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Calcium in PDB 3elm: Crystal Structure of Mmp-13 Complexed with Inhibitor 24F

Protein crystallography data

The structure of Crystal Structure of Mmp-13 Complexed with Inhibitor 24F, PDB code: 3elm was solved by R.Kulathila, L.Monovich, J.Koehn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.56 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.500, 36.070, 95.180, 90.00, 130.53, 90.00
R / Rfree (%) n/a / n/a

Other elements in 3elm:

The structure of Crystal Structure of Mmp-13 Complexed with Inhibitor 24F also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F (pdb code 3elm). 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 of Mmp-13 Complexed with Inhibitor 24F, PDB code: 3elm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3elm

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Calcium binding site 1 out of 7 in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F


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 Mmp-13 Complexed with Inhibitor 24F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:13.4
occ:1.00
 OE2 A:GLU205 2.2 17.6 1.0
O A:GLY180 2.3 12.8 1.0
OD2 A:ASP202 2.3 12.6 1.0
O A:LEU184 2.3 14.7 1.0
O A:SER182 2.3 18.3 1.0
OD1 A:ASP179 2.4 15.4 1.0
CG A:ASP202 3.4 12.6 1.0
CD A:GLU205 3.4 16.6 1.0
C A:SER182 3.4 19.9 1.0
C A:GLY180 3.5 12.2 1.0
C A:LEU184 3.5 15.4 1.0
CG A:ASP179 3.6 17.0 1.0
N A:SER182 3.8 16.1 1.0
N A:LEU184 3.9 14.3 1.0
C A:PRO181 4.0 17.1 1.0
CB A:ASP202 4.1 12.6 1.0
N A:GLY180 4.1 14.2 1.0
OD2 A:ASP179 4.1 17.2 1.0
C A:GLY183 4.2 17.1 1.0
CA A:SER182 4.2 20.2 1.0
CA A:LEU184 4.2 16.6 1.0
OE1 A:GLU205 4.2 16.6 1.0
N A:ASP179 4.3 14.6 1.0
C A:ASP179 4.3 15.1 1.0
OD1 A:ASP202 4.3 10.2 1.0
CG A:GLU205 4.3 13.3 1.0
O A:PRO181 4.3 16.9 1.0
N A:PRO181 4.4 14.5 1.0
N A:GLY183 4.4 19.1 1.0
CA A:PRO181 4.4 15.0 1.0
CA A:GLY180 4.4 13.5 1.0
CB A:LEU184 4.5 18.8 1.0
O A:HOH1078 4.5 27.1 1.0
CA A:GLY183 4.6 17.4 1.0
N A:LEU185 4.6 13.3 1.0
CA A:ASP179 4.6 16.1 1.0
O A:GLY183 4.7 17.7 1.0
O A:ASP179 4.7 15.9 1.0
CB A:ASP179 4.7 16.4 1.0
CA A:LEU185 4.8 12.3 1.0

Calcium binding site 2 out of 7 in 3elm

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Calcium binding site 2 out of 7 in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F


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 Mmp-13 Complexed with Inhibitor 24F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:25.8
occ:1.00
 O A:HOH1184 2.3 22.4 1.0
O A:GLU205 2.3 14.1 1.0
OD2 A:ASP128 2.4 12.8 1.0
OD2 A:ASP203 2.4 15.3 1.0
O A:ASP203 2.5 13.5 1.0
CG A:ASP128 3.2 16.0 1.0
C A:ASP203 3.3 12.8 1.0
OD1 A:ASP128 3.3 18.1 1.0
CG A:ASP203 3.5 17.1 1.0
C A:GLU205 3.6 14.6 1.0
CA A:ASP203 3.7 12.7 1.0
OG1 A:THR126 3.7 10.4 1.0
CD1 A:TRP207 3.9 11.8 1.0
CB A:ASP203 4.0 14.5 1.0
N A:GLU205 4.2 12.9 1.0
CA A:THR206 4.3 13.4 1.0
N A:ASP204 4.3 12.6 1.0
N A:THR206 4.4 14.0 1.0
CD A:PRO127 4.4 12.7 1.0
C A:ASP204 4.4 14.1 1.0
NE1 A:TRP207 4.5 11.4 1.0
OD1 A:ASP203 4.5 15.8 1.0
N A:TRP207 4.5 12.2 1.0
CA A:GLU205 4.6 12.8 1.0
CB A:ASP128 4.6 12.6 1.0
CA A:ASP204 4.7 13.1 1.0
O A:ASP202 4.9 13.4 1.0
C A:THR206 5.0 13.5 1.0
CG A:TRP207 5.0 11.2 1.0
CB A:THR126 5.0 10.8 1.0

Calcium binding site 3 out of 7 in 3elm

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Calcium binding site 3 out of 7 in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F


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 Mmp-13 Complexed with Inhibitor 24F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:20.5
occ:1.00
 O A:GLY196 2.2 13.9 1.0
O A:ASN194 2.4 22.7 1.0
O A:ASP162 2.4 13.3 1.0
OD1 A:ASP198 2.4 13.9 1.0
O A:HOH1183 2.5 13.2 1.0
O A:HOH1132 2.5 14.8 1.0
C A:GLY196 3.4 14.7 1.0
CG A:ASP198 3.4 15.8 1.0
C A:ASP162 3.5 13.0 1.0
C A:ASN194 3.6 22.0 1.0
N A:GLY196 3.8 16.6 1.0
C A:TYR195 3.8 17.9 1.0
OD2 A:ASP198 3.9 16.6 1.0
O A:HOH1044 4.0 25.1 1.0
N A:ASP198 4.1 11.2 1.0
O A:TYR195 4.1 15.9 1.0
O A:ALA161 4.2 15.5 1.0
CA A:GLY196 4.2 14.7 1.0
CA A:TYR195 4.2 20.6 1.0
CA A:ASP162 4.3 13.7 1.0
N A:TYR195 4.4 21.5 1.0
N A:GLY197 4.4 12.6 1.0
O A:GLY192 4.4 17.2 1.0
N A:ILE163 4.5 11.8 1.0
CA A:GLY197 4.5 12.9 1.0
C A:GLY197 4.5 12.4 1.0
CA A:ASN194 4.6 22.8 1.0
CB A:ASP198 4.6 12.2 1.0
CH2 A:TRP113 4.6 14.8 1.0
N A:MET164 4.7 10.6 1.0
CA A:ILE163 4.7 11.8 1.0
O A:HOH1027 4.7 20.6 1.0
CA A:ASP198 4.7 11.7 1.0
N A:ASN194 4.7 20.7 1.0
CG A:MET164 4.8 13.6 1.0

Calcium binding site 4 out of 7 in 3elm

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Calcium binding site 4 out of 7 in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Mmp-13 Complexed with Inhibitor 24F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:32.8
occ:1.00
 O A:HOH1187 2.3 23.4 1.0
O A:THR149 2.3 13.1 1.0
O A:SER146 2.4 14.4 1.0
O A:HOH1020 2.5 15.4 1.0
O A:HOH1003 2.5 15.6 1.0
O A:HOH1007 2.6 15.9 1.0
C A:THR149 3.5 12.9 1.0
C A:SER146 3.7 15.9 1.0
N A:THR149 4.0 14.3 1.0
O A:HOH1140 4.1 30.6 1.0
C A:ASP147 4.3 16.5 1.0
CA A:PRO150 4.3 13.6 1.0
N A:PRO150 4.3 13.0 1.0
CA A:THR149 4.4 13.1 1.0
CA A:ASP147 4.4 16.8 1.0
O A:HOH1156 4.4 35.9 1.0
N A:ASP270 4.5 16.1 1.0
O A:ASP147 4.5 16.1 1.0
N A:ASP147 4.5 16.8 1.0
N A:VAL148 4.5 14.8 1.0
CA A:GLY269 4.6 15.3 1.0
CA A:SER146 4.6 15.4 1.0
O A:LEU151 4.7 16.3 1.0
O A:PRO268 4.7 16.6 1.0
C A:PRO150 4.7 15.1 1.0
N A:LEU151 4.9 13.9 1.0
O A:HOH1097 4.9 21.5 1.0
C A:VAL148 4.9 13.2 1.0
O A:ASP270 5.0 16.8 1.0

Calcium binding site 5 out of 7 in 3elm

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Calcium binding site 5 out of 7 in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Mmp-13 Complexed with Inhibitor 24F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:17.1
occ:1.00
 OE2 B:GLU205 2.2 20.8 1.0
O B:GLY180 2.3 20.3 1.0
O B:LEU184 2.3 16.3 1.0
OD1 B:ASP179 2.3 18.0 1.0
OD2 B:ASP202 2.3 14.0 1.0
O B:SER182 2.4 21.7 1.0
C B:LEU184 3.4 15.8 1.0
CG B:ASP202 3.4 15.7 1.0
C B:SER182 3.5 23.0 1.0
CD B:GLU205 3.5 18.3 1.0
C B:GLY180 3.5 19.3 1.0
CG B:ASP179 3.5 18.8 1.0
N B:SER182 3.8 20.8 1.0
N B:LEU184 3.9 18.5 1.0
C B:PRO181 4.0 20.0 1.0
N B:GLY180 4.0 18.7 1.0
OD2 B:ASP179 4.1 20.0 1.0
CB B:ASP202 4.1 13.5 1.0
CA B:LEU184 4.1 17.9 1.0
CA B:SER182 4.2 23.3 1.0
C B:ASP179 4.2 18.9 1.0
N B:ASP179 4.2 16.5 1.0
C B:GLY183 4.2 19.0 1.0
CG B:GLU205 4.3 19.3 1.0
OE1 B:GLU205 4.4 19.2 1.0
O B:PRO181 4.4 20.5 1.0
OD1 B:ASP202 4.4 15.5 1.0
N B:PRO181 4.4 19.2 1.0
CA B:GLY180 4.4 18.4 1.0
CA B:PRO181 4.5 19.6 1.0
CB B:LEU184 4.5 17.1 1.0
N B:LEU185 4.5 13.6 1.0
N B:GLY183 4.5 20.7 1.0
CA B:ASP179 4.6 18.1 1.0
CB B:ASP179 4.6 18.5 1.0
O B:ASP179 4.7 17.3 1.0
CA B:GLY183 4.7 20.3 1.0
O B:GLY183 4.7 17.0 1.0
CA B:LEU185 4.8 14.4 1.0

Calcium binding site 6 out of 7 in 3elm

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Calcium binding site 6 out of 7 in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Mmp-13 Complexed with Inhibitor 24F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:26.7
occ:1.00
 O B:HOH1143 2.2 26.9 1.0
O B:GLU205 2.3 15.0 1.0
OD2 B:ASP128 2.4 17.6 1.0
O B:ASP203 2.4 16.8 1.0
OD2 B:ASP203 2.4 13.7 1.0
O B:HOH1201 3.0 30.2 1.0
CG B:ASP128 3.1 18.2 1.0
OD1 B:ASP128 3.2 19.1 1.0
C B:ASP203 3.3 16.2 1.0
C B:GLU205 3.5 16.2 1.0
CG B:ASP203 3.5 15.3 1.0
CA B:ASP203 3.7 15.3 1.0
OG1 B:THR126 3.8 11.9 1.0
CB B:ASP203 4.0 15.0 1.0
CD1 B:TRP207 4.0 15.1 1.0
N B:GLU205 4.1 14.0 1.0
CA B:THR206 4.1 13.9 1.0
N B:THR206 4.3 15.2 1.0
N B:ASP204 4.3 14.8 1.0
C B:ASP204 4.4 15.4 1.0
NE1 B:TRP207 4.5 13.6 1.0
CA B:GLU205 4.5 14.8 1.0
N B:TRP207 4.5 14.0 1.0
OD1 B:ASP203 4.5 15.2 1.0
CB B:ASP128 4.6 16.3 1.0
CA B:ASP204 4.6 15.0 1.0
CD B:PRO127 4.6 12.4 1.0
O B:HOH1188 4.9 34.1 1.0
C B:THR206 4.9 14.0 1.0
O B:ASP202 4.9 14.1 1.0

Calcium binding site 7 out of 7 in 3elm

Go back to Calcium Binding Sites List in 3elm
Calcium binding site 7 out of 7 in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Mmp-13 Complexed with Inhibitor 24F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:18.0
occ:1.00
 O B:ASP162 2.3 12.4 1.0
O B:GLY196 2.3 14.5 1.0
O B:HOH1186 2.3 17.2 1.0
O B:ASN194 2.4 20.5 1.0
OD1 B:ASP198 2.4 12.4 1.0
O B:HOH1185 2.4 15.7 1.0
C B:ASP162 3.4 13.7 1.0
C B:GLY196 3.4 15.3 1.0
CG B:ASP198 3.5 13.0 1.0
C B:ASN194 3.5 21.7 1.0
C B:TYR195 3.9 19.0 1.0
N B:GLY196 3.9 16.6 1.0
OD2 B:ASP198 4.0 13.4 1.0
O B:TYR195 4.1 17.8 1.0
O B:ALA161 4.1 15.1 1.0
N B:ASP198 4.1 13.7 1.0
O B:HOH1082 4.2 19.9 1.0
CA B:ASP162 4.2 14.7 1.0
CA B:GLY196 4.2 14.7 1.0
CA B:TYR195 4.3 20.1 1.0
N B:TYR195 4.4 18.9 1.0
O B:GLY192 4.4 21.4 1.0
N B:ILE163 4.4 12.7 1.0
N B:GLY197 4.4 13.2 1.0
CA B:ASN194 4.5 23.4 1.0
N B:ASN194 4.5 23.3 1.0
CA B:ILE163 4.6 12.5 1.0
CA B:GLY197 4.6 13.6 1.0
C B:GLY197 4.6 14.1 1.0
N B:MET164 4.6 11.6 1.0
CB B:ASP198 4.6 13.1 1.0
CA B:ASP198 4.8 14.0 1.0
O B:HOH1115 4.8 21.2 1.0
CH2 B:TRP113 4.8 19.3 1.0
C B:PRO193 4.8 23.1 1.0
CG B:MET164 4.8 14.2 1.0

Reference:

L.G.Monovich, R.A.Tommasi, R.A.Fujimoto, V.Blancuzzi, K.Clark, W.D.Cornell, R.Doti, J.Doughty, J.Fang, D.Farley, J.Fitt, V.Ganu, R.Goldberg, R.Goldstein, S.Lavoie, R.Kulathila, W.Macchia, D.T.Parker, R.Melton, E.O'byrne, G.Pastor, T.Pellas, E.Quadros, N.Reel, D.M.Roland, Y.Sakane, H.Singh, J.Skiles, J.Somers, K.Toscano, A.Wigg, S.Zhou, L.Zhu, W.C.Shieh, S.Xue, L.W.Mcquire. Discovery of Potent, Selective, and Orally Active Carboxylic Acid Based Inhibitors of Matrix Metalloproteinase-13 J.Med.Chem. V. 52 3523 2009.
ISSN: ISSN 0022-2623
PubMed: 19422229
DOI: 10.1021/JM801394M
Page generated: Tue Jul 8 11:57:45 2025

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