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Zinc in PDB 5n8c: Crystal Structure of Pseudomonas Aeruginosa Lpxc Complexed with Inhibitor

Enzymatic activity of Crystal Structure of Pseudomonas Aeruginosa Lpxc Complexed with Inhibitor

All present enzymatic activity of Crystal Structure of Pseudomonas Aeruginosa Lpxc Complexed with Inhibitor:
3.5.1.108;

Protein crystallography data

The structure of Crystal Structure of Pseudomonas Aeruginosa Lpxc Complexed with Inhibitor, PDB code: 5n8c was solved by J.B.Cross, M.D.Ryan, J.Zhang, R.K.Cheng, M.Wood, O.A.Andersen, M.Brooks, J.Kwong, J.Barker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.59 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.440, 95.310, 89.720, 90.00, 96.34, 90.00
R / Rfree (%) 14.9 / 20.3

Other elements in 5n8c:

The structure of Crystal Structure of Pseudomonas Aeruginosa Lpxc Complexed with Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Pseudomonas Aeruginosa Lpxc Complexed with Inhibitor (pdb code 5n8c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Pseudomonas Aeruginosa Lpxc Complexed with Inhibitor, PDB code: 5n8c:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5n8c

Go back to Zinc Binding Sites List in 5n8c
Zinc binding site 1 out of 4 in the Crystal Structure of Pseudomonas Aeruginosa Lpxc Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Pseudomonas Aeruginosa Lpxc Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:10.2
occ:1.00
OD1 A:ASP241 2.0 9.9 1.0
O2 A:8Q8403 2.0 12.2 1.0
NE2 A:HIS78 2.1 10.0 1.0
NE2 A:HIS237 2.1 7.9 1.0
O3 A:8Q8403 2.1 14.4 1.0
CG A:ASP241 2.7 10.3 1.0
OD2 A:ASP241 2.8 11.6 1.0
C27 A:8Q8403 2.8 14.7 1.0
N5 A:8Q8403 2.9 15.5 1.0
CD2 A:HIS78 3.0 11.3 1.0
CD2 A:HIS237 3.0 8.4 1.0
CE1 A:HIS237 3.1 8.6 1.0
CE1 A:HIS78 3.1 11.8 1.0
OG1 A:THR190 4.0 11.6 1.0
CG A:HIS78 4.2 11.3 1.0
ND1 A:HIS237 4.2 9.5 1.0
CG A:HIS237 4.2 9.2 1.0
ND1 A:HIS78 4.2 11.3 1.0
CB A:ASP241 4.2 10.5 1.0
CG A:GLU77 4.3 12.2 1.0
CB A:THR190 4.3 10.9 1.0
C4 A:8Q8403 4.3 14.6 1.0
OE2 A:GLU77 4.4 15.5 1.0
CE1 A:HIS264 4.7 13.0 1.0
C1 A:8Q8403 4.8 13.6 1.0
CA A:ASP241 4.9 9.7 1.0
NE2 A:HIS264 4.9 13.2 1.0
C3 A:8Q8403 4.9 13.4 1.0
O A:HIS237 4.9 9.4 1.0
C2 A:8Q8403 4.9 13.7 1.0
CD A:GLU77 4.9 14.2 1.0
CA A:THR190 5.0 10.9 1.0

Zinc binding site 2 out of 4 in 5n8c

Go back to Zinc Binding Sites List in 5n8c
Zinc binding site 2 out of 4 in the Crystal Structure of Pseudomonas Aeruginosa Lpxc Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Pseudomonas Aeruginosa Lpxc Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:15.2
occ:0.50
N4 A:8Q8403 2.0 21.6 1.0
OE1 A:GLU198 2.1 24.6 1.0
C22 A:8Q8403 2.8 22.9 1.0
C23 A:8Q8403 3.1 22.6 1.0
CD A:GLU198 3.2 22.5 1.0
C24 A:8Q8403 3.5 27.3 1.0
OE2 A:GLU198 3.7 27.9 1.0
C21 A:8Q8403 4.1 23.9 1.0
N3 A:8Q8403 4.2 24.6 1.0
O1 A:8Q8403 4.5 34.2 1.0
CG A:ARG201 4.5 17.3 1.0
CG A:GLU198 4.5 17.6 1.0
CB A:ARG201 4.7 14.9 1.0
CA A:GLU198 5.0 14.7 1.0

Zinc binding site 3 out of 4 in 5n8c

Go back to Zinc Binding Sites List in 5n8c
Zinc binding site 3 out of 4 in the Crystal Structure of Pseudomonas Aeruginosa Lpxc Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Pseudomonas Aeruginosa Lpxc Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:8.9
occ:1.00
OD1 B:ASP241 2.1 7.0 1.0
O2 B:8Q8403 2.1 12.6 1.0
NE2 B:HIS78 2.1 8.3 1.0
NE2 B:HIS237 2.1 7.6 1.0
O3 B:8Q8403 2.2 12.1 1.0
CG B:ASP241 2.8 7.8 1.0
OD2 B:ASP241 2.8 8.2 1.0
C27 B:8Q8403 2.8 12.5 1.0
N5 B:8Q8403 2.9 12.4 1.0
CE1 B:HIS78 3.0 9.0 1.0
CE1 B:HIS237 3.0 7.4 1.0
CD2 B:HIS78 3.1 8.3 1.0
CD2 B:HIS237 3.1 7.5 1.0
OG1 B:THR190 4.0 11.8 1.0
ND1 B:HIS237 4.2 7.8 1.0
ND1 B:HIS78 4.2 9.5 1.0
CG B:HIS78 4.2 8.4 1.0
CG B:HIS237 4.2 7.9 1.0
CB B:THR190 4.2 10.9 1.0
CB B:ASP241 4.3 8.1 1.0
CG B:GLU77 4.3 13.2 1.0
C4 B:8Q8403 4.3 12.3 1.0
OE2 B:GLU77 4.4 14.6 1.0
CE1 B:HIS264 4.8 13.7 1.0
CA B:ASP241 4.9 8.0 1.0
C1 B:8Q8403 4.9 12.7 1.0
C3 B:8Q8403 4.9 12.3 1.0
CD B:GLU77 4.9 14.8 1.0
C2 B:8Q8403 4.9 12.4 1.0
CA B:THR190 4.9 10.8 1.0
O B:HIS237 5.0 8.0 1.0
NE2 B:HIS264 5.0 13.4 1.0

Zinc binding site 4 out of 4 in 5n8c

Go back to Zinc Binding Sites List in 5n8c
Zinc binding site 4 out of 4 in the Crystal Structure of Pseudomonas Aeruginosa Lpxc Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Pseudomonas Aeruginosa Lpxc Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:18.7
occ:0.50
O1 B:8Q8403 2.1 29.6 1.0
N4 B:8Q8403 2.1 23.0 1.0
C23 B:8Q8403 2.9 21.9 1.0
OE2 B:GLU198 3.0 19.4 1.0
C24 B:8Q8403 3.0 24.8 1.0
C22 B:8Q8403 3.1 21.6 1.0
CG B:GLU198 3.5 18.5 1.0
CD B:GLU198 3.7 20.7 1.0
N3 B:8Q8403 4.1 19.6 1.0
C21 B:8Q8403 4.2 20.6 1.0
CB B:GLU198 4.7 15.4 1.0
OE1 B:GLU198 5.0 23.7 1.0

Reference:

J.Zhang, A.Chan, B.Lippa, J.B.Cross, C.Liu, N.Yin, J.A.Romero, J.Lawrence, R.Heney, P.Herradura, J.Goss, C.Clark, C.Abel, Y.Zhang, K.M.Poutsiaka, F.Epie, M.Conrad, A.Mahamoon, K.Nguyen, A.Chavan, E.Clark, T.C.Li, R.K.Cheng, M.Wood, O.A.Andersen, M.Brooks, J.Kwong, J.Barker, I.B.Parr, Y.Gu, M.D.Ryan, S.Coleman, C.A.Metcalf. Structure-Based Discovery of Lpxc Inhibitors. Bioorg. Med. Chem. Lett. V. 27 1670 2017.
ISSN: ESSN 1464-3405
PubMed: 28302397
DOI: 10.1016/J.BMCL.2017.03.006
Page generated: Wed Dec 16 06:34:57 2020

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