Atomistry » Calcium » PDB 4h84-4hte » 4hma
Atomistry »
  Calcium »
    PDB 4h84-4hte »
      4hma »

Calcium in PDB 4hma: Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain

Enzymatic activity of Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain

All present enzymatic activity of Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain:
3.4.24.35;

Protein crystallography data

The structure of Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain, PDB code: 4hma was solved by E.A.Stura, C.Antoni, L.Vera, E.Nuti, L.Carafa, E.Cassar-Lajeunesse, V.Dive, A.Rossello, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.72 / 1.94
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 73.870, 98.240, 47.440, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 28.3

Other elements in 4hma:

The structure of Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain (pdb code 4hma). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain, PDB code: 4hma:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4hma

Go back to Calcium Binding Sites List in 4hma
Calcium binding site 1 out of 6 in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 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 An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:30.1
occ:1.00
 O A:HOH446 2.2 23.4 1.0
O A:ASP165 2.3 23.9 1.0
OD1 A:ASP201 2.3 23.5 1.0
O A:HOH445 2.3 24.9 1.0
O A:GLY197 2.3 33.4 1.0
O A:GLN199 2.4 30.6 0.5
O A:GLN199 2.5 30.3 0.5
CG A:ASP201 3.4 29.0 1.0
C A:ASP165 3.4 24.1 1.0
C A:GLY197 3.6 34.3 1.0
C A:GLN199 3.6 30.6 0.5
C A:GLN199 3.6 30.3 0.5
O A:HOH460 3.8 41.5 1.0
OD2 A:ASP201 3.9 32.3 1.0
O A:ILE198 4.0 32.5 1.0
C A:ILE198 4.1 32.1 1.0
O A:ALA164 4.1 25.9 1.0
N A:ASP201 4.1 26.3 1.0
CA A:ASP165 4.2 24.8 1.0
N A:GLY197 4.3 33.2 1.0
C A:GLY200 4.3 28.8 1.0
CA A:GLY200 4.3 29.1 1.0
N A:ILE166 4.3 23.5 1.0
N A:GLY200 4.4 30.5 1.0
N A:GLN199 4.4 30.9 0.5
N A:GLN199 4.4 31.2 0.5
O A:GLY195 4.4 30.1 1.0
CA A:GLY197 4.4 33.1 1.0
CA A:ILE166 4.5 23.6 1.0
N A:ILE198 4.5 33.6 1.0
CB A:ASP201 4.5 25.9 1.0
CA A:GLN199 4.6 31.3 0.5
CA A:GLN199 4.6 30.8 0.5
N A:VAL167 4.6 23.4 1.0
O A:HOH447 4.6 34.1 1.0
CA A:ILE198 4.6 33.4 1.0
CA A:ASP201 4.7 26.1 1.0
CH2 A:TRP116 4.7 27.7 1.0
C A:PRO196 4.8 33.5 1.0
O A:GLY200 4.9 28.7 1.0

Calcium binding site 2 out of 6 in 4hma

Go back to Calcium Binding Sites List in 4hma
Calcium binding site 2 out of 6 in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 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 An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:34.1
occ:1.00
 OE1 A:GLU208 2.2 41.7 1.0
OD2 A:ASP182 2.3 42.2 1.0
O A:LEU187 2.4 32.3 1.0
O A:GLY183 2.4 43.3 1.0
O A:ASP185 2.4 39.5 1.0
OD2 A:ASP205 2.4 31.7 1.0
CD A:GLU208 3.4 36.2 1.0
C A:ASP185 3.5 40.7 1.0
C A:LEU187 3.5 31.2 1.0
CG A:ASP182 3.5 41.4 1.0
CG A:ASP205 3.6 31.3 1.0
C A:GLY183 3.6 42.4 1.0
N A:LEU187 3.7 32.6 1.0
N A:ASP185 3.9 42.6 1.0
CA A:LEU187 4.0 32.3 1.0
OD1 A:ASP182 4.1 33.0 1.0
C A:GLY186 4.1 34.5 1.0
N A:ASP182 4.2 41.9 1.0
C A:LYS184 4.2 43.4 1.0
CB A:ASP205 4.2 30.1 1.0
CG A:GLU208 4.2 32.5 1.0
CA A:ASP185 4.3 42.2 1.0
C A:ASP182 4.3 41.4 1.0
OE2 A:GLU208 4.3 37.6 1.0
CB A:LEU187 4.3 32.5 1.0
N A:GLY183 4.4 41.5 1.0
N A:GLY186 4.4 38.3 1.0
OD1 A:ASP205 4.4 26.1 1.0
N A:LYS184 4.5 41.8 1.0
CA A:LYS184 4.5 43.3 1.0
CA A:GLY186 4.6 36.6 1.0
N A:LEU188 4.6 28.1 1.0
O A:ASP182 4.6 40.9 1.0
CA A:ASP182 4.6 41.5 1.0
CA A:GLY183 4.6 40.9 1.0
CB A:ASP182 4.7 41.3 1.0
O A:GLY186 4.7 34.2 1.0
CA A:LEU188 4.7 26.7 1.0
O A:LYS184 4.8 44.7 1.0

Calcium binding site 3 out of 6 in 4hma

Go back to Calcium Binding Sites List in 4hma
Calcium binding site 3 out of 6 in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 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 An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:55.1
occ:1.00
 O A:GLU208 2.2 34.2 1.0
OD1 A:ASP131 2.2 41.2 1.0
OD1 A:ASP206 2.5 34.1 1.0
O A:ASP206 2.5 33.8 1.0
CG A:ASP131 3.1 38.8 1.0
C A:GLU208 3.4 33.8 1.0
C A:ASP206 3.4 33.3 1.0
OD2 A:ASP131 3.4 41.7 1.0
CG A:ASP206 3.5 36.3 1.0
CA A:ASP206 3.8 33.1 1.0
CD1 A:TRP210 3.9 25.5 1.0
OG A:SER129 3.9 30.8 1.0
N A:GLU208 4.1 33.9 1.0
CA A:LEU209 4.1 35.2 1.0
N A:LEU209 4.2 34.1 1.0
CB A:ASP206 4.2 33.3 1.0
CA A:GLU208 4.3 33.0 1.0
N A:TRP210 4.3 34.3 1.0
N A:ASP207 4.4 34.2 1.0
C A:ASP207 4.4 34.5 1.0
O A:HOH509 4.4 41.1 1.0
OD2 A:ASP206 4.5 37.5 1.0
NE1 A:TRP210 4.5 28.0 1.0
CB A:ASP131 4.5 36.4 1.0
CA A:ASP207 4.7 33.5 1.0
C A:LEU209 4.8 34.6 1.0
CG A:TRP210 4.9 28.5 1.0
CB A:SER129 5.0 35.8 1.0
O A:ASP205 5.0 30.6 1.0

Calcium binding site 4 out of 6 in 4hma

Go back to Calcium Binding Sites List in 4hma
Calcium binding site 4 out of 6 in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 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 4 of Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:29.6
occ:1.00
 O B:GLN199 2.3 24.8 1.0
O B:ASP165 2.3 23.2 1.0
O B:HOH612 2.4 25.2 1.0
O B:HOH611 2.4 27.1 1.0
OD1 B:ASP201 2.4 25.5 1.0
O B:GLY197 2.4 28.9 1.0
CG B:ASP201 3.4 29.0 1.0
C B:ASP165 3.4 22.6 1.0
C B:GLN199 3.5 26.9 1.0
C B:GLY197 3.6 29.0 1.0
OD2 B:ASP201 3.9 30.9 1.0
N B:ASP201 4.1 26.6 1.0
O B:HOH652 4.1 33.7 1.0
O B:ALA164 4.2 26.5 1.0
CA B:GLY200 4.2 26.8 1.0
N B:GLY197 4.2 28.2 1.0
O B:GLY195 4.2 26.5 1.0
C B:ILE198 4.2 29.3 1.0
C B:GLY200 4.2 26.6 1.0
N B:GLN199 4.3 27.6 1.0
CA B:ASP165 4.3 24.6 1.0
N B:GLY200 4.3 27.0 1.0
CA B:GLY197 4.3 28.2 1.0
O B:ILE198 4.4 29.9 1.0
N B:ILE166 4.4 23.0 1.0
CA B:GLN199 4.5 27.5 1.0
CA B:ILE166 4.6 23.4 1.0
N B:ILE198 4.6 29.6 1.0
CB B:ASP201 4.6 26.0 1.0
CA B:ASP201 4.7 25.1 1.0
O B:HOH668 4.7 39.8 1.0
N B:VAL167 4.7 24.8 1.0
C B:PRO196 4.7 28.3 1.0
CH2 B:TRP116 4.8 23.1 1.0
CA B:ILE198 4.8 30.1 1.0
O B:GLY200 5.0 26.3 1.0

Calcium binding site 5 out of 6 in 4hma

Go back to Calcium Binding Sites List in 4hma
Calcium binding site 5 out of 6 in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 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 5 of Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:29.5
occ:1.00
 OE1 B:GLU208 2.1 29.8 1.0
OD2 B:ASP205 2.2 28.5 1.0
O B:GLY183 2.2 37.2 1.0
O B:ASP185 2.3 37.4 1.0
O B:LEU187 2.4 29.4 1.0
OD1 B:ASP182 2.4 39.0 1.0
CD B:GLU208 3.4 30.2 1.0
CG B:ASP205 3.4 29.4 1.0
C B:ASP185 3.5 36.8 1.0
C B:GLY183 3.5 37.8 1.0
C B:LEU187 3.5 29.6 1.0
CG B:ASP182 3.6 39.1 1.0
N B:LEU187 3.8 32.2 1.0
N B:ASP185 3.9 36.7 1.0
C B:LYS184 4.1 37.6 1.0
CB B:ASP205 4.1 26.4 1.0
CA B:LEU187 4.2 31.1 1.0
N B:GLY183 4.2 38.1 1.0
OD2 B:ASP182 4.2 38.8 1.0
OE2 B:GLU208 4.2 33.6 1.0
CA B:ASP185 4.2 38.1 1.0
CG B:GLU208 4.2 29.1 1.0
C B:GLY186 4.3 34.4 1.0
C B:ASP182 4.3 37.6 1.0
OD1 B:ASP205 4.3 26.8 1.0
N B:LYS184 4.3 37.2 1.0
N B:ASP182 4.4 37.9 1.0
CA B:LYS184 4.4 37.3 1.0
CA B:GLY183 4.4 37.2 1.0
N B:GLY186 4.5 35.9 1.0
CB B:LEU187 4.5 31.1 1.0
O B:LYS184 4.6 37.0 1.0
N B:LEU188 4.6 27.0 1.0
O B:ASP182 4.6 37.7 1.0
CA B:GLY186 4.7 35.2 1.0
CA B:ASP182 4.7 38.0 1.0
CB B:ASP182 4.8 38.1 1.0
CA B:LEU188 4.8 26.4 1.0
O B:GLY186 4.8 34.3 1.0

Calcium binding site 6 out of 6 in 4hma

Go back to Calcium Binding Sites List in 4hma
Calcium binding site 6 out of 6 in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 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 6 of Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca505

b:55.8
occ:1.00
 O B:GLU208 2.2 28.0 1.0
OD2 B:ASP131 2.3 31.8 1.0
O B:HOH681 2.5 42.2 1.0
OD1 B:ASP206 2.6 32.9 1.0
O B:ASP206 2.6 31.5 1.0
CG B:ASP131 3.1 35.3 1.0
OD1 B:ASP131 3.3 38.9 1.0
C B:GLU208 3.4 28.7 1.0
C B:ASP206 3.5 31.2 1.0
CG B:ASP206 3.5 34.0 1.0
CA B:ASP206 4.0 30.6 1.0
CA B:LEU209 4.0 28.1 1.0
N B:LEU209 4.1 28.0 1.0
OG B:SER129 4.2 31.2 1.0
CD1 B:TRP210 4.2 26.3 1.0
N B:GLU208 4.2 31.4 1.0
OD2 B:ASP206 4.2 35.2 1.0
CB B:ASP206 4.3 30.6 1.0
CA B:GLU208 4.4 29.5 1.0
C B:ASP207 4.4 32.4 1.0
N B:TRP210 4.5 26.9 1.0
N B:ASP207 4.5 32.7 1.0
CB B:ASP131 4.6 30.7 1.0
C B:LEU209 4.8 27.6 1.0
CA B:ASP207 4.8 32.9 1.0
NE1 B:TRP210 4.8 26.1 1.0
O B:ASP207 5.0 32.7 1.0

Reference:

C.Antoni, L.Vera, L.Devel, M.P.Catalani, B.Czarny, E.Cassar-Lajeunesse, E.Nuti, A.Rossello, V.Dive, E.A.Stura. Crystallization of Bi-Functional Ligand Protein Complexes. J.Struct.Biol. V. 182 246 2013.
ISSN: ISSN 1047-8477
PubMed: 23567804
DOI: 10.1016/J.JSB.2013.03.015
Page generated: Sun Jul 14 07:49:18 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy