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Chlorine 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:

Manganese (Mn) 3 atoms
Fluorine (F) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7fvs

Go back to Chlorine Binding Sites List in 7fvs
Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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:Cl1502

b:43.5
occ:1.00
 O B:HOH1702 2.4 38.7 1.0
O A:HOH1604 3.5 31.9 1.0
O A:HOH1670 3.8 35.1 1.0
NE A:ARG1429 3.9 35.6 1.0
NH1 B:ARG1429 4.1 37.2 1.0
NH2 B:ARG1429 4.2 40.3 1.0
CD A:ARG1429 4.5 33.0 1.0
NH1 A:ARG1432 4.6 36.0 1.0
CZ B:ARG1429 4.7 36.4 1.0
CG A:ARG1429 4.8 31.8 1.0
CZ A:ARG1429 4.9 34.6 1.0
NH2 A:ARG1429 5.0 35.1 1.0

Chlorine binding site 2 out of 2 in 7fvs

Go back to Chlorine Binding Sites List in 7fvs
Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl 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:Cl1504

b:47.2
occ:1.00
 CL15 B:61I1504 0.0 47.2 1.0
C14 B:61I1504 1.7 35.8 1.0
N13 B:61I1504 2.6 37.9 1.0
C8 B:61I1504 2.6 35.0 1.0
C7 B:61I1504 3.1 35.4 1.0
C2 D:DC11 3.2 34.4 1.0
N3 D:DC11 3.3 35.5 1.0
C2 D:DG10 3.4 34.4 1.0
N1 D:DC11 3.5 38.5 1.0
N2 D:DG10 3.5 36.3 1.0
O2 D:DC11 3.5 35.5 1.0
N1 D:DG10 3.6 33.2 1.0
C4 D:DC11 3.7 35.0 1.0
N3 D:DG10 3.8 35.1 1.0
C12 B:61I1504 3.8 36.5 1.0
C6 D:DC11 3.9 37.9 1.0
C9 B:61I1504 3.9 36.3 1.0
O4' D:DC11 3.9 39.5 1.0
C5 D:DC11 4.0 35.9 1.0
N3 C:DC11 4.2 34.9 1.0
C1' D:DC11 4.2 38.2 1.0
C6 D:DG10 4.2 34.6 1.0
C4 D:DG10 4.3 34.8 1.0
C11 B:61I1504 4.4 36.4 1.0
N4 D:DC11 4.4 34.3 1.0
N2 C:DG10 4.4 32.1 1.0
O2 C:DC11 4.5 37.7 1.0
C6 B:61I1504 4.5 35.0 1.0
C2 C:DC11 4.5 37.4 1.0
C5 D:DG10 4.5 34.9 1.0
N1 C:DG10 4.6 30.2 1.0
C2 C:DG10 4.7 32.6 1.0
C4 C:DC11 4.8 36.3 1.0
O6 D:DG10 4.9 37.6 1.0
C10 B:61I1504 4.9 38.9 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: Mon Jul 29 20:59:37 2024

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