Zinc in PDB 3kry: Crystal Structure of Mmp-13 in Complex with Sc-78080

The structure of Crystal Structure of Mmp-13 in Complex with Sc-78080, PDB code: 3kry was solved by J.R.Kiefer, J.M.Williams, D.P.Becker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.68 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	36.317, 70.016, 69.094, 92.42, 94.23, 104.94
R / Rfree (%)	20.6 / 25.6

The structure of Crystal Structure of Mmp-13 in Complex with Sc-78080 also contains other interesting chemical elements:

Fluorine	(F)	12 atoms
Calcium	(Ca)	8 atoms

The binding sites of Zinc atom in the Crystal Structure of Mmp-13 in Complex with Sc-78080 (pdb code 3kry). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Mmp-13 in Complex with Sc-78080, PDB code: 3kry:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Mmp-13 in Complex with Sc-78080


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 Mmp-13 in Complex with Sc-78080 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1998 b:12.9 occ:1.00 OD2 A:ASP174 1.9 7.5 1.0 NE2 A:HIS187 2.0 12.2 1.0 ND1 A:HIS200 2.0 12.0 1.0 NE2 A:HIS172 2.0 7.8 1.0 CE1 A:HIS187 2.8 12.6 1.0 CG A:ASP174 2.9 7.7 1.0 CE1 A:HIS200 2.9 14.2 1.0 CD2 A:HIS172 2.9 10.1 1.0 CD2 A:HIS187 3.0 13.2 1.0 CE1 A:HIS172 3.1 9.8 1.0 CG A:HIS200 3.1 12.3 1.0 OD1 A:ASP174 3.1 5.0 1.0 CB A:HIS200 3.5 11.9 1.0 ND1 A:HIS187 4.0 12.0 1.0 NE2 A:HIS200 4.1 12.0 1.0 CG A:HIS172 4.1 9.1 1.0 ND1 A:HIS172 4.1 10.0 1.0 CG A:HIS187 4.1 10.3 1.0 O A:TYR176 4.1 10.6 1.0 CD2 A:HIS200 4.2 12.9 1.0 CB A:ASP174 4.3 8.4 1.0 CB A:TYR176 4.6 11.2 1.0 CE1 A:PHE189 4.6 15.9 1.0 CZ A:PHE189 4.6 16.6 1.0 CE2 A:PHE178 4.8 9.2 1.0 C A:TYR176 4.9 10.2 1.0 O A:HOH444 4.9 5.6 1.0 CZ A:PHE178 4.9 10.0 1.0 CA A:HIS200 5.0 11.9 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Mmp-13 in Complex with Sc-78080


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 Mmp-13 in Complex with Sc-78080 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1999 b:13.5 occ:1.00 O11 A:3KR1800 2.0 18.3 1.0 NE2 A:HIS222 2.1 10.7 1.0 NE2 A:HIS226 2.2 7.7 1.0 O14 A:3KR1800 2.2 25.4 1.0 NE2 A:HIS232 2.3 12.1 1.0 N10 A:3KR1800 2.8 20.9 1.0 C9 A:3KR1800 2.9 23.9 1.0 CD2 A:HIS222 3.0 10.6 1.0 CD2 A:HIS226 3.1 9.4 1.0 CD2 A:HIS232 3.1 9.8 1.0 CE1 A:HIS226 3.1 8.8 1.0 CE1 A:HIS222 3.2 9.8 1.0 CE1 A:HIS232 3.3 12.2 1.0 O A:HOH299 4.0 12.9 1.0 OE2 A:GLU223 4.0 11.0 1.0 CG A:HIS222 4.2 10.4 1.0 ND1 A:HIS222 4.2 9.6 1.0 ND1 A:HIS226 4.3 8.8 1.0 CG A:HIS226 4.3 8.8 1.0 CG A:HIS232 4.3 10.0 1.0 ND1 A:HIS232 4.3 12.1 1.0 C8 A:3KR1800 4.4 25.5 1.0 C7 A:3KR1800 4.6 18.8 1.0 OE1 A:GLU223 4.6 10.7 1.0 CD A:GLU223 4.6 11.1 1.0 CE A:MET240 4.8 7.9 1.0 C6 A:3KR1800 4.8 18.1 1.0 C15 A:3KR1800 4.9 27.2 1.0 C2 A:3KR1800 5.0 20.9 1.0 CB A:PRO242 5.0 11.7 1.0 O A:HOH46 5.0 25.2 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Mmp-13 in Complex with Sc-78080


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 Mmp-13 in Complex with Sc-78080 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2998 b:12.8 occ:1.00 OD2 B:ASP174 1.9 12.4 1.0 NE2 B:HIS187 1.9 13.2 1.0 NE2 B:HIS172 2.0 9.4 1.0 ND1 B:HIS200 2.1 14.6 1.0 CE1 B:HIS187 2.8 14.0 1.0 CG B:ASP174 2.8 13.4 1.0 CD2 B:HIS172 2.9 12.6 1.0 CE1 B:HIS200 3.0 16.3 1.0 CD2 B:HIS187 3.0 13.8 1.0 CE1 B:HIS172 3.1 10.4 1.0 CG B:HIS200 3.2 14.5 1.0 OD1 B:ASP174 3.2 11.9 1.0 CB B:HIS200 3.5 13.5 1.0 ND1 B:HIS187 4.0 15.0 1.0 CG B:HIS172 4.1 12.3 1.0 CG B:HIS187 4.1 13.9 1.0 O B:TYR176 4.1 15.4 1.0 ND1 B:HIS172 4.1 12.2 1.0 NE2 B:HIS200 4.2 15.7 1.0 CB B:ASP174 4.2 13.9 1.0 CD2 B:HIS200 4.3 14.8 1.0 CE1 B:PHE189 4.5 18.7 1.0 CB B:TYR176 4.6 17.1 1.0 CZ B:PHE189 4.7 19.4 1.0 C B:TYR176 4.9 16.1 1.0 CE2 B:PHE178 4.9 13.4 1.0 O B:HOH292 5.0 2.2 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Mmp-13 in Complex with Sc-78080


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 Mmp-13 in Complex with Sc-78080 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2999 b:13.4 occ:1.00 NE2 B:HIS222 2.0 15.7 1.0 NE2 B:HIS232 2.1 20.1 1.0 NE2 B:HIS226 2.1 13.6 1.0 O14 B:3KR2800 2.2 25.6 1.0 O11 B:3KR2800 2.2 20.1 1.0 CD2 B:HIS222 2.9 14.2 1.0 N10 B:3KR2800 2.9 23.7 1.0 C9 B:3KR2800 2.9 25.3 1.0 CD2 B:HIS232 3.0 18.1 1.0 CD2 B:HIS226 3.1 12.7 1.0 CE1 B:HIS226 3.1 15.1 1.0 CE1 B:HIS222 3.1 14.6 1.0 CE1 B:HIS232 3.1 21.6 1.0 OE2 B:GLU223 4.1 16.0 1.0 CG B:HIS222 4.1 14.0 1.0 ND1 B:HIS222 4.2 14.3 1.0 O B:HOH302 4.2 17.0 1.0 CG B:HIS232 4.2 18.7 1.0 ND1 B:HIS232 4.2 20.1 1.0 ND1 B:HIS226 4.2 14.1 1.0 CG B:HIS226 4.2 13.3 1.0 C8 B:3KR2800 4.4 26.0 1.0 C7 B:3KR2800 4.7 18.2 1.0 OE1 B:GLU223 4.7 16.1 1.0 CD B:GLU223 4.7 14.3 1.0 C16 B:3KR2800 4.8 30.1 1.0 CE B:MET240 4.8 12.9 1.0 C15 B:3KR2800 4.8 28.5 1.0 C6 B:3KR2800 4.9 17.5 1.0 CB B:PRO242 4.9 19.8 1.0 C2 B:3KR2800 5.0 20.6 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Mmp-13 in Complex with Sc-78080


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Mmp-13 in Complex with Sc-78080 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn3998 b:15.8 occ:1.00 OD2 C:ASP174 1.9 15.4 1.0 NE2 C:HIS172 2.0 14.5 1.0 NE2 C:HIS187 2.0 16.5 1.0 ND1 C:HIS200 2.1 14.9 1.0 CG C:ASP174 2.9 16.4 1.0 CE1 C:HIS187 2.9 17.1 1.0 CD2 C:HIS172 3.0 14.6 1.0 CE1 C:HIS172 3.0 15.3 1.0 CE1 C:HIS200 3.0 15.2 1.0 CD2 C:HIS187 3.1 16.7 1.0 CG C:HIS200 3.1 14.6 1.0 OD1 C:ASP174 3.2 15.4 1.0 CB C:HIS200 3.4 14.6 1.0 ND1 C:HIS187 4.1 17.8 1.0 ND1 C:HIS172 4.1 16.6 1.0 CG C:HIS172 4.1 15.0 1.0 NE2 C:HIS200 4.1 15.9 1.0 CG C:HIS187 4.2 16.4 1.0 CD2 C:HIS200 4.2 14.7 1.0 CB C:ASP174 4.2 15.1 1.0 O C:TYR176 4.3 18.8 1.0 CZ C:PHE178 4.6 16.8 1.0 CE2 C:PHE178 4.6 16.4 1.0 CE1 C:PHE189 4.7 20.2 1.0 CB C:TYR176 4.7 19.8 1.0 O C:HOH437 4.8 16.3 1.0 CZ C:PHE189 4.9 20.6 1.0 CA C:HIS200 4.9 14.6 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Mmp-13 in Complex with Sc-78080


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Mmp-13 in Complex with Sc-78080 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn3999 b:18.0 occ:1.00 NE2 C:HIS232 2.1 25.1 1.0 NE2 C:HIS222 2.1 15.6 1.0 NE2 C:HIS226 2.1 14.2 1.0 O11 C:3KR3800 2.2 31.2 1.0 O14 C:3KR3800 2.2 35.4 1.0 N10 C:3KR3800 2.9 34.2 1.0 C9 C:3KR3800 2.9 34.5 1.0 CD2 C:HIS222 2.9 14.5 1.0 CD2 C:HIS232 3.0 25.4 1.0 CD2 C:HIS226 3.1 14.8 1.0 CE1 C:HIS226 3.1 15.1 1.0 CE1 C:HIS232 3.1 25.8 1.0 CE1 C:HIS222 3.2 16.7 1.0 OE2 C:GLU223 4.1 17.4 1.0 CG C:HIS232 4.1 25.7 1.0 CG C:HIS222 4.1 15.8 1.0 ND1 C:HIS232 4.2 26.6 1.0 ND1 C:HIS226 4.2 16.6 1.0 O C:HOH368 4.2 24.0 1.0 ND1 C:HIS222 4.2 16.0 1.0 CG C:HIS226 4.2 15.9 1.0 C8 C:3KR3800 4.4 34.0 1.0 C7 C:3KR3800 4.6 26.5 1.0 CD C:GLU223 4.8 15.8 1.0 C15 C:3KR3800 4.9 35.9 1.0 CE C:MET240 4.9 20.7 1.0 C6 C:3KR3800 4.9 24.4 1.0 OE1 C:GLU223 4.9 15.7 1.0 C16 C:3KR3800 5.0 37.2 1.0 C2 C:3KR3800 5.0 28.1 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Mmp-13 in Complex with Sc-78080


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Mmp-13 in Complex with Sc-78080 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn4998 b:14.4 occ:1.00 OD2 D:ASP174 1.9 16.3 1.0 NE2 D:HIS172 1.9 14.2 1.0 ND1 D:HIS200 2.1 15.2 1.0 NE2 D:HIS187 2.1 18.4 1.0 CD2 D:HIS172 2.9 14.8 1.0 CG D:ASP174 2.9 16.8 1.0 CE1 D:HIS200 3.0 14.9 1.0 CE1 D:HIS172 3.0 15.0 1.0 CE1 D:HIS187 3.0 18.7 1.0 CG D:HIS200 3.1 13.9 1.0 CD2 D:HIS187 3.1 18.3 1.0 OD1 D:ASP174 3.2 15.9 1.0 CB D:HIS200 3.5 13.5 1.0 CG D:HIS172 4.0 15.5 1.0 ND1 D:HIS172 4.1 15.2 1.0 NE2 D:HIS200 4.1 15.7 1.0 ND1 D:HIS187 4.1 19.7 1.0 CD2 D:HIS200 4.2 15.0 1.0 O D:TYR176 4.2 18.9 1.0 CG D:HIS187 4.2 18.3 1.0 CB D:ASP174 4.3 16.2 1.0 CZ D:PHE178 4.6 17.1 1.0 CE2 D:PHE178 4.6 17.5 1.0 CE1 D:PHE189 4.7 21.7 1.0 O D:HOH430 4.8 17.7 1.0 CB D:TYR176 4.8 20.0 1.0 O D:HOH268 4.9 28.9 1.0 O D:HOH346 4.9 44.7 1.0 CA D:HIS200 4.9 13.5 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Mmp-13 in Complex with Sc-78080


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Mmp-13 in Complex with Sc-78080 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn4999 b:16.6 occ:1.00 NE2 D:HIS232 2.1 22.7 1.0 NE2 D:HIS222 2.1 17.8 1.0 O11 D:3KR4800 2.2 29.0 1.0 NE2 D:HIS226 2.2 15.9 1.0 O14 D:3KR4800 2.3 33.1 1.0 N10 D:3KR4800 2.9 32.6 1.0 C9 D:3KR4800 3.0 33.1 1.0 CD2 D:HIS232 3.0 23.5 1.0 CE1 D:HIS232 3.0 23.4 1.0 CD2 D:HIS222 3.0 16.1 1.0 CD2 D:HIS226 3.1 16.1 1.0 CE1 D:HIS222 3.1 16.9 1.0 CE1 D:HIS226 3.2 16.4 1.0 ND1 D:HIS232 4.1 24.1 1.0 CG D:HIS232 4.1 23.3 1.0 OE2 D:GLU223 4.1 17.0 1.0 CG D:HIS222 4.2 16.8 1.0 ND1 D:HIS222 4.2 15.4 1.0 CG D:HIS226 4.3 16.0 1.0 ND1 D:HIS226 4.3 17.5 1.0 O D:HOH382 4.3 25.4 1.0 C8 D:3KR4800 4.5 34.0 1.0 C7 D:3KR4800 4.7 27.3 1.0 CE D:MET240 4.9 17.9 1.0 CD D:GLU223 4.9 15.8 1.0 OE1 D:GLU223 4.9 16.0 1.0 C6 D:3KR4800 4.9 26.2 1.0 CB D:PRO242 4.9 21.7 1.0 C15 D:3KR4800 5.0 35.5 1.0

D.P.Becker, T.E.Barta, L.J.Bedell, T.L.Boehm, B.R.Bond, J.Carroll, C.P.Carron, G.A.Decrescenzo, A.M.Easton, J.N.Freskos, C.L.Funckes-Shippy, M.Heron, S.Hockerman, C.P.Howard, J.R.Kiefer, M.H.Li, K.J.Mathis, J.J.Mcdonald, P.P.Mehta, G.E.Munie, T.Sunyer, C.A.Swearingen, C.I.Villamil, D.Welsch, J.M.Williams, Y.Yu, J.Yao. Orally-Active Mmp-1 Sparing Alpha-Tetrahydropyranyl and Alpha-Piperidinyl Sulfone Matrix Metalloproteinase (Mmp) Inhibitors with Efficacy in Cancer, Arthritis, and Cardiovascular Disease J.Med.Chem. V. 53 6653 2010.
ISSN: ISSN 0022-2623
PubMed: 20726512
DOI: 10.1021/JM100669J