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Calcium in PDB 4a7b: MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22

Protein crystallography data

The structure of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22, PDB code: 4a7b was solved by D.Hargreaves, S.Gerhardt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.02 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 135.854, 36.220, 95.568, 90.00, 131.10, 90.00
R / Rfree (%) 19.3 / 25.3

Other elements in 4a7b:

The structure of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22 (pdb code 4a7b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22, PDB code: 4a7b:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4a7b

Go back to Calcium Binding Sites List in 4a7b
Calcium binding site 1 out of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1277

b:25.8
occ:1.00
 O A:HOH2048 2.3 20.5 1.0
O A:GLY196 2.3 23.2 1.0
O A:ASN194 2.4 31.2 1.0
O A:ASP162 2.4 23.1 1.0
O A:HOH2049 2.4 25.4 1.0
OD1 A:ASP198 2.5 22.2 1.0
CG A:ASP198 3.4 21.8 1.0
C A:GLY196 3.5 22.9 1.0
C A:ASN194 3.5 28.9 1.0
C A:ASP162 3.6 21.5 1.0
OD2 A:ASP198 3.9 22.4 1.0
N A:GLY196 3.9 23.9 1.0
C A:TYR195 4.0 24.5 1.0
N A:ASP198 4.1 20.4 1.0
O A:ALA161 4.1 24.8 1.0
O A:HOH2072 4.1 34.0 1.0
O A:TYR195 4.2 24.7 1.0
CA A:GLY196 4.2 22.9 1.0
CA A:ASP162 4.4 24.0 1.0
O A:GLY192 4.4 25.5 1.0
N A:TYR195 4.4 29.4 1.0
CA A:ASN194 4.4 31.4 1.0
N A:ASN194 4.4 31.5 1.0
CA A:TYR195 4.5 28.2 1.0
O A:HOH2050 4.5 29.9 1.0
N A:GLY197 4.5 21.9 1.0
N A:ILE163 4.6 21.3 1.0
CB A:ASP198 4.6 19.7 1.0
C A:GLY197 4.7 21.1 1.0
CA A:GLY197 4.7 20.2 1.0
C A:PRO193 4.7 29.7 1.0
CA A:ASP198 4.8 20.6 1.0
CH2 A:TRP113 4.8 25.6 1.0
CA A:ILE163 4.8 20.9 1.0
N A:MET164 4.8 21.7 1.0
CG A:MET164 4.8 21.0 1.0
O A:PRO193 4.9 31.0 1.0

Calcium binding site 2 out of 4 in 4a7b

Go back to Calcium Binding Sites List in 4a7b
Calcium binding site 2 out of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1279

b:24.1
occ:1.00
 O A:GLY180 2.2 24.8 1.0
OE2 A:GLU205 2.3 28.6 1.0
OD2 A:ASP202 2.3 22.7 1.0
O A:SER182 2.3 32.2 1.0
O A:LEU184 2.4 24.3 1.0
OD1 A:ASP179 2.4 24.5 1.0
CG A:ASP202 3.4 22.5 1.0
C A:GLY180 3.4 25.6 1.0
CD A:GLU205 3.5 25.8 1.0
C A:SER182 3.5 31.3 1.0
C A:LEU184 3.5 24.7 1.0
CG A:ASP179 3.6 28.6 1.0
N A:SER182 3.9 26.0 1.0
CB A:ASP202 3.9 19.9 1.0
C A:PRO181 4.0 25.7 1.0
N A:LEU184 4.0 27.6 1.0
OD2 A:ASP179 4.1 31.5 1.0
N A:GLY180 4.2 26.4 1.0
CA A:SER182 4.2 29.4 1.0
OE1 A:GLU205 4.3 25.3 1.0
C A:GLY183 4.3 31.8 1.0
N A:ASP179 4.3 26.0 1.0
CA A:LEU184 4.3 26.7 1.0
OD1 A:ASP202 4.3 19.3 1.0
O A:PRO181 4.3 25.8 1.0
CA A:PRO181 4.3 25.9 1.0
N A:PRO181 4.3 26.1 1.0
CG A:GLU205 4.4 24.3 1.0
C A:ASP179 4.4 26.7 1.0
CA A:GLY180 4.4 25.4 1.0
N A:LEU185 4.4 22.0 1.0
N A:GLY183 4.5 31.2 1.0
CA A:GLY183 4.5 30.3 1.0
CA A:LEU185 4.6 21.7 1.0
CA A:ASP179 4.7 27.8 1.0
CB A:ASP179 4.8 25.7 1.0
O A:ASP179 4.8 29.8 1.0
CB A:LEU184 4.9 27.3 1.0
O A:GLY183 5.0 30.4 1.0

Calcium binding site 3 out of 4 in 4a7b

Go back to Calcium Binding Sites List in 4a7b
Calcium binding site 3 out of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1275

b:22.5
occ:1.00
 O B:HOH2048 2.3 20.2 1.0
O B:ASP162 2.3 20.4 1.0
O B:ASN194 2.3 28.6 1.0
O B:GLY196 2.4 23.7 1.0
OD1 B:ASP198 2.4 21.1 1.0
O B:HOH2047 2.4 24.8 1.0
CG B:ASP198 3.4 21.0 1.0
C B:ASP162 3.4 21.8 1.0
C B:GLY196 3.5 24.2 1.0
C B:ASN194 3.6 29.9 1.0
OD2 B:ASP198 3.7 21.1 1.0
C B:TYR195 3.9 27.7 1.0
N B:GLY196 4.0 26.1 1.0
O B:ALA161 4.1 23.7 1.0
O B:TYR195 4.1 24.6 1.0
N B:ASP198 4.2 20.9 1.0
CA B:ASP162 4.2 21.8 1.0
CA B:GLY196 4.3 25.3 1.0
O B:HOH2060 4.3 42.8 1.0
O B:HOH2061 4.3 28.0 1.0
CA B:TYR195 4.4 30.1 1.0
N B:TYR195 4.4 29.4 1.0
N B:ASN194 4.4 32.3 1.0
N B:ILE163 4.4 21.2 1.0
O B:GLY192 4.4 26.2 1.0
N B:GLY197 4.5 23.2 1.0
CA B:ASN194 4.5 32.9 1.0
N B:MET164 4.6 20.4 1.0
CB B:ASP198 4.6 19.9 1.0
CA B:GLY197 4.6 20.9 1.0
CA B:ILE163 4.6 21.0 1.0
C B:GLY197 4.7 21.1 1.0
C B:PRO193 4.7 30.9 1.0
CG B:MET164 4.8 19.2 1.0
CA B:ASP198 4.8 20.2 1.0
O B:PRO193 5.0 27.8 1.0

Calcium binding site 4 out of 4 in 4a7b

Go back to Calcium Binding Sites List in 4a7b
Calcium binding site 4 out of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1276

b:30.7
occ:1.00
 OE2 B:GLU205 2.2 27.1 1.0
O B:LEU184 2.2 27.4 1.0
O B:SER182 2.3 31.9 1.0
OD1 B:ASP179 2.3 31.8 1.0
O B:GLY180 2.4 31.8 1.0
OD2 B:ASP202 2.5 28.7 1.0
C B:LEU184 3.4 30.4 1.0
C B:SER182 3.4 35.4 1.0
CD B:GLU205 3.4 28.2 1.0
CG B:ASP179 3.4 29.9 1.0
CG B:ASP202 3.5 27.2 1.0
C B:GLY180 3.7 32.2 1.0
N B:SER182 3.8 35.3 1.0
N B:LEU184 3.9 31.1 1.0
OD2 B:ASP179 3.9 32.3 1.0
CB B:ASP202 4.0 26.0 1.0
C B:PRO181 4.0 35.6 1.0
CA B:SER182 4.1 35.8 1.0
CA B:LEU184 4.1 31.1 1.0
N B:GLY180 4.2 30.9 1.0
OE1 B:GLU205 4.2 30.6 1.0
C B:GLY183 4.2 33.1 1.0
C B:ASP179 4.3 31.6 1.0
N B:ASP179 4.3 30.5 1.0
CG B:GLU205 4.3 27.8 1.0
OD1 B:ASP202 4.4 27.4 1.0
O B:PRO181 4.4 36.6 1.0
N B:LEU185 4.4 27.8 1.0
N B:GLY183 4.4 33.8 1.0
CA B:PRO181 4.5 34.0 1.0
N B:PRO181 4.6 32.3 1.0
CA B:GLY180 4.6 30.4 1.0
CB B:LEU184 4.6 31.8 1.0
CB B:ASP179 4.6 30.8 1.0
CA B:ASP179 4.6 31.6 1.0
CA B:GLY183 4.6 32.6 1.0
CA B:LEU185 4.6 27.8 1.0
O B:ASP179 4.7 30.4 1.0
O B:GLY183 4.8 31.3 1.0

Reference:

C.De Savi, A.D.Morley, I.Nash, G.Karoutchi, K.Page, A.Ting, S.Gerhardt. Lead Optimisation of Selective Non-Zinc Binding Inhibitors of MMP13. Part 2. Bioorg.Med.Chem.Lett. V. 22 271 2012.
ISSN: ISSN 0960-894X
PubMed: 22153941
DOI: 10.1016/J.BMCL.2011.11.034
Page generated: Tue Jul 8 18:25:12 2025

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