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Manganese in PDB 5iwi: 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna

Enzymatic activity of 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna

All present enzymatic activity of 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna:
5.99.1.3;

Protein crystallography data

The structure of 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna, PDB code: 5iwi was solved by B.D.Bax, T.J.Miles, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.00 / 1.98
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 92.897, 92.897, 410.784, 90.00, 90.00, 120.00
R / Rfree (%) 16.6 / 20.2

Other elements in 5iwi:

The structure of 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna also contains other interesting chemical elements:

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

Manganese Binding Sites:

The binding sites of Manganese atom in the 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna (pdb code 5iwi). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna, PDB code: 5iwi:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 5iwi

Go back to Manganese Binding Sites List in 5iwi
Manganese binding site 1 out of 5 in the 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:24.3
occ:0.55
 MN B:MN701 0.0 24.3 0.6
OP1 E:DG9 1.9 22.5 0.6
O B:HOH821 2.0 44.1 0.6
O B:HOH809 2.1 24.0 0.6
OE2 B:GLU435 2.1 29.2 0.6
OD2 B:ASP508 2.2 22.9 0.6
OE2 B:GLU435 2.3 40.1 0.5
O B:HOH821 2.5 20.4 0.5
O3' E:DG8 2.5 24.9 0.6
P E:DG9 2.7 26.2 0.6
CD B:GLU435 2.9 28.2 0.6
OD2 B:ASP508 3.0 31.9 0.5
O B:HOH809 3.1 21.7 0.5
O3' F:DT1008 3.1 28.4 0.5
CG B:ASP508 3.2 25.0 0.6
CD B:GLU435 3.2 38.0 0.5
OE1 B:GLU435 3.2 26.3 0.6
C3' F:DT1008 3.3 30.3 0.5
O B:HOH806 3.5 34.7 1.0
MN B:MN701 3.5 33.8 0.5
CB B:ASP508 3.6 26.1 0.6
CG B:ASP508 3.6 29.9 0.5
O5' E:DG9 3.6 24.9 0.6
OE1 B:GLU435 3.8 33.5 0.5
C3' E:DG8 3.9 22.6 0.6
CB B:GLU435 3.9 43.5 0.5
OP2 E:DG9 4.0 23.6 0.6
OD1 B:ASP508 4.0 31.1 0.5
O E:HOH201 4.0 28.9 0.5
OD2 B:ASP510 4.1 29.3 0.6
CG B:GLU435 4.2 37.8 0.5
CG B:GLU435 4.2 28.7 0.6
OD1 B:ASP508 4.3 28.5 0.6
C4' E:DG8 4.3 21.7 0.6
C2' F:DT1008 4.4 30.6 0.5
C4' F:DT1008 4.4 27.9 0.5
CB B:GLU435 4.4 32.0 0.6
CA B:GLY582 4.4 47.9 0.5
CB B:ASP508 4.4 28.0 0.5
OD1 B:ASP510 4.6 25.6 0.6
O B:LYS581 4.6 53.2 0.6
C2' E:DG8 4.6 23.4 0.6
C5' F:DT1008 4.7 28.8 0.5
O B:GLU435 4.7 48.5 0.5
CG B:ASP510 4.8 27.6 0.6
CE1 C:PHE123 4.8 43.8 1.0
CZ C:PHE123 4.8 44.3 1.0
C5' E:DG8 4.9 22.4 0.6
CA B:ASP508 4.9 25.5 0.6
C5' E:DG9 5.0 28.1 0.6

Manganese binding site 2 out of 5 in 5iwi

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Manganese binding site 2 out of 5 in the 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:33.8
occ:0.45
 MN B:MN701 0.0 33.8 0.5
OD2 B:ASP510 0.8 29.3 0.6
O B:HOH821 1.8 20.4 0.5
O B:HOH821 2.0 44.1 0.6
CG B:ASP510 2.0 27.6 0.6
OD2 B:ASP510 2.2 25.6 0.5
O B:HOH802 2.2 22.8 0.5
OD2 B:ASP508 2.4 31.9 0.5
O B:HOH809 2.4 21.7 0.5
O B:LYS581 2.7 53.2 0.6
OD1 B:ASP510 2.8 25.6 0.6
CB B:ASP510 3.1 28.0 0.6
CG B:ASP510 3.1 25.8 0.5
O B:HOH809 3.2 24.0 0.6
OD1 B:ASP510 3.3 27.9 0.5
CG B:ASP508 3.4 29.9 0.5
MN B:MN701 3.5 24.3 0.6
CB B:ASP508 3.6 28.0 0.5
N B:GLY582 3.8 55.3 0.5
C B:LYS581 3.9 52.3 0.6
O A:HOH809 4.0 43.3 1.0
CB B:ASP508 4.0 26.1 0.6
O B:HOH807 4.1 39.5 1.0
CA B:GLY582 4.3 47.9 0.5
OP1 F:DT1008 4.3 29.5 0.5
CA B:ASP510 4.4 30.2 0.6
OD2 B:ASP508 4.5 22.9 0.6
CB B:ASP510 4.5 25.4 0.5
N B:ASP510 4.5 30.9 0.6
OD1 B:ASP508 4.5 31.1 0.5
OP1 E:DG9 4.6 22.5 0.6
C5' F:DT1008 4.7 28.8 0.5
CA B:LYS581 4.7 54.9 0.6
C B:LYS581 4.7 60.9 0.5
OE2 B:GLU435 4.7 40.1 0.5
CG B:ASP508 4.8 25.0 0.6
O3' E:DG8 4.8 24.9 0.6
NH1 C:ARG122 4.8 21.6 0.5
CA B:LYS581 4.8 60.6 0.5
OP1 E:DG8 4.9 21.8 0.6
C5' E:DG8 4.9 22.4 0.6
N B:GLY582 4.9 42.3 0.6

Manganese binding site 3 out of 5 in 5iwi

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Manganese binding site 3 out of 5 in the 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1001

b:32.1
occ:0.55
 MN D:MN1001 0.0 32.1 0.6
OD2 D:ASP510 0.9 28.1 0.5
O D:HOH1148 1.6 25.7 0.6
CG D:ASP510 1.9 26.9 0.5
OD2 D:ASP510 2.1 27.0 0.6
O D:HOH1148 2.2 23.4 0.5
O D:HOH1101 2.2 26.2 0.6
OD2 D:ASP508 2.3 41.2 0.5
O D:HOH1126 2.4 23.1 0.6
OD1 D:ASP510 2.6 24.5 0.5
O D:LYS581 2.7 61.8 0.5
CG D:ASP508 2.7 41.5 0.5
CG D:ASP510 3.1 29.4 0.6
OD1 D:ASP508 3.1 48.1 0.5
CB D:ASP510 3.2 28.0 0.5
O D:LYS581 3.2 92.8 0.6
O D:HOH1126 3.3 22.4 0.5
OD1 D:ASP510 3.4 29.7 0.6
MN D:MN1001 3.5 26.1 0.5
CB D:ASP508 3.6 39.5 0.5
C D:LYS581 3.7 86.5 0.6
CB D:ASP508 3.8 34.3 0.6
C D:LYS581 3.9 61.3 0.5
OD2 D:ASP508 4.0 34.0 0.6
O D:HOH1110 4.1 30.9 1.0
O C:HOH865 4.2 45.0 1.0
N D:GLY582 4.2 73.9 0.6
CA D:ASP510 4.3 29.4 0.5
CA D:LYS581 4.3 87.0 0.6
CG D:ASP508 4.4 35.7 0.6
CB D:LYS581 4.4 91.8 0.6
N D:ASP510 4.4 30.8 0.5
OP1 F:DT1008 4.4 28.7 0.6
CA D:GLY582 4.5 58.5 0.6
CB D:ASP510 4.5 30.7 0.6
NH2 A:ARG122 4.5 30.4 0.6
CA D:LYS581 4.8 67.5 0.5
OE2 D:GLU435 4.8 38.2 0.6
O3' E:DG8 4.9 23.7 0.5
N D:GLY582 4.9 46.7 0.5
CA D:ASP508 4.9 37.5 0.5
C5' F:DT1008 4.9 27.4 0.6
OP1 E:DG8 5.0 23.0 0.5
CA D:GLY582 5.0 39.5 0.5
OE1 D:GLU435 5.0 26.7 0.5
C5' E:DG8 5.0 23.0 0.5
OP1 E:DG9 5.0 25.9 0.5

Manganese binding site 4 out of 5 in 5iwi

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Manganese binding site 4 out of 5 in the 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1001

b:26.1
occ:0.45
 MN D:MN1001 0.0 26.1 0.5
OE2 D:GLU435 2.0 30.6 0.5
OD2 D:ASP508 2.1 34.0 0.6
O D:HOH1126 2.1 22.4 0.5
OP1 E:DG9 2.2 25.9 0.5
O D:HOH1148 2.2 25.7 0.6
OE2 D:GLU435 2.2 38.2 0.6
O3' E:DG8 2.5 23.7 0.5
O D:HOH1148 2.7 23.4 0.5
CD D:GLU435 2.8 27.8 0.5
P E:DG9 2.9 26.8 0.5
O D:HOH1126 3.1 23.1 0.6
OD2 D:ASP508 3.1 41.2 0.5
OE1 D:GLU435 3.1 26.7 0.5
O3' F:DT1008 3.2 30.3 0.6
CD D:GLU435 3.2 38.0 0.6
CG D:ASP508 3.2 35.7 0.6
C3' F:DT1008 3.4 29.8 0.6
O D:HOH1105 3.4 49.6 1.0
CB D:ASP508 3.4 39.5 0.5
MN D:MN1001 3.5 32.1 0.6
CG D:ASP508 3.7 41.5 0.5
OE1 D:GLU435 3.8 33.4 0.6
CB D:ASP508 3.9 34.3 0.6
C3' E:DG8 3.9 23.2 0.5
CB D:GLU435 4.0 50.0 0.6
OP2 E:DG9 4.0 23.8 0.5
O5' E:DG9 4.0 25.4 0.5
CG D:GLU435 4.1 30.1 0.5
CG D:GLU435 4.2 42.2 0.6
OD2 D:ASP510 4.2 28.1 0.5
OD1 D:ASP508 4.2 35.9 0.6
C4' E:DG8 4.2 23.9 0.5
C5' E:DG9 4.3 26.8 0.5
CB D:GLU435 4.3 35.1 0.5
C2' F:DT1008 4.4 30.5 0.6
C4' F:DT1008 4.4 29.7 0.6
OD1 D:ASP510 4.5 24.5 0.5
C2' E:DG8 4.6 22.7 0.5
C5' F:DT1008 4.7 27.4 0.6
O D:LYS581 4.7 61.8 0.5
C5' E:DG8 4.8 23.0 0.5
CG D:ASP510 4.8 26.9 0.5
CA D:ASP508 4.8 37.5 0.5
CE1 A:PHE123 4.9 40.0 1.0
OD1 D:ASP508 4.9 48.1 0.5
O D:HOH1101 4.9 26.2 0.6
CZ A:PHE123 4.9 41.3 1.0
NH2 A:ARG122 4.9 30.4 0.6

Manganese binding site 5 out of 5 in 5iwi

Go back to Manganese Binding Sites List in 5iwi
Manganese binding site 5 out of 5 in the 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:75.0
occ:1.00
 NE2 C:HIS390 2.3 38.9 1.0
O C:HOH901 2.5 55.2 1.0
O C:HOH706 2.5 59.2 1.0
CE1 C:HIS390 3.0 39.9 1.0
CD2 C:HIS390 3.4 38.2 1.0
ND1 C:HIS390 4.2 39.1 1.0
CG C:HIS390 4.4 37.7 1.0
CB C:ASP389 4.5 32.0 1.0
OD2 C:ASP389 4.6 36.9 1.0

Reference:

T.J.Miles, A.J.Hennessy, B.Bax, G.Brooks, B.S.Brown, P.Brown, N.Cailleau, D.Chen, S.Dabbs, D.T.Davies, J.M.Esken, I.Giordano, J.L.Hoover, G.E.Jones, S.K.Kusalakumari Sukmar, R.E.Markwell, E.A.Minthorn, S.Rittenhouse, M.N.Gwynn, N.D.Pearson. Novel Tricyclics (E.G., GSK945237) As Potent Inhibitors of Bacterial Type Iia Topoisomerases. Bioorg.Med.Chem.Lett. V. 26 2464 2016.
ISSN: ESSN 1464-3405
PubMed: 27055939
DOI: 10.1016/J.BMCL.2016.03.106
Page generated: Sun Oct 6 01:28:34 2024

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