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Zinc in PDB 5drq: Crystal Structure of the Pseudomonas Aeruginosa Lpxc/Lpc-040 Complex

Protein crystallography data

The structure of Crystal Structure of the Pseudomonas Aeruginosa Lpxc/Lpc-040 Complex, PDB code: 5drq was solved by C.-J.Lee, J.Najeeb, P.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.87 / 1.63
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.433, 74.001, 88.629, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Pseudomonas Aeruginosa Lpxc/Lpc-040 Complex (pdb code 5drq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Pseudomonas Aeruginosa Lpxc/Lpc-040 Complex, PDB code: 5drq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5drq

Go back to Zinc Binding Sites List in 5drq
Zinc binding site 1 out of 2 in the Crystal Structure of the Pseudomonas Aeruginosa Lpxc/Lpc-040 Complex


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 the Pseudomonas Aeruginosa Lpxc/Lpc-040 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:16.2
occ:1.00
OD1 A:ASP241 2.0 14.1 1.0
NE2 A:HIS237 2.1 14.2 1.0
NE2 A:HIS78 2.1 15.3 1.0
O01 A:5EM303 2.1 15.2 1.0
O04 A:5EM303 2.2 16.6 1.0
CG A:ASP241 2.7 18.2 1.0
OD2 A:ASP241 2.8 16.3 1.0
C02 A:5EM303 2.9 17.2 1.0
N03 A:5EM303 2.9 16.9 1.0
CE1 A:HIS237 3.0 14.3 1.0
CD2 A:HIS78 3.0 15.1 1.0
CE1 A:HIS78 3.1 17.7 1.0
CD2 A:HIS237 3.1 14.3 1.0
OG1 A:THR190 4.0 16.3 1.0
ND1 A:HIS237 4.1 14.1 1.0
O A:HOH626 4.2 39.4 1.0
ND1 A:HIS78 4.2 15.6 1.0
CG A:HIS78 4.2 15.6 1.0
CG A:HIS237 4.2 15.1 1.0
CB A:ASP241 4.2 16.5 1.0
C05 A:5EM303 4.3 15.5 1.0
CG A:GLU77 4.3 17.5 1.0
CB A:THR190 4.3 16.3 1.0
OE2 A:GLU77 4.4 22.0 1.0
C29 A:5EM303 4.5 19.8 1.0
CE1 A:HIS264 4.7 16.8 1.0
C28 A:5EM303 4.8 19.1 1.0
CA A:ASP241 4.8 13.6 1.0
C26 A:5EM303 4.8 17.4 1.0
O A:HIS237 4.9 14.7 1.0
NE2 A:HIS264 4.9 16.8 1.0
CD A:GLU77 4.9 23.0 1.0
N06 A:5EM303 4.9 17.1 1.0
CA A:THR190 5.0 15.5 1.0

Zinc binding site 2 out of 2 in 5drq

Go back to Zinc Binding Sites List in 5drq
Zinc binding site 2 out of 2 in the Crystal Structure of the Pseudomonas Aeruginosa Lpxc/Lpc-040 Complex


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 the Pseudomonas Aeruginosa Lpxc/Lpc-040 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:26.1
occ:0.94
ND1 A:HIS162 2.0 23.2 1.0
OE1 A:GLU219 2.1 38.7 1.0
OE2 A:GLU219 2.6 35.8 1.0
CD A:GLU219 2.7 36.4 1.0
CE1 A:HIS162 2.8 23.3 1.0
CG A:HIS162 3.1 21.2 1.0
CB A:HIS162 3.6 19.0 1.0
CA A:HIS162 3.8 21.2 1.0
NE2 A:HIS162 4.0 30.8 1.0
CG A:GLU219 4.2 31.2 1.0
CD2 A:HIS162 4.2 26.4 1.0
CD A:PRO163 4.4 19.5 1.0
N A:HIS162 4.4 19.3 1.0
O2 A:NO3332 4.6 37.1 0.8
CB A:GLU219 4.9 25.9 1.0

Reference:

C.J.Lee, X.Liang, Q.Wu, J.Najeeb, J.Zhao, R.Gopalaswamy, M.Titecat, F.Sebbane, N.Lemaitre, E.J.Toone, P.Zhou. Drug Design From the Cryptic Inhibitor Envelope. Nat Commun V. 7 10638 2016.
ISSN: ESSN 2041-1723
PubMed: 26912110
DOI: 10.1038/NCOMMS10638
Page generated: Wed Dec 16 06:08:43 2020

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