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Chlorine in PDB 7fvt: Crystal Structure of S. Aureus Gyrase in Complex with 6-[5-[2-[(4- Chloro-2,3-Dihydro-1H-Inden-2-Yl)Methylamino]Ethyl]-2-Oxo-1,3- Oxazolidin-3-Yl]-4H-Pyrido[3,2-B][1,4]Oxazin-3-One

Enzymatic activity of Crystal Structure of S. Aureus Gyrase in Complex with 6-[5-[2-[(4- Chloro-2,3-Dihydro-1H-Inden-2-Yl)Methylamino]Ethyl]-2-Oxo-1,3- Oxazolidin-3-Yl]-4H-Pyrido[3,2-B][1,4]Oxazin-3-One

All present enzymatic activity of Crystal Structure of S. Aureus Gyrase in Complex with 6-[5-[2-[(4- Chloro-2,3-Dihydro-1H-Inden-2-Yl)Methylamino]Ethyl]-2-Oxo-1,3- Oxazolidin-3-Yl]-4H-Pyrido[3,2-B][1,4]Oxazin-3-One:
5.6.2.2;

Protein crystallography data

The structure of Crystal Structure of S. Aureus Gyrase in Complex with 6-[5-[2-[(4- Chloro-2,3-Dihydro-1H-Inden-2-Yl)Methylamino]Ethyl]-2-Oxo-1,3- Oxazolidin-3-Yl]-4H-Pyrido[3,2-B][1,4]Oxazin-3-One, PDB code: 7fvt was solved by B.Xu, J.Benz, J.G.Cumming, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.16 / 2.08
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 92.938, 92.938, 407.651, 90, 90, 120
R / Rfree (%) 20 / 24.8

Other elements in 7fvt:

The structure of Crystal Structure of S. Aureus Gyrase in Complex with 6-[5-[2-[(4- Chloro-2,3-Dihydro-1H-Inden-2-Yl)Methylamino]Ethyl]-2-Oxo-1,3- Oxazolidin-3-Yl]-4H-Pyrido[3,2-B][1,4]Oxazin-3-One also contains other interesting chemical elements:

Manganese (Mn) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of S. Aureus Gyrase in Complex with 6-[5-[2-[(4- Chloro-2,3-Dihydro-1H-Inden-2-Yl)Methylamino]Ethyl]-2-Oxo-1,3- Oxazolidin-3-Yl]-4H-Pyrido[3,2-B][1,4]Oxazin-3-One (pdb code 7fvt). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of S. Aureus Gyrase in Complex with 6-[5-[2-[(4- Chloro-2,3-Dihydro-1H-Inden-2-Yl)Methylamino]Ethyl]-2-Oxo-1,3- Oxazolidin-3-Yl]-4H-Pyrido[3,2-B][1,4]Oxazin-3-One, PDB code: 7fvt:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7fvt

Go back to Chlorine Binding Sites List in 7fvt
Chlorine binding site 1 out of 4 in the Crystal Structure of S. Aureus Gyrase in Complex with 6-[5-[2-[(4- Chloro-2,3-Dihydro-1H-Inden-2-Yl)Methylamino]Ethyl]-2-Oxo-1,3- Oxazolidin-3-Yl]-4H-Pyrido[3,2-B][1,4]Oxazin-3-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 6-[5-[2-[(4- Chloro-2,3-Dihydro-1H-Inden-2-Yl)Methylamino]Ethyl]-2-Oxo-1,3- Oxazolidin-3-Yl]-4H-Pyrido[3,2-B][1,4]Oxazin-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1502

b:60.8
occ:1.00
 O B:HOH1826 2.8 55.7 1.0
NE A:ARG1429 3.7 46.1 1.0
O A:HOH1671 3.8 47.8 1.0
NH2 A:ARG1429 3.9 52.8 1.0
NH2 B:ARG1429 3.9 61.4 1.0
NH1 B:ARG1429 4.1 51.5 1.0
CZ A:ARG1429 4.2 50.8 1.0
CZ B:ARG1429 4.5 58.2 1.0
O A:HOH1801 4.6 44.6 1.0
CD A:ARG1429 4.6 37.7 1.0
CG A:ARG1429 4.7 38.2 1.0

Chlorine binding site 2 out of 4 in 7fvt

Go back to Chlorine Binding Sites List in 7fvt
Chlorine binding site 2 out of 4 in the Crystal Structure of S. Aureus Gyrase in Complex with 6-[5-[2-[(4- Chloro-2,3-Dihydro-1H-Inden-2-Yl)Methylamino]Ethyl]-2-Oxo-1,3- Oxazolidin-3-Yl]-4H-Pyrido[3,2-B][1,4]Oxazin-3-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 6-[5-[2-[(4- Chloro-2,3-Dihydro-1H-Inden-2-Yl)Methylamino]Ethyl]-2-Oxo-1,3- Oxazolidin-3-Yl]-4H-Pyrido[3,2-B][1,4]Oxazin-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1503

b:58.4
occ:1.00
 CA B:ASP1138 3.4 42.4 1.0
N B:ASN1140 3.5 29.8 1.0
N B:ASP1138 3.6 39.9 1.0
C B:ASP1138 3.6 42.9 1.0
CB B:ASN1140 3.7 41.5 1.0
N B:ILE1139 3.7 41.5 1.0
CE B:LYS1141 3.8 58.2 1.0
ND2 B:ASN1140 4.0 52.9 1.0
NZ B:LYS1141 4.0 56.6 1.0
CA B:ASN1140 4.0 42.2 1.0
CG B:LYS1141 4.1 50.0 1.0
CG B:ASN1140 4.2 50.1 1.0
O B:ASP1138 4.4 35.8 1.0
CD B:LYS1141 4.4 57.5 1.0
C B:ASN1140 4.4 47.5 1.0
N B:LYS1141 4.5 43.9 1.0
C B:ILE1139 4.5 32.2 1.0
CA B:ILE1139 4.7 35.3 1.0
C B:ARG1137 4.8 41.1 1.0
CG2 B:ILE1139 4.8 30.4 1.0
CB B:ASP1138 4.8 42.6 1.0
OD1 B:ASP1138 4.9 50.6 1.0
O B:LEU1136 5.0 29.4 1.0

Chlorine binding site 3 out of 4 in 7fvt

Go back to Chlorine Binding Sites List in 7fvt
Chlorine binding site 3 out of 4 in the Crystal Structure of S. Aureus Gyrase in Complex with 6-[5-[2-[(4- Chloro-2,3-Dihydro-1H-Inden-2-Yl)Methylamino]Ethyl]-2-Oxo-1,3- Oxazolidin-3-Yl]-4H-Pyrido[3,2-B][1,4]Oxazin-3-One


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of S. Aureus Gyrase in Complex with 6-[5-[2-[(4- Chloro-2,3-Dihydro-1H-Inden-2-Yl)Methylamino]Ethyl]-2-Oxo-1,3- Oxazolidin-3-Yl]-4H-Pyrido[3,2-B][1,4]Oxazin-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1504

b:60.6
occ:1.00
 NH1 B:ARG1272 3.4 57.7 1.0
N B:ASN1269 3.8 36.1 1.0
CD B:ARG1272 4.0 51.4 1.0
CA B:VAL1268 4.1 31.8 1.0
CG1 B:VAL1268 4.4 28.0 1.0
C B:VAL1268 4.5 35.4 1.0
CZ B:ARG1272 4.5 61.7 1.0
O B:GLN1267 4.5 31.1 1.0
CG2 B:VAL1268 4.6 25.7 1.0
CB B:ASN1269 4.6 42.4 1.0
CG B:PRO1326 4.6 33.1 1.0
CB B:VAL1268 4.6 32.3 1.0
NE B:ARG1272 4.7 57.9 1.0
CA B:ASN1269 4.8 37.2 1.0
CB B:PRO1326 4.8 37.1 1.0
NZ B:LYS1276 4.8 65.6 1.0
O B:ASN1269 4.9 34.0 1.0
CG B:ARG1272 5.0 46.1 1.0
C4' C:DC3 5.0 48.6 1.0

Chlorine binding site 4 out of 4 in 7fvt

Go back to Chlorine Binding Sites List in 7fvt
Chlorine binding site 4 out of 4 in the Crystal Structure of S. Aureus Gyrase in Complex with 6-[5-[2-[(4- Chloro-2,3-Dihydro-1H-Inden-2-Yl)Methylamino]Ethyl]-2-Oxo-1,3- Oxazolidin-3-Yl]-4H-Pyrido[3,2-B][1,4]Oxazin-3-One


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of S. Aureus Gyrase in Complex with 6-[5-[2-[(4- Chloro-2,3-Dihydro-1H-Inden-2-Yl)Methylamino]Ethyl]-2-Oxo-1,3- Oxazolidin-3-Yl]-4H-Pyrido[3,2-B][1,4]Oxazin-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl101

b:123.3
occ:1.00
 CL31 D:6I0101 0.0 123.3 1.0
C30 D:6I0101 1.7 95.0 1.0
C29 D:6I0101 2.7 84.2 1.0
C24 D:6I0101 2.7 81.6 1.0
C5 C:DC11 3.2 60.5 1.0
C23 D:6I0101 3.3 77.3 1.0
C4 C:DC11 3.3 57.9 1.0
C6 C:DC11 3.6 63.4 1.0
C2 C:DG10 3.7 45.8 1.0
N3 C:DG10 3.7 44.9 1.0
C4 C:DG10 3.8 50.0 1.0
N4 C:DC11 3.8 57.6 1.0
N3 C:DC11 3.8 60.2 1.0
N1 C:DG10 3.8 45.3 1.0
C5 C:DG10 3.9 51.2 1.0
C28 D:6I0101 4.0 75.0 1.0
C25 D:6I0101 4.0 74.1 1.0
N1 C:DC11 4.0 63.2 1.0
C6 C:DG10 4.0 49.3 1.0
C2 C:DC11 4.1 61.4 1.0
N2 C:DG10 4.2 41.9 1.0
N9 C:DG10 4.4 53.0 1.0
C27 D:6I0101 4.5 73.1 1.0
O4' C:DC11 4.7 66.9 1.0
N3 D:DC11 4.7 45.4 1.0
N7 C:DG10 4.7 52.6 1.0
O6 C:DG10 4.7 54.8 1.0
C1 D:6I0101 4.7 80.0 1.0
C2' C:DG10 4.8 45.1 1.0
C8 C:DG10 4.9 51.3 1.0
N4 D:DC11 5.0 50.4 1.0
C1' C:DC11 5.0 63.4 1.0
O2 C:DC11 5.0 59.6 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 Jul 13 00:48:00 2025

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