Atomistry » Zinc » PDB 5dor-5e6a » 5drp
Atomistry »
  Zinc »
    PDB 5dor-5e6a »
      5drp »

Zinc in PDB 5drp: Structure of the Aalpxc/Lpc-023 Complex

Protein crystallography data

The structure of Structure of the Aalpxc/Lpc-023 Complex, PDB code: 5drp was solved by J.Najeeb, C.-J.Lee, P.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.81 / 1.89
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 45.657, 50.419, 61.730, 80.26, 71.71, 88.90
R / Rfree (%) 15.6 / 19.2

Other elements in 5drp:

The structure of Structure of the Aalpxc/Lpc-023 Complex also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Aalpxc/Lpc-023 Complex (pdb code 5drp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the Aalpxc/Lpc-023 Complex, PDB code: 5drp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5drp

Go back to Zinc Binding Sites List in 5drp
Zinc binding site 1 out of 2 in the Structure of the Aalpxc/Lpc-023 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Aalpxc/Lpc-023 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:22.4
occ:1.00
OD1 A:ASP230 2.0 20.9 1.0
O01 A:5EP402 2.0 23.6 1.0
NE2 A:HIS226 2.1 22.0 1.0
NE2 A:HIS74 2.1 25.3 1.0
O04 A:5EP402 2.2 25.2 1.0
CG A:ASP230 2.7 20.3 1.0
OD2 A:ASP230 2.8 22.9 1.0
C02 A:5EP402 2.8 32.6 1.0
N03 A:5EP402 2.8 28.1 1.0
CE1 A:HIS226 3.0 24.6 1.0
CD2 A:HIS226 3.1 20.8 1.0
CD2 A:HIS74 3.1 22.8 1.0
CE1 A:HIS74 3.1 35.3 1.0
OE2 A:GLU73 4.1 28.3 1.0
ND1 A:HIS226 4.1 25.2 1.0
OG1 A:THR179 4.1 28.1 1.0
C05 A:5EP402 4.2 31.7 1.0
CG A:HIS226 4.2 25.1 1.0
ND1 A:HIS74 4.2 38.1 1.0
CB A:ASP230 4.2 19.2 1.0
CG A:GLU73 4.2 26.6 1.0
CG A:HIS74 4.2 28.3 1.0
CB A:THR179 4.3 26.4 1.0
O A:HOH537 4.6 43.6 1.0
C29 A:5EP402 4.7 38.8 1.0
CD A:GLU73 4.7 26.4 1.0
C26 A:5EP402 4.7 36.9 1.0
C27 A:5EP402 4.7 35.2 1.0
N06 A:5EP402 4.8 31.1 1.0
CA A:ASP230 4.8 20.5 1.0
NE2 A:HIS253 4.9 28.7 1.0
CA A:THR179 4.9 24.1 1.0
CE1 A:HIS253 4.9 26.6 1.0
O A:HIS226 5.0 22.3 1.0

Zinc binding site 2 out of 2 in 5drp

Go back to Zinc Binding Sites List in 5drp
Zinc binding site 2 out of 2 in the Structure of the Aalpxc/Lpc-023 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Aalpxc/Lpc-023 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:19.3
occ:1.00
NE2 B:HIS74 2.0 23.5 1.0
OD1 B:ASP230 2.0 13.1 1.0
NE2 B:HIS226 2.0 15.6 1.0
O01 B:5EP402 2.1 20.4 1.0
O04 B:5EP402 2.3 24.1 1.0
CG B:ASP230 2.7 19.7 1.0
OD2 B:ASP230 2.7 21.6 1.0
C02 B:5EP402 2.9 22.9 1.0
N03 B:5EP402 2.9 26.9 1.0
CE1 B:HIS226 3.0 19.4 1.0
CE1 B:HIS74 3.0 28.6 1.0
CD2 B:HIS74 3.0 20.4 1.0
CD2 B:HIS226 3.0 18.6 1.0
OE2 B:GLU73 4.0 23.9 1.0
ND1 B:HIS226 4.1 19.3 1.0
CG B:GLU73 4.1 22.7 1.0
ND1 B:HIS74 4.1 30.2 1.0
CG B:HIS74 4.1 22.3 1.0
CG B:HIS226 4.1 20.2 1.0
CB B:ASP230 4.2 17.9 1.0
C05 B:5EP402 4.2 27.0 1.0
OG1 B:THR179 4.3 20.9 1.0
C27 B:5EP402 4.5 35.9 1.0
CB B:THR179 4.6 19.9 1.0
CD B:GLU73 4.6 25.2 1.0
C26 B:5EP402 4.7 34.6 1.0
O B:HOH507 4.7 57.4 1.0
C29 B:5EP402 4.8 37.7 1.0
CA B:ASP230 4.8 16.6 1.0
O B:HIS226 4.8 17.5 1.0
N06 B:5EP402 4.9 25.4 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

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy