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Manganese in PDB 2xct: The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna

Enzymatic activity of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna

All present enzymatic activity of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna:
5.99.1.3;

Protein crystallography data

The structure of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna, PDB code: 2xct was solved by B.D.Bax, P.Chan, D.S.Eggleston, A.Fosberry, D.R.Gentry, F.Gorrec, I.Giordano, M.M.Hann, A.Hennessy, M.Hibbs, J.Huang, E.Jones, J.Jones, K.K.Brown, C.J.Lewis, E.May, O.Singh, C.Spitzfaden, C.Shen, A.Shillings, A.Theobald, A.Wohlkonig, N.D.Pearson, M.N.Gwynn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.956 / 3.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 88.984, 123.166, 170.418, 90.00, 90.25, 90.00
R / Rfree (%) 16.64 / 23.63

Other elements in 2xct:

The structure of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna (pdb code 2xct). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna, PDB code: 2xct:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 2xct

Go back to Manganese Binding Sites List in 2xct
Manganese binding site 1 out of 8 in the The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2492

b:76.5
occ:1.00
 OD2 B:ASP510 1.7 64.2 1.0
CG B:ASP510 2.9 60.6 1.0
OD2 B:ASP508 3.0 43.6 1.0
OD1 B:ASP510 3.7 59.8 1.0
CG B:ASP508 3.7 44.1 1.0
CB B:ASP510 3.9 59.1 1.0
OE1 B:GLU435 4.0 61.8 1.0
OD1 B:ASP508 4.1 43.9 1.0
OP1 E:DT8 4.7 47.2 1.0
CB B:ASP508 4.8 44.3 1.0
CD B:GLU435 4.8 63.2 1.0
O3' E:DT8 5.0 52.0 1.0

Manganese binding site 2 out of 8 in 2xct

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Manganese binding site 2 out of 8 in the The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2492

b:85.5
occ:1.00
 OD2 D:ASP510 2.0 79.0 1.0
OD2 D:ASP508 2.6 72.5 1.0
CG D:ASP510 3.2 75.6 1.0
CG D:ASP508 3.6 73.5 1.0
CB D:ASP510 4.0 73.0 1.0
CB D:ASP508 4.1 73.9 1.0
OD1 D:ASP510 4.1 76.0 1.0
OP1 F:DG8 4.6 48.8 1.0
OD1 D:ASP508 4.6 73.7 1.0
OE1 D:GLU435 4.7 57.9 1.0
CA D:GLY582 4.8 49.6 1.0

Manganese binding site 3 out of 8 in 2xct

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Manganese binding site 3 out of 8 in the The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn2000

b:86.0
occ:1.00
 O3 H:CPF1020 2.1 86.0 1.0
O2 H:CPF1020 2.1 86.0 1.0
C4 H:CPF1020 3.3 86.0 1.0
C3 H:CPF1020 3.4 86.0 1.0
C2 H:CPF1020 3.8 86.0 1.0
O6 H:DG9 3.9 89.0 1.0
O6 F:DG8 4.1 51.5 1.0
OG D:SER1084 4.2 49.1 1.0
CB D:SER1084 4.3 47.2 1.0
C5 H:CPF1020 4.4 86.0 1.0
O1 H:CPF1020 4.4 86.0 1.0
C6 H:CPF1020 4.5 86.0 1.0
C6 H:DG9 4.8 90.1 1.0
N1 H:DG9 4.9 90.8 1.0

Manganese binding site 4 out of 8 in 2xct

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Manganese binding site 4 out of 8 in the The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn2000

b:70.5
occ:1.00
 O2 G:CPF1020 2.1 70.5 1.0
O3 G:CPF1020 2.1 70.5 1.0
C4 G:CPF1020 3.4 70.5 1.0
C3 G:CPF1020 3.4 70.5 1.0
C2 G:CPF1020 3.9 70.5 1.0
O6 G:DG9 4.0 91.5 1.0
CB B:SER1084 4.1 73.2 1.0
OG B:SER1084 4.2 73.6 1.0
O1 G:CPF1020 4.4 70.5 1.0
C5 G:CPF1020 4.5 70.5 1.0
N7 G:DG9 4.6 89.5 1.0
OE2 B:GLU1088 4.6 81.1 1.0
O4 E:DT8 4.6 45.8 1.0
C6 G:DG9 4.8 91.6 1.0
C6 G:CPF1020 4.8 70.5 1.0

Manganese binding site 5 out of 8 in 2xct

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Manganese binding site 5 out of 8 in the The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mn2492

b:70.0
occ:1.00
 OD2 S:ASP508 2.1 76.9 1.0
OD2 S:ASP510 2.3 66.1 1.0
OD1 S:ASP510 2.7 61.7 1.0
CG S:ASP508 2.8 77.2 1.0
CG S:ASP510 2.8 62.4 1.0
OD1 S:ASP508 2.8 76.4 1.0
OE2 S:GLU435 3.8 88.6 1.0
CB S:ASP508 4.3 77.9 1.0
CB S:ASP510 4.3 60.8 1.0
O3' W:DG8 4.4 76.9 1.0
O5' W:DG8 4.4 70.4 1.0
C3' W:DG8 4.6 74.5 1.0
N S:GLY513 4.7 86.9 1.0
CB S:ASP512 4.8 55.3 1.0
CD S:GLU435 4.9 89.9 1.0

Manganese binding site 6 out of 8 in 2xct

Go back to Manganese Binding Sites List in 2xct
Manganese binding site 6 out of 8 in the The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mn2492

b:64.0
occ:1.00
 OD2 U:ASP510 2.6 65.9 1.0
CG U:ASP510 3.3 67.6 1.0
OD1 U:ASP510 3.5 69.7 1.0
OD1 U:ASP508 3.5 48.1 1.0
OD2 U:ASP508 3.5 52.5 1.0
CG U:ASP508 3.6 50.4 1.0
OP1 V:DT8 4.4 63.0 1.0
CB U:ASP510 4.6 66.5 1.0
CB U:ASP508 4.6 50.9 1.0
CB U:ASP512 4.8 66.9 1.0
OE1 U:GLU435 4.8 59.3 1.0
O3' V:DT8 4.9 66.2 1.0

Manganese binding site 7 out of 8 in 2xct

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Manganese binding site 7 out of 8 in the The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mn2000

b:86.1
occ:1.00
 O3 X:CPF1020 2.1 86.1 1.0
O2 X:CPF1020 2.1 86.1 1.0
C4 X:CPF1020 3.3 86.1 1.0
C3 X:CPF1020 3.4 86.1 1.0
O6 Y:DG9 3.7 91.8 1.0
C2 X:CPF1020 3.9 86.1 1.0
OG U:SER1084 3.9 59.0 1.0
CB U:SER1084 4.1 57.8 1.0
C6 Y:DG9 4.2 93.0 1.0
O1 X:CPF1020 4.4 86.1 1.0
C5 X:CPF1020 4.5 86.1 1.0
C6 X:CPF1020 4.6 86.1 1.0
O6 W:DG8 4.8 74.2 1.0
C5 Y:DG9 4.8 93.9 1.0
N1 Y:DG9 4.8 93.8 1.0
N4 X:DC12 4.8 0.7 1.0

Manganese binding site 8 out of 8 in 2xct

Go back to Manganese Binding Sites List in 2xct
Manganese binding site 8 out of 8 in the The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mn2001

b:76.7
occ:1.00
 O3 Y:CPF1020 2.1 76.7 1.0
O2 Y:CPF1020 2.1 76.7 1.0
C4 Y:CPF1020 3.3 76.7 1.0
C3 Y:CPF1020 3.4 76.7 1.0
OG S:SER1084 3.8 77.9 1.0
C2 Y:CPF1020 3.8 76.7 1.0
CB S:SER1084 4.1 78.0 1.0
O6 X:DG9 4.2 94.1 1.0
N4 Y:DC12 4.3 96.3 1.0
C5 Y:CPF1020 4.4 76.7 1.0
OE1 S:GLU1088 4.4 72.6 1.0
O1 Y:CPF1020 4.4 76.7 1.0
C6 Y:CPF1020 4.6 76.7 1.0
C6 X:DG9 4.8 93.3 1.0
N7 X:DG9 4.8 91.9 1.0
O4 V:DT8 4.9 59.8 1.0
OE2 S:GLU1088 5.0 72.7 1.0

Reference:

B.D.Bax, P.F.Chan, D.S.Eggleston, A.Fosberry, D.R.Gentry, F.Gorrec, I.Giordano, M.M.Hann, A.Hennessy, M.Hibbs, J.Huang, E.Jones, J.Jones, K.K.Brown, C.J.Lewis, E.W.May, M.R.Saunders, O.Singh, C.Spitzfaden, C.Shen, A.Shillings, A.F.Theobald, A.Wohlkonig, N.D.Pearson, M.N.Gwynn. Type Iia Topoisomerase Inhibition By A New Class of Antibacterial Agents. Nature V. 466 935 2010.
ISSN: ISSN 0028-0836
PubMed: 20686482
DOI: 10.1038/NATURE09197
Page generated: Tue Dec 15 04:06:31 2020

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