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Manganese 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:

Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 3 binding sites of Manganese 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 Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 7fvt

Go back to Manganese Binding Sites List in 7fvt
Manganese binding site 1 out of 3 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 Manganese with other atoms in the Mn 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:Mn1501

b:40.5
occ:1.00
 OD2 A:ASP508 2.1 43.1 1.0
OE2 A:GLU435 2.1 36.2 1.0
O A:HOH1620 2.2 35.8 1.0
OP1 D:DG9 2.4 29.8 1.0
O A:HOH1645 2.4 28.6 1.0
O3' D:DG8 2.7 26.4 1.0
CD A:GLU435 2.9 35.5 1.0
CG A:ASP508 3.1 45.8 1.0
OE1 A:GLU435 3.1 37.9 1.0
P D:DG9 3.2 32.8 1.0
CB A:ASP508 3.5 41.9 1.0
O D:HOH209 3.6 32.4 1.0
OD2 A:ASP510 4.0 52.4 1.0
C3' D:DG8 4.0 31.5 1.0
CG A:GLU435 4.2 36.0 1.0
O5' D:DG9 4.3 38.6 1.0
OD1 A:ASP508 4.3 42.9 1.0
OP2 D:DG9 4.3 28.9 1.0
C5' D:DG9 4.3 34.9 1.0
C4' D:DG8 4.3 37.0 1.0
OD1 A:ASP510 4.4 50.3 1.0
CB A:GLU435 4.4 41.7 1.0
O A:LYS581 4.6 59.2 1.0
CG A:ASP510 4.6 47.4 1.0
C2' D:DG8 4.8 30.3 1.0
C5' D:DG8 4.8 28.9 1.0
CA A:ASP508 4.9 42.2 1.0
CZ B:PHE1123 5.0 44.1 1.0
CE1 B:PHE1123 5.0 50.0 1.0

Manganese binding site 2 out of 3 in 7fvt

Go back to Manganese Binding Sites List in 7fvt
Manganese binding site 2 out of 3 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 Manganese with other atoms in the Mn 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:Mn1501

b:40.0
occ:1.00
 OD2 B:ASP508 2.1 37.9 1.0
OE2 B:GLU435 2.1 35.5 1.0
O B:HOH1713 2.3 31.4 1.0
O B:HOH1634 2.3 28.1 1.0
OP1 C:DG9 2.3 25.7 1.0
O3' C:DG8 2.8 30.9 1.0
CD B:GLU435 2.9 34.4 1.0
CG B:ASP508 3.0 27.1 1.0
OE1 B:GLU435 3.2 32.0 1.0
P C:DG9 3.2 30.9 1.0
CB B:ASP508 3.3 30.4 1.0
O B:HOH1611 3.6 30.6 1.0
C3' C:DG8 4.1 26.6 1.0
OD2 B:ASP510 4.1 32.9 1.0
OD1 B:ASP508 4.2 31.4 1.0
CG B:GLU435 4.3 32.4 1.0
O5' C:DG9 4.3 28.7 1.0
OP2 C:DG9 4.3 29.7 1.0
C5' C:DG9 4.3 25.6 1.0
C4' C:DG8 4.4 29.7 1.0
OD1 B:ASP510 4.4 30.8 1.0
O B:LYS581 4.5 60.9 1.0
CB B:GLU435 4.5 31.3 1.0
CG B:ASP510 4.7 35.0 1.0
CA B:ASP508 4.7 34.2 1.0
C2' C:DG8 4.8 34.8 1.0
C5' C:DG8 4.9 25.8 1.0
N B:ASP508 4.9 33.1 1.0
O C:HOH128 4.9 42.9 1.0
CA B:GLY582 5.0 37.1 1.0

Manganese binding site 3 out of 3 in 7fvt

Go back to Manganese Binding Sites List in 7fvt
Manganese binding site 3 out of 3 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 Manganese with other atoms in the Mn 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:Mn1502

b:65.6
occ:1.00
 O B:TYR1322 2.2 31.9 1.0
O B:GLN1328 2.3 36.8 1.0
O B:THR1325 2.3 36.5 1.0
O B:HOH1801 2.4 46.2 1.0
O B:HOH1799 2.6 50.6 1.0
C B:GLN1328 3.3 40.9 1.0
C B:TYR1322 3.4 34.7 1.0
C B:THR1325 3.5 39.1 1.0
O B:LYS1323 3.6 52.3 1.0
CB B:GLN1328 3.7 39.9 1.0
CA B:GLN1328 3.8 41.6 1.0
N B:GLN1328 3.8 33.0 1.0
C B:LYS1323 3.9 44.8 1.0
N B:THR1325 4.0 30.4 1.0
CG B:GLN1328 4.3 41.2 1.0
CA B:LYS1323 4.3 39.6 1.0
N B:LYS1323 4.3 37.5 1.0
CA B:TYR1322 4.4 33.5 1.0
N B:PRO1326 4.4 30.7 1.0
CA B:THR1325 4.4 34.9 1.0
CA B:PRO1326 4.4 36.6 1.0
N B:THR1329 4.4 37.0 1.0
N B:GLN1324 4.5 36.4 1.0
C B:PRO1326 4.7 41.0 1.0
O B:LEU1321 4.7 38.7 1.0
N B:LEU1327 4.8 34.5 1.0
C B:GLN1324 4.8 37.4 1.0
CA B:THR1329 4.9 40.0 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 08:48:29 2024

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