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Calcium in PDB 4xct: Crystal Structure of A Hydroxamate Based Inhibitor ARP101 (EN73) in Complex with the Mmp-9 Catalytic Domain.

Enzymatic activity of Crystal Structure of A Hydroxamate Based Inhibitor ARP101 (EN73) in Complex with the Mmp-9 Catalytic Domain.

All present enzymatic activity of Crystal Structure of A Hydroxamate Based Inhibitor ARP101 (EN73) in Complex with the Mmp-9 Catalytic Domain.:
3.4.24.35;

Protein crystallography data

The structure of Crystal Structure of A Hydroxamate Based Inhibitor ARP101 (EN73) in Complex with the Mmp-9 Catalytic Domain., PDB code: 4xct was solved by E.A.Stura, L.Tepshi, E.Nuti, V.Dive, E.Cassar-Lajeunesse, L.Vera, A.Rossello, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.30 / 1.30
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 39.600, 39.600, 163.960, 90.00, 90.00, 120.00
R / Rfree (%) 16.7 / 23.1

Other elements in 4xct:

The structure of Crystal Structure of A Hydroxamate Based Inhibitor ARP101 (EN73) in Complex with the Mmp-9 Catalytic Domain. also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Hydroxamate Based Inhibitor ARP101 (EN73) in Complex with the Mmp-9 Catalytic Domain. (pdb code 4xct). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of A Hydroxamate Based Inhibitor ARP101 (EN73) in Complex with the Mmp-9 Catalytic Domain., PDB code: 4xct:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4xct

Go back to Calcium Binding Sites List in 4xct
Calcium binding site 1 out of 3 in the Crystal Structure of A Hydroxamate Based Inhibitor ARP101 (EN73) in Complex with the Mmp-9 Catalytic Domain.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Hydroxamate Based Inhibitor ARP101 (EN73) in Complex with the Mmp-9 Catalytic Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:21.4
occ:1.00
O A:LEU187 2.3 23.8 1.0
O A:GLY183 2.3 23.3 1.0
OD2 A:ASP205 2.3 20.1 1.0
O A:ASP185 2.3 25.8 1.0
OE2 A:GLU208 2.3 22.0 1.0
OD1 A:ASP182 2.4 25.1 1.0
CG A:ASP205 3.4 22.1 1.0
C A:ASP185 3.4 27.4 1.0
C A:LEU187 3.4 23.5 1.0
C A:GLY183 3.5 25.6 1.0
CD A:GLU208 3.6 22.3 1.0
CG A:ASP182 3.6 27.4 1.0
N A:ASP185 3.8 26.2 1.0
N A:LEU187 3.9 23.6 1.0
C A:LYS184 4.0 28.1 1.0
CB A:ASP205 4.1 19.9 1.0
N A:GLY183 4.1 23.4 1.0
CA A:ASP185 4.1 27.5 1.0
CA A:LEU187 4.1 22.2 1.0
C A:GLY186 4.2 23.3 1.0
OD2 A:ASP182 4.2 27.6 1.0
C A:ASP182 4.3 24.8 1.0
N A:ASP182 4.3 22.5 1.0
OD1 A:ASP205 4.3 20.0 1.0
OE1 A:GLU208 4.4 23.0 1.0
CA A:GLY183 4.4 23.1 1.0
N A:LYS184 4.4 27.4 1.0
N A:GLY186 4.4 26.5 1.0
CG A:GLU208 4.4 22.0 1.0
CA A:LYS184 4.4 32.4 1.0
O A:LYS184 4.5 28.9 1.0
CB A:LEU187 4.5 28.2 1.0
N A:LEU188 4.5 21.2 1.0
CA A:GLY186 4.6 23.3 1.0
O A:GLY186 4.6 26.3 1.0
CA A:ASP182 4.7 25.3 1.0
CB A:ASP182 4.7 24.6 1.0
CA A:LEU188 4.8 20.7 1.0
O A:HOH466 4.8 45.7 1.0
O A:ASP182 4.8 26.3 1.0

Calcium binding site 2 out of 3 in 4xct

Go back to Calcium Binding Sites List in 4xct
Calcium binding site 2 out of 3 in the Crystal Structure of A Hydroxamate Based Inhibitor ARP101 (EN73) in Complex with the Mmp-9 Catalytic Domain.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Hydroxamate Based Inhibitor ARP101 (EN73) in Complex with the Mmp-9 Catalytic Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:26.1
occ:1.00
O A:GLN199 2.3 27.6 1.0
O A:HOH520 2.3 30.4 1.0
O A:HOH530 2.3 28.9 1.0
O A:GLY197 2.3 27.4 1.0
OD1 A:ASP201 2.3 22.7 1.0
O A:ASP165 2.3 21.7 1.0
CG A:ASP201 3.4 23.4 1.0
C A:GLN199 3.4 25.6 1.0
C A:ASP165 3.5 19.6 1.0
C A:GLY197 3.5 27.5 1.0
OD2 A:ASP201 3.8 25.7 1.0
N A:ASP201 4.0 21.6 1.0
O A:ALA164 4.1 30.4 1.0
C A:ILE198 4.1 24.9 1.0
N A:GLN199 4.2 25.0 1.0
CA A:GLY200 4.2 22.5 1.0
CA A:ASP165 4.3 24.6 1.0
C A:GLY200 4.3 24.5 1.0
N A:GLY200 4.3 24.4 1.0
O A:GLY195 4.3 30.2 1.0
O A:ILE198 4.3 26.5 1.0
O A:HOH548 4.4 41.5 1.0
N A:GLY197 4.4 29.7 1.0
CA A:GLY197 4.4 29.5 1.0
CA A:GLN199 4.4 26.1 1.0
N A:ILE198 4.4 27.3 1.0
N A:ILE166 4.5 22.6 1.0
CA A:ILE198 4.5 26.0 1.0
CB A:ASP201 4.6 21.8 1.0
N A:VAL167 4.6 20.4 1.0
CA A:ILE166 4.6 21.9 1.0
CA A:ASP201 4.6 23.2 1.0
C A:PRO196 4.7 30.1 1.0
O A:HOH536 4.7 35.0 1.0
CH2 A:TRP116 4.8 26.1 1.0
O A:PRO196 4.9 31.1 1.0

Calcium binding site 3 out of 3 in 4xct

Go back to Calcium Binding Sites List in 4xct
Calcium binding site 3 out of 3 in the Crystal Structure of A Hydroxamate Based Inhibitor ARP101 (EN73) in Complex with the Mmp-9 Catalytic Domain.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Hydroxamate Based Inhibitor ARP101 (EN73) in Complex with the Mmp-9 Catalytic Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca306

b:20.1
occ:1.00
O A:HOH456 2.3 27.6 1.0
OD2 A:ASP131 2.4 22.0 1.0
O A:GLU208 2.4 21.1 1.0
O A:ASP206 2.4 19.7 1.0
OD1 A:ASP206 2.4 20.3 1.0
O A:HOH459 2.4 28.1 1.0
OD1 A:ASP131 2.6 24.3 1.0
CG A:ASP131 2.8 20.3 1.0
C A:ASP206 3.4 20.0 1.0
CG A:ASP206 3.4 22.4 1.0
C A:GLU208 3.5 21.1 1.0
CA A:ASP206 3.9 17.7 1.0
OG A:SER129 4.0 20.7 1.0
CB A:ASP206 4.2 20.8 1.0
OD2 A:ASP206 4.2 24.4 1.0
CA A:LEU209 4.2 20.0 1.0
O A:HOH413 4.2 42.3 1.0
N A:LEU209 4.3 21.0 1.0
CB A:ASP131 4.3 21.0 1.0
N A:GLU208 4.3 22.2 1.0
CD1 A:TRP210 4.4 18.0 1.0
O A:HOH446 4.4 51.2 1.0
N A:ASP207 4.5 19.7 1.0
O A:HOH468 4.5 30.9 1.0
C A:ASP207 4.5 22.4 1.0
CA A:GLU208 4.6 19.6 1.0
N A:TRP210 4.7 18.8 1.0
CA A:ASP207 4.7 19.9 1.0
NE1 A:TRP210 4.9 18.9 1.0

Reference:

E.Nuti, C.Camodeca, A.R.Cantelmo, T.Tuccinardi, L.Vera, L.Tepshi, E.Orlandini, S.Nencetti, E.A.Stura, A.Albini, A.Martinelli, V.Dive, A.Rossello. N-O-Isopropyl Sulphonamido-Based Hydroxamates As Matrix Metalloproteinase Inhibitors: Hit Selection and in Vivo Antiangiogenic Activity. Journal of Medicinalchemistry.
Page generated: Sat Dec 12 05:11:56 2020

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