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Chlorine 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:

Magnesium (Mg) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine where determined in the S. Aureus Gyrb Atpase Domain in Complex with A Small Molecule Inhibitor, PDB code: 3u2k:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3u2k

Go back to Chlorine Binding Sites List in 3u2k
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl1

b:30.5
occ:1.00
 CL1 A:0871 0.0 30.5 1.0
C21 A:0871 1.7 22.9 1.0
N22 A:0871 2.6 21.0 1.0
C20 A:0871 2.7 22.9 1.0
O A:HOH342 3.1 27.9 1.0
O A:HOH395 3.7 19.0 1.0
C17 A:0871 3.8 17.8 1.0
C19 A:0871 4.0 23.1 1.0
CG A:PRO87 4.1 13.7 1.0
C18 A:0871 4.4 19.1 1.0
N14 A:0871 4.9 14.8 1.0

Chlorine binding site 2 out of 6 in 3u2k

Go back to Chlorine Binding Sites List in 3u2k
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl1

b:24.0
occ:1.00
 CL2 A:0871 0.0 24.0 1.0
C4 A:0871 1.7 12.3 1.0
O A:HOH339 2.4 18.8 1.0
C3 A:0871 2.7 10.4 1.0
C5 A:0871 2.8 10.2 1.0
N10 A:0871 3.2 9.8 1.0
CL3 A:0871 3.3 4.9 1.0
C8 A:0871 3.5 10.2 1.0
O A:HOH306 3.6 18.7 1.0
CD1 A:ILE86 3.6 11.5 1.0
CG1 A:ILE86 3.7 11.6 1.0
OD1 A:ASN54 3.7 16.7 1.0
CG A:ASN54 3.8 13.2 1.0
CB A:ASN54 3.9 10.6 1.0
C2 A:0871 3.9 9.6 1.0
N6 A:0871 3.9 9.7 1.0
ND2 A:ASN54 4.4 13.9 1.0
CG2 A:ILE102 4.4 14.4 1.0
C11 A:0871 4.6 10.2 1.0
O9 A:0871 4.7 10.3 1.0
C12 A:0871 4.8 12.1 1.0
CG2 A:ILE86 4.8 10.5 1.0
CB A:ILE86 4.9 10.7 1.0
O A:HOH390 4.9 31.7 1.0

Chlorine binding site 3 out of 6 in 3u2k

Go back to Chlorine Binding Sites List in 3u2k
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl1

b:4.9
occ:1.00
 CL3 A:0871 0.0 4.9 1.0
C3 A:0871 1.8 10.4 1.0
C4 A:0871 2.8 12.3 1.0
C2 A:0871 2.8 9.6 1.0
CL2 A:0871 3.3 24.0 1.0
C1 A:0871 3.4 8.5 1.0
ND2 A:ASN54 3.7 13.9 1.0
CG1 A:ILE175 3.8 11.2 1.0
N6 A:0871 3.9 9.7 1.0
C5 A:0871 4.0 10.2 1.0
CG A:ASN54 4.1 13.2 1.0
CB A:ASN54 4.1 10.6 1.0
CD1 A:ILE175 4.2 11.4 1.0
CD1 A:ILE86 4.2 11.5 1.0
CG2 A:ILE51 4.3 10.4 1.0
CD1 A:ILE51 4.3 8.6 1.0
CD2 A:LEU103 4.5 12.5 1.0
O A:ILE51 4.6 10.0 1.0
OD1 A:ASN54 4.8 16.7 1.0
CG2 A:THR173 4.9 9.4 1.0
CA A:ILE51 4.9 9.9 1.0

Chlorine binding site 4 out of 6 in 3u2k

Go back to Chlorine Binding Sites List in 3u2k
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl2

b:31.5
occ:1.00
 CL1 B:0872 0.0 31.5 1.0
C21 B:0872 1.7 21.4 1.0
N22 B:0872 2.6 17.3 1.0
C20 B:0872 2.7 20.3 1.0
O B:HOH358 3.5 23.6 1.0
C17 B:0872 3.9 15.4 1.0
C19 B:0872 4.0 19.6 1.0
C18 B:0872 4.5 15.4 1.0
O B:HOH105 4.8 20.3 1.0
CG B:PRO87 4.8 11.1 1.0
O B:HOH271 4.9 36.2 1.0
N14 B:0872 5.0 11.3 1.0

Chlorine binding site 5 out of 6 in 3u2k

Go back to Chlorine Binding Sites List in 3u2k
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl2

b:23.9
occ:1.00
 CL2 B:0872 0.0 23.9 1.0
C4 B:0872 1.7 13.4 1.0
O B:HOH360 2.6 38.9 1.0
C3 B:0872 2.7 13.2 1.0
C5 B:0872 2.8 12.3 1.0
O B:HOH341 3.2 28.0 1.0
CL3 B:0872 3.2 8.3 1.0
N10 B:0872 3.2 10.6 1.0
C8 B:0872 3.5 11.4 1.0
CD1 B:ILE86 3.5 9.7 1.0
CG1 B:ILE86 3.7 10.3 1.0
C2 B:0872 3.9 11.4 1.0
CB B:ASN54 3.9 11.8 1.0
N6 B:0872 3.9 10.9 1.0
CG B:ASN54 4.0 15.7 1.0
ND2 B:ASN54 4.2 18.8 1.0
OD1 B:ASN54 4.4 22.1 1.0
C11 B:0872 4.6 10.6 1.0
CG2 B:ILE102 4.7 12.8 1.0
O9 B:0872 4.7 11.4 1.0
C12 B:0872 4.8 12.6 1.0
O B:HOH243 4.9 9.6 1.0
CB B:ILE86 4.9 9.6 1.0
CG2 B:ILE86 5.0 10.6 1.0

Chlorine binding site 6 out of 6 in 3u2k

Go back to Chlorine Binding Sites List in 3u2k
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl2

b:8.3
occ:1.00
 CL3 B:0872 0.0 8.3 1.0
C3 B:0872 1.7 13.2 1.0
C4 B:0872 2.8 13.4 1.0
C2 B:0872 2.8 11.4 1.0
CL2 B:0872 3.2 23.9 1.0
C1 B:0872 3.4 11.8 1.0
ND2 B:ASN54 3.5 18.8 1.0
CG1 B:ILE175 3.6 12.7 1.0
N6 B:0872 3.9 10.9 1.0
C5 B:0872 3.9 12.3 1.0
CD1 B:ILE175 4.0 14.2 1.0
CB B:ASN54 4.1 11.8 1.0
CG B:ASN54 4.1 15.7 1.0
CD1 B:ILE51 4.2 11.4 1.0
CG2 B:ILE51 4.2 10.3 1.0
CD1 B:ILE86 4.4 9.7 1.0
O B:ILE51 4.6 11.1 1.0
CD2 B:LEU103 4.7 12.2 1.0
CB B:ILE175 4.8 11.0 1.0
CG2 B:THR173 4.8 9.7 1.0
CA B:ILE51 4.9 10.7 1.0
CB B:ILE51 5.0 10.9 1.0

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: Sun Jul 21 05:48:10 2024

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