Zinc in PDB 6yjm: Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972, PDB code: 6yjm was solved by A.Goepfert, P.Leonard, N.Triballeau, D.Fleury, P.Mollat, M.Lamers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.47 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.32, 80.24, 51.05, 90, 90.2, 90
R / Rfree (%) 21.3 / 25.6

Other elements in 6yjm:

The structure of Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 (pdb code 6yjm). 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 Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972, PDB code: 6yjm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6yjm

Go back to Zinc Binding Sites List in 6yjm
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972


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 Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:10.7
occ:1.00
N5 A:OU5505 2.1 9.9 1.0
NE2 A:HIS410 2.1 12.0 1.0
NE2 A:HIS420 2.1 16.6 1.0
NE2 A:HIS414 2.2 12.7 1.0
C6 A:OU5505 2.9 13.4 1.0
O9 A:OU5505 2.9 13.8 1.0
CD2 A:HIS420 3.0 13.7 1.0
CD2 A:HIS410 3.0 11.9 1.0
CD2 A:HIS414 3.1 11.6 1.0
CE1 A:HIS420 3.1 14.7 1.0
CE1 A:HIS410 3.1 12.8 1.0
CE1 A:HIS414 3.2 12.8 1.0
C4 A:OU5505 3.2 11.3 1.0
O8 A:OU5505 3.7 20.9 1.0
C20 A:OU5505 3.9 11.7 1.0
O A:HOH648 4.0 19.0 1.0
N7 A:OU5505 4.1 12.9 1.0
CG A:HIS420 4.2 13.4 1.0
ND1 A:HIS420 4.2 16.1 1.0
CG A:HIS410 4.2 11.7 1.0
ND1 A:HIS410 4.2 9.6 1.0
O A:HOH619 4.2 14.1 1.0
CG A:HIS414 4.3 13.7 1.0
ND1 A:HIS414 4.3 13.1 1.0
C3 A:OU5505 4.4 15.1 1.0
N15 A:OU5505 4.5 11.2 1.0
CE A:MET439 4.8 15.5 1.0
C1 A:OU5505 4.9 11.6 1.0

Zinc binding site 2 out of 2 in 6yjm

Go back to Zinc Binding Sites List in 6yjm
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972


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 Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:13.2
occ:1.00
NE2 B:HIS420 2.1 13.3 1.0
NE2 B:HIS410 2.1 14.1 1.0
NE2 B:HIS414 2.1 12.6 1.0
N5 B:OU5505 2.3 12.2 1.0
CD2 B:HIS420 2.9 13.7 1.0
CD2 B:HIS410 3.0 15.3 1.0
CE1 B:HIS414 3.1 15.6 1.0
C6 B:OU5505 3.1 9.3 1.0
CD2 B:HIS414 3.2 13.9 1.0
CE1 B:HIS410 3.2 13.2 1.0
O9 B:OU5505 3.2 9.6 1.0
CE1 B:HIS420 3.2 16.6 1.0
C4 B:OU5505 3.4 12.7 1.0
O8 B:OU5505 3.8 11.3 1.0
C20 B:OU5505 4.0 10.4 1.0
O B:HOH641 4.1 19.7 1.0
CG B:HIS420 4.1 12.6 1.0
ND1 B:HIS414 4.2 12.2 1.0
ND1 B:HIS420 4.2 8.8 1.0
CG B:HIS410 4.2 10.8 1.0
ND1 B:HIS410 4.2 16.8 1.0
CG B:HIS414 4.3 12.0 1.0
N7 B:OU5505 4.4 11.9 1.0
O B:HOH623 4.5 12.3 1.0
N15 B:OU5505 4.6 9.3 1.0
C3 B:OU5505 4.6 11.0 1.0
CE B:MET439 4.7 10.7 1.0

Reference:

P.Leonard, N.Triballeau, P.Mollat. Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 To Be Published.
Page generated: Sat Apr 17 17:45:12 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy