Atomistry » Calcium » PDB 5hsa-5i6w » 5i12
Atomistry »
  Calcium »
    PDB 5hsa-5i6w »
      5i12 »

Calcium in PDB 5i12: Crystal Structure of the Catalytic Domain of Mmp-9 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27).

Enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-9 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27).

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-9 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27).:
3.4.24.35;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Mmp-9 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27)., PDB code: 5i12 was solved by E.A.Stura, L.Rosalia, D.Cuffaro, L.Tepshi, L.Ciccone, A.Rossello, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.26 / 1.59
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 39.560, 39.560, 163.550, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 22.8

Other elements in 5i12:

The structure of Crystal Structure of the Catalytic Domain of Mmp-9 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27). also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Mmp-9 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27). (pdb code 5i12). 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 the Catalytic Domain of Mmp-9 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27)., PDB code: 5i12:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5i12

Go back to Calcium Binding Sites List in 5i12
Calcium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Mmp-9 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27).


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 the Catalytic Domain of Mmp-9 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:25.0
occ:1.00
 O A:LEU187 2.3 26.2 1.0
O A:GLY183 2.3 23.7 1.0
OE2 A:GLU208 2.3 31.4 1.0
O A:ASP185 2.3 30.4 1.0
OD2 A:ASP205 2.4 23.3 1.0
OD1 A:ASP182 2.4 24.8 1.0
CG A:ASP205 3.4 22.6 1.0
C A:ASP185 3.4 30.8 1.0
C A:LEU187 3.4 24.3 1.0
CG A:ASP182 3.5 30.1 1.0
C A:GLY183 3.5 27.9 1.0
CD A:GLU208 3.5 26.2 1.0
N A:ASP185 3.8 30.0 1.0
N A:LEU187 3.9 26.0 1.0
C A:LYS184 4.1 28.9 1.0
N A:GLY183 4.1 31.1 1.0
OD2 A:ASP182 4.1 28.2 1.0
CB A:ASP205 4.1 19.2 1.0
CA A:LEU187 4.1 24.6 1.0
CA A:ASP185 4.1 26.9 1.0
C A:GLY186 4.2 27.2 1.0
N A:ASP182 4.3 25.8 1.0
C A:ASP182 4.3 30.2 1.0
OD1 A:ASP205 4.3 22.1 1.0
CG A:GLU208 4.4 24.2 1.0
OE1 A:GLU208 4.4 31.0 1.0
CA A:GLY183 4.4 27.0 1.0
N A:LYS184 4.4 25.6 1.0
CA A:LYS184 4.5 26.4 1.0
N A:GLY186 4.5 31.8 1.0
O A:LYS184 4.5 31.0 1.0
N A:LEU188 4.5 19.6 1.0
CB A:LEU187 4.5 31.0 1.0
CA A:GLY186 4.6 33.8 1.0
CA A:ASP182 4.6 27.8 1.0
CB A:ASP182 4.7 29.4 1.0
CA A:LEU188 4.7 19.7 1.0
O A:GLY186 4.7 28.5 1.0
O A:ASP182 4.8 35.1 1.0

Calcium binding site 2 out of 3 in 5i12

Go back to Calcium Binding Sites List in 5i12
Calcium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Mmp-9 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27).


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 the Catalytic Domain of Mmp-9 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:29.0
occ:1.00
 O A:GLY197 2.3 34.1 1.0
O A:HOH424 2.3 32.9 1.0
OD1 A:ASP201 2.3 27.2 1.0
O A:GLN199 2.4 30.3 1.0
O A:ASP165 2.4 28.2 1.0
O A:HOH420 2.4 31.0 1.0
CG A:ASP201 3.4 23.6 1.0
C A:GLN199 3.5 29.1 1.0
C A:GLY197 3.5 37.3 1.0
C A:ASP165 3.6 25.2 1.0
OD2 A:ASP201 3.9 27.6 1.0
N A:ASP201 4.0 25.6 1.0
O A:ALA164 4.0 33.8 1.0
C A:ILE198 4.1 29.9 1.0
O A:ILE198 4.1 30.9 1.0
N A:GLN199 4.2 28.3 1.0
C A:GLY200 4.3 26.1 1.0
CA A:GLY200 4.3 27.7 1.0
N A:GLY197 4.3 43.2 1.0
O A:HOH416 4.3 38.0 1.0
CA A:ASP165 4.3 27.5 1.0
N A:GLY200 4.3 26.5 1.0
O A:GLY195 4.4 38.0 1.0
CA A:GLY197 4.4 38.1 1.0
CA A:GLN199 4.5 28.1 1.0
N A:ILE198 4.5 35.2 1.0
CB A:ASP201 4.5 21.7 1.0
N A:ILE166 4.5 26.4 1.0
CA A:ILE198 4.6 30.1 1.0
N A:VAL167 4.6 24.0 1.0
CA A:ASP201 4.6 25.9 1.0
CA A:ILE166 4.7 23.7 1.0
C A:PRO196 4.7 35.6 1.0
CH2 A:TRP116 4.8 28.9 1.0
CG2 A:VAL167 4.8 28.6 1.0
O A:HOH413 4.9 44.0 1.0
O A:PRO196 5.0 35.6 1.0
O A:GLY200 5.0 25.0 1.0

Calcium binding site 3 out of 3 in 5i12

Go back to Calcium Binding Sites List in 5i12
Calcium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Mmp-9 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27).


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 the Catalytic Domain of Mmp-9 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:32.3
occ:1.00
 O A:HOH451 2.3 41.0 1.0
O A:GLU208 2.3 23.7 1.0
O A:ASP206 2.4 20.8 1.0
OD2 A:ASP131 2.4 21.7 1.0
OD1 A:ASP206 2.4 22.4 1.0
O A:HOH476 3.1 77.5 1.0
CG A:ASP131 3.1 28.3 1.0
OD1 A:ASP131 3.2 29.4 1.0
C A:ASP206 3.3 22.7 1.0
CG A:ASP206 3.4 21.6 1.0
C A:GLU208 3.5 19.8 1.0
CA A:ASP206 3.7 16.8 1.0
OG A:SER129 3.9 22.8 1.0
CD1 A:TRP210 4.1 17.9 1.0
CB A:ASP206 4.1 18.2 1.0
O A:HOH446 4.1 42.9 1.0
O A:HOH510 4.2 55.0 1.0
OD2 A:ASP206 4.2 26.9 1.0
N A:GLU208 4.2 20.6 1.0
CA A:LEU209 4.3 21.7 1.0
O A:HOH508 4.3 26.2 1.0
N A:LEU209 4.3 20.9 1.0
N A:ASP207 4.4 20.1 1.0
C A:ASP207 4.5 22.6 1.0
CB A:ASP131 4.5 24.9 1.0
CA A:GLU208 4.5 22.4 1.0
O A:HOH487 4.6 45.2 1.0
N A:TRP210 4.6 20.8 1.0
CA A:ASP207 4.6 19.9 1.0
O A:HOH426 4.6 29.2 1.0
NE1 A:TRP210 4.6 20.0 1.0
CB A:SER129 5.0 22.3 1.0
C A:LEU209 5.0 24.2 1.0

Reference:

E.Nuti, D.Cuffaro, F.D'andrea, L.Rosalia, L.Tepshi, M.Fabbi, G.Carbotti, S.Ferrini, S.Santamaria, C.Camodeca, L.Ciccone, E.Orlandini, S.Nencetti, E.A.Stura, V.Dive, A.Rossello. Sugar-Based Arylsulfonamide Carboxylates As Selective and Water-Soluble Matrix Metalloproteinase-12 Inhibitors. Chemmedchem V. 11 1626 2016.
ISSN: ESSN 1860-7187
PubMed: 27356908
DOI: 10.1002/CMDC.201600235
Page generated: Sun Jul 14 20:18:18 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