2 0.5 1.0
CB b:ASP508 3.4 96.3 1.0
OE1 b:GLU435 3.7 0.5 1.0
OE2 b:GLU435 4.2 0.7 1.0
OD1 b:ASP508 4.2 0.7 1.0
CD b:GLU435 4.4 1.0 1.0
CB b:ASP510 4.4 95.9 1.0
C5' f:DT-1 4.9 78.9 1.0
CA b:ASP508 4.9 97.0 1.0

Manganese binding site 4 out of 4 in 6fqm

Go back to Manganese Binding Sites List in 6fqm
Manganese binding site 4 out of 4 in the 3.06A Complex of S.Aureus Gyrase with Imidazopyrazinone T1 and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of 3.06A Complex of S.Aureus Gyrase with Imidazopyrazinone T1 and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
d:Mn901

b:0.7
occ:1.00
 O d:HOH1002 2.1 0.7 1.0
O d:HOH1004 2.1 0.6 1.0
O d:HOH1001 2.1 0.4 1.0
O d:HOH1003 2.1 0.0 1.0
OD2 d:ASP508 2.1 0.5 1.0
OD2 d:ASP510 2.2 0.8 1.0
CG d:ASP508 3.2 0.1 1.0
CG d:ASP510 3.3 0.3 1.0
CB d:ASP508 3.7 0.2 1.0
OD1 d:ASP510 3.8 0.7 1.0
OE2 d:GLU435 3.9 0.3 1.0
OD1 d:ASP508 4.3 0.3 1.0
CB d:ASP510 4.5 0.5 1.0
OP1 e:DT-1 4.8 81.2 1.0
CD d:GLU435 5.0 0.8 1.0
OG d:SER438 5.0 0.8 1.0

Reference:

T.Germe, J.Voros, F.Jeannot, T.Taillier, R.A.Stavenger, E.Bacque, A.Maxwell, B.D.Bax. A New Class of Antibacterials, the Imidazopyrazinones, Reveal Structural Transitions Involved in Dna Gyrase Poisoning and Mechanisms of Resistance. Nucleic Acids Res. V. 46 4114 2018.
ISSN: ESSN 1362-4962
PubMed: 29538767
DOI: 10.1093/NAR/GKY181
Page generated: Sun Oct 6 04:37:43 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy