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Magnesium in PDB 3u2k: S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor

Enzymatic activity of S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor

All present enzymatic activity of S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor:
5.99.1.3;

Protein crystallography data

The structure of S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor, PDB code: 3u2k was solved by P.A.Boriack-Sjodin, D.B.Prince, A.E.Eakin, B.A.Sherer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.17 / 1.64
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 143.175, 55.497, 51.349, 90.00, 100.67, 90.00
R / Rfree (%) 15.6 / 18.2

Other elements in 3u2k:

The structure of S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor (pdb code 3u2k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor, PDB code: 3u2k:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3u2k

Go back to Magnesium Binding Sites List in 3u2k
Magnesium binding site 1 out of 6 in the S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg234

b:30.1
occ:1.00
 O A:HOH326 2.0 20.2 1.0
O A:HOH320 2.1 26.9 1.0
O A:HOH341 2.2 12.2 0.5
O A:HOH9 2.2 10.8 1.0
O A:HOH306 2.4 18.7 1.0
OD2 A:ASP57 3.9 18.1 1.0
O A:HOH11 4.0 10.9 1.0
CB A:ASP57 4.1 11.5 1.0
OD1 A:ASN54 4.2 16.7 1.0
O A:HOH340 4.3 26.0 1.0
CG A:ASP57 4.5 14.4 1.0
C12 A:0871 4.6 12.1 1.0
O A:ASN54 4.8 9.7 1.0
O A:HOH413 4.8 37.9 1.0
CA A:ASN54 4.9 10.6 1.0

Magnesium binding site 2 out of 6 in 3u2k

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Magnesium binding site 2 out of 6 in the S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2

b:27.4
occ:1.00
 O A:HOH345 1.9 30.9 1.0
O A:HOH346 2.0 20.9 1.0
O A:HOH344 2.0 29.8 1.0
O A:GLY208 2.1 16.1 1.0
O A:HOH264 2.2 24.4 1.0
NE2 A:HIS228 2.5 23.1 1.0
C A:GLY208 3.2 15.1 1.0
CE1 A:HIS228 3.2 23.3 1.0
CD2 A:HIS228 3.5 21.1 1.0
CA A:GLY208 3.7 16.0 1.0
O A:HOH270 4.1 24.3 1.0
ND2 A:ASN65 4.1 19.8 1.0
O A:HOH281 4.1 25.6 1.0
N A:ILE209 4.3 13.3 1.0
ND1 A:HIS228 4.3 22.1 1.0
CB A:ASN65 4.4 12.0 1.0
O A:ASN65 4.4 11.1 1.0
CG A:HIS228 4.5 19.2 1.0
N A:GLN210 4.6 11.6 1.0
CG A:ASN65 4.6 14.3 1.0
CA A:ILE209 4.6 12.4 1.0
C A:ILE209 4.8 12.1 1.0

Magnesium binding site 3 out of 6 in 3u2k

Go back to Magnesium Binding Sites List in 3u2k
Magnesium binding site 3 out of 6 in the S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3

b:47.1
occ:1.00
 O A:HOH381 1.9 32.0 1.0
O A:HOH355 2.0 23.5 1.0
O A:HOH244 2.2 31.1 1.0
O A:HOH350 2.4 38.1 1.0
OE1 A:GLU50 2.8 24.1 1.0
CD A:GLU50 3.8 20.5 1.0
OD2 A:ASP53 4.1 16.7 0.5
OE2 A:GLU50 4.2 25.9 1.0
O A:GLU50 4.4 12.2 1.0
CG A:ASP53 4.9 13.5 0.5
CB A:ASP53 4.9 11.8 0.5
CA A:GLU50 4.9 11.9 1.0

Magnesium binding site 4 out of 6 in 3u2k

Go back to Magnesium Binding Sites List in 3u2k
Magnesium binding site 4 out of 6 in the S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4

b:30.2
occ:1.00
 O B:HOH374 2.0 28.2 1.0
O B:HOH318 2.0 29.1 1.0
O B:HOH336 2.0 20.0 1.0
O A:HOH373 2.1 30.3 1.0
O A:HOH315 2.2 27.5 1.0
O B:LEU60 4.1 14.1 1.0
OE1 A:GLU164 4.1 19.9 1.0
OE2 A:GLU164 4.2 20.4 1.0
O B:HOH293 4.4 11.2 1.0
O A:HOH316 4.4 22.8 1.0
CA B:ALA61 4.5 13.3 1.0
O B:HOH261 4.5 10.3 1.0
CD A:GLU164 4.6 17.8 1.0
C B:LEU60 4.7 12.7 1.0
N B:ALA61 4.9 12.6 1.0
O A:HOH275 4.9 24.9 1.0

Magnesium binding site 5 out of 6 in 3u2k

Go back to Magnesium Binding Sites List in 3u2k
Magnesium binding site 5 out of 6 in the S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg5

b:26.0
occ:1.00
 O B:GLY208 2.0 13.9 1.0
O B:HOH321 2.0 20.7 1.0
O B:HOH255 2.1 19.6 1.0
O B:HOH269 2.1 13.1 1.0
O B:HOH343 2.2 17.4 1.0
NE2 B:HIS228 2.3 18.1 1.0
CE1 B:HIS228 3.0 18.7 1.0
C B:GLY208 3.1 13.1 1.0
CD2 B:HIS228 3.4 17.5 1.0
CA B:GLY208 3.8 14.1 1.0
ND1 B:HIS228 4.2 16.7 1.0
O B:HOH284 4.2 26.4 1.0
N B:ILE209 4.2 12.2 1.0
O B:HOH263 4.2 20.0 1.0
O B:ASN65 4.4 10.4 1.0
CG B:HIS228 4.4 15.4 1.0
CA B:ILE209 4.5 11.2 1.0
N B:GLN210 4.5 10.7 1.0
CB B:ASN65 4.7 11.8 1.0
C B:ILE209 4.8 11.0 1.0

Magnesium binding site 6 out of 6 in 3u2k

Go back to Magnesium Binding Sites List in 3u2k
Magnesium binding site 6 out of 6 in the S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg6

b:42.7
occ:1.00
 O B:HOH371 2.0 37.8 1.0
O B:HOH397 2.0 30.7 1.0
O B:HOH252 2.1 21.4 1.0
O B:HOH292 2.1 26.2 1.0
O B:HOH268 2.2 37.9 1.0
OD1 B:ASN54 2.5 22.1 1.0
CG B:ASN54 3.5 15.7 1.0
OD2 B:ASP53 3.7 17.1 0.5
O B:HOH289 4.0 29.4 1.0
ND2 B:ASN54 4.1 18.8 1.0
O B:HOH356 4.1 24.6 1.0
O B:GLU50 4.3 12.3 1.0
OD2 B:ASP57 4.4 17.4 1.0
N B:ASN54 4.4 11.3 1.0
CB B:ASP53 4.5 13.0 0.5
CG B:ASP53 4.5 14.7 0.5
CB B:ASP53 4.6 13.0 0.5
CA B:ASN54 4.6 11.5 1.0
CB B:ASN54 4.6 11.8 1.0
OE1 B:GLU50 4.6 24.2 1.0
C B:ASP53 4.8 11.9 0.5
C B:ASP53 4.8 11.9 0.5

Reference:

A.E.Eakin, O.Green, N.Hales, G.K.Walkup, S.Bist, A.Singh, G.Mullen, J.Bryant, K.Embrey, N.Gao, A.Breeze, D.Timms, B.Andrews, M.Uria-Nickelsen, J.Demeritt, J.T.Loch, K.Hull, A.Blodgett, R.N.Illingworth, B.Prince, P.A.Boriack-Sjodin, S.Hauck, L.J.Macpherson, H.Ni, B.Sherer. Pyrrolamide Dna Gyrase Inhibitors: Fragment-Based Nuclear Magnetic Resonance Screening to Identify Antibacterial Agents. Antimicrob.Agents Chemother. V. 56 1240 2012.
ISSN: ISSN 0066-4804
PubMed: 22183167
DOI: 10.1128/AAC.05485-11
Page generated: Thu Aug 15 12:19:09 2024

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