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Magnesium in PDB 2y3p: Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8

Enzymatic activity of Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8

All present enzymatic activity of Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8:
5.99.1.3;

Protein crystallography data

The structure of Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8, PDB code: 2y3p was solved by M.J.Edwards, R.H.Flatman, L.A.Mitchenall, C.E.M.Stevenson, T.B.K.Le, T.A.Clarke, A.R.Mckay, H.-P.Fiedler, M.J.Buttner, D.M.Lawson, A.Maxwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.47 / 2.62
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 143.910, 153.090, 177.700, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 24.1

Other elements in 2y3p:

The structure of Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8 (pdb code 2y3p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8, PDB code: 2y3p:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2y3p

Go back to Magnesium Binding Sites List in 2y3p
Magnesium binding site 1 out of 4 in the Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg951

b:58.4
occ:1.00
 O1B B:SM8901 2.3 52.3 1.0
O1A B:SM8901 2.7 51.1 1.0
C1D B:SM8901 3.3 50.6 1.0
O4E B:SM8901 3.7 60.3 1.0
C1B B:SM8901 3.8 50.7 1.0
C1C B:SM8901 4.1 49.7 1.0
C1E B:SM8901 4.5 54.2 1.0
C1F B:SM8901 4.7 53.9 1.0
C1A B:SM8901 5.0 49.9 1.0

Magnesium binding site 2 out of 4 in 2y3p

Go back to Magnesium Binding Sites List in 2y3p
Magnesium binding site 2 out of 4 in the Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg952

b:37.0
occ:1.00
 O1F B:SM8901 2.3 50.5 1.0
O1D B:SM8901 2.5 52.2 1.0
C1H B:SM8901 3.3 54.4 1.0
C1N B:SM8901 3.3 53.5 1.0
C1G B:SM8901 3.4 55.1 1.0
C1O B:SM8901 4.1 54.5 1.0
O1G B:SM8901 4.4 51.1 1.0
C1P B:SM8901 4.5 51.6 1.0
C1M B:SM8901 4.5 54.7 1.0
C1F B:SM8901 4.7 53.9 1.0
C1J B:SM8901 4.7 55.6 1.0
C1E B:SM8901 4.7 54.2 1.0

Magnesium binding site 3 out of 4 in 2y3p

Go back to Magnesium Binding Sites List in 2y3p
Magnesium binding site 3 out of 4 in the Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg951

b:61.0
occ:1.00
 O1B A:SM8901 2.4 53.1 1.0
O1A A:SM8901 2.5 55.6 1.0
C1D A:SM8901 3.7 52.6 1.0
C1B A:SM8901 3.8 55.9 1.0
C1C A:SM8901 4.3 55.2 1.0
C1E A:SM8901 4.9 53.0 1.0
C1A A:SM8901 4.9 56.6 1.0

Magnesium binding site 4 out of 4 in 2y3p

Go back to Magnesium Binding Sites List in 2y3p
Magnesium binding site 4 out of 4 in the Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg952

b:31.1
occ:1.00
 O1F A:SM8901 2.4 45.8 1.0
O1D A:SM8901 2.5 49.1 1.0
C1H A:SM8901 3.5 51.2 1.0
C1N A:SM8901 3.6 51.9 1.0
C1J A:SM8901 4.0 53.3 1.0
C1O A:SM8901 4.4 53.7 1.0
O1G A:SM8901 4.5 55.4 1.0
O4E A:SM8901 4.6 50.8 1.0
C1P A:SM8901 4.7 55.4 1.0
C1M A:SM8901 4.7 53.0 1.0
C1G A:SM8901 4.8 50.5 1.0

Reference:

M.J.Edwards, R.H.Flatman, L.A.Mitchenall, C.E.M.Stevenson, T.B.K.Le, T.A.Clarke, A.R.Mckay, H.-P.Fiedler, M.J.Buttner, D.M.Lawson, A.Maxwell. A Crystal Structure of the Bifunctional Antibiotic Simocyclinone D8, Bound to Dna Gyrase. Science V. 326 1415 2009.
ISSN: ISSN 0036-8075
PubMed: 19965760
DOI: 10.1126/SCIENCE.1179123
Page generated: Mon Dec 14 07:48:00 2020

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