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Calcium in PDB 3i7g: Mmp-13 in Complex with A Non Zinc-Chelating Inhibitor

Protein crystallography data

The structure of Mmp-13 in Complex with A Non Zinc-Chelating Inhibitor, PDB code: 3i7g was solved by N.A.Farrow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.37 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 133.770, 36.100, 95.333, 90.00, 130.77, 90.00
R / Rfree (%) 17.3 / 22.8

Other elements in 3i7g:

The structure of Mmp-13 in Complex with A Non Zinc-Chelating Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Mmp-13 in Complex with A Non Zinc-Chelating Inhibitor (pdb code 3i7g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Mmp-13 in Complex with A Non Zinc-Chelating Inhibitor, PDB code: 3i7g:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3i7g

Go back to Calcium Binding Sites List in 3i7g
Calcium binding site 1 out of 6 in the Mmp-13 in Complex with A Non Zinc-Chelating 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 A Non Zinc-Chelating Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1263

b:44.6
occ:1.00
 O A:GLU205 2.6 19.4 1.0
OD2 A:ASP128 2.7 19.9 1.0
O A:ASP203 2.9 19.8 1.0
OD2 A:ASP203 2.9 20.8 1.0
CG A:ASP128 3.3 27.2 1.0
OD1 A:ASP128 3.3 31.9 1.0
C A:ASP203 3.6 15.8 1.0
O A:HOH325 3.7 32.9 1.0
OG1 A:THR126 3.7 15.2 1.0
C A:GLU205 3.8 22.1 1.0
CG A:ASP203 3.9 24.3 1.0
CA A:ASP203 4.1 14.8 1.0
CD A:PRO127 4.3 16.7 1.0
CD1 A:TRP207 4.3 16.5 1.0
N A:GLU205 4.4 17.2 1.0
CB A:ASP203 4.5 16.8 1.0
CA A:THR206 4.6 18.9 1.0
C A:ASP204 4.6 19.5 1.0
N A:ASP204 4.6 11.4 1.0
CB A:ASP128 4.6 20.9 1.0
N A:THR206 4.7 15.0 1.0
OD1 A:ASP203 4.7 26.5 1.0
CA A:ASP204 4.8 16.4 1.0
CA A:GLU205 4.8 13.0 1.0
CG A:PRO127 4.8 18.9 1.0
NE1 A:TRP207 4.9 15.6 1.0
N A:TRP207 4.9 16.4 1.0
CB A:THR126 5.0 15.8 1.0

Calcium binding site 2 out of 6 in 3i7g

Go back to Calcium Binding Sites List in 3i7g
Calcium binding site 2 out of 6 in the Mmp-13 in Complex with A Non Zinc-Chelating 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 A Non Zinc-Chelating Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1264

b:22.7
occ:1.00
 O A:GLY180 2.3 24.6 1.0
OD2 A:ASP202 2.3 12.1 1.0
O A:LEU184 2.4 23.8 1.0
OE2 A:GLU205 2.4 26.4 1.0
O A:SER182 2.5 31.2 1.0
OD1 A:ASP179 2.5 20.7 1.0
CG A:ASP202 3.4 18.9 1.0
C A:GLY180 3.5 15.4 1.0
C A:LEU184 3.6 20.1 1.0
CD A:GLU205 3.6 26.7 1.0
C A:SER182 3.6 40.5 1.0
CG A:ASP179 3.7 28.8 1.0
N A:SER182 3.8 20.4 1.0
C A:PRO181 3.9 27.8 1.0
N A:LEU184 4.0 27.0 1.0
N A:GLY180 4.1 23.2 1.0
CB A:ASP202 4.1 12.5 1.0
CG A:GLU205 4.2 18.4 1.0
C A:ASP179 4.2 26.8 1.0
N A:ASP179 4.2 18.1 1.0
OD2 A:ASP179 4.3 24.2 1.0
CA A:PRO181 4.3 20.9 1.0
CA A:LEU184 4.3 19.9 1.0
OD1 A:ASP202 4.3 12.4 1.0
N A:PRO181 4.3 26.4 1.0
CA A:SER182 4.3 37.1 1.0
C A:GLY183 4.4 29.0 1.0
O A:PRO181 4.4 37.8 1.0
CA A:GLY180 4.4 21.8 1.0
N A:GLY183 4.6 33.0 1.0
O A:ASP179 4.6 24.9 1.0
N A:LEU185 4.6 21.6 1.0
OE1 A:GLU205 4.6 24.5 1.0
CA A:ASP179 4.6 25.7 1.0
CB A:LEU184 4.6 32.9 1.0
CA A:GLY183 4.7 30.2 1.0
CB A:ASP179 4.7 22.6 1.0
CA A:LEU185 4.8 20.7 1.0
O A:GLY183 4.9 29.5 1.0
O A:HOH47 5.0 12.9 1.0

Calcium binding site 3 out of 6 in 3i7g

Go back to Calcium Binding Sites List in 3i7g
Calcium binding site 3 out of 6 in the Mmp-13 in Complex with A Non Zinc-Chelating 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 A Non Zinc-Chelating Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1265

b:32.7
occ:1.00
 O A:GLY196 2.5 18.4 1.0
O A:HOH277 2.5 26.8 1.0
OD1 A:ASP198 2.5 14.6 1.0
O A:ASN194 2.6 26.5 1.0
O A:ASP162 2.6 19.6 1.0
O A:HOH319 2.8 23.8 1.0
CG A:ASP198 3.5 18.2 1.0
C A:ASP162 3.6 20.2 1.0
C A:GLY196 3.6 15.1 1.0
C A:ASN194 3.7 22.5 1.0
C A:TYR195 3.8 18.5 1.0
OD2 A:ASP198 3.8 17.1 1.0
O A:ALA161 3.9 17.7 1.0
N A:GLY196 4.0 16.9 1.0
CA A:TYR195 4.1 27.1 1.0
O A:TYR195 4.1 17.7 1.0
O A:HOH290 4.2 19.8 1.0
N A:ASP198 4.2 12.6 1.0
CA A:ASP162 4.3 14.9 1.0
N A:TYR195 4.4 19.0 1.0
CA A:GLY196 4.5 14.6 1.0
N A:ILE163 4.5 12.0 1.0
O A:HOH315 4.6 21.4 1.0
N A:GLY197 4.6 13.2 1.0
N A:MET164 4.6 14.7 1.0
CG A:MET164 4.6 14.7 1.0
CB A:ASP198 4.6 13.1 1.0
CA A:GLY197 4.6 13.5 1.0
C A:GLY197 4.7 14.0 1.0
CA A:ILE163 4.7 13.4 1.0
CA A:ASP198 4.8 12.5 1.0
CA A:ASN194 4.8 28.0 1.0
C A:ALA161 4.9 16.9 1.0
CH2 A:TRP113 4.9 20.4 1.0

Calcium binding site 4 out of 6 in 3i7g

Go back to Calcium Binding Sites List in 3i7g
Calcium binding site 4 out of 6 in the Mmp-13 in Complex with A Non Zinc-Chelating 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 A Non Zinc-Chelating Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2263

b:49.8
occ:1.00
 OD2 B:ASP128 2.7 23.2 1.0
O B:GLU205 2.9 16.7 1.0
OD2 B:ASP203 2.9 19.9 1.0
O B:ASP203 3.0 18.0 1.0
CG B:ASP128 3.3 23.1 1.0
OD1 B:ASP128 3.4 22.3 1.0
OG1 B:THR126 3.6 15.7 1.0
C B:ASP203 3.8 16.1 1.0
O B:HOH322 3.9 33.9 1.0
CG B:ASP203 3.9 17.0 1.0
C B:GLU205 4.1 19.6 1.0
CD B:PRO127 4.1 17.6 1.0
CA B:ASP203 4.3 18.6 1.0
CD1 B:TRP207 4.5 18.9 1.0
CB B:ASP203 4.5 14.8 1.0
CB B:ASP128 4.5 18.4 1.0
CA B:THR206 4.6 19.0 1.0
CG B:PRO127 4.7 18.4 1.0
N B:GLU205 4.8 16.3 1.0
OD1 B:ASP203 4.8 17.7 1.0
N B:THR206 4.8 18.4 1.0
N B:ASP204 4.9 15.8 1.0
N B:ASP128 4.9 15.3 1.0
N B:PRO127 4.9 16.6 1.0
C B:ASP204 4.9 20.5 1.0
CB B:THR126 5.0 14.6 1.0
N B:TRP207 5.0 18.0 1.0

Calcium binding site 5 out of 6 in 3i7g

Go back to Calcium Binding Sites List in 3i7g
Calcium binding site 5 out of 6 in the Mmp-13 in Complex with A Non Zinc-Chelating 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 A Non Zinc-Chelating Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2264

b:21.3
occ:1.00
 OE1 B:GLU205 2.2 20.0 1.0
O B:LEU184 2.3 22.1 1.0
OD2 B:ASP202 2.3 13.1 1.0
O B:GLY180 2.4 22.4 1.0
OD1 B:ASP179 2.5 23.4 1.0
O B:SER182 2.5 27.7 1.0
CG B:ASP202 3.4 17.2 1.0
C B:LEU184 3.5 24.1 1.0
CD B:GLU205 3.5 23.2 1.0
C B:GLY180 3.6 23.5 1.0
CG B:ASP179 3.6 28.0 1.0
C B:SER182 3.6 34.5 1.0
N B:SER182 3.9 28.5 1.0
N B:LEU184 4.0 21.9 1.0
C B:PRO181 4.0 24.0 1.0
CB B:ASP202 4.1 16.1 1.0
OD2 B:ASP179 4.1 33.6 1.0
N B:GLY180 4.2 24.0 1.0
CA B:LEU184 4.2 23.9 1.0
N B:ASP179 4.2 17.8 1.0
OE2 B:GLU205 4.3 20.7 1.0
C B:ASP179 4.3 28.1 1.0
CA B:SER182 4.3 37.8 1.0
C B:GLY183 4.3 24.6 1.0
OD1 B:ASP202 4.3 12.4 1.0
CG B:GLU205 4.4 19.0 1.0
O B:PRO181 4.4 29.1 1.0
CA B:PRO181 4.4 22.5 1.0
N B:PRO181 4.4 19.8 1.0
CB B:LEU184 4.5 22.7 1.0
N B:LEU185 4.5 13.1 1.0
CA B:GLY180 4.5 20.7 1.0
N B:GLY183 4.6 27.8 1.0
CA B:LEU185 4.6 19.1 1.0
CA B:ASP179 4.7 19.5 1.0
O B:ASP179 4.7 27.2 1.0
CB B:ASP179 4.7 24.4 1.0
CA B:GLY183 4.7 24.7 1.0
O B:GLY183 4.8 28.7 1.0

Calcium binding site 6 out of 6 in 3i7g

Go back to Calcium Binding Sites List in 3i7g
Calcium binding site 6 out of 6 in the Mmp-13 in Complex with A Non Zinc-Chelating 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 A Non Zinc-Chelating Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2265

b:27.9
occ:1.00
 O B:GLY196 2.3 20.1 1.0
O B:ASP162 2.4 20.9 1.0
OD1 B:ASP198 2.5 15.2 1.0
O B:HOH311 2.5 25.4 1.0
O B:ASN194 2.5 24.6 1.0
O B:HOH292 2.7 24.0 1.0
CG B:ASP198 3.4 18.2 1.0
C B:GLY196 3.5 20.1 1.0
C B:ASP162 3.5 16.3 1.0
C B:ASN194 3.7 25.4 1.0
OD2 B:ASP198 3.9 19.4 1.0
C B:TYR195 3.9 25.3 1.0
O B:TYR195 4.0 20.6 1.0
O B:ALA161 4.0 21.3 1.0
N B:GLY196 4.0 17.8 1.0
O B:HOH30 4.1 18.4 1.0
N B:ASP198 4.1 16.0 1.0
CA B:ASP162 4.3 18.6 1.0
CA B:GLY196 4.3 19.7 1.0
CA B:TYR195 4.4 20.5 1.0
N B:GLY197 4.4 17.5 1.0
N B:ILE163 4.5 17.2 1.0
CA B:GLY197 4.5 20.0 1.0
N B:TYR195 4.5 24.1 1.0
O B:GLY192 4.5 26.7 1.0
C B:GLY197 4.6 20.4 1.0
CB B:ASP198 4.6 17.3 1.0
N B:MET164 4.6 14.7 1.0
N B:ASN194 4.6 28.1 1.0
CA B:ILE163 4.6 15.2 1.0
CA B:ASN194 4.7 33.7 1.0
CA B:ASP198 4.7 15.1 1.0
CG B:MET164 4.8 15.7 1.0
CH2 B:TRP113 4.9 29.6 1.0
C B:PRO193 4.9 31.8 1.0
O B:HOH324 5.0 25.7 1.0
C B:ALA161 5.0 17.4 1.0

Reference:

A.Heim-Riether, S.J.Taylor, S.Liang, D.A.Gao, Z.Xiong, E.Michael August, B.K.Collins, B.T.Farmer, K.Haverty, M.Hill-Drzewi, H.D.Junker, S.Mariana Margarit, N.Moss, T.Neumann, J.R.Proudfoot, L.S.Keenan, R.Sekul, Q.Zhang, J.Li, N.A.Farrow. Improving Potency and Selectivity of A New Class of Non-Zn-Chelating Mmp-13 Inhibitors. Bioorg.Med.Chem.Lett. V. 19 5321 2009.
ISSN: ISSN 0960-894X
PubMed: 19692239
DOI: 10.1016/J.BMCL.2009.07.151
Page generated: Sat Jul 13 11:24:08 2024

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