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Manganese in PDB 7fvs: Crystal Structure of S. Aureus Gyrase in Complex with 4-[[1-[(1- Chloro-6,7-Dihydro-5H-Cyclopenta[C]Pyridin-6-Yl)Methyl]Azetidin-3- Yl]Methylamino]-6-Fluorochromen-2-One

Enzymatic activity of Crystal Structure of S. Aureus Gyrase in Complex with 4-[[1-[(1- Chloro-6,7-Dihydro-5H-Cyclopenta[C]Pyridin-6-Yl)Methyl]Azetidin-3- Yl]Methylamino]-6-Fluorochromen-2-One

All present enzymatic activity of Crystal Structure of S. Aureus Gyrase in Complex with 4-[[1-[(1- Chloro-6,7-Dihydro-5H-Cyclopenta[C]Pyridin-6-Yl)Methyl]Azetidin-3- Yl]Methylamino]-6-Fluorochromen-2-One:
5.6.2.2;

Protein crystallography data

The structure of Crystal Structure of S. Aureus Gyrase in Complex with 4-[[1-[(1- Chloro-6,7-Dihydro-5H-Cyclopenta[C]Pyridin-6-Yl)Methyl]Azetidin-3- Yl]Methylamino]-6-Fluorochromen-2-One, PDB code: 7fvs was solved by B.Xu, J.Benz, J.G.Cumming, L.Kreis, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.47 / 2.16
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 92.915, 92.915, 407.576, 90, 90, 120
R / Rfree (%) 18.5 / 22.1

Other elements in 7fvs:

The structure of Crystal Structure of S. Aureus Gyrase in Complex with 4-[[1-[(1- Chloro-6,7-Dihydro-5H-Cyclopenta[C]Pyridin-6-Yl)Methyl]Azetidin-3- Yl]Methylamino]-6-Fluorochromen-2-One also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Fluorine (F) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of S. Aureus Gyrase in Complex with 4-[[1-[(1- Chloro-6,7-Dihydro-5H-Cyclopenta[C]Pyridin-6-Yl)Methyl]Azetidin-3- Yl]Methylamino]-6-Fluorochromen-2-One (pdb code 7fvs). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of S. Aureus Gyrase in Complex with 4-[[1-[(1- Chloro-6,7-Dihydro-5H-Cyclopenta[C]Pyridin-6-Yl)Methyl]Azetidin-3- Yl]Methylamino]-6-Fluorochromen-2-One, PDB code: 7fvs:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 7fvs

Go back to Manganese Binding Sites List in 7fvs
Manganese binding site 1 out of 3 in the Crystal Structure of S. Aureus Gyrase in Complex with 4-[[1-[(1- Chloro-6,7-Dihydro-5H-Cyclopenta[C]Pyridin-6-Yl)Methyl]Azetidin-3- Yl]Methylamino]-6-Fluorochromen-2-One


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of S. Aureus Gyrase in Complex with 4-[[1-[(1- Chloro-6,7-Dihydro-5H-Cyclopenta[C]Pyridin-6-Yl)Methyl]Azetidin-3- Yl]Methylamino]-6-Fluorochromen-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1501

b:31.6
occ:1.00
 O A:HOH1609 1.9 33.2 1.0
O A:HOH1613 2.0 29.9 1.0
OD2 A:ASP508 2.1 32.9 1.0
OE2 A:GLU435 2.1 30.6 1.0
OP1 D:DG9 2.1 30.5 1.0
O3' D:DG8 2.6 30.1 1.0
CD A:GLU435 2.7 30.9 1.0
OE1 A:GLU435 2.9 31.8 1.0
P D:DG9 2.9 29.4 1.0
CG A:ASP508 3.1 33.5 1.0
O D:HOH112 3.4 32.2 1.0
CB A:ASP508 3.7 33.2 1.0
OD2 A:ASP510 3.9 35.3 1.0
O5' D:DG9 3.9 29.8 1.0
C3' D:DG8 3.9 27.4 1.0
C5' D:DG9 4.0 29.4 1.0
CG A:GLU435 4.0 27.9 1.0
OP2 D:DG9 4.1 29.0 1.0
OD1 A:ASP508 4.2 32.9 1.0
CB A:GLU435 4.3 29.5 1.0
OD1 A:ASP510 4.4 36.0 1.0
C4' D:DG8 4.4 28.6 1.0
CG A:ASP510 4.6 33.8 1.0
C2' D:DG8 4.6 28.1 1.0
O A:LYS581 4.6 40.3 1.0
CE1 B:PHE1123 4.8 33.4 1.0
CZ B:PHE1123 4.9 31.9 1.0
CA A:GLY582 4.9 33.3 1.0
C5' D:DG8 5.0 29.5 1.0
CA A:ASP508 5.0 31.8 1.0

Manganese binding site 2 out of 3 in 7fvs

Go back to Manganese Binding Sites List in 7fvs
Manganese binding site 2 out of 3 in the Crystal Structure of S. Aureus Gyrase in Complex with 4-[[1-[(1- Chloro-6,7-Dihydro-5H-Cyclopenta[C]Pyridin-6-Yl)Methyl]Azetidin-3- Yl]Methylamino]-6-Fluorochromen-2-One


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of S. Aureus Gyrase in Complex with 4-[[1-[(1- Chloro-6,7-Dihydro-5H-Cyclopenta[C]Pyridin-6-Yl)Methyl]Azetidin-3- Yl]Methylamino]-6-Fluorochromen-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1501

b:32.4
occ:1.00
 O B:HOH1602 1.7 31.4 1.0
OD2 B:ASP508 2.0 28.9 1.0
OE2 B:GLU435 2.1 30.8 1.0
OP1 C:DG9 2.1 29.1 1.0
O B:HOH1709 2.3 30.8 1.0
O3' C:DG8 2.5 27.8 1.0
P C:DG9 2.9 22.8 1.0
CG B:ASP508 3.1 31.6 1.0
CD B:GLU435 3.1 30.0 1.0
OE1 B:GLU435 3.6 31.8 1.0
CB B:ASP508 3.7 31.2 1.0
C3' C:DG8 3.8 28.1 1.0
O B:HOH1746 3.8 29.7 1.0
O5' C:DG9 3.9 28.8 1.0
C5' C:DG9 4.0 28.1 1.0
OP2 C:DG9 4.0 29.0 1.0
OD1 B:ASP508 4.0 31.5 1.0
OD2 B:ASP510 4.1 31.7 1.0
C4' C:DG8 4.2 26.2 1.0
CG B:GLU435 4.4 26.2 1.0
CB B:GLU435 4.4 28.3 1.0
C2' C:DG8 4.5 26.9 1.0
O B:LYS581 4.7 35.5 1.0
C5' C:DG8 4.8 26.3 1.0
OD1 B:ASP510 4.8 31.9 1.0
CG B:ASP510 4.9 29.6 1.0
CE1 A:PHE1123 5.0 29.0 1.0

Manganese binding site 3 out of 3 in 7fvs

Go back to Manganese Binding Sites List in 7fvs
Manganese binding site 3 out of 3 in the Crystal Structure of S. Aureus Gyrase in Complex with 4-[[1-[(1- Chloro-6,7-Dihydro-5H-Cyclopenta[C]Pyridin-6-Yl)Methyl]Azetidin-3- Yl]Methylamino]-6-Fluorochromen-2-One


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of S. Aureus Gyrase in Complex with 4-[[1-[(1- Chloro-6,7-Dihydro-5H-Cyclopenta[C]Pyridin-6-Yl)Methyl]Azetidin-3- Yl]Methylamino]-6-Fluorochromen-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1502

b:46.9
occ:1.00
 O B:HOH1722 1.9 35.4 1.0
O B:THR1325 2.1 30.8 1.0
O B:TYR1322 2.1 32.5 1.0
O B:GLN1328 2.2 30.6 1.0
O B:HOH1723 2.2 37.6 1.0
C B:GLN1328 3.2 30.1 1.0
C B:THR1325 3.2 31.7 1.0
O B:HOH1601 3.2 40.4 1.0
C B:TYR1322 3.4 33.1 1.0
N B:GLN1328 3.6 29.2 1.0
CA B:GLN1328 3.7 30.2 1.0
N B:THR1325 3.8 33.3 1.0
CB B:GLN1328 3.8 30.6 1.0
O B:LYS1323 4.0 36.0 1.0
C B:LYS1323 4.1 33.7 1.0
N B:PRO1326 4.1 30.4 1.0
CA B:THR1325 4.1 30.6 1.0
CA B:PRO1326 4.1 29.9 1.0
CA B:TYR1322 4.3 31.0 1.0
C B:PRO1326 4.3 30.3 1.0
N B:LYS1323 4.3 34.5 1.0
O B:HOH1652 4.3 34.7 1.0
N B:THR1329 4.3 28.7 1.0
CA B:LYS1323 4.4 33.6 1.0
O B:LEU1321 4.4 32.6 1.0
N B:LEU1327 4.4 31.6 1.0
N B:GLN1324 4.5 33.0 1.0
CG B:GLN1328 4.5 29.1 1.0
OG1 B:THR1329 4.7 30.9 1.0
C B:GLN1324 4.7 33.3 1.0
CA B:THR1329 4.8 27.6 1.0
C B:LEU1327 4.8 29.0 1.0
O B:PRO1326 4.8 28.8 1.0
OG1 B:THR1325 4.9 33.0 1.0

Reference:

J.G.Cumming, C.Kramer, H.Kuehne, M.G.Rudolph. Crystal Structure of A S. Aureus Gyrase Complex Acs Med.Chem.Lett. 2023.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.3C00187
Page generated: Sun Oct 6 08:46:41 2024

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