Atomistry » Calcium » PDB 3nur-3ojk » 3o2x
Atomistry »
  Calcium »
    PDB 3nur-3ojk »
      3o2x »

Calcium in PDB 3o2x: Mmp-13 in Complex with Selective Tetrazole Core Inhibitor

Protein crystallography data

The structure of Mmp-13 in Complex with Selective Tetrazole Core Inhibitor, PDB code: 3o2x was solved by J.R.Kiefer, T.E.Barta, D.P.Becker, K.J.Mathis, J.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.72 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.864, 95.257, 120.076, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21

Other elements in 3o2x:

The structure of Mmp-13 in Complex with Selective Tetrazole Core Inhibitor also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Zinc (Zn) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Mmp-13 in Complex with Selective Tetrazole Core Inhibitor (pdb code 3o2x). 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-13 in Complex with Selective Tetrazole Core Inhibitor, PDB code: 3o2x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3o2x

Go back to Calcium Binding Sites List in 3o2x
Calcium binding site 1 out of 8 in the Mmp-13 in Complex with Selective Tetrazole Core Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mmp-13 in Complex with Selective Tetrazole Core Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1996

b:37.7
occ:1.00
O A:ASN1194 2.5 17.4 1.0
O A:HOH479 2.7 22.7 1.0
OD1 A:ASP1198 2.9 8.7 1.0
O A:HOH167 3.1 8.7 1.0
O A:ASP1162 3.1 9.1 1.0
O A:GLY1196 3.2 11.8 1.0
O A:HOH201 3.6 15.0 1.0
C A:ASN1194 3.6 17.2 1.0
CG A:ASP1198 3.6 9.0 1.0
O A:ALA1161 3.7 9.7 1.0
OD2 A:ASP1198 3.8 9.0 1.0
C A:ASP1162 3.9 8.8 1.0
C A:TYR1195 4.1 15.3 1.0
CG A:MET1164 4.1 9.2 1.0
C A:GLY1196 4.3 12.2 1.0
N A:GLY1196 4.3 14.1 1.0
CA A:TYR1195 4.3 16.4 1.0
O A:TYR1195 4.3 14.7 1.0
N A:TYR1195 4.4 16.7 1.0
CA A:ASP1162 4.6 9.0 1.0
N A:MET1164 4.6 8.8 1.0
CA A:ASN1194 4.6 17.6 1.0
N A:ILE1163 4.7 8.9 1.0
C A:ALA1161 4.8 9.3 1.0
CA A:GLY1196 4.9 13.0 1.0
CB A:MET1164 4.9 8.8 1.0
N A:ASP1198 4.9 9.6 1.0
CA A:ILE1163 4.9 8.7 1.0
CB A:ASP1198 5.0 9.6 1.0

Calcium binding site 2 out of 8 in 3o2x

Go back to Calcium Binding Sites List in 3o2x
Calcium binding site 2 out of 8 in the Mmp-13 in Complex with Selective Tetrazole Core Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mmp-13 in Complex with Selective Tetrazole Core Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1997

b:6.7
occ:1.00
OE2 A:GLU1205 2.2 9.9 1.0
O A:GLY1180 2.3 7.4 1.0
OD2 A:ASP1202 2.3 5.2 1.0
O A:SER1182 2.3 7.7 1.0
O A:LEU1184 2.3 8.4 1.0
OD1 A:ASP1179 2.4 6.8 1.0
CG A:ASP1202 3.4 6.8 1.0
CD A:GLU1205 3.4 8.9 1.0
C A:LEU1184 3.5 8.5 1.0
C A:GLY1180 3.5 7.2 1.0
C A:SER1182 3.5 8.0 1.0
CG A:ASP1179 3.6 7.6 1.0
N A:LEU1184 3.8 8.6 1.0
N A:SER1182 4.0 7.7 1.0
CB A:ASP1202 4.1 7.4 1.0
C A:PRO1181 4.1 7.3 1.0
N A:GLY1180 4.1 6.8 1.0
CA A:LEU1184 4.1 8.6 1.0
OD2 A:ASP1179 4.2 8.7 1.0
C A:GLY1183 4.2 8.6 1.0
OE1 A:GLU1205 4.3 9.1 1.0
N A:ASP1179 4.3 6.5 1.0
C A:ASP1179 4.3 6.8 1.0
OD1 A:ASP1202 4.3 7.3 1.0
CG A:GLU1205 4.3 8.7 1.0
CA A:SER1182 4.3 7.8 1.0
N A:PRO1181 4.4 7.3 1.0
CA A:PRO1181 4.4 7.4 1.0
CA A:GLY1180 4.4 7.1 1.0
CB A:LEU1184 4.5 8.6 1.0
O A:HOH223 4.5 21.4 1.0
N A:GLY1183 4.5 8.3 1.0
O A:PRO1181 4.5 7.3 1.0
N A:LEU1185 4.6 8.2 1.0
CA A:GLY1183 4.6 8.5 1.0
CA A:ASP1179 4.6 6.7 1.0
CB A:ASP1179 4.7 6.9 1.0
O A:GLY1183 4.7 8.8 1.0
O A:ASP1179 4.8 6.5 1.0
CA A:LEU1185 4.8 8.1 1.0

Calcium binding site 3 out of 8 in 3o2x

Go back to Calcium Binding Sites List in 3o2x
Calcium binding site 3 out of 8 in the Mmp-13 in Complex with Selective Tetrazole Core Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mmp-13 in Complex with Selective Tetrazole Core Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2996

b:34.6
occ:1.00
O B:ASN2194 2.7 17.3 1.0
OD1 B:ASP2198 2.7 9.4 1.0
O B:HOH435 2.8 13.8 1.0
O B:GLY2196 2.9 12.6 1.0
O B:HOH92 3.1 7.8 1.0
O B:ASP2162 3.2 7.6 1.0
CG B:ASP2198 3.4 10.0 1.0
OD2 B:ASP2198 3.6 9.7 1.0
O B:HOH308 3.6 11.1 1.0
O B:HOH461 3.8 29.1 1.0
C B:ASN2194 3.8 17.2 1.0
C B:TYR2195 3.9 15.4 1.0
C B:GLY2196 4.0 12.9 1.0
CG B:MET2164 4.1 8.0 1.0
O B:ALA2161 4.1 7.0 1.0
N B:GLY2196 4.1 14.4 1.0
CA B:TYR2195 4.1 16.5 1.0
O B:TYR2195 4.2 14.8 1.0
C B:ASP2162 4.2 7.2 1.0
O B:HOH361 4.3 10.4 1.0
N B:TYR2195 4.4 16.8 1.0
CA B:GLY2196 4.6 13.6 1.0
N B:ASP2198 4.7 10.4 1.0
N B:MET2164 4.7 7.8 1.0
CB B:ASP2198 4.8 9.9 1.0
CB B:MET2164 4.8 7.8 1.0
CA B:ASP2162 4.9 7.0 1.0
CA B:ASN2194 5.0 17.4 1.0

Calcium binding site 4 out of 8 in 3o2x

Go back to Calcium Binding Sites List in 3o2x
Calcium binding site 4 out of 8 in the Mmp-13 in Complex with Selective Tetrazole Core Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mmp-13 in Complex with Selective Tetrazole Core Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2997

b:11.9
occ:1.00
OE2 B:GLU2205 2.2 10.8 1.0
O B:GLY2180 2.2 10.5 1.0
OD2 B:ASP2202 2.3 5.6 1.0
OD1 B:ASP2179 2.3 9.3 1.0
O B:LEU2184 2.4 9.9 1.0
O B:SER2182 2.4 11.7 1.0
CD B:GLU2205 3.4 8.6 1.0
CG B:ASP2202 3.5 7.3 1.0
C B:GLY2180 3.5 10.5 1.0
C B:LEU2184 3.5 10.0 1.0
CG B:ASP2179 3.5 9.7 1.0
C B:SER2182 3.5 11.7 1.0
N B:LEU2184 3.8 10.7 1.0
N B:SER2182 4.0 11.8 1.0
N B:GLY2180 4.0 9.7 1.0
C B:PRO2181 4.1 11.5 1.0
OD2 B:ASP2179 4.1 9.7 1.0
CA B:LEU2184 4.2 10.5 1.0
CB B:ASP2202 4.2 7.2 1.0
N B:ASP2179 4.2 8.8 1.0
C B:ASP2179 4.2 9.5 1.0
C B:GLY2183 4.2 11.1 1.0
OE1 B:GLU2205 4.2 8.0 1.0
CG B:GLU2205 4.3 7.3 1.0
CA B:SER2182 4.3 12.0 1.0
OD1 B:ASP2202 4.4 7.7 1.0
CA B:GLY2180 4.4 10.2 1.0
N B:PRO2181 4.4 10.9 1.0
O B:HOH730 4.4 25.9 1.0
O B:PRO2181 4.5 11.2 1.0
CA B:PRO2181 4.5 11.2 1.0
N B:GLY2183 4.5 11.5 1.0
N B:LEU2185 4.5 9.2 1.0
CB B:LEU2184 4.5 10.7 1.0
CA B:ASP2179 4.6 9.1 1.0
CA B:GLY2183 4.6 11.4 1.0
CB B:ASP2179 4.6 9.2 1.0
O B:ASP2179 4.7 9.4 1.0
CA B:LEU2185 4.8 8.9 1.0
O B:GLY2183 4.8 11.2 1.0

Calcium binding site 5 out of 8 in 3o2x

Go back to Calcium Binding Sites List in 3o2x
Calcium binding site 5 out of 8 in the Mmp-13 in Complex with Selective Tetrazole Core Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Mmp-13 in Complex with Selective Tetrazole Core Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1996

b:35.4
occ:1.00
O C:HOH256 2.6 13.1 1.0
O C:ASN1194 2.6 10.4 1.0
OD1 C:ASP1198 2.7 9.2 1.0
O C:HOH185 3.1 6.8 1.0
O C:ASP1162 3.1 8.1 1.0
O C:GLY1196 3.2 9.0 1.0
O C:HOH44 3.5 6.9 1.0
CG C:ASP1198 3.5 8.2 1.0
OD2 C:ASP1198 3.7 8.9 1.0
C C:ASN1194 3.7 10.3 1.0
C C:TYR1195 3.7 9.7 1.0
O C:TYR1195 3.9 9.4 1.0
CA C:TYR1195 4.0 9.9 1.0
O C:ALA1161 4.0 7.4 1.0
C C:ASP1162 4.0 7.7 1.0
N C:GLY1196 4.1 9.4 1.0
C C:GLY1196 4.2 9.0 1.0
CG C:MET1164 4.3 8.5 1.0
N C:TYR1195 4.3 10.1 1.0
O C:HOH758 4.5 18.0 1.0
CA C:GLY1196 4.7 9.3 1.0
CA C:ASP1162 4.7 7.4 1.0
N C:ASP1198 4.7 8.3 1.0
N C:MET1164 4.8 8.3 1.0
CB C:ASP1198 4.8 8.5 1.0
CA C:ASN1194 4.9 10.3 1.0
N C:ILE1163 4.9 7.8 1.0
CB C:MET1164 5.0 8.6 1.0
N C:ASN1194 5.0 10.3 1.0

Calcium binding site 6 out of 8 in 3o2x

Go back to Calcium Binding Sites List in 3o2x
Calcium binding site 6 out of 8 in the Mmp-13 in Complex with Selective Tetrazole Core Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Mmp-13 in Complex with Selective Tetrazole Core Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1997

b:8.0
occ:1.00
OE2 C:GLU1205 2.2 10.9 1.0
O C:LEU1184 2.3 8.6 1.0
OD2 C:ASP1202 2.3 7.7 1.0
O C:GLY1180 2.3 7.3 1.0
O C:SER1182 2.4 8.4 1.0
OD1 C:ASP1179 2.4 6.2 1.0
CG C:ASP1202 3.4 7.6 1.0
C C:LEU1184 3.4 8.1 1.0
CD C:GLU1205 3.4 10.4 1.0
C C:GLY1180 3.5 7.4 1.0
C C:SER1182 3.5 8.5 1.0
CG C:ASP1179 3.6 7.7 1.0
N C:SER1182 3.9 8.0 1.0
N C:LEU1184 3.9 7.9 1.0
C C:PRO1181 4.0 7.6 1.0
CB C:ASP1202 4.0 8.2 1.0
CA C:LEU1184 4.1 8.1 1.0
OD2 C:ASP1179 4.1 8.2 1.0
OE1 C:GLU1205 4.2 11.3 1.0
N C:GLY1180 4.2 7.6 1.0
C C:GLY1183 4.3 8.2 1.0
CA C:SER1182 4.3 8.5 1.0
OD1 C:ASP1202 4.3 6.5 1.0
N C:ASP1179 4.3 7.3 1.0
CA C:PRO1181 4.3 7.4 1.0
O C:PRO1181 4.4 7.4 1.0
CG C:GLU1205 4.4 9.7 1.0
N C:PRO1181 4.4 7.3 1.0
C C:ASP1179 4.4 7.5 1.0
CB C:LEU1184 4.5 8.0 1.0
N C:LEU1185 4.5 7.9 1.0
CA C:GLY1180 4.5 7.6 1.0
N C:GLY1183 4.5 8.5 1.0
O C:HOH118 4.6 18.4 1.0
CA C:ASP1179 4.7 7.5 1.0
CA C:GLY1183 4.7 8.3 1.0
CA C:LEU1185 4.7 7.8 1.0
CB C:ASP1179 4.8 7.3 1.0
O C:GLY1183 4.8 7.7 1.0
O C:ASP1179 4.9 7.7 1.0

Calcium binding site 7 out of 8 in 3o2x

Go back to Calcium Binding Sites List in 3o2x
Calcium binding site 7 out of 8 in the Mmp-13 in Complex with Selective Tetrazole Core Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Mmp-13 in Complex with Selective Tetrazole Core Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2996

b:37.2
occ:1.00
O D:HOH62 2.5 16.9 1.0
OD1 D:ASP2198 2.7 6.8 1.0
O D:ASN2194 2.7 9.3 1.0
O D:ASP2162 3.1 8.8 1.0
O D:HOH16 3.2 5.4 1.0
O D:GLY2196 3.3 8.2 1.0
CG D:ASP2198 3.4 7.9 1.0
O D:HOH72 3.5 13.0 1.0
OD2 D:ASP2198 3.6 7.4 1.0
O D:ALA2161 3.8 8.3 1.0
C D:ASN2194 3.8 9.2 1.0
C D:TYR2195 3.9 8.5 1.0
C D:ASP2162 3.9 8.4 1.0
CG D:MET2164 4.0 8.3 1.0
CA D:TYR2195 4.1 8.7 1.0
O D:TYR2195 4.1 8.6 1.0
N D:GLY2196 4.2 8.2 1.0
C D:GLY2196 4.3 7.8 1.0
N D:TYR2195 4.4 8.9 1.0
N D:MET2164 4.6 8.1 1.0
CA D:ASP2162 4.7 8.3 1.0
N D:ILE2163 4.8 8.3 1.0
CB D:ASP2198 4.8 7.5 1.0
N D:ASP2198 4.8 7.3 1.0
CB D:MET2164 4.8 8.3 1.0
CA D:GLY2196 4.9 8.2 1.0
C D:ALA2161 4.9 7.7 1.0
CA D:ILE2163 5.0 8.2 1.0
CA D:ASN2194 5.0 9.4 1.0

Calcium binding site 8 out of 8 in 3o2x

Go back to Calcium Binding Sites List in 3o2x
Calcium binding site 8 out of 8 in the Mmp-13 in Complex with Selective Tetrazole Core Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Mmp-13 in Complex with Selective Tetrazole Core Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2997

b:7.2
occ:1.00
O D:LEU2184 2.2 9.3 1.0
OE2 D:GLU2205 2.3 9.8 1.0
OD2 D:ASP2202 2.3 6.1 1.0
OD1 D:ASP2179 2.3 6.5 1.0
O D:GLY2180 2.3 8.0 1.0
O D:SER2182 2.3 9.2 1.0
CG D:ASP2202 3.4 7.4 1.0
C D:LEU2184 3.4 9.1 1.0
CG D:ASP2179 3.5 6.8 1.0
C D:SER2182 3.5 9.5 1.0
CD D:GLU2205 3.5 9.7 1.0
C D:GLY2180 3.6 8.0 1.0
N D:LEU2184 3.8 9.1 1.0
N D:SER2182 3.9 9.3 1.0
OD2 D:ASP2179 4.1 6.7 1.0
CB D:ASP2202 4.1 7.8 1.0
C D:PRO2181 4.1 8.8 1.0
CA D:LEU2184 4.1 9.2 1.0
N D:GLY2180 4.2 7.2 1.0
C D:GLY2183 4.2 9.1 1.0
N D:ASP2179 4.2 7.0 1.0
CA D:SER2182 4.3 9.8 1.0
OE1 D:GLU2205 4.3 9.6 1.0
OD1 D:ASP2202 4.3 6.9 1.0
C D:ASP2179 4.3 7.1 1.0
CB D:LEU2184 4.4 9.4 1.0
CG D:GLU2205 4.4 8.8 1.0
CA D:PRO2181 4.4 8.6 1.0
N D:PRO2181 4.5 8.2 1.0
N D:LEU2185 4.5 8.6 1.0
CA D:GLY2180 4.5 7.6 1.0
N D:GLY2183 4.5 9.1 1.0
O D:PRO2181 4.5 8.7 1.0
CA D:ASP2179 4.6 7.0 1.0
CA D:GLY2183 4.6 9.2 1.0
CB D:ASP2179 4.7 6.8 1.0
O D:GLY2183 4.7 9.0 1.0
CA D:LEU2185 4.8 8.6 1.0
O D:ASP2179 4.8 6.9 1.0

Reference:

T.E.Barta, D.P.Becker, L.J.Bedell, S.L.Hockerman, J.R.Kiefer, M.H.Li, C.I.Villamill, J.G.Rico, J.J.Mcdonald. Mmp-13 in Complex with Selective Tetrazole Core Inhibitor To Be Published.
Page generated: Sat Dec 12 04:22:53 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy