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Zinc 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
Calcium (Ca) 6 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 3kej

Go back to Zinc Binding Sites List in 3kej
Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn901

b:3.6
occ:1.00
NE2 A:HIS232 2.0 11.1 1.0
NE2 A:HIS222 2.1 4.2 1.0
NE2 A:HIS226 2.3 11.8 1.0
CD2 A:HIS232 2.9 10.7 1.0
CE1 A:HIS232 3.0 11.8 1.0
CD2 A:HIS222 3.0 5.7 1.0
CD2 A:HIS226 3.1 11.0 1.0
O A:HOH2067 3.1 16.0 1.0
CE1 A:HIS222 3.2 5.7 1.0
CE1 A:HIS226 3.4 11.4 1.0
OE2 A:GLU223 3.8 17.7 1.0
ND1 A:HIS232 4.0 10.8 1.0
CG A:HIS232 4.1 10.7 1.0
CG A:HIS222 4.2 8.1 1.0
ND1 A:HIS222 4.3 6.7 1.0
CG A:HIS226 4.3 10.3 1.0
O A:HOH2007 4.3 2.0 1.0
ND1 A:HIS226 4.4 11.0 1.0
CD A:GLU223 4.5 16.1 1.0
O A:HOH2102 4.6 2.3 1.0
OE1 A:GLU223 4.6 17.4 1.0
CE A:MET240 4.7 8.2 1.0
CA A:PRO242 4.9 6.1 1.0
F32 A:3EJ801 4.9 5.1 1.0

Zinc binding site 2 out of 4 in 3kej

Go back to Zinc Binding Sites List in 3kej
Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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:Zn902

b:2.0
occ:1.00
ND1 A:HIS200 2.0 7.6 1.0
OD2 A:ASP174 2.1 11.1 1.0
NE2 A:HIS172 2.1 6.8 1.0
CE1 A:HIS187 2.1 10.5 1.0
NE2 A:HIS187 2.5 10.6 1.0
CG A:ASP174 2.9 8.9 1.0
CD2 A:HIS172 2.9 6.5 1.0
CE1 A:HIS200 3.0 8.9 1.0
OD1 A:ASP174 3.0 10.7 1.0
CG A:HIS200 3.1 8.1 1.0
CE1 A:HIS172 3.1 6.8 1.0
ND1 A:HIS187 3.4 11.5 1.0
CB A:HIS200 3.4 8.6 1.0
CD2 A:HIS187 3.8 9.2 1.0
CG A:HIS172 4.1 7.9 1.0
NE2 A:HIS200 4.1 8.9 1.0
ND1 A:HIS172 4.2 7.3 1.0
CD2 A:HIS200 4.2 8.6 1.0
CG A:HIS187 4.2 10.5 1.0
O A:TYR176 4.3 8.4 1.0
CB A:ASP174 4.3 8.2 1.0
CB A:TYR176 4.6 10.3 1.0
CZ A:PHE178 4.7 7.8 1.0
CE2 A:PHE178 4.8 7.6 1.0
O A:HOH2248 4.8 14.9 1.0
CE1 A:PHE189 4.9 14.0 1.0
CZ A:PHE189 4.9 13.2 1.0
CA A:HIS200 4.9 8.5 1.0
O A:HOH2328 5.0 11.3 1.0

Zinc binding site 3 out of 4 in 3kej

Go back to Zinc Binding Sites List in 3kej
Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn 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
B:Zn901

b:6.1
occ:1.00
NE2 B:HIS232 2.1 10.5 1.0
NE2 B:HIS222 2.2 5.5 1.0
NE2 B:HIS226 2.2 8.7 1.0
O B:HOH2235 2.2 8.7 1.0
CD2 B:HIS222 3.0 5.8 1.0
CD2 B:HIS232 3.0 10.2 1.0
CE1 B:HIS232 3.0 11.5 1.0
CD2 B:HIS226 3.1 7.6 1.0
CE1 B:HIS226 3.1 9.0 1.0
CE1 B:HIS222 3.2 5.3 1.0
OE2 B:GLU223 4.0 13.4 1.0
ND1 B:HIS232 4.1 11.5 1.0
CG B:HIS232 4.1 10.6 1.0
CG B:HIS222 4.2 6.3 1.0
ND1 B:HIS226 4.3 9.0 1.0
ND1 B:HIS222 4.3 5.1 1.0
CG B:HIS226 4.3 8.1 1.0
O B:HOH2165 4.4 24.4 1.0
O B:HOH2078 4.5 2.0 1.0
O B:HOH2145 4.6 11.4 1.0
OE1 B:GLU223 4.6 15.3 1.0
CD B:GLU223 4.6 12.3 1.0
O B:HOH2357 4.8 38.0 1.0
CE B:MET240 4.8 6.7 1.0
F32 B:3EJ801 4.8 4.0 1.0
CA B:PRO242 5.0 7.4 1.0

Zinc binding site 4 out of 4 in 3kej

Go back to Zinc Binding Sites List in 3kej
Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn 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:Zn902

b:2.0
occ:1.00
OD2 B:ASP174 1.9 3.6 1.0
NE2 B:HIS172 2.0 5.9 1.0
NE2 B:HIS187 2.0 8.8 1.0
ND1 B:HIS200 2.0 8.7 1.0
CG B:ASP174 2.9 3.4 1.0
CE1 B:HIS187 2.9 9.5 1.0
CE1 B:HIS172 2.9 6.4 1.0
CE1 B:HIS200 2.9 8.9 1.0
CD2 B:HIS172 3.0 5.1 1.0
CG B:HIS200 3.1 7.9 1.0
CD2 B:HIS187 3.1 8.2 1.0
OD1 B:ASP174 3.2 4.2 1.0
CB B:HIS200 3.4 7.8 1.0
ND1 B:HIS187 4.0 8.2 1.0
ND1 B:HIS172 4.0 6.4 1.0
NE2 B:HIS200 4.1 7.5 1.0
CG B:HIS172 4.1 5.7 1.0
CD2 B:HIS200 4.2 8.1 1.0
CB B:ASP174 4.2 5.0 1.0
CG B:HIS187 4.2 9.3 1.0
O B:TYR176 4.2 7.6 1.0
CE1 B:PHE189 4.5 11.7 1.0
CZ B:PHE178 4.6 9.7 1.0
CZ B:PHE189 4.7 12.5 1.0
CE2 B:PHE178 4.7 9.7 1.0
O B:HOH2013 4.7 2.0 1.0
CA B:HIS200 4.9 8.0 1.0
CB B:TYR176 5.0 8.7 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: Wed Dec 16 04:30:00 2020

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