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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

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