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Calcium in PDB 5boy: X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate

Protein crystallography data

The structure of X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate, PDB code: 5boy was solved by N.A.Farrow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.42 / 2.03
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 135.079, 36.051, 95.908, 90.00, 131.26, 90.00
R / Rfree (%) 16 / 19

Other elements in 5boy:

The structure of X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate (pdb code 5boy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate, PDB code: 5boy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5boy

Go back to Calcium Binding Sites List in 5boy
Calcium binding site 1 out of 6 in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:48.7
occ:1.00
 OD2 A:ASP128 2.7 20.6 1.0
O A:GLU205 2.8 19.6 1.0
O A:ASP203 2.8 18.8 1.0
OD2 A:ASP203 2.8 23.5 1.0
OD1 A:ASP128 3.0 25.1 1.0
CG A:ASP128 3.2 24.9 1.0
C A:ASP203 3.6 15.3 1.0
OG1 A:THR126 3.6 12.5 1.0
CG A:ASP203 3.8 19.6 1.0
C A:GLU205 4.0 17.9 1.0
CD A:PRO127 4.0 12.1 1.0
O A:HOH491 4.0 30.4 1.0
CA A:ASP203 4.1 14.8 1.0
CB A:ASP203 4.4 14.2 1.0
CD1 A:TRP207 4.5 12.1 1.0
CG A:PRO127 4.5 17.1 1.0
CB A:ASP128 4.6 16.7 1.0
N A:GLU205 4.6 14.6 1.0
N A:ASP204 4.6 11.1 1.0
CA A:THR206 4.7 17.6 1.0
C A:ASP204 4.8 16.2 1.0
OD1 A:ASP203 4.8 22.5 1.0
CB A:THR126 4.8 12.4 1.0
N A:THR206 4.8 16.1 1.0
N A:ASP128 4.9 13.3 1.0
CA A:ASP204 4.9 13.6 1.0
N A:PRO127 5.0 12.7 1.0
CA A:GLU205 5.0 16.1 1.0

Calcium binding site 2 out of 6 in 5boy

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Calcium binding site 2 out of 6 in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:15.4
occ:1.00
 OD2 A:ASP202 2.4 14.1 1.0
O A:GLY180 2.4 17.3 1.0
OE2 A:GLU205 2.4 23.5 1.0
O A:LEU184 2.4 16.3 1.0
O A:SER182 2.5 19.7 1.0
OD1 A:ASP179 2.5 16.7 1.0
CG A:ASP202 3.5 13.1 1.0
C A:SER182 3.5 23.6 1.0
C A:GLY180 3.5 17.0 1.0
C A:LEU184 3.6 16.7 1.0
CD A:GLU205 3.6 23.4 1.0
CG A:ASP179 3.7 20.8 1.0
N A:LEU184 3.9 14.5 1.0
N A:SER182 3.9 19.5 1.0
C A:PRO181 4.1 22.6 1.0
N A:GLY180 4.1 15.8 1.0
C A:GLY183 4.2 21.8 1.0
CB A:ASP202 4.2 9.5 1.0
CA A:LEU184 4.2 20.8 1.0
OD2 A:ASP179 4.3 22.4 1.0
C A:ASP179 4.3 17.3 1.0
N A:ASP179 4.3 16.5 1.0
CG A:GLU205 4.3 16.9 1.0
CA A:SER182 4.3 24.1 1.0
OD1 A:ASP202 4.4 7.9 1.0
CA A:GLY180 4.4 15.0 1.0
CA A:PRO181 4.4 18.5 1.0
N A:PRO181 4.4 21.1 1.0
N A:GLY183 4.5 22.4 1.0
O A:PRO181 4.5 26.6 1.0
CA A:GLY183 4.5 22.7 1.0
OE1 A:GLU205 4.5 24.6 1.0
N A:LEU185 4.6 16.0 1.0
CA A:ASP179 4.6 17.0 1.0
CB A:LEU184 4.6 23.9 1.0
O A:ASP179 4.7 20.2 1.0
O A:GLY183 4.7 19.4 1.0
CB A:ASP179 4.8 22.0 1.0
CA A:LEU185 4.8 15.5 1.0
O A:HOH461 5.0 9.6 1.0

Calcium binding site 3 out of 6 in 5boy

Go back to Calcium Binding Sites List in 5boy
Calcium binding site 3 out of 6 in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:36.8
occ:1.00
 O A:GLY196 2.4 15.3 1.0
O A:ASN194 2.6 24.6 1.0
OD1 A:ASP198 2.6 17.2 1.0
O A:HOH411 2.7 24.3 1.0
O A:ASP162 2.7 16.7 1.0
O A:HOH488 2.9 22.9 1.0
CG A:ASP198 3.5 17.2 1.0
C A:GLY196 3.5 14.7 1.0
C A:ASP162 3.7 15.9 1.0
C A:TYR195 3.7 20.3 1.0
C A:ASN194 3.7 22.4 1.0
N A:GLY196 3.8 16.6 1.0
OD2 A:ASP198 3.9 16.8 1.0
O A:ALA161 3.9 13.9 1.0
O A:TYR195 3.9 15.7 1.0
O A:HOH402 4.0 29.7 1.0
CA A:TYR195 4.1 21.3 1.0
N A:ASP198 4.2 11.2 1.0
CA A:GLY196 4.3 15.5 1.0
N A:TYR195 4.4 22.1 1.0
CA A:ASP162 4.4 14.5 1.0
N A:GLY197 4.5 11.6 1.0
CG A:MET164 4.6 16.9 1.0
N A:ILE163 4.6 11.4 1.0
CB A:ASP198 4.6 14.2 1.0
N A:MET164 4.7 12.6 1.0
C A:GLY197 4.7 13.9 1.0
CA A:GLY197 4.7 11.7 1.0
O A:HOH455 4.7 27.4 1.0
CA A:ILE163 4.8 12.1 1.0
CA A:ASP198 4.8 13.3 1.0
CH2 A:TRP113 4.8 19.7 1.0
CA A:ASN194 4.8 26.8 1.0
C A:ALA161 4.9 14.8 1.0
O A:GLY192 4.9 16.2 1.0

Calcium binding site 4 out of 6 in 5boy

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Calcium binding site 4 out of 6 in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:50.0
occ:1.00
 OD2 B:ASP128 2.8 21.2 1.0
OD2 B:ASP203 2.9 19.0 1.0
O B:GLU205 2.9 18.4 1.0
O B:ASP203 2.9 16.1 1.0
OD1 B:ASP128 3.2 24.2 1.0
CG B:ASP128 3.3 20.1 1.0
OG1 B:THR126 3.6 12.0 1.0
C B:ASP203 3.7 13.7 1.0
CG B:ASP203 3.8 17.0 1.0
O B:HOH472 4.0 31.0 1.0
C B:GLU205 4.0 16.1 1.0
CA B:ASP203 4.2 14.5 1.0
CD B:PRO127 4.2 14.9 1.0
CB B:ASP203 4.4 14.2 1.0
CD1 B:TRP207 4.6 11.1 1.0
CA B:THR206 4.6 16.8 1.0
CB B:ASP128 4.6 15.2 1.0
CG B:PRO127 4.7 14.2 1.0
N B:GLU205 4.7 15.0 1.0
OD1 B:ASP203 4.7 18.6 1.0
N B:ASP204 4.7 12.8 1.0
N B:THR206 4.8 15.4 1.0
C B:ASP204 4.9 19.8 1.0
N B:ASP128 4.9 13.9 1.0
N B:TRP207 5.0 13.3 1.0
CB B:THR126 5.0 11.3 1.0
CA B:ASP204 5.0 15.1 1.0

Calcium binding site 5 out of 6 in 5boy

Go back to Calcium Binding Sites List in 5boy
Calcium binding site 5 out of 6 in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:24.4
occ:1.00
 OE1 B:GLU205 2.4 23.6 1.0
O B:GLY180 2.4 23.6 1.0
OD2 B:ASP202 2.4 14.5 1.0
O B:LEU184 2.5 24.6 1.0
OD1 B:ASP179 2.6 26.0 1.0
O B:SER182 2.7 31.8 1.0
CG B:ASP202 3.5 17.3 1.0
CD B:GLU205 3.6 24.8 1.0
C B:SER182 3.6 36.4 1.0
C B:GLY180 3.6 28.1 1.0
C B:LEU184 3.6 23.1 1.0
CG B:ASP179 3.7 29.7 1.0
N B:SER182 4.0 28.9 1.0
N B:LEU184 4.0 23.8 1.0
N B:GLY180 4.1 23.9 1.0
C B:PRO181 4.1 30.7 1.0
CB B:ASP202 4.2 11.3 1.0
C B:ASP179 4.2 25.5 1.0
N B:ASP179 4.2 21.0 1.0
CG B:GLU205 4.2 20.2 1.0
OD2 B:ASP179 4.3 32.5 1.0
C B:GLY183 4.3 26.9 1.0
CA B:SER182 4.3 33.3 1.0
CA B:LEU184 4.3 24.7 1.0
OD1 B:ASP202 4.4 11.4 1.0
CA B:GLY180 4.5 24.7 1.0
N B:GLY183 4.5 32.7 1.0
O B:PRO181 4.5 33.5 1.0
CA B:PRO181 4.5 28.9 1.0
N B:PRO181 4.5 23.3 1.0
O B:ASP179 4.5 28.9 1.0
CA B:ASP179 4.6 24.1 1.0
OE2 B:GLU205 4.6 30.5 1.0
CA B:GLY183 4.6 28.9 1.0
CB B:LEU184 4.6 27.1 1.0
N B:LEU185 4.7 18.5 1.0
CB B:ASP179 4.7 27.6 1.0
CA B:LEU185 4.8 18.0 1.0
O B:GLY183 4.8 26.7 1.0

Calcium binding site 6 out of 6 in 5boy

Go back to Calcium Binding Sites List in 5boy
Calcium binding site 6 out of 6 in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:30.9
occ:1.00
 O B:GLY196 2.5 18.0 1.0
O B:ASP162 2.6 12.9 1.0
O B:HOH461 2.6 27.5 1.0
OD1 B:ASP198 2.7 19.1 1.0
O B:HOH442 2.7 19.9 1.0
O B:ASN194 2.8 25.9 1.0
CG B:ASP198 3.5 17.4 1.0
C B:GLY196 3.5 18.6 1.0
C B:ASP162 3.7 15.7 1.0
C B:TYR195 3.9 20.1 1.0
O B:HOH411 3.9 23.6 1.0
OD2 B:ASP198 3.9 20.7 1.0
C B:ASN194 3.9 26.6 1.0
N B:GLY196 4.0 22.5 1.0
O B:ALA161 4.0 15.4 1.0
O B:TYR195 4.0 17.3 1.0
N B:ASP198 4.2 13.7 1.0
CA B:GLY196 4.3 18.7 1.0
CA B:TYR195 4.4 22.0 1.0
CA B:ASP162 4.4 16.4 1.0
N B:GLY197 4.5 15.8 1.0
N B:ILE163 4.6 12.2 1.0
N B:TYR195 4.6 28.0 1.0
CB B:ASP198 4.6 13.9 1.0
O B:GLY192 4.6 23.4 1.0
CA B:GLY197 4.7 16.5 1.0
N B:MET164 4.7 12.5 1.0
C B:GLY197 4.7 15.7 1.0
CA B:ILE163 4.7 13.8 1.0
CG B:MET164 4.8 15.0 1.0
CA B:ASP198 4.8 13.8 1.0
N B:ASN194 5.0 37.2 1.0
C B:ALA161 5.0 18.3 1.0

Reference:

S.J.Taylor, A.Abeywardane, S.Liang, I.Muegge, A.K.Padyana, Z.Xiong, M.Hill-Drzewi, B.Farmer, X.Li, B.Collins, J.X.Li, A.Heim-Riether, J.Proudfoot, Q.Zhang, D.Goldberg, L.Zuvela-Jelaska, H.Zaher, J.Li, N.A.Farrow. Fragment-Based Discovery of Indole Inhibitors of Matrix Metalloproteinase-13. J. Med. Chem. V. 54 8174 2011.
ISSN: ISSN 1520-4804
PubMed: 22017539
DOI: 10.1021/JM201129M
Page generated: Wed Jul 9 04:26:12 2025

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