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Calcium in PDB 2yig: MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor

Protein crystallography data

The structure of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor, PDB code: 2yig was solved by S.Gerhardt, D.Hargreaves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.12 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.417, 36.074, 95.206, 90.00, 131.49, 90.00
R / Rfree (%) 18.4 / 22.1

Other elements in 2yig:

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

Zinc (Zn) 4 atoms
Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor (pdb code 2yig). 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, PDB code: 2yig:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2yig

Go back to Calcium Binding Sites List in 2yig
Calcium binding site 1 out of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:12.1
occ:1.00
 O A:ASP162 2.2 10.2 1.0
O A:ASN194 2.3 13.7 1.0
O A:GLY196 2.3 10.9 1.0
O A:HOH431 2.4 9.3 1.0
OD1 A:ASP198 2.4 10.6 1.0
O A:HOH464 2.4 12.8 1.0
C A:ASP162 3.4 11.9 1.0
CG A:ASP198 3.4 10.5 1.0
C A:ASN194 3.5 15.8 1.0
C A:GLY196 3.5 10.4 1.0
C A:TYR195 3.9 12.2 1.0
OD2 A:ASP198 3.9 11.1 1.0
N A:GLY196 4.0 12.2 1.0
O A:TYR195 4.1 11.8 1.0
O A:ALA161 4.1 12.2 1.0
N A:ASP198 4.2 8.5 1.0
CA A:TYR195 4.2 14.1 1.0
CA A:ASP162 4.3 11.8 1.0
N A:TYR195 4.3 14.7 1.0
CA A:GLY196 4.4 10.5 1.0
N A:ILE163 4.4 10.9 1.0
CA A:ASN194 4.4 17.4 1.0
O A:GLY192 4.5 12.3 1.0
N A:GLY197 4.5 8.7 1.0
O A:HOH471 4.5 14.7 1.0
O A:HOH453 4.5 12.2 1.0
N A:ASN194 4.5 16.8 1.0
CA A:GLY197 4.6 8.5 1.0
CA A:ILE163 4.6 10.5 1.0
C A:GLY197 4.6 8.4 1.0
CB A:ASP198 4.6 9.8 1.0
N A:MET164 4.7 9.9 1.0
CG A:MET164 4.7 11.8 1.0
CA A:ASP198 4.8 8.6 1.0
CH2 A:TRP113 4.8 12.7 1.0
C A:PRO193 4.9 16.0 1.0

Calcium binding site 2 out of 4 in 2yig

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:11.8
occ:1.00
 OE2 A:GLU205 2.2 12.0 1.0
OD2 A:ASP202 2.3 9.4 1.0
O A:GLY180 2.3 11.3 1.0
O A:LEU184 2.3 9.4 1.0
O A:SER182 2.3 12.8 1.0
OD1 A:ASP179 2.4 11.2 1.0
CG A:ASP202 3.4 8.4 1.0
C A:LEU184 3.4 10.2 1.0
CD A:GLU205 3.5 11.0 1.0
C A:GLY180 3.5 11.7 1.0
C A:SER182 3.5 14.1 1.0
CG A:ASP179 3.6 12.6 1.0
N A:SER182 3.9 13.4 1.0
N A:LEU184 4.0 10.9 1.0
C A:PRO181 4.0 12.5 1.0
CB A:ASP202 4.0 8.0 1.0
N A:GLY180 4.0 11.7 1.0
CA A:SER182 4.2 14.1 1.0
OD2 A:ASP179 4.2 13.5 1.0
C A:GLY183 4.3 12.1 1.0
OE1 A:GLU205 4.3 11.9 1.0
C A:ASP179 4.3 11.7 1.0
N A:ASP179 4.3 10.9 1.0
CA A:LEU184 4.3 11.3 1.0
OD1 A:ASP202 4.3 7.5 1.0
O A:PRO181 4.3 13.5 1.0
CG A:GLU205 4.4 9.6 1.0
N A:PRO181 4.4 12.5 1.0
CA A:PRO181 4.4 12.4 1.0
N A:LEU185 4.4 8.5 1.0
CA A:GLY180 4.4 12.1 1.0
CA A:LEU185 4.5 8.9 1.0
N A:GLY183 4.5 13.0 1.0
CA A:GLY183 4.6 12.8 1.0
O A:ASP179 4.7 11.8 1.0
CA A:ASP179 4.7 11.7 1.0
CB A:ASP179 4.7 12.6 1.0
CB A:LEU184 4.8 10.9 1.0
O A:GLY183 4.8 11.6 1.0

Calcium binding site 3 out of 4 in 2yig

Go back to Calcium Binding Sites List in 2yig
Calcium binding site 3 out of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:12.1
occ:1.00
 O B:GLY196 2.3 11.5 1.0
O B:ASP162 2.3 9.4 1.0
O B:ASN194 2.3 15.0 1.0
O B:HOH416 2.4 12.5 1.0
O B:HOH414 2.4 12.0 1.0
OD1 B:ASP198 2.5 11.1 1.0
CG B:ASP198 3.4 10.9 1.0
C B:ASP162 3.4 9.5 1.0
C B:GLY196 3.5 11.9 1.0
C B:ASN194 3.5 14.7 1.0
OD2 B:ASP198 3.8 12.4 1.0
C B:TYR195 3.9 12.5 1.0
N B:GLY196 4.0 13.1 1.0
O B:ALA161 4.1 10.6 1.0
O B:HOH435 4.1 14.8 1.0
O B:TYR195 4.2 10.6 1.0
CA B:ASP162 4.2 10.4 1.0
N B:ASP198 4.2 11.5 1.0
CA B:GLY196 4.3 12.7 1.0
O B:GLY192 4.3 15.6 1.0
CA B:TYR195 4.4 13.9 1.0
N B:TYR195 4.4 14.0 1.0
N B:GLY197 4.5 11.3 1.0
CA B:ASN194 4.5 15.9 1.0
N B:ASN194 4.5 16.2 1.0
N B:ILE163 4.5 9.5 1.0
CB B:ASP198 4.6 10.5 1.0
CA B:GLY197 4.6 11.4 1.0
N B:MET164 4.6 9.1 1.0
C B:GLY197 4.7 11.0 1.0
CA B:ILE163 4.7 9.1 1.0
C B:PRO193 4.8 16.1 1.0
CG B:MET164 4.8 10.0 1.0
CA B:ASP198 4.8 10.1 1.0
O B:PRO193 4.9 16.5 1.0

Calcium binding site 4 out of 4 in 2yig

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:13.9
occ:1.00
 OE2 B:GLU205 2.2 15.3 1.0
O B:LEU184 2.2 12.8 1.0
O B:SER182 2.3 16.2 1.0
OD2 B:ASP202 2.3 10.4 1.0
O B:GLY180 2.3 15.1 1.0
OD1 B:ASP179 2.4 13.4 1.0
C B:LEU184 3.4 13.3 1.0
CG B:ASP202 3.4 10.7 1.0
C B:SER182 3.4 18.0 1.0
CD B:GLU205 3.5 13.7 1.0
CG B:ASP179 3.5 14.6 1.0
C B:GLY180 3.6 15.8 1.0
N B:SER182 3.8 16.5 1.0
N B:LEU184 3.9 15.9 1.0
CB B:ASP202 4.0 10.1 1.0
OD2 B:ASP179 4.1 14.6 1.0
C B:PRO181 4.1 16.6 1.0
CA B:LEU184 4.1 15.0 1.0
CA B:SER182 4.2 18.6 1.0
OE1 B:GLU205 4.2 14.4 1.0
C B:GLY183 4.2 17.5 1.0
N B:GLY180 4.3 15.2 1.0
N B:ASP179 4.3 13.6 1.0
C B:ASP179 4.3 15.0 1.0
OD1 B:ASP202 4.3 9.8 1.0
CG B:GLU205 4.4 13.1 1.0
N B:LEU185 4.4 11.9 1.0
CA B:PRO181 4.4 16.9 1.0
CA B:GLY180 4.5 15.0 1.0
N B:PRO181 4.5 16.5 1.0
N B:GLY183 4.5 19.2 1.0
O B:PRO181 4.5 17.7 1.0
CB B:LEU184 4.5 16.4 1.0
O B:ASP179 4.6 16.0 1.0
CA B:LEU185 4.6 11.6 1.0
CB B:ASP179 4.6 14.3 1.0
CA B:GLY183 4.7 17.6 1.0
CA B:ASP179 4.7 14.8 1.0
O B:GLY183 4.8 17.1 1.0

Reference:

C.D.Savi, A.D.Morley, A.Ting, I.Nash, K.Karabelas, C.M.Wood, M.James, S.J.Norris, G.Karoutchi, N.Rankine, G.Hamlin, P.A.Macfaul, D.Ryan, S.V.Baker, D.Hargreaves, S.Gerhardt. Selective Non Zinc Binding Inhibitors of MMP13. Bioorg.Med.Chem.Lett. V. 21 4215 2011.
ISSN: ISSN 0960-894X
PubMed: 21669521
DOI: 10.1016/J.BMCL.2011.05.075
Page generated: Tue Jul 8 09:40:26 2025

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