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Calcium in PDB 3kek: 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: 3kek 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) 26.14 / 1.97
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 120.846, 95.740, 36.443, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 21.8

Other elements in 3kek:

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 3kek). 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: 3kek:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3kek

Go back to Calcium Binding Sites List in 3kek
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:17.1
occ:1.00
 OE2 A:GLU205 2.2 15.5 1.0
O A:LEU184 2.2 16.7 1.0
O A:GLY180 2.2 18.6 1.0
OD2 A:ASP202 2.3 12.2 1.0
O A:SER182 2.4 21.2 1.0
OD1 A:ASP179 2.4 15.4 1.0
C A:LEU184 3.3 16.7 1.0
CG A:ASP202 3.4 13.3 1.0
CD A:GLU205 3.5 15.4 1.0
C A:GLY180 3.5 19.8 1.0
C A:SER182 3.6 21.9 1.0
CG A:ASP179 3.6 19.3 1.0
N A:LEU184 3.9 19.2 1.0
N A:SER182 3.9 21.9 1.0
C A:PRO181 4.0 21.9 1.0
CB A:ASP202 4.0 13.1 1.0
N A:GLY180 4.1 19.1 1.0
CA A:LEU184 4.1 18.1 1.0
OD2 A:ASP179 4.2 20.2 1.0
OE1 A:GLU205 4.2 16.7 1.0
N A:ASP179 4.3 17.5 1.0
N A:LEU185 4.3 15.2 1.0
CA A:PRO181 4.3 21.4 1.0
CA A:SER182 4.3 22.7 1.0
OD1 A:ASP202 4.4 10.9 1.0
C A:ASP179 4.4 19.4 1.0
C A:GLY183 4.4 19.8 1.0
N A:PRO181 4.4 21.1 1.0
CA A:GLY180 4.4 20.0 1.0
CG A:GLU205 4.4 14.4 1.0
O A:PRO181 4.5 22.4 1.0
CA A:LEU185 4.5 14.3 1.0
N A:GLY183 4.6 22.1 1.0
CB A:LEU184 4.6 18.5 1.0
CA A:ASP179 4.7 18.8 1.0
O A:HOH2045 4.7 25.9 1.0
CB A:ASP179 4.8 18.9 1.0
CA A:GLY183 4.8 21.5 1.0
O A:ASP179 4.9 20.3 1.0
O A:GLY183 4.9 19.1 1.0
CD2 A:LEU185 5.0 12.0 1.0

Calcium binding site 2 out of 6 in 3kek

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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:47.3
occ:1.00
 O A:HOH2266 2.4 38.2 1.0
OD1 A:ASP198 2.6 13.3 1.0
O A:ASP162 2.7 16.9 1.0
O A:ASN194 2.8 25.5 1.0
O A:HOH2007 2.8 17.1 1.0
O A:GLY196 2.9 16.2 1.0
CG A:ASP198 3.5 14.2 1.0
O A:HOH2211 3.5 35.2 1.0
O A:ALA161 3.5 18.5 1.0
C A:ASP162 3.6 16.8 1.0
OD2 A:ASP198 3.8 15.0 1.0
C A:ASN194 3.9 26.2 1.0
O A:HOH2071 4.0 23.3 1.0
C A:TYR195 4.0 20.3 1.0
C A:GLY196 4.0 16.8 1.0
O A:TYR195 4.2 18.9 1.0
CA A:ASP162 4.3 18.2 1.0
N A:GLY196 4.3 20.2 1.0
CA A:TYR195 4.3 22.5 1.0
CG A:MET164 4.3 17.2 1.0
N A:ILE163 4.5 15.7 1.0
N A:MET164 4.5 15.0 1.0
N A:TYR195 4.6 24.8 1.0
N A:ASP198 4.6 13.8 1.0
C A:ALA161 4.6 18.6 1.0
CA A:ILE163 4.7 14.7 1.0
CA A:GLY196 4.8 18.5 1.0
CB A:ASP198 4.8 14.0 1.0
O A:HOH2013 4.9 21.8 1.0
N A:ASP162 5.0 18.4 1.0
CB A:MET164 5.0 16.1 1.0
N A:GLY197 5.0 14.9 1.0
O A:GLY192 5.0 26.2 1.0

Calcium binding site 3 out of 6 in 3kek

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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:48.1
occ:1.00
 OD2 A:ASP128 2.8 24.1 1.0
O A:ASP203 2.8 12.9 1.0
O A:GLU205 2.9 16.5 1.0
OD2 A:ASP203 3.1 18.7 1.0
OD1 A:ASP128 3.1 22.6 1.0
O A:HOH2002 3.2 12.5 1.0
CG A:ASP128 3.3 22.5 1.0
O A:HOH2206 3.7 39.8 1.0
C A:ASP203 3.8 13.0 1.0
C A:GLU205 4.1 16.7 1.0
OG1 A:THR126 4.1 15.9 1.0
CG A:ASP203 4.2 14.8 1.0
CA A:ASP203 4.4 12.8 1.0
CD A:PRO127 4.5 18.5 1.0
O A:HOH2151 4.6 35.1 1.0
CB A:ASP128 4.6 21.6 1.0
N A:GLU205 4.7 14.8 1.0
C A:ASP204 4.7 15.1 1.0
N A:ASP204 4.7 13.4 1.0
CB A:ASP203 4.7 13.0 1.0
CA A:ASP204 4.8 14.7 1.0
CD1 A:TRP207 4.8 15.7 1.0
CG A:PRO127 4.8 20.2 1.0
O A:HOH2084 4.8 36.2 1.0
N A:THR206 4.9 18.0 1.0
CA A:THR206 4.9 19.1 1.0

Calcium binding site 4 out of 6 in 3kek

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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:33.0
occ:1.00
 O B:LEU184 2.2 29.3 1.0
O B:GLY180 2.2 33.0 1.0
OE2 B:GLU205 2.4 28.3 1.0
O B:SER182 2.4 36.4 1.0
OD1 B:ASP179 2.4 33.7 1.0
OD2 B:ASP202 2.5 24.2 1.0
C B:LEU184 3.3 29.5 1.0
C B:GLY180 3.4 34.3 1.0
CD B:GLU205 3.6 26.6 1.0
C B:SER182 3.6 37.5 1.0
CG B:ASP179 3.6 34.4 1.0
CG B:ASP202 3.6 21.5 1.0
N B:LEU184 3.7 34.1 1.0
N B:SER182 3.9 37.0 1.0
CA B:LEU184 4.0 31.9 1.0
C B:PRO181 4.0 37.4 1.0
N B:GLY180 4.2 33.7 1.0
CB B:ASP202 4.2 21.5 1.0
OD2 B:ASP179 4.2 36.4 1.0
N B:PRO181 4.3 36.1 1.0
C B:ASP179 4.3 34.4 1.0
CA B:PRO181 4.3 36.3 1.0
N B:ASP179 4.3 30.6 1.0
CB B:LEU184 4.3 32.5 1.0
N B:LEU185 4.3 27.4 1.0
CA B:SER182 4.3 38.0 1.0
OE1 B:GLU205 4.3 26.5 1.0
C B:GLY183 4.4 35.3 1.0
CA B:GLY180 4.4 34.6 1.0
CG B:GLU205 4.4 24.2 1.0
O B:PRO181 4.4 39.0 1.0
CA B:LEU185 4.6 25.3 1.0
N B:GLY183 4.6 38.4 1.0
OD1 B:ASP202 4.6 20.5 1.0
CA B:ASP179 4.6 33.5 1.0
O B:ASP179 4.7 36.2 1.0
CB B:ASP179 4.7 34.7 1.0
CA B:GLY183 4.8 38.0 1.0

Calcium binding site 5 out of 6 in 3kek

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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:47.6
occ:1.00
 OD1 B:ASP198 2.6 18.3 1.0
O B:ASN194 2.7 28.3 1.0
O B:ASP162 2.9 19.6 1.0
O B:GLY196 3.1 20.4 1.0
O B:HOH2026 3.2 21.5 1.0
O B:ALA161 3.3 19.6 1.0
O B:HOH2138 3.3 32.3 1.0
CG B:ASP198 3.5 18.4 1.0
O B:HOH2108 3.5 37.7 1.0
O B:HOH2027 3.5 23.2 1.0
OD2 B:ASP198 3.7 20.5 1.0
C B:ASP162 3.7 19.1 1.0
C B:ASN194 3.9 29.2 1.0
C B:TYR195 4.0 24.9 1.0
C B:GLY196 4.2 21.4 1.0
CG B:MET164 4.2 17.8 1.0
N B:GLY196 4.3 24.9 1.0
O B:TYR195 4.3 23.3 1.0
CA B:TYR195 4.3 26.8 1.0
CA B:ASP162 4.3 19.9 1.0
C B:ALA161 4.4 19.6 1.0
N B:TYR195 4.5 28.6 1.0
N B:MET164 4.5 16.8 1.0
N B:ILE163 4.5 18.0 1.0
N B:ASP198 4.7 17.6 1.0
CB B:ASP198 4.8 17.7 1.0
CA B:GLY196 4.8 23.7 1.0
CA B:ILE163 4.9 17.2 1.0
N B:ASP162 4.9 19.8 1.0
CB B:MET164 4.9 17.0 1.0
CA B:ASN194 4.9 31.8 1.0

Calcium binding site 6 out of 6 in 3kek

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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:52.0
occ:1.00
 O B:HOH2254 2.5 48.5 1.0
OG1 B:THR206 3.2 24.7 1.0
O B:HOH2002 3.3 19.1 1.0
O B:GLU205 3.5 23.0 1.0
OD1 B:ASP128 3.5 26.6 1.0
OD2 B:ASP128 3.5 25.7 1.0
O A:HOH2126 3.6 47.1 1.0
CA B:THR206 3.6 22.7 1.0
CG B:ASP128 3.8 25.1 1.0
CB B:THR206 3.9 24.6 1.0
C B:GLU205 4.0 23.6 1.0
N B:THR206 4.0 23.4 1.0
OG A:SER182 4.1 28.1 1.0
O B:HOH2163 4.1 31.7 1.0
O A:HOH2176 4.2 26.2 1.0
CB A:SER182 4.2 25.0 1.0
CG2 B:THR206 4.2 25.2 1.0
O B:ASP203 4.9 25.6 1.0
C B:THR206 5.0 20.9 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 2009.
ISSN: ISSN 0960-894X
PubMed: 20005097
DOI: 10.1016/J.BMCL.2009.11.081
Page generated: Tue Jul 8 13:46:47 2025

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