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Calcium in PDB 2ow9: Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor

Protein crystallography data

The structure of Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor, PDB code: 2ow9 was solved by A.G.Pavlovsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.71 / 1.74
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 140.764, 36.343, 71.684, 90.00, 93.53, 90.00
R / Rfree (%) 16.7 / 19.1

Other elements in 2ow9:

The structure of Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor (pdb code 2ow9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor, PDB code: 2ow9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 2ow9

Go back to Calcium Binding Sites List in 2ow9
Calcium binding site 1 out of 7 in the Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:10.3
occ:1.00
 O A:LEU163 2.2 12.6 1.0
OD2 A:ASP181 2.3 9.6 1.0
O A:GLY159 2.3 11.5 1.0
OE2 A:GLU184 2.3 11.2 1.0
O A:SER161 2.3 12.4 1.0
OD1 A:ASP158 2.4 11.9 1.0
C A:LEU163 3.3 12.1 1.0
CG A:ASP181 3.4 9.2 1.0
C A:SER161 3.5 13.0 1.0
CD A:GLU184 3.5 10.8 1.0
C A:GLY159 3.5 12.2 1.0
CG A:ASP158 3.6 13.2 1.0
N A:LEU163 3.9 12.4 1.0
N A:SER161 3.9 13.0 1.0
C A:PRO160 4.0 12.8 1.0
CB A:ASP181 4.0 9.6 1.0
N A:GLY159 4.1 11.8 1.0
CA A:LEU163 4.1 13.0 1.0
OD2 A:ASP158 4.2 14.3 1.0
OE1 A:GLU184 4.2 10.8 1.0
CA A:SER161 4.2 13.5 1.0
N A:LEU164 4.3 11.5 1.0
N A:ASP158 4.3 11.9 1.0
C A:GLY162 4.3 12.8 1.0
C A:ASP158 4.3 12.1 1.0
OD1 A:ASP181 4.4 8.4 1.0
O A:PRO160 4.4 12.8 1.0
CA A:PRO160 4.4 12.7 1.0
N A:PRO160 4.4 12.4 1.0
CA A:LEU164 4.4 10.6 1.0
CA A:GLY159 4.4 12.0 1.0
CG A:GLU184 4.5 10.7 1.0
N A:GLY162 4.5 12.8 1.0
CB A:LEU163 4.5 13.5 1.0
O A:HOH865 4.6 17.1 1.0
CA A:ASP158 4.7 12.1 1.0
CA A:GLY162 4.7 12.7 1.0
CB A:ASP158 4.8 12.4 1.0
O A:ASP158 4.8 11.9 1.0
O A:GLY162 4.9 12.8 1.0
CD2 A:LEU164 5.0 11.1 1.0

Calcium binding site 2 out of 7 in 2ow9

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Calcium binding site 2 out of 7 in the Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca604

b:13.8
occ:1.00
 O A:GLY175 2.3 11.6 1.0
O A:HOH726 2.3 14.9 1.0
O A:ASN173 2.3 16.7 1.0
O A:ASP141 2.4 10.7 1.0
O A:HOH702 2.4 10.5 1.0
OD1 A:ASP177 2.5 11.5 1.0
C A:GLY175 3.5 12.0 1.0
CG A:ASP177 3.5 10.2 1.0
C A:ASP141 3.5 11.1 1.0
C A:ASN173 3.5 16.9 1.0
C A:TYR174 3.9 15.0 1.0
OD2 A:ASP177 3.9 10.7 1.0
N A:GLY175 4.0 13.8 1.0
O A:TYR174 4.0 14.3 1.0
N A:ASP177 4.1 9.7 1.0
O A:ALA140 4.1 11.5 1.0
CA A:GLY175 4.2 12.9 1.0
CA A:ASP141 4.3 11.0 1.0
O A:HOH738 4.3 22.6 1.0
O A:GLY171 4.4 15.1 1.0
N A:TYR174 4.4 16.2 1.0
CA A:ASN173 4.4 17.6 1.0
O A:HOH855 4.4 28.3 1.0
CA A:TYR174 4.4 16.1 1.0
N A:ASN173 4.4 17.2 1.0
N A:GLY176 4.4 11.1 1.0
N A:ILE142 4.5 10.7 1.0
O A:HOH854 4.5 36.0 1.0
CB A:ASP177 4.6 9.7 1.0
CA A:GLY176 4.6 10.5 1.0
C A:GLY176 4.6 10.0 1.0
CA A:ILE142 4.6 10.8 1.0
N A:MET143 4.7 10.7 1.0
O A:HOH715 4.7 11.5 1.0
CA A:ASP177 4.7 9.6 1.0
C A:PRO172 4.8 16.9 1.0
CH2 A:TRP92 4.9 11.9 1.0
CG A:MET143 4.9 11.1 1.0
O A:PRO172 5.0 16.9 1.0

Calcium binding site 3 out of 7 in 2ow9

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Calcium binding site 3 out of 7 in the Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca605

b:29.6
occ:1.00
 OD2 A:ASP107 2.5 17.9 1.0
O A:GLU184 2.6 11.9 1.0
O A:ASP182 2.6 11.0 1.0
OD1 A:ASP182 2.8 12.8 1.0
OD1 A:ASP107 2.8 16.8 1.0
CG A:ASP107 3.0 15.0 1.0
C A:ASP182 3.5 10.7 1.0
C A:GLU184 3.8 11.6 1.0
CG A:ASP182 3.9 11.2 1.0
OG1 A:THR105 3.9 10.8 1.0
CA A:ASP182 4.1 10.6 1.0
O A:HOH912 4.2 34.0 1.0
CB A:ASP182 4.4 11.0 1.0
CD1 A:TRP186 4.4 11.4 1.0
CB A:ASP107 4.4 13.2 1.0
N A:GLU184 4.4 11.0 1.0
N A:ASP183 4.5 10.5 1.0
CA A:THR185 4.6 12.6 1.0
N A:THR185 4.6 11.8 1.0
C A:ASP183 4.6 10.8 1.0
CD A:PRO106 4.7 11.9 1.0
CA A:ASP183 4.8 10.7 1.0
CA A:GLU184 4.8 11.2 1.0
O A:HOH845 4.8 27.9 1.0
N A:TRP186 4.9 12.4 1.0
OD2 A:ASP182 4.9 12.8 1.0
NE1 A:TRP186 4.9 10.8 1.0

Calcium binding site 4 out of 7 in 2ow9

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Calcium binding site 4 out of 7 in the Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca608

b:14.2
occ:1.00
 O B:LEU163 2.2 18.1 1.0
OD2 B:ASP181 2.3 11.7 1.0
OE2 B:GLU184 2.3 15.7 1.0
O B:GLY159 2.3 16.1 1.0
OD1 B:ASP158 2.3 14.3 1.0
O B:SER161 2.4 17.8 1.0
C B:LEU163 3.4 18.0 1.0
CG B:ASP181 3.4 12.1 1.0
CG B:ASP158 3.5 15.6 1.0
CD B:GLU184 3.5 14.5 1.0
C B:SER161 3.5 18.6 1.0
C B:GLY159 3.5 16.3 1.0
N B:LEU163 3.9 18.9 1.0
N B:SER161 3.9 18.2 1.0
C B:PRO160 4.0 17.9 1.0
CA B:LEU163 4.1 18.6 1.0
OD2 B:ASP158 4.1 16.4 1.0
CB B:ASP181 4.1 11.3 1.0
N B:GLY159 4.1 15.0 1.0
N B:ASP158 4.3 14.4 1.0
CA B:SER161 4.3 18.6 1.0
C B:GLY162 4.3 18.9 1.0
C B:ASP158 4.3 15.1 1.0
OD1 B:ASP181 4.4 12.0 1.0
N B:LEU164 4.4 17.0 1.0
OE1 B:GLU184 4.4 13.9 1.0
CG B:GLU184 4.4 13.9 1.0
O B:PRO160 4.4 18.0 1.0
N B:PRO160 4.4 17.0 1.0
CA B:GLY159 4.5 15.7 1.0
CA B:PRO160 4.5 17.4 1.0
CB B:LEU163 4.5 18.7 1.0
N B:GLY162 4.5 18.4 1.0
CA B:LEU164 4.6 15.9 1.0
CA B:ASP158 4.6 15.0 1.0
CB B:ASP158 4.7 14.9 1.0
CA B:GLY162 4.7 18.8 1.0
O B:ASP158 4.8 15.0 1.0
O B:GLY162 4.9 19.4 1.0

Calcium binding site 5 out of 7 in 2ow9

Go back to Calcium Binding Sites List in 2ow9
Calcium binding site 5 out of 7 in the Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca609

b:18.7
occ:1.00
 O B:ASN173 2.3 20.4 1.0
O B:GLY175 2.3 16.3 1.0
O B:HOH630 2.3 15.4 1.0
O B:ASP141 2.3 12.7 1.0
O B:HOH621 2.4 14.9 1.0
OD1 B:ASP177 2.5 13.6 1.0
CG B:ASP177 3.4 13.6 1.0
C B:ASP141 3.5 12.9 1.0
C B:GLY175 3.5 16.2 1.0
C B:ASN173 3.5 20.6 1.0
OD2 B:ASP177 3.8 13.3 1.0
C B:TYR174 3.9 18.8 1.0
O B:ALA140 3.9 14.2 1.0
O B:HOH637 4.0 18.4 1.0
O B:TYR174 4.0 18.1 1.0
N B:GLY175 4.1 17.8 1.0
N B:ASP177 4.1 13.8 1.0
CA B:ASP141 4.2 13.5 1.0
CA B:GLY175 4.3 16.9 1.0
N B:TYR174 4.4 20.0 1.0
CA B:TYR174 4.4 19.7 1.0
CA B:ASN173 4.4 21.0 1.0
O B:GLY171 4.4 19.6 1.0
N B:GLY176 4.4 15.7 1.0
N B:ILE142 4.5 12.6 1.0
N B:ASN173 4.5 20.6 1.0
CA B:GLY176 4.5 14.8 1.0
C B:GLY176 4.6 14.3 1.0
O B:HOH810 4.6 37.3 1.0
CB B:ASP177 4.6 13.2 1.0
N B:MET143 4.7 12.0 1.0
CA B:ILE142 4.7 12.4 1.0
CA B:ASP177 4.7 13.1 1.0
O B:HOH624 4.7 19.9 1.0
C B:PRO172 4.8 20.2 1.0
CG B:MET143 4.8 12.8 1.0
C B:ALA140 4.9 14.5 1.0
O B:PRO172 4.9 20.1 1.0

Calcium binding site 6 out of 7 in 2ow9

Go back to Calcium Binding Sites List in 2ow9
Calcium binding site 6 out of 7 in the Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca610

b:11.8
occ:1.00
 O B:ASP182 2.4 11.2 1.0
OD2 B:ASP107 2.4 12.9 1.0
O B:HOH629 2.4 16.6 1.0
O B:GLU184 2.4 13.1 1.0
OD1 B:ASP182 2.5 10.9 1.0
O B:HOH653 2.5 12.7 1.0
OD1 B:ASP107 2.6 12.7 1.0
CG B:ASP107 2.8 12.9 1.0
C B:ASP182 3.3 11.3 1.0
CG B:ASP182 3.5 11.5 1.0
C B:GLU184 3.6 12.9 1.0
CA B:ASP182 3.8 11.3 1.0
OG1 B:THR105 4.0 11.2 1.0
CB B:ASP182 4.1 11.5 1.0
CA B:THR185 4.3 12.7 1.0
CB B:ASP107 4.3 12.7 1.0
CD1 B:TRP186 4.4 12.6 1.0
N B:THR185 4.4 12.7 1.0
N B:ASP183 4.4 11.5 1.0
N B:GLU184 4.4 12.3 1.0
OD2 B:ASP182 4.5 11.3 1.0
C B:ASP183 4.6 12.1 1.0
CA B:GLU184 4.7 13.0 1.0
CA B:ASP183 4.7 11.7 1.0
O B:HOH676 4.7 23.2 1.0
N B:TRP186 4.7 12.2 1.0
O B:HOH777 4.7 36.1 1.0
NE1 B:TRP186 4.9 11.7 1.0

Calcium binding site 7 out of 7 in 2ow9

Go back to Calcium Binding Sites List in 2ow9
Calcium binding site 7 out of 7 in the Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca611

b:17.5
occ:1.00
 O B:HOH789 2.2 29.2 1.0
NE2 B:HIS230 2.3 23.3 1.0
O B:HOH790 2.8 33.6 1.0
CD2 B:HIS230 3.2 23.3 1.0
CE1 B:HIS230 3.3 23.7 1.0
CG B:HIS230 4.3 22.8 1.0
ND1 B:HIS230 4.4 24.0 1.0

Reference:

A.R.Johnson, A.G.Pavlovsky, D.F.Ortwine, F.Prior, C.F.Man, D.A.Bornemeier, C.A.Banotai, W.T.Mueller, P.Mcconnell, C.Yan, V.Baragi, C.Lesch, W.H.Roark, M.Wilson, K.Datta, R.Guzman, H.K.Han, R.D.Dyer. Discovery and Characterization of A Novel Inhibitor of Matrix Metalloprotease-13 That Reduces Cartilage Damage in Vivo Without Joint Fibroplasia Side Effects. J.Biol.Chem. V. 282 27781 2007.
ISSN: ISSN 0021-9258
PubMed: 17623656
DOI: 10.1074/JBC.M703286200
Page generated: Fri Jul 12 14:47:20 2024

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