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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

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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

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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

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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

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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

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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: Fri Jul 12 14:47:20 2024

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