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Calcium in PDB 3kej: Crystal Structure of Human Mmp-13 Complexed with A (Pyridin-4-Yl)-2H- Tetrazole Compound

Protein crystallography data

The structure of Crystal Structure of Human Mmp-13 Complexed with A (Pyridin-4-Yl)-2H- Tetrazole Compound, PDB code: 3kej was solved by H.-S.Shieh, B.Collins, M.E.Schnute, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.80 / 2.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 120.883, 96.457, 36.638, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23.6

Other elements in 3kej:

The structure of Crystal Structure of Human Mmp-13 Complexed with A (Pyridin-4-Yl)-2H- Tetrazole Compound also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Mmp-13 Complexed with A (Pyridin-4-Yl)-2H- Tetrazole Compound (pdb code 3kej). 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 (Pyridin-4-Yl)-2H- Tetrazole Compound, PDB code: 3kej:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3kej

Go back to Calcium Binding Sites List in 3kej
Calcium binding site 1 out of 6 in the Crystal Structure of Human Mmp-13 Complexed with A (Pyridin-4-Yl)-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 (Pyridin-4-Yl)-2H- Tetrazole Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:2.0
occ:1.00
 O A:GLY180 2.2 8.2 1.0
O A:SER182 2.3 10.8 1.0
OD2 A:ASP202 2.3 5.1 1.0
OE2 A:GLU205 2.3 10.1 1.0
O A:LEU184 2.3 10.5 1.0
OD1 A:ASP179 2.5 8.0 1.0
C A:LEU184 3.4 10.8 1.0
CG A:ASP202 3.5 6.6 1.0
C A:GLY180 3.5 8.5 1.0
C A:SER182 3.5 10.9 1.0
CG A:ASP179 3.6 8.0 1.0
CD A:GLU205 3.6 8.6 1.0
N A:LEU184 3.8 11.1 1.0
N A:SER182 4.1 10.7 1.0
N A:GLY180 4.1 8.2 1.0
OD2 A:ASP179 4.1 7.6 1.0
C A:PRO181 4.1 9.9 1.0
CA A:LEU184 4.1 11.2 1.0
CB A:ASP202 4.1 7.2 1.0
C A:GLY183 4.2 11.1 1.0
N A:ASP179 4.2 7.9 1.0
OE1 A:GLU205 4.3 7.8 1.0
C A:ASP179 4.3 8.1 1.0
CA A:SER182 4.3 11.3 1.0
CA A:GLY180 4.4 8.4 1.0
N A:PRO181 4.4 9.1 1.0
OD1 A:ASP202 4.4 4.5 1.0
N A:LEU185 4.4 10.5 1.0
N A:GLY183 4.4 11.2 1.0
CA A:PRO181 4.4 9.7 1.0
O A:PRO181 4.5 9.9 1.0
CA A:GLY183 4.6 11.0 1.0
CG A:GLU205 4.6 8.8 1.0
CB A:LEU184 4.6 11.7 1.0
CA A:ASP179 4.6 7.9 1.0
CA A:LEU185 4.6 10.2 1.0
CB A:ASP179 4.7 8.0 1.0
O A:GLY183 4.7 11.0 1.0
O A:ASP179 4.8 8.3 1.0
CD2 A:LEU185 4.9 8.9 1.0

Calcium binding site 2 out of 6 in 3kej

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Calcium binding site 2 out of 6 in the Crystal Structure of Human Mmp-13 Complexed with A (Pyridin-4-Yl)-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 (Pyridin-4-Yl)-2H- Tetrazole Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:39.6
occ:1.00
 OD1 A:ASP198 2.8 11.2 1.0
O A:ASN194 2.8 11.4 1.0
O A:ASP162 2.9 8.9 1.0
O A:HOH2011 2.9 2.0 1.0
O A:GLY196 3.1 9.1 1.0
O A:ALA161 3.4 9.1 1.0
O A:HOH2105 3.5 22.2 1.0
C A:ASP162 3.7 9.0 1.0
CG A:ASP198 3.7 10.8 1.0
C A:ASN194 4.0 11.4 1.0
OD2 A:ASP198 4.0 12.5 1.0
C A:TYR195 4.1 11.2 1.0
C A:GLY196 4.2 9.4 1.0
CG A:MET164 4.2 8.9 1.0
CA A:ASP162 4.2 9.3 1.0
CA A:TYR195 4.3 11.6 1.0
N A:GLY196 4.3 10.6 1.0
O A:TYR195 4.4 10.6 1.0
C A:ALA161 4.5 9.2 1.0
N A:ILE163 4.5 8.8 1.0
N A:MET164 4.6 8.5 1.0
N A:TYR195 4.6 11.4 1.0
CA A:ILE163 4.8 8.8 1.0
N A:ASP162 4.9 9.2 1.0
N A:ASP198 4.9 9.4 1.0
CA A:GLY196 4.9 10.0 1.0
O A:HOH2088 5.0 8.9 1.0

Calcium binding site 3 out of 6 in 3kej

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Calcium binding site 3 out of 6 in the Crystal Structure of Human Mmp-13 Complexed with A (Pyridin-4-Yl)-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 (Pyridin-4-Yl)-2H- Tetrazole Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:37.4
occ:1.00
 OD2 A:ASP128 2.6 16.9 1.0
O A:GLU205 2.9 9.2 1.0
O A:ASP203 2.9 8.3 1.0
OD2 A:ASP203 3.0 13.9 1.0
O A:HOH2003 3.2 2.0 1.0
CG A:ASP128 3.3 14.3 1.0
OD1 A:ASP128 3.5 16.9 1.0
OG1 A:THR126 3.5 9.1 1.0
C A:ASP203 3.8 8.4 1.0
O A:HOH2203 4.0 20.8 1.0
C A:GLU205 4.1 9.3 1.0
CG A:ASP203 4.1 11.1 1.0
CD A:PRO127 4.2 10.3 1.0
CA A:ASP203 4.4 8.8 1.0
CB A:ASP128 4.5 12.6 1.0
CD1 A:TRP207 4.6 9.6 1.0
N A:GLU205 4.6 9.2 1.0
CB A:ASP203 4.7 9.3 1.0
N A:ASP204 4.8 8.4 1.0
CG A:PRO127 4.8 10.6 1.0
CA A:THR206 4.9 9.6 1.0
N A:THR206 4.9 9.3 1.0
C A:ASP204 4.9 8.8 1.0
CB A:THR126 4.9 9.2 1.0
N A:ASP128 4.9 11.8 1.0
CA A:ASP204 4.9 8.6 1.0

Calcium binding site 4 out of 6 in 3kej

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Calcium binding site 4 out of 6 in the Crystal Structure of Human Mmp-13 Complexed with A (Pyridin-4-Yl)-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 (Pyridin-4-Yl)-2H- Tetrazole Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca903

b:16.6
occ:1.00
 O B:GLY180 2.2 17.6 1.0
OE2 B:GLU205 2.3 17.0 1.0
OD2 B:ASP202 2.4 10.0 1.0
O B:SER182 2.4 20.4 1.0
O B:LEU184 2.4 15.7 1.0
OD1 B:ASP179 2.6 18.4 1.0
C B:SER182 3.4 20.0 1.0
C B:GLY180 3.5 17.6 1.0
CD B:GLU205 3.5 15.3 1.0
CG B:ASP202 3.5 10.3 1.0
C B:LEU184 3.5 15.9 1.0
N B:LEU184 3.6 17.9 1.0
CG B:ASP179 3.7 17.0 1.0
N B:GLY180 4.0 16.7 1.0
N B:SER182 4.0 19.5 1.0
C B:ASP179 4.1 15.8 1.0
CA B:LEU184 4.1 17.1 1.0
C B:PRO181 4.2 19.0 1.0
CB B:ASP202 4.2 10.8 1.0
N B:ASP179 4.2 13.9 1.0
C B:GLY183 4.2 18.7 1.0
N B:GLY183 4.2 19.8 1.0
CA B:SER182 4.3 19.9 1.0
OD2 B:ASP179 4.3 19.5 1.0
O B:HOH2338 4.3 47.3 1.0
CG B:GLU205 4.3 14.0 1.0
CA B:GLY180 4.3 17.1 1.0
OE1 B:GLU205 4.4 18.4 1.0
CA B:GLY183 4.4 19.2 1.0
N B:PRO181 4.4 18.1 1.0
OD1 B:ASP202 4.5 9.9 1.0
O B:ASP179 4.5 16.0 1.0
CA B:ASP179 4.5 15.2 1.0
CA B:PRO181 4.5 18.6 1.0
CB B:LEU184 4.6 17.2 1.0
N B:LEU185 4.6 14.8 1.0
O B:PRO181 4.6 19.4 1.0
CB B:ASP179 4.7 15.4 1.0
CA B:LEU185 4.9 14.0 1.0

Calcium binding site 5 out of 6 in 3kej

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Calcium binding site 5 out of 6 in the Crystal Structure of Human Mmp-13 Complexed with A (Pyridin-4-Yl)-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 (Pyridin-4-Yl)-2H- Tetrazole Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca904

b:30.4
occ:1.00
 OD1 B:ASP198 2.6 12.1 1.0
O B:ASN194 2.8 14.1 1.0
O B:GLY196 2.9 9.3 1.0
O B:HOH2308 3.0 26.1 1.0
O B:ASP162 3.0 8.3 1.0
O B:HOH2046 3.2 2.0 1.0
O B:HOH2042 3.3 13.8 1.0
CG B:ASP198 3.4 10.4 1.0
O B:ALA161 3.5 8.2 1.0
OD2 B:ASP198 3.5 12.1 1.0
C B:ASP162 3.8 8.5 1.0
C B:ASN194 4.0 13.8 1.0
C B:GLY196 4.1 9.9 1.0
CG B:MET164 4.1 9.4 1.0
C B:TYR195 4.1 12.6 1.0
O B:TYR195 4.2 11.4 1.0
CA B:TYR195 4.3 14.0 1.0
N B:GLY196 4.3 11.4 1.0
CA B:ASP162 4.4 8.4 1.0
N B:MET164 4.5 8.5 1.0
N B:ILE163 4.5 8.5 1.0
C B:ALA161 4.6 8.1 1.0
N B:TYR195 4.6 14.0 1.0
N B:ASP198 4.7 9.1 1.0
CB B:ASP198 4.7 9.0 1.0
CA B:GLY196 4.8 10.6 1.0
CB B:MET164 4.8 8.9 1.0
CA B:ILE163 4.8 8.1 1.0

Calcium binding site 6 out of 6 in 3kej

Go back to Calcium Binding Sites List in 3kej
Calcium binding site 6 out of 6 in the Crystal Structure of Human Mmp-13 Complexed with A (Pyridin-4-Yl)-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 (Pyridin-4-Yl)-2H- Tetrazole Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca905

b:35.5
occ:1.00
 O A:HOH2185 2.8 20.4 1.0
O B:GLU205 2.9 11.7 1.0
O B:HOH2005 2.9 11.3 1.0
O A:HOH2290 3.4 34.8 1.0
OD1 B:ASP128 3.4 12.6 1.0
OD2 B:ASP128 3.5 13.1 1.0
C B:GLU205 3.5 11.8 1.0
OG1 B:THR206 3.5 10.8 1.0
CA B:THR206 3.7 10.3 1.0
CG B:ASP128 3.8 11.6 1.0
N B:THR206 3.8 10.9 1.0
CB B:THR206 4.1 10.4 1.0
O B:HOH2242 4.2 23.1 1.0
O B:ASP204 4.3 13.4 1.0
O B:ASP203 4.4 13.3 1.0
OG A:SER182 4.4 14.4 1.0
C B:ASP204 4.4 13.1 1.0
O A:HOH2272 4.5 14.1 1.0
CG2 B:THR206 4.6 10.3 1.0
CA B:GLU205 4.6 12.4 1.0
N B:GLU205 4.7 12.7 1.0
CB A:SER182 4.9 11.6 1.0
CA B:ASP204 5.0 13.6 1.0
C B:THR206 5.0 9.7 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: Sat Jul 13 12:11:46 2024

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