Chlorine in PDB 7ci6: Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor

Enzymatic activity of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor

All present enzymatic activity of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor:
3.5.1.108;

Protein crystallography data

The structure of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor, PDB code: 7ci6 was solved by M.Mima, L.M.Baker, A.Surgenor, A.Robertson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.32 / 2.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.475, 50.772, 76.063, 76.18, 72.38, 61.57
R / Rfree (%) 25.2 / 33.7

Other elements in 7ci6:

The structure of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor (pdb code 7ci6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor, PDB code: 7ci6:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7ci6

Go back to Chlorine Binding Sites List in 7ci6
Chlorine binding site 1 out of 4 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1300

b:92.7
occ:1.00
CL1 A:FY61300 0.0 92.7 1.0
C1 A:FY61300 1.8 77.8 1.0
C2 A:FY61300 2.7 69.5 1.0
C6 A:FY61300 2.7 78.1 1.0
C3 A:FY61300 4.0 68.3 1.0
C5 A:FY61300 4.0 70.3 1.0
CA A:GLY209 4.0 49.7 1.0
C A:GLY209 4.1 48.7 1.0
NH1 A:ARG201 4.3 80.8 1.0
O A:GLY209 4.4 50.3 1.0
CB A:ALA206 4.4 62.3 1.0
N A:SER210 4.5 49.8 1.0
CG2 A:VAL216 4.5 56.2 1.0
C4 A:FY61300 4.5 67.5 1.0
CA A:GLY192 4.8 48.1 1.0

Chlorine binding site 2 out of 4 in 7ci6

Go back to Chlorine Binding Sites List in 7ci6
Chlorine binding site 2 out of 4 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1302

b:57.9
occ:1.00
NH2 A:ARG41 3.9 64.8 1.0
CD A:LYS72 4.1 55.3 1.0
CB A:SER98 4.2 41.9 1.0
N A:LYS72 4.2 51.9 1.0
CG A:LYS72 4.2 50.0 1.0
NH1 A:ARG41 4.4 56.6 1.0
O A:HOH1445 4.5 43.3 1.0
O A:ASP70 4.6 48.7 1.0
CZ A:ARG41 4.6 57.9 1.0
CA A:VAL71 4.7 54.9 1.0
O A:LYS72 4.7 52.3 1.0
CB A:LYS72 4.8 48.0 1.0
C A:VAL71 4.9 54.8 1.0
CA A:LYS72 5.0 49.8 1.0

Chlorine binding site 3 out of 4 in 7ci6

Go back to Chlorine Binding Sites List in 7ci6
Chlorine binding site 3 out of 4 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1300

b:78.0
occ:1.00
CL1 B:FY61300 0.0 78.0 1.0
C1 B:FY61300 1.8 64.0 1.0
C6 B:FY61300 2.7 63.4 1.0
C2 B:FY61300 2.8 62.9 1.0
CB B:ALA206 3.7 64.0 1.0
CD1 B:LEU200 3.9 71.0 1.0
C5 B:FY61300 4.0 62.3 1.0
C3 B:FY61300 4.1 56.9 1.0
CA B:GLY192 4.5 52.1 1.0
C4 B:FY61300 4.6 56.5 1.0
NH1 B:ARG201 4.6 86.3 1.0
CD1 B:ILE197 4.7 99.5 1.0
CA B:GLY209 4.8 47.5 1.0

Chlorine binding site 4 out of 4 in 7ci6

Go back to Chlorine Binding Sites List in 7ci6
Chlorine binding site 4 out of 4 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1302

b:53.5
occ:1.00
NH2 B:ARG41 3.8 64.7 1.0
NH1 B:ARG41 3.9 55.3 1.0
CB B:SER98 4.3 44.1 1.0
CZ B:ARG41 4.3 57.7 1.0
N B:LYS72 4.4 58.7 1.0
CD B:LYS72 4.5 56.8 1.0
CG B:LYS72 4.6 54.1 1.0
O B:LYS72 4.6 62.9 1.0
O B:ASP70 4.7 51.7 1.0
CA B:VAL71 4.9 61.1 1.0
CB B:LYS72 5.0 54.4 1.0

Reference:

Y.Yamada, H.Takashima, D.L.Walmsley, F.Ushiyama, Y.Matsuda, H.Kanazawa, T.Yamaguchi-Sasaki, N.Tanaka-Yamamoto, J.Yamagishi, R.Kurimoto-Tsuruta, Y.Ogata, N.Ohtake, H.Angove, L.Baker, R.Harris, A.Macias, A.Robertson, A.Surgenor, H.Watanabe, K.Nakano, M.Mima, K.Iwamoto, A.Okada, I.Takata, K.Hitaka, A.Tanaka, K.Fujita, H.Sugiyama, R.E.Hubbard. Fragment-Based Discovery of Novel Non-Hydroxamate Lpxc Inhibitors with Antibacterial Activity. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 33210531
DOI: 10.1021/ACS.JMEDCHEM.0C01215
Page generated: Sun Dec 13 10:27:43 2020

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