Calcium in PDB 1ztq: Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033, PDB code: 1ztq was solved by J.Wu, T.S.Rush Iii, R.Hotchandani, X.Du, M.Geck, E.Collins, Z.B.Xu, J.Skotnicki, J.I.Levin, F.Lovering, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.46 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.937, 135.252, 69.385, 90.00, 104.95, 90.00
R / Rfree (%)	23.6 / 28.7

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033 also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033 (pdb code 1ztq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033, PDB code: 1ztq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033


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 the Catalytic Domain of Mmp-13 Complexed with Way-033 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca560 b:11.2 occ:1.00 O A:LEU159 2.2 12.5 1.0 O A:GLY155 2.4 13.5 1.0 OD1 A:ASP177 2.4 7.8 1.0 OE1 A:GLU180 2.5 4.6 1.0 O A:SER157 2.5 12.1 1.0 OD2 A:ASP154 2.5 12.1 1.0 C A:LEU159 3.4 11.6 1.0 C A:SER157 3.5 12.5 1.0 CD A:GLU180 3.5 2.2 1.0 CG A:ASP177 3.5 5.4 1.0 CG A:ASP154 3.6 12.4 1.0 C A:GLY155 3.6 14.8 1.0 N A:LEU159 3.8 12.0 1.0 CG A:GLU180 3.8 2.3 1.0 N A:SER157 4.0 14.4 1.0 C A:PRO156 4.0 13.6 1.0 O A:HOH665 4.1 27.2 1.0 C A:GLY158 4.1 11.6 1.0 CA A:LEU159 4.1 12.1 1.0 OD1 A:ASP154 4.2 15.6 1.0 N A:GLY155 4.2 14.7 1.0 O A:PRO156 4.2 16.4 1.0 C A:ASP154 4.2 14.1 1.0 N A:ASP154 4.3 15.2 1.0 CA A:SER157 4.3 13.3 1.0 CB A:ASP177 4.3 4.7 1.0 OD2 A:ASP177 4.3 7.5 1.0 N A:GLY158 4.4 12.7 1.0 N A:LEU160 4.4 11.9 1.0 CA A:PRO156 4.5 14.1 1.0 CA A:GLY158 4.5 11.9 1.0 N A:PRO156 4.5 15.3 1.0 O A:ASP154 4.5 14.2 1.0 CA A:GLY155 4.5 14.3 1.0 CA A:LEU160 4.6 11.7 1.0 CA A:ASP154 4.6 14.8 1.0 O A:GLY158 4.6 11.7 1.0 OE2 A:GLU180 4.6 6.3 1.0 CB A:ASP154 4.6 15.0 1.0 CB A:LEU159 4.7 13.3 1.0

Calcium binding site 2 out of 12 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033


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 the Catalytic Domain of Mmp-13 Complexed with Way-033 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca561 b:15.4 occ:1.00 O A:ASP137 2.1 2.2 1.0 O A:ASN169 2.2 17.2 1.0 O A:HOH659 2.3 14.5 1.0 OD2 A:ASP173 2.4 8.4 1.0 O A:GLY171 2.5 8.2 1.0 C A:ASN169 3.3 15.3 1.0 C A:ASP137 3.3 3.9 1.0 CG A:ASP173 3.4 9.9 1.0 C A:GLY171 3.6 9.1 1.0 OD1 A:ASP173 3.8 11.5 1.0 O A:HOH615 3.9 9.2 1.0 N A:GLY171 3.9 10.7 1.0 C A:TYR170 4.0 12.3 1.0 O A:ALA136 4.0 7.3 1.0 CA A:ASN169 4.1 15.9 1.0 N A:ASN169 4.1 16.3 1.0 CA A:ASP137 4.1 5.6 1.0 N A:ASP173 4.2 10.7 1.0 O A:TYR170 4.2 10.2 1.0 N A:TYR170 4.3 14.0 1.0 CA A:GLY171 4.3 10.5 1.0 N A:ILE138 4.3 2.2 1.0 O A:GLY167 4.3 13.0 1.0 CA A:TYR170 4.4 13.5 1.0 CA A:ILE138 4.4 2.5 1.0 C A:PRO168 4.5 15.2 1.0 CB A:ASP173 4.6 9.2 1.0 N A:GLY172 4.6 8.3 1.0 CH2 A:TRP88 4.6 10.9 1.0 N A:MET139 4.7 3.4 1.0 C A:GLY172 4.7 9.4 1.0 CA A:ASP173 4.7 7.6 1.0 CA A:GLY172 4.8 9.7 1.0 O A:PRO168 4.8 14.5 1.0 C A:ALA136 4.9 8.4 1.0 CG A:MET139 5.0 5.9 1.0

Calcium binding site 3 out of 12 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033


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 the Catalytic Domain of Mmp-13 Complexed with Way-033 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca562 b:15.1 occ:1.00 O A:HOH622 2.3 10.2 1.0 O A:ASP178 2.4 6.0 1.0 O A:GLU180 2.6 9.5 1.0 OD1 A:ASP103 2.6 3.8 1.0 OD2 A:ASP178 2.7 8.8 1.0 CG A:ASP103 3.3 5.5 1.0 OD2 A:ASP103 3.3 5.2 1.0 C A:ASP178 3.4 6.1 1.0 OG1 A:THR101 3.6 6.5 1.0 CG A:ASP178 3.7 5.1 1.0 C A:GLU180 3.7 7.6 1.0 CA A:ASP178 3.8 5.2 1.0 CD1 A:TRP182 4.0 6.3 1.0 CB A:ASP178 4.1 6.3 1.0 N A:GLU180 4.2 7.8 1.0 O D:HOH609 4.2 9.0 1.0 CA A:THR181 4.4 12.8 1.0 NE1 A:TRP182 4.4 3.2 1.0 N A:THR181 4.5 9.4 1.0 N A:ASP179 4.5 4.7 1.0 CD A:PRO102 4.5 7.3 1.0 CG A:PRO102 4.6 10.4 1.0 CB A:ASP103 4.7 6.9 1.0 CA A:GLU180 4.7 7.5 1.0 N A:TRP182 4.7 14.0 1.0 OD1 A:ASP178 4.8 5.1 1.0 OD2 D:ASP133 4.8 17.9 1.0 C A:ASP179 4.8 5.7 1.0 CA A:ASP179 4.9 5.5 1.0 CB A:THR101 4.9 4.9 1.0

Calcium binding site 4 out of 12 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033


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 the Catalytic Domain of Mmp-13 Complexed with Way-033 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca563 b:18.2 occ:1.00 O B:LEU159 2.2 10.9 1.0 OD1 B:ASP177 2.3 6.0 1.0 OD2 B:ASP154 2.3 8.9 1.0 O B:GLY155 2.4 16.6 1.0 OE2 B:GLU180 2.5 8.2 1.0 O B:SER157 2.8 19.8 1.0 C B:LEU159 3.4 10.6 1.0 CG B:ASP177 3.4 7.3 1.0 CD B:GLU180 3.5 9.6 1.0 CG B:ASP154 3.5 14.3 1.0 C B:GLY155 3.7 17.1 1.0 C B:SER157 3.7 17.9 1.0 CG B:GLU180 3.7 9.7 1.0 N B:LEU159 3.8 12.4 1.0 CA B:LEU159 4.1 10.6 1.0 N B:GLY155 4.1 16.0 1.0 C B:ASP154 4.1 15.9 1.0 N B:SER157 4.1 18.9 1.0 OD1 B:ASP154 4.1 15.2 1.0 N B:ASP154 4.2 17.0 1.0 OD2 B:ASP177 4.2 6.5 1.0 O B:HOH607 4.2 22.0 1.0 C B:GLY158 4.2 13.2 1.0 CB B:ASP177 4.2 8.2 1.0 C B:PRO156 4.3 18.6 1.0 N B:LEU160 4.4 10.2 1.0 CB B:LEU159 4.4 12.4 1.0 CA B:SER157 4.5 19.3 1.0 O B:ASP154 4.5 17.1 1.0 CA B:ASP154 4.5 17.4 1.0 CA B:GLY155 4.5 15.9 1.0 N B:GLY158 4.5 17.5 1.0 CB B:ASP154 4.6 16.0 1.0 CA B:LEU160 4.6 9.9 1.0 OE1 B:GLU180 4.6 8.6 1.0 N B:PRO156 4.6 16.4 1.0 CA B:GLY158 4.7 14.2 1.0 O B:PRO156 4.7 21.8 1.0 CA B:PRO156 4.7 17.3 1.0 O B:GLY158 4.7 12.5 1.0 O B:HOH606 5.0 7.9 1.0

Calcium binding site 5 out of 12 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033


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 the Catalytic Domain of Mmp-13 Complexed with Way-033 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca564 b:9.4 occ:1.00 O B:ASN169 2.2 14.1 1.0 O B:HOH720 2.3 19.7 1.0 O B:HOH641 2.3 5.1 1.0 O B:ASP137 2.3 4.5 1.0 OD2 B:ASP173 2.5 14.3 1.0 O B:GLY171 2.6 15.2 1.0 C B:ASN169 3.4 17.2 1.0 C B:ASP137 3.5 7.8 1.0 CG B:ASP173 3.6 13.7 1.0 C B:GLY171 3.7 14.5 1.0 O B:ALA136 3.9 12.2 1.0 C B:TYR170 4.0 14.4 1.0 OD1 B:ASP173 4.0 14.7 1.0 O B:TYR170 4.2 15.1 1.0 O B:HOH635 4.2 6.0 1.0 N B:GLY171 4.2 12.9 1.0 N B:ASP173 4.2 10.2 1.0 CA B:ASP137 4.3 8.4 1.0 CA B:ASN169 4.3 18.9 1.0 O B:GLY167 4.3 15.5 1.0 N B:ASN169 4.3 18.8 1.0 N B:TYR170 4.4 16.2 1.0 CA B:TYR170 4.4 15.7 1.0 N B:ILE138 4.5 8.7 1.0 CA B:GLY171 4.5 12.9 1.0 O B:HOH696 4.5 23.6 1.0 N B:MET139 4.6 10.8 1.0 C B:PRO168 4.6 18.5 1.0 CA B:ILE138 4.6 8.8 1.0 N B:GLY172 4.7 11.8 1.0 CB B:ASP173 4.7 11.1 1.0 O B:PRO168 4.8 18.1 1.0 CA B:GLY172 4.8 8.9 1.0 C B:GLY172 4.8 8.6 1.0 CA B:ASP173 4.8 9.6 1.0 CH2 B:TRP88 4.9 21.5 1.0 C B:ALA136 4.9 10.9 1.0

Calcium binding site 6 out of 12 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033


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 the Catalytic Domain of Mmp-13 Complexed with Way-033 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca565 b:13.2 occ:1.00 O B:ASP178 2.4 10.4 1.0 O C:HOH615 2.4 4.8 1.0 O B:HOH618 2.5 14.2 1.0 OD1 B:ASP103 2.6 11.9 1.0 O B:GLU180 2.7 14.3 1.0 OD2 B:ASP178 3.1 7.5 1.0 OD2 B:ASP103 3.2 14.8 1.0 CG B:ASP103 3.2 12.5 1.0 C B:ASP178 3.3 9.8 1.0 C B:GLU180 3.6 12.3 1.0 CA B:ASP178 3.9 8.0 1.0 OD2 C:ASP133 3.9 22.5 1.0 OG1 B:THR101 4.0 3.2 1.0 CG B:ASP178 4.1 10.3 1.0 O C:HOH625 4.1 10.0 1.0 CA B:THR181 4.1 12.7 1.0 N B:GLU180 4.2 12.6 1.0 N B:THR181 4.3 12.5 1.0 N B:ASP179 4.3 8.1 1.0 CB B:ASP178 4.4 8.9 1.0 CD1 B:TRP182 4.5 7.0 1.0 C B:ASP179 4.5 10.0 1.0 CA B:GLU180 4.6 12.6 1.0 CA B:ASP179 4.6 10.2 1.0 CB B:ASP103 4.7 13.4 1.0 CG B:PRO102 4.8 11.8 1.0 N B:TRP182 4.8 11.6 1.0 CD B:PRO102 4.8 8.2 1.0 OG1 B:THR181 4.9 13.7 1.0 NE1 B:TRP182 5.0 7.4 1.0

Calcium binding site 7 out of 12 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca566 b:7.0 occ:1.00 OD2 C:ASP177 2.1 9.4 1.0 O C:LEU159 2.2 11.2 1.0 O C:SER157 2.3 11.0 1.0 OE1 C:GLU180 2.3 17.6 1.0 O C:GLY155 2.4 6.6 1.0 OD2 C:ASP154 2.5 10.7 1.0 CG C:ASP177 3.2 9.1 1.0 CD C:GLU180 3.3 15.6 1.0 C C:LEU159 3.4 13.0 1.0 C C:SER157 3.4 11.5 1.0 C C:GLY155 3.6 9.0 1.0 CG C:ASP154 3.7 12.3 1.0 N C:LEU159 3.7 14.1 1.0 CG C:GLU180 3.9 11.8 1.0 N C:SER157 3.9 12.2 1.0 OD1 C:ASP177 3.9 12.0 1.0 CA C:LEU159 4.0 11.6 1.0 C C:GLY158 4.1 14.4 1.0 CB C:ASP177 4.1 7.3 1.0 C C:PRO156 4.1 12.7 1.0 N C:GLY155 4.1 9.6 1.0 CA C:SER157 4.2 11.0 1.0 OD1 C:ASP154 4.2 12.9 1.0 C C:ASP154 4.3 10.7 1.0 N C:ASP154 4.3 12.2 1.0 OE2 C:GLU180 4.3 16.2 1.0 CB C:LEU159 4.4 13.2 1.0 N C:GLY158 4.4 12.2 1.0 CA C:GLY155 4.5 10.5 1.0 N C:LEU160 4.5 12.2 1.0 N C:PRO156 4.5 11.3 1.0 CA C:GLY158 4.5 14.5 1.0 CA C:PRO156 4.5 11.1 1.0 O C:PRO156 4.6 13.2 1.0 CA C:ASP154 4.7 9.8 1.0 O C:GLY158 4.7 14.7 1.0 O C:ASP154 4.7 10.7 1.0 CB C:ASP154 4.7 8.6 1.0 O C:HOH632 4.9 10.7 1.0 CA C:LEU160 4.9 11.1 1.0

Calcium binding site 8 out of 12 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca567 b:24.9 occ:1.00 O C:ASN169 2.1 25.2 1.0 O C:HOH604 2.3 4.4 1.0 O C:ASP137 2.5 15.2 1.0 OD2 C:ASP173 2.5 14.2 1.0 O C:GLY171 2.8 18.3 1.0 C C:ASN169 3.3 26.2 1.0 C C:ASP137 3.5 10.9 1.0 CG C:ASP173 3.6 13.1 1.0 C C:GLY171 3.8 16.9 1.0 O C:HOH689 3.8 19.3 1.0 O C:ALA136 3.9 7.7 1.0 OD1 C:ASP173 4.0 11.6 1.0 C C:TYR170 4.0 21.3 1.0 N C:ASP173 4.1 13.6 1.0 N C:GLY171 4.2 20.3 1.0 O C:TYR170 4.3 20.5 1.0 CA C:ASN169 4.3 28.3 1.0 N C:TYR170 4.3 23.8 1.0 CA C:TYR170 4.3 22.7 1.0 CA C:ASP137 4.3 12.8 1.0 N C:ILE138 4.4 11.9 1.0 N C:ASN169 4.5 27.0 1.0 CA C:GLY171 4.6 18.2 1.0 CG C:MET139 4.6 6.2 1.0 N C:GLY172 4.6 17.1 1.0 CA C:ILE138 4.6 9.5 1.0 CA C:GLY172 4.6 15.4 1.0 N C:MET139 4.7 8.8 1.0 O C:GLY167 4.7 20.5 1.0 C C:GLY172 4.7 14.5 1.0 CB C:ASP173 4.7 13.3 1.0 CA C:ASP173 4.8 12.2 1.0 C C:PRO168 4.9 25.9 1.0 CH2 C:TRP88 4.9 13.7 1.0 C C:ALA136 4.9 9.4 1.0 O C:PRO168 5.0 25.4 1.0

Calcium binding site 9 out of 12 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca568 b:40.1 occ:1.00 OD1 C:ASP103 2.5 18.7 1.0 O C:GLU180 2.6 9.9 1.0 O B:HOH717 2.8 22.1 1.0 OD2 C:ASP103 2.9 15.9 1.0 O C:HOH731 2.9 19.9 1.0 OD2 C:ASP178 2.9 10.1 1.0 CG C:ASP103 2.9 15.6 1.0 O C:ASP178 3.4 10.4 1.0 C C:GLU180 3.8 10.0 1.0 OG1 C:THR101 3.8 7.3 1.0 C C:ASP178 3.9 10.6 1.0 O B:HOH694 4.0 19.1 1.0 CD1 C:TRP182 4.1 6.1 1.0 CG C:ASP178 4.1 6.4 1.0 CA C:THR181 4.2 7.5 1.0 CB C:ASP103 4.3 14.1 1.0 CA C:ASP178 4.3 7.6 1.0 N C:THR181 4.5 8.0 1.0 CG C:PRO102 4.5 12.2 1.0 N C:GLU180 4.5 8.8 1.0 O B:HOH699 4.6 24.3 1.0 NE1 C:TRP182 4.6 6.8 1.0 CD C:PRO102 4.6 15.3 1.0 N C:TRP182 4.7 8.6 1.0 N C:ASP179 4.7 10.8 1.0 CB C:ASP178 4.8 9.6 1.0 N C:ASP103 4.8 14.4 1.0 CA C:GLU180 4.9 9.9 1.0 C C:ASP179 4.9 9.2 1.0 C C:THR181 5.0 8.5 1.0

Calcium binding site 10 out of 12 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca569 b:8.3 occ:1.00 O D:GLY155 2.1 10.9 1.0 O D:SER157 2.3 10.2 1.0 OD1 D:ASP177 2.3 9.3 1.0 O D:LEU159 2.4 12.9 1.0 OE2 D:GLU180 2.4 14.5 1.0 OD1 D:ASP154 2.6 8.5 1.0 C D:GLY155 3.3 11.2 1.0 C D:SER157 3.4 11.0 1.0 CD D:GLU180 3.5 15.1 1.0 CG D:ASP177 3.5 8.4 1.0 C D:LEU159 3.6 12.0 1.0 CG D:ASP154 3.6 11.3 1.0 N D:GLY155 3.8 12.0 1.0 N D:LEU159 3.9 12.7 1.0 N D:SER157 4.0 11.8 1.0 C D:PRO156 4.1 11.6 1.0 CG D:GLU180 4.1 12.0 1.0 C D:GLY158 4.1 12.8 1.0 C D:ASP154 4.2 10.4 1.0 CA D:GLY155 4.2 12.4 1.0 OD2 D:ASP154 4.2 11.8 1.0 N D:ASP154 4.3 10.7 1.0 CA D:LEU159 4.3 11.6 1.0 N D:PRO156 4.3 11.9 1.0 CB D:ASP177 4.3 9.3 1.0 CA D:SER157 4.3 11.8 1.0 OD2 D:ASP177 4.4 7.3 1.0 N D:GLY158 4.4 11.9 1.0 CA D:GLY158 4.4 13.0 1.0 OE1 D:GLU180 4.4 15.4 1.0 CA D:PRO156 4.5 10.6 1.0 O D:PRO156 4.5 8.9 1.0 CA D:ASP154 4.6 10.3 1.0 O D:GLY158 4.6 13.1 1.0 N D:LEU160 4.6 11.9 1.0 CB D:ASP154 4.7 10.1 1.0 O D:ASP154 4.7 10.3 1.0 CB D:LEU159 4.8 10.2 1.0 CA D:LEU160 4.9 10.6 1.0 O D:HOH610 4.9 12.7 1.0

J.Wu, T.S.Rush Iii, R.Hotchandani, X.Du, M.Geck, E.Collins, Z.B.Xu, J.Skotnicki, J.I.Levin, F.E.Lovering. Identification of Potent and Selective Mmp-13 Inhibitors Bioorg.Med.Chem.Lett. V. 15 4105 2005.
ISSN: ISSN 0960-894X
PubMed: 16005220
DOI: 10.1016/J.BMCL.2005.06.019