Atomistry » Calcium » PDB 2ovu-2p9i » 2ow0
Atomistry »
  Calcium »
    PDB 2ovu-2p9i »
      2ow0 »

Calcium in PDB 2ow0: Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor

Enzymatic activity of Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor

All present enzymatic activity of Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor:
3.4.24.35;

Protein crystallography data

The structure of Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor, PDB code: 2ow0 was solved by A.Tochowicz, W.Bode, K.Maskos, P.Goettig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 55.190, 55.190, 260.361, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 27.1

Other elements in 2ow0:

The structure of Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor also contains other interesting chemical elements:

Iodine (I) 2 atoms
Chlorine (Cl) 6 atoms
Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor (pdb code 2ow0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor, PDB code: 2ow0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2ow0

Go back to Calcium Binding Sites List in 2ow0
Calcium binding site 1 out of 8 in the Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca446

b:28.6
occ:1.00
O A:GLN199 2.4 21.9 1.0
O A:HOH564 2.4 21.4 1.0
O A:HOH583 2.4 25.7 1.0
O A:ASP165 2.5 17.5 1.0
O A:GLY197 2.5 32.2 1.0
OD1 A:ASP201 2.6 20.0 1.0
C A:GLN199 3.5 23.8 1.0
C A:ASP165 3.6 19.5 1.0
CG A:ASP201 3.6 20.3 1.0
C A:GLY197 3.7 34.1 1.0
C A:ILE198 4.0 30.8 1.0
N A:ASP201 4.1 19.5 1.0
OD2 A:ASP201 4.1 21.1 1.0
O A:ALA164 4.1 23.7 1.0
N A:GLN199 4.1 28.8 1.0
O A:ILE198 4.2 30.6 1.0
O A:HOH531 4.2 23.9 1.0
CA A:ASP165 4.3 20.7 1.0
O A:GLY195 4.3 33.5 1.0
N A:GLY200 4.4 19.3 1.0
CA A:GLY200 4.4 18.5 1.0
C A:GLY200 4.4 17.4 1.0
CA A:GLN199 4.4 26.6 1.0
CA A:ILE198 4.5 32.9 1.0
N A:ILE198 4.5 33.0 1.0
N A:ILE166 4.5 18.0 1.0
N A:GLY197 4.6 35.6 1.0
O A:HOH594 4.6 28.5 1.0
CA A:GLY197 4.6 34.6 1.0
CA A:ILE166 4.7 16.9 1.0
CH2 A:TRP116 4.7 20.8 1.0
CB A:ASP201 4.7 19.4 1.0
CA A:ASP201 4.8 18.9 1.0
N A:VAL167 4.8 14.8 1.0
C A:PRO196 4.8 35.7 1.0
CG2 A:VAL167 5.0 16.9 1.0

Calcium binding site 2 out of 8 in 2ow0

Go back to Calcium Binding Sites List in 2ow0
Calcium binding site 2 out of 8 in the Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca447

b:21.4
occ:1.00
O A:GLY183 2.1 37.3 1.0
OE2 A:GLU208 2.2 20.2 1.0
OD2 A:ASP205 2.2 16.3 1.0
O A:LEU187 2.2 22.4 1.0
O A:ASP185 2.3 36.7 1.0
OD1 A:ASP182 2.4 35.1 1.0
C A:GLY183 3.3 38.3 1.0
CG A:ASP205 3.3 17.1 1.0
CD A:GLU208 3.3 20.1 1.0
C A:LEU187 3.4 23.4 1.0
C A:ASP185 3.4 37.5 1.0
CG A:ASP182 3.7 36.2 1.0
N A:GLY183 3.7 36.8 1.0
N A:LEU187 3.8 27.9 1.0
N A:ASP185 3.9 38.6 1.0
CG A:GLU208 3.9 20.8 1.0
CB A:ASP205 4.0 16.1 1.0
C A:LYS184 4.1 39.2 1.0
CA A:GLY183 4.1 37.5 1.0
CA A:LEU187 4.1 26.0 1.0
CA A:ASP185 4.2 38.7 1.0
C A:GLY186 4.2 29.9 1.0
C A:ASP182 4.2 35.5 1.0
OD1 A:ASP205 4.2 14.9 1.0
N A:ASP182 4.3 31.7 1.0
N A:LYS184 4.3 38.0 1.0
O A:LYS184 4.4 38.5 1.0
OE1 A:GLU208 4.4 19.0 1.0
OD2 A:ASP182 4.4 36.5 1.0
N A:LEU188 4.4 20.3 1.0
N A:GLY186 4.4 35.4 1.0
CA A:LYS184 4.5 39.9 1.0
CB A:LEU187 4.6 27.1 1.0
CA A:GLY186 4.6 32.4 1.0
CA A:ASP182 4.6 34.3 1.0
CA A:LEU188 4.6 20.3 1.0
CB A:ASP182 4.7 35.6 1.0
O A:GLY186 4.8 29.4 1.0
O A:ASP182 4.9 35.1 1.0
CB A:PHE181 5.0 23.1 1.0

Calcium binding site 3 out of 8 in 2ow0

Go back to Calcium Binding Sites List in 2ow0
Calcium binding site 3 out of 8 in the Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca448

b:35.4
occ:1.00
OD1 A:ASP131 2.2 13.8 1.0
O A:GLU208 2.3 22.1 1.0
O A:ASP206 2.4 19.2 1.0
OD1 A:ASP206 2.5 20.2 1.0
CG A:ASP131 3.0 20.0 1.0
C A:ASP206 3.2 19.4 1.0
OD2 A:ASP131 3.3 15.2 1.0
CG A:ASP206 3.4 22.3 1.0
C A:GLU208 3.5 20.7 1.0
CA A:ASP206 3.7 18.3 1.0
CD1 A:TRP210 3.9 15.2 1.0
OG A:SER129 3.9 17.1 1.0
N A:GLU208 4.0 18.6 1.0
CB A:ASP206 4.2 19.7 1.0
OD2 A:ASP206 4.2 23.3 1.0
N A:ASP207 4.2 18.5 1.0
C A:ASP207 4.3 19.7 1.0
CB A:ASP131 4.3 19.6 1.0
CA A:LEU209 4.3 21.3 1.0
N A:LEU209 4.4 21.6 1.0
N A:TRP210 4.4 16.8 1.0
CA A:GLU208 4.5 20.4 1.0
CA A:ASP207 4.5 19.6 1.0
NE1 A:TRP210 4.6 13.4 1.0
O A:ASP207 4.9 18.1 1.0
CG A:TRP210 4.9 14.4 1.0
C A:LEU209 4.9 19.9 1.0
O A:ASP205 4.9 14.4 1.0
N A:ASP131 5.0 19.1 1.0

Calcium binding site 4 out of 8 in 2ow0

Go back to Calcium Binding Sites List in 2ow0
Calcium binding site 4 out of 8 in the Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca449

b:40.8
occ:1.00
O A:SER149 2.1 20.6 1.0
O A:HOH535 2.3 22.9 1.0
O A:THR152 2.3 24.3 1.0
O A:HOH547 2.4 21.1 1.0
O A:HOH528 2.7 20.0 1.0
C A:SER149 3.3 21.2 1.0
C A:THR152 3.5 23.5 1.0
N A:THR152 4.0 23.0 1.0
C A:ALA150 4.2 20.5 1.0
CA A:SER149 4.2 18.8 1.0
N A:ALA150 4.3 19.4 1.0
CA A:ALA150 4.3 21.1 1.0
O A:LEU154 4.3 16.8 1.0
O A:ALA150 4.3 19.3 1.0
N A:PRO153 4.3 23.6 1.0
CA A:PRO153 4.3 24.4 1.0
CA A:THR152 4.4 23.1 1.0
N A:VAL151 4.5 20.6 1.0
O A:HOH609 4.6 29.1 1.0
CB A:SER149 4.7 18.4 1.0
C A:PRO153 4.7 23.8 1.0
N A:LEU154 4.9 21.9 1.0
C A:VAL151 5.0 22.0 1.0

Calcium binding site 5 out of 8 in 2ow0

Go back to Calcium Binding Sites List in 2ow0
Calcium binding site 5 out of 8 in the Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca446

b:26.5
occ:1.00
O B:GLN199 2.4 19.1 1.0
O B:ASP165 2.5 17.3 1.0
O B:HOH540 2.5 20.6 1.0
OD1 B:ASP201 2.5 15.7 1.0
O B:HOH505 2.5 19.5 1.0
O B:GLY197 2.5 24.3 1.0
CG B:ASP201 3.5 16.9 1.0
C B:GLN199 3.5 20.5 1.0
C B:ASP165 3.5 17.8 1.0
C B:GLY197 3.7 23.0 1.0
OD2 B:ASP201 3.9 16.5 1.0
O B:ALA164 4.0 21.7 1.0
N B:ASP201 4.0 15.0 1.0
C B:ILE198 4.0 23.3 1.0
O B:HOH547 4.1 23.0 1.0
N B:GLN199 4.2 21.5 1.0
O B:ILE198 4.2 21.4 1.0
CA B:ASP165 4.3 19.1 1.0
C B:GLY200 4.3 17.4 1.0
CA B:GLY200 4.3 16.0 1.0
N B:GLY200 4.3 19.7 1.0
O B:GLY195 4.3 19.2 1.0
CA B:ILE198 4.5 24.1 1.0
CA B:GLN199 4.5 21.9 1.0
N B:ILE166 4.5 16.8 1.0
N B:ILE198 4.6 24.2 1.0
CB B:ASP201 4.6 15.4 1.0
N B:VAL167 4.6 15.4 1.0
CA B:ASP201 4.7 16.7 1.0
CA B:ILE166 4.7 15.9 1.0
N B:GLY197 4.7 24.2 1.0
CH2 B:TRP116 4.7 19.2 1.0
CA B:GLY197 4.7 24.3 1.0
CG2 B:VAL167 4.8 16.1 1.0
C B:ALA164 4.9 22.2 1.0
C B:PRO196 5.0 23.7 1.0

Calcium binding site 6 out of 8 in 2ow0

Go back to Calcium Binding Sites List in 2ow0
Calcium binding site 6 out of 8 in the Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca447

b:19.9
occ:1.00
OE2 B:GLU208 2.2 23.1 1.0
O B:GLY183 2.2 23.1 1.0
O B:LEU187 2.2 21.3 1.0
O B:ASP185 2.3 25.7 1.0
OD1 B:ASP182 2.4 25.0 1.0
OD2 B:ASP205 2.4 21.0 1.0
CD B:GLU208 3.3 20.8 1.0
CG B:ASP205 3.4 20.7 1.0
C B:LEU187 3.4 21.9 1.0
C B:GLY183 3.4 23.2 1.0
C B:ASP185 3.5 27.2 1.0
CG B:ASP182 3.6 25.0 1.0
N B:LEU187 3.8 24.3 1.0
N B:GLY183 3.9 23.0 1.0
N B:ASP185 3.9 26.4 1.0
CB B:ASP205 4.0 19.4 1.0
OE1 B:GLU208 4.1 18.1 1.0
C B:LYS184 4.1 26.4 1.0
CA B:LEU187 4.2 24.3 1.0
C B:GLY186 4.2 25.9 1.0
C B:ASP182 4.2 23.3 1.0
CA B:GLY183 4.2 24.0 1.0
OD2 B:ASP182 4.3 27.3 1.0
CG B:GLU208 4.3 21.6 1.0
OD1 B:ASP205 4.3 17.4 1.0
CA B:ASP185 4.3 27.2 1.0
N B:ASP182 4.4 20.5 1.0
N B:LYS184 4.4 23.7 1.0
N B:LEU188 4.4 20.9 1.0
N B:GLY186 4.5 26.8 1.0
CA B:LYS184 4.5 25.6 1.0
O B:LYS184 4.5 24.4 1.0
CA B:GLY186 4.6 26.5 1.0
CA B:LEU188 4.6 20.6 1.0
CA B:ASP182 4.6 23.1 1.0
CB B:ASP182 4.7 23.8 1.0
CB B:LEU187 4.7 28.4 1.0
O B:ASP182 4.8 21.7 1.0
O B:GLY186 4.8 25.8 1.0
O B:HOH521 5.0 16.4 1.0

Calcium binding site 7 out of 8 in 2ow0

Go back to Calcium Binding Sites List in 2ow0
Calcium binding site 7 out of 8 in the Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca448

b:35.7
occ:1.00
OD2 B:ASP131 2.2 14.0 1.0
O B:GLU208 2.2 20.9 1.0
O B:ASP206 2.5 16.8 1.0
OD1 B:ASP206 2.7 17.7 1.0
CG B:ASP131 3.1 16.3 1.0
C B:ASP206 3.3 19.7 1.0
C B:GLU208 3.4 21.0 1.0
OD1 B:ASP131 3.5 15.2 1.0
CG B:ASP206 3.6 20.9 1.0
CA B:ASP206 3.8 19.4 1.0
CD1 B:TRP210 3.8 13.0 1.0
N B:GLU208 4.0 21.7 1.0
OG B:SER129 4.1 19.0 1.0
CA B:LEU209 4.1 19.5 1.0
N B:LEU209 4.1 19.3 1.0
N B:TRP210 4.2 16.4 1.0
CB B:ASP206 4.2 18.8 1.0
N B:ASP207 4.3 19.9 1.0
C B:ASP207 4.3 21.9 1.0
CA B:GLU208 4.4 20.7 1.0
OD2 B:ASP206 4.4 22.5 1.0
CB B:ASP131 4.4 16.1 1.0
NE1 B:TRP210 4.5 13.6 1.0
C B:LEU209 4.6 17.2 1.0
CA B:ASP207 4.6 22.5 1.0
CG B:TRP210 4.7 13.6 1.0
O B:ASP205 4.9 19.4 1.0
O B:ASP207 4.9 22.1 1.0

Calcium binding site 8 out of 8 in 2ow0

Go back to Calcium Binding Sites List in 2ow0
Calcium binding site 8 out of 8 in the Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Mmp-9 Active Site Mutant with Iodine-Labeled Carboxylate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca449

b:43.4
occ:1.00
O B:THR152 2.2 26.2 1.0
O B:SER149 2.3 25.6 1.0
O B:HOH528 2.5 23.4 1.0
O B:HOH552 2.5 32.5 1.0
O B:HOH593 2.6 30.1 1.0
O B:HOH551 2.6 20.2 1.0
C B:THR152 3.3 25.7 1.0
C B:SER149 3.5 25.5 1.0
N B:THR152 4.0 26.0 1.0
CA B:PRO153 4.2 25.6 1.0
N B:PRO153 4.2 25.9 1.0
O B:HOH543 4.2 28.8 1.0
C B:ALA150 4.3 27.2 1.0
CA B:THR152 4.3 25.1 1.0
O B:LEU154 4.3 20.5 1.0
O B:HOH512 4.4 32.7 1.0
CA B:SER149 4.4 23.4 1.0
N B:ALA150 4.4 26.3 1.0
CA B:ALA150 4.4 27.4 1.0
O B:ALA150 4.4 25.8 1.0
C B:PRO153 4.6 25.6 1.0
N B:VAL151 4.7 26.1 1.0
N B:LEU154 4.8 23.9 1.0
CB B:SER149 4.8 23.1 1.0
C B:VAL151 5.0 26.2 1.0

Reference:

A.Tochowicz, K.Maskos, R.Huber, R.Oltenfreiter, V.Dive, A.Yiotakis, M.Zanda, W.Bode, P.Goettig. Crystal Structures of Mmp-9 Complexes with Five Inhibitors: Contribution of the Flexible ARG424 Side-Chain to Selectivity. J.Mol.Biol. V. 371 989 2007.
ISSN: ISSN 0022-2836
PubMed: 17599356
DOI: 10.1016/J.JMB.2007.05.068
Page generated: Sat Dec 12 03:49:04 2020

Last articles

Zn in 7M6U
Zn in 7NNG
Zn in 7NEE
Zn in 7NEU
Zn in 7M3K
Zn in 7KWD
Zn in 7KYH
Zn in 7KNG
Zn in 7KY2
Zn in 7KYF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy