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Calcium in PDB 3kec: Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound

Protein crystallography data

The structure of Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound, PDB code: 3kec was solved by H.-S.Shieh, A.G.Pavlovsky, B.Collins, M.E.Schnute, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.05
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 133.209, 72.348, 36.356, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.4

Other elements in 3kec:

The structure of Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound (pdb code 3kec). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound, PDB code: 3kec:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3kec

Go back to Calcium Binding Sites List in 3kec
Calcium binding site 1 out of 6 in the Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound


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 Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:12.5
occ:1.00
 OE2 A:GLU205 2.2 12.4 1.0
O A:LEU184 2.2 16.1 1.0
O A:GLY180 2.3 15.8 1.0
O A:SER182 2.3 17.5 1.0
OD2 A:ASP202 2.4 10.0 1.0
OD1 A:ASP179 2.4 16.2 1.0
C A:LEU184 3.4 16.2 1.0
CG A:ASP202 3.5 11.3 1.0
C A:SER182 3.5 18.5 1.0
CD A:GLU205 3.5 14.0 1.0
C A:GLY180 3.5 16.9 1.0
CG A:ASP179 3.6 17.2 1.0
N A:SER182 3.9 18.4 1.0
C A:PRO181 4.0 18.4 1.0
N A:LEU184 4.0 17.6 1.0
CB A:ASP202 4.1 11.8 1.0
N A:GLY180 4.1 16.5 1.0
CA A:SER182 4.2 19.1 1.0
CA A:LEU184 4.2 17.2 1.0
OD2 A:ASP179 4.2 17.2 1.0
OE1 A:GLU205 4.2 14.5 1.0
O A:PRO181 4.3 18.2 1.0
C A:GLY183 4.3 18.2 1.0
C A:ASP179 4.3 17.2 1.0
N A:LEU185 4.3 15.4 1.0
N A:ASP179 4.3 16.0 1.0
O A:HOH304 4.3 18.1 1.0
OD1 A:ASP202 4.4 10.8 1.0
CA A:PRO181 4.4 17.9 1.0
N A:PRO181 4.4 17.7 1.0
CA A:GLY180 4.4 16.9 1.0
CG A:GLU205 4.4 15.0 1.0
CA A:LEU185 4.5 15.0 1.0
N A:GLY183 4.5 19.2 1.0
CA A:GLY183 4.7 18.8 1.0
CA A:ASP179 4.7 16.9 1.0
CB A:LEU184 4.7 17.1 1.0
O A:ASP179 4.8 18.4 1.0
CB A:ASP179 4.8 17.2 1.0
O A:GLY183 4.8 17.9 1.0
CD2 A:LEU185 4.9 14.1 1.0

Calcium binding site 2 out of 6 in 3kec

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Calcium binding site 2 out of 6 in the Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound


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 Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:14.8
occ:1.00
 O A:ASP162 2.3 15.4 1.0
O A:HOH57 2.3 15.0 1.0
O A:GLY196 2.4 15.6 1.0
O A:HOH3 2.4 14.3 1.0
O A:ASN194 2.4 19.2 1.0
OD1 A:ASP198 2.5 14.5 1.0
C A:ASP162 3.4 15.3 1.0
CG A:ASP198 3.5 13.3 1.0
C A:GLY196 3.5 15.3 1.0
C A:ASN194 3.5 19.9 1.0
C A:TYR195 3.9 17.8 1.0
O A:HOH81 3.9 17.5 1.0
OD2 A:ASP198 4.0 13.8 1.0
N A:GLY196 4.0 17.4 1.0
O A:TYR195 4.0 17.0 1.0
O A:ALA161 4.1 16.8 1.0
N A:ASP198 4.2 12.9 1.0
CA A:ASP162 4.3 16.4 1.0
CA A:GLY196 4.3 16.6 1.0
O A:GLY192 4.4 17.8 1.0
N A:TYR195 4.4 19.6 1.0
N A:ASN194 4.4 20.8 1.0
CA A:TYR195 4.4 19.2 1.0
N A:ILE163 4.4 14.6 1.0
CA A:ASN194 4.5 21.2 1.0
N A:GLY197 4.5 14.6 1.0
CA A:GLY197 4.6 13.8 1.0
C A:GLY197 4.6 13.1 1.0
CB A:ASP198 4.6 13.1 1.0
CA A:ILE163 4.7 13.8 1.0
N A:MET164 4.7 13.6 1.0
O A:HOH31 4.7 19.9 1.0
CA A:ASP198 4.8 12.6 1.0
C A:PRO193 4.8 20.1 1.0
CH2 A:TRP113 4.9 16.4 1.0
CG A:MET164 4.9 15.0 1.0

Calcium binding site 3 out of 6 in 3kec

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Calcium binding site 3 out of 6 in the Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound


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 Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:46.3
occ:1.00
 OD1 A:ASP128 2.7 26.4 1.0
O A:GLU205 2.8 16.8 1.0
O A:ASP203 2.8 14.7 1.0
OD1 A:ASP203 3.2 17.7 1.0
CG A:ASP128 3.3 23.8 1.0
OD2 A:ASP128 3.4 28.8 1.0
C A:ASP203 3.8 14.1 1.0
C A:GLU205 3.9 17.1 1.0
OG1 A:THR126 4.1 12.3 1.0
CG A:ASP203 4.2 15.5 1.0
CA A:ASP203 4.4 13.6 1.0
CD A:PRO127 4.5 15.7 1.0
CB A:ASP128 4.5 20.6 1.0
N A:GLU205 4.6 15.7 1.0
CD1 A:TRP207 4.7 15.5 1.0
C A:ASP204 4.7 15.7 1.0
CA A:THR206 4.7 19.1 1.0
N A:THR206 4.7 18.4 1.0
N A:ASP204 4.7 14.5 1.0
CB A:ASP203 4.7 13.5 1.0
CA A:ASP204 4.8 15.3 1.0
CG A:PRO127 4.9 16.4 1.0
CA A:GLU205 4.9 16.4 1.0

Calcium binding site 4 out of 6 in 3kec

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Calcium binding site 4 out of 6 in the Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound


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 Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca903

b:16.4
occ:1.00
 OE2 B:GLU205 2.2 16.7 1.0
OD2 B:ASP202 2.3 13.1 1.0
O B:LEU184 2.3 16.7 1.0
O B:GLY180 2.3 17.7 1.0
OD1 B:ASP179 2.4 14.7 1.0
O B:SER182 2.4 20.8 1.0
C B:LEU184 3.4 17.3 1.0
CG B:ASP202 3.4 13.9 1.0
CD B:GLU205 3.5 17.2 1.0
C B:GLY180 3.5 18.3 1.0
CG B:ASP179 3.5 18.1 1.0
C B:SER182 3.5 21.5 1.0
N B:LEU184 3.9 19.8 1.0
N B:SER182 3.9 20.6 1.0
C B:PRO181 4.0 20.4 1.0
OD2 B:ASP179 4.1 19.6 1.0
CB B:ASP202 4.1 13.6 1.0
N B:GLY180 4.1 17.7 1.0
CA B:LEU184 4.2 18.6 1.0
OE1 B:GLU205 4.2 16.2 1.0
CA B:SER182 4.3 21.8 1.0
N B:ASP179 4.3 16.5 1.0
C B:ASP179 4.4 17.9 1.0
C B:GLY183 4.4 20.5 1.0
OD1 B:ASP202 4.4 12.8 1.0
O B:PRO181 4.4 20.9 1.0
CG B:GLU205 4.4 15.4 1.0
N B:LEU185 4.4 16.4 1.0
CA B:GLY180 4.4 18.3 1.0
N B:PRO181 4.4 19.4 1.0
CA B:PRO181 4.4 19.7 1.0
CB B:LEU184 4.5 18.9 1.0
N B:GLY183 4.5 22.1 1.0
CA B:LEU185 4.6 15.8 1.0
CA B:ASP179 4.7 17.5 1.0
CB B:ASP179 4.7 18.2 1.0
CA B:GLY183 4.7 21.7 1.0
O B:ASP179 4.8 18.6 1.0
O B:GLY183 5.0 20.5 1.0

Calcium binding site 5 out of 6 in 3kec

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Calcium binding site 5 out of 6 in the Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound


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 Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca904

b:17.3
occ:1.00
 O B:GLY196 2.2 16.7 1.0
O B:ASN194 2.3 21.4 1.0
O B:HOH22 2.3 14.5 1.0
O B:HOH46 2.4 16.6 1.0
O B:ASP162 2.4 14.8 1.0
OD1 B:ASP198 2.5 16.4 1.0
C B:GLY196 3.4 17.0 1.0
C B:ASP162 3.5 15.1 1.0
CG B:ASP198 3.5 15.5 1.0
C B:ASN194 3.5 22.1 1.0
N B:GLY196 3.9 18.9 1.0
C B:TYR195 3.9 19.5 1.0
OD2 B:ASP198 4.0 14.4 1.0
O B:HOH62 4.0 27.0 1.0
O B:ALA161 4.1 15.0 1.0
CA B:GLY196 4.2 18.1 1.0
N B:ASP198 4.2 14.8 1.0
O B:TYR195 4.2 18.5 1.0
CA B:ASP162 4.2 15.6 1.0
O B:GLY192 4.3 21.3 1.0
N B:GLY197 4.4 16.2 1.0
CA B:TYR195 4.4 20.7 1.0
N B:ASN194 4.4 23.2 1.0
N B:TYR195 4.4 21.4 1.0
CA B:ASN194 4.5 23.3 1.0
N B:ILE163 4.5 15.1 1.0
CA B:GLY197 4.6 15.6 1.0
O B:HOH29 4.6 20.2 1.0
C B:GLY197 4.6 14.8 1.0
CB B:ASP198 4.7 14.5 1.0
O B:HOH315 4.7 38.4 1.0
C B:PRO193 4.7 23.0 1.0
CA B:ILE163 4.7 15.0 1.0
N B:MET164 4.7 14.5 1.0
CA B:ASP198 4.8 14.4 1.0
O B:PRO193 4.9 22.5 1.0
CG B:MET164 5.0 15.0 1.0
CH2 B:TRP113 5.0 19.0 1.0

Calcium binding site 6 out of 6 in 3kec

Go back to Calcium Binding Sites List in 3kec
Calcium binding site 6 out of 6 in the Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound


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 Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca905

b:14.9
occ:1.00
 O B:HOH277 2.3 18.0 1.0
OD2 B:ASP128 2.4 13.9 1.0
O B:GLU205 2.4 14.9 1.0
O B:ASP203 2.5 15.0 1.0
OD1 B:ASP203 2.5 16.9 1.0
O B:HOH45 2.6 22.3 1.0
OD1 B:ASP128 2.6 17.4 1.0
CG B:ASP128 2.9 14.7 1.0
C B:ASP203 3.4 14.7 1.0
CG B:ASP203 3.6 15.0 1.0
C B:GLU205 3.6 15.0 1.0
CA B:ASP203 3.8 14.2 1.0
OG1 B:THR126 4.0 12.4 1.0
CB B:ASP203 4.1 14.2 1.0
CA B:THR206 4.3 14.9 1.0
CD1 B:TRP207 4.3 12.2 1.0
N B:THR206 4.4 15.2 1.0
CB B:ASP128 4.4 14.7 1.0
N B:GLU205 4.4 14.8 1.0
N B:ASP204 4.5 14.9 1.0
OD2 B:ASP203 4.6 15.4 1.0
C B:ASP204 4.6 15.0 1.0
CA B:GLU205 4.7 15.2 1.0
N B:TRP207 4.7 14.0 1.0
CA B:ASP204 4.8 15.0 1.0
NE1 B:TRP207 4.8 11.9 1.0

Reference:

M.E.Schnute, P.M.O'brien, J.Nahra, M.Morris, W.Howard Roark, C.E.Hanau, P.G.Ruminski, J.A.Scholten, T.R.Fletcher, B.C.Hamper, J.N.Carroll, W.C.Patt, H.S.Shieh, B.Collins, A.G.Pavlovsky, K.E.Palmquist, K.W.Aston, J.Hitchcock, M.D.Rogers, J.Mcdonald, A.R.Johnson, G.E.Munie, A.J.Wittwer, C.F.Man, S.L.Settle, O.Nemirovskiy, L.E.Vickery, A.Agawal, R.D.Dyer, T.Sunyer. Discovery of (Pyridin-4-Yl)-2H-Tetrazole As A Novel Scaffold to Identify Highly Selective Matrix Metalloproteinase-13 Inhibitors For the Treatment of Osteoarthritis. Bioorg.Med.Chem.Lett. V. 20 576 2010.
ISSN: ISSN 0960-894X
PubMed: 20005097
DOI: 10.1016/J.BMCL.2009.11.081
Page generated: Tue Jul 8 13:46:41 2025

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