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Calcium in PDB 5bot: X-Ray Co-Structure of Mmp-13 with Ethyl 5-Carbamoyl-1H-Indole-2- Carboxylate

Protein crystallography data

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

Resolution Low / High (Å) 50.98 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.641, 35.953, 95.824, 90.00, 130.78, 90.00
R / Rfree (%) n/a / 22.9

Other elements in 5bot:

The structure of X-Ray Co-Structure of Mmp-13 with Ethyl 5-Carbamoyl-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-Carbamoyl-1H-Indole-2- Carboxylate (pdb code 5bot). 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-Carbamoyl-1H-Indole-2- Carboxylate, PDB code: 5bot:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5bot

Go back to Calcium Binding Sites List in 5bot
Calcium binding site 1 out of 6 in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-Carbamoyl-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-Carbamoyl-1H-Indole-2- Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:30.1
occ:1.00
 O A:GLU205 2.5 20.1 1.0
OD2 A:ASP128 2.5 20.7 1.0
O A:HOH564 2.6 28.5 1.0
O A:ASP203 2.7 22.5 1.0
O A:HOH534 2.7 29.9 1.0
OD2 A:ASP203 2.7 25.0 1.0
OD1 A:ASP128 3.0 27.8 1.0
CG A:ASP128 3.1 22.5 1.0
C A:ASP203 3.5 18.2 1.0
C A:GLU205 3.6 20.8 1.0
CG A:ASP203 3.8 18.1 1.0
O A:HOH503 3.8 34.6 1.0
OG1 A:THR126 3.8 14.2 1.0
CA A:ASP203 4.0 14.4 1.0
N A:GLU205 4.3 18.2 1.0
CB A:ASP203 4.3 16.3 1.0
CA A:THR206 4.4 17.0 1.0
CD1 A:TRP207 4.4 17.9 1.0
N A:THR206 4.4 17.7 1.0
CD A:PRO127 4.4 16.9 1.0
N A:ASP204 4.5 15.8 1.0
CB A:ASP128 4.6 15.3 1.0
C A:ASP204 4.6 19.6 1.0
CA A:GLU205 4.6 19.0 1.0
CA A:ASP204 4.7 17.6 1.0
OD1 A:ASP203 4.8 22.7 1.0
N A:TRP207 4.8 15.9 1.0
CG A:PRO127 5.0 19.5 1.0

Calcium binding site 2 out of 6 in 5bot

Go back to Calcium Binding Sites List in 5bot
Calcium binding site 2 out of 6 in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-Carbamoyl-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-Carbamoyl-1H-Indole-2- Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:19.5
occ:1.00
 OE2 A:GLU205 2.3 25.4 1.0
O A:GLY180 2.4 18.9 1.0
O A:LEU184 2.4 18.2 1.0
OD2 A:ASP202 2.4 16.1 1.0
OD1 A:ASP179 2.4 18.7 1.0
O A:SER182 2.5 22.6 1.0
CG A:ASP202 3.5 18.7 1.0
CG A:ASP179 3.5 22.9 1.0
CD A:GLU205 3.5 23.7 1.0
C A:LEU184 3.5 18.2 1.0
C A:GLY180 3.6 19.6 1.0
C A:SER182 3.6 24.5 1.0
N A:SER182 3.9 20.0 1.0
N A:LEU184 3.9 19.1 1.0
C A:PRO181 4.0 22.7 1.0
OD2 A:ASP179 4.0 23.2 1.0
CA A:LEU184 4.2 20.8 1.0
CB A:ASP202 4.2 15.5 1.0
N A:GLY180 4.2 20.8 1.0
CG A:GLU205 4.2 18.9 1.0
C A:ASP179 4.3 22.0 1.0
N A:ASP179 4.3 18.3 1.0
CA A:SER182 4.3 24.2 1.0
C A:GLY183 4.3 21.0 1.0
OD1 A:ASP202 4.4 15.5 1.0
CA A:PRO181 4.4 18.2 1.0
N A:PRO181 4.5 21.9 1.0
OE1 A:GLU205 4.5 18.3 1.0
O A:PRO181 4.5 25.5 1.0
CB A:LEU184 4.5 23.1 1.0
CA A:GLY180 4.5 21.1 1.0
N A:GLY183 4.6 22.3 1.0
N A:LEU185 4.6 13.2 1.0
CA A:ASP179 4.6 21.6 1.0
O A:ASP179 4.7 20.7 1.0
CB A:ASP179 4.7 19.5 1.0
CA A:GLY183 4.7 22.6 1.0
CA A:LEU185 4.8 14.3 1.0
O A:GLY183 4.9 18.6 1.0
O A:HOH457 5.0 14.3 1.0

Calcium binding site 3 out of 6 in 5bot

Go back to Calcium Binding Sites List in 5bot
Calcium binding site 3 out of 6 in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-Carbamoyl-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-Carbamoyl-1H-Indole-2- Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca306

b:17.0
occ:1.00
 O A:GLY196 2.3 15.7 1.0
O A:ASP162 2.4 15.3 1.0
O A:ASN194 2.4 19.4 1.0
O A:HOH491 2.4 15.9 1.0
OD1 A:ASP198 2.5 15.8 1.0
O A:HOH409 2.5 14.8 1.0
CG A:ASP198 3.5 17.0 1.0
C A:GLY196 3.5 18.1 1.0
C A:ASP162 3.5 13.8 1.0
C A:ASN194 3.6 22.8 1.0
OD2 A:ASP198 3.9 18.6 1.0
C A:TYR195 3.9 18.8 1.0
N A:GLY196 4.0 18.2 1.0
O A:ALA161 4.2 16.0 1.0
O A:TYR195 4.2 16.0 1.0
N A:ASP198 4.2 15.3 1.0
CA A:GLY196 4.3 16.2 1.0
CA A:ASP162 4.3 15.9 1.0
CA A:TYR195 4.4 20.5 1.0
O A:HOH416 4.4 21.9 1.0
O A:GLY192 4.5 21.9 1.0
N A:TYR195 4.5 21.2 1.0
N A:ILE163 4.5 14.0 1.0
CA A:ASN194 4.5 24.9 1.0
N A:ASN194 4.5 21.8 1.0
N A:GLY197 4.5 13.9 1.0
CB A:ASP198 4.6 13.2 1.0
O A:HOH586 4.6 34.7 1.0
N A:MET164 4.6 16.3 1.0
CA A:GLY197 4.6 12.9 1.0
C A:GLY197 4.6 14.6 1.0
O A:HOH504 4.6 38.5 1.0
CA A:ILE163 4.7 15.2 1.0
CG A:MET164 4.7 15.9 1.0
O A:HOH419 4.7 21.1 1.0
CA A:ASP198 4.8 14.6 1.0
C A:PRO193 4.9 20.8 1.0
CH2 A:TRP113 4.9 20.4 1.0

Calcium binding site 4 out of 6 in 5bot

Go back to Calcium Binding Sites List in 5bot
Calcium binding site 4 out of 6 in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-Carbamoyl-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-Carbamoyl-1H-Indole-2- Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:24.6
occ:1.00
 O B:GLU205 2.5 18.8 1.0
OD2 B:ASP128 2.5 19.8 1.0
OD2 B:ASP203 2.6 18.2 1.0
O B:ASP203 2.6 21.6 1.0
OD1 B:ASP128 3.0 24.4 1.0
CG B:ASP128 3.1 19.9 1.0
C B:ASP203 3.4 19.2 1.0
C B:GLU205 3.6 19.6 1.0
CG B:ASP203 3.6 14.8 1.0
CA B:ASP203 3.9 15.4 1.0
OG1 B:THR126 4.0 13.4 1.0
CA B:THR206 4.1 17.2 1.0
CB B:ASP203 4.2 17.3 1.0
N B:THR206 4.3 15.7 1.0
CD1 B:TRP207 4.3 16.3 1.0
N B:GLU205 4.3 18.6 1.0
N B:ASP204 4.4 14.1 1.0
CB B:ASP128 4.5 18.6 1.0
C B:ASP204 4.5 19.0 1.0
O B:HOH536 4.6 32.7 1.0
CA B:GLU205 4.6 17.2 1.0
OD1 B:ASP203 4.6 19.1 1.0
N B:TRP207 4.6 18.5 1.0
CA B:ASP204 4.7 20.4 1.0
CD B:PRO127 4.8 18.3 1.0
NE1 B:TRP207 4.9 15.6 1.0
OG1 B:THR206 4.9 18.5 1.0
C B:THR206 5.0 18.6 1.0

Calcium binding site 5 out of 6 in 5bot

Go back to Calcium Binding Sites List in 5bot
Calcium binding site 5 out of 6 in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-Carbamoyl-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-Carbamoyl-1H-Indole-2- Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:21.8
occ:1.00
 OE1 B:GLU205 2.3 27.5 1.0
O B:LEU184 2.3 24.2 1.0
O B:GLY180 2.4 23.0 1.0
OD2 B:ASP202 2.4 16.4 1.0
OD1 B:ASP179 2.4 23.8 1.0
O B:SER182 2.5 25.8 1.0
CG B:ASP202 3.5 18.6 1.0
C B:LEU184 3.5 24.1 1.0
CG B:ASP179 3.5 26.5 1.0
CD B:GLU205 3.5 26.2 1.0
C B:GLY180 3.6 25.0 1.0
C B:SER182 3.6 27.2 1.0
N B:SER182 3.9 26.6 1.0
N B:LEU184 3.9 19.9 1.0
C B:PRO181 4.0 25.6 1.0
OD2 B:ASP179 4.1 24.2 1.0
N B:GLY180 4.1 21.1 1.0
CA B:LEU184 4.1 22.8 1.0
CB B:ASP202 4.2 17.8 1.0
N B:ASP179 4.2 17.5 1.0
CG B:GLU205 4.2 21.3 1.0
C B:ASP179 4.2 23.3 1.0
C B:GLY183 4.2 24.5 1.0
CA B:SER182 4.3 27.2 1.0
OD1 B:ASP202 4.4 15.8 1.0
CA B:PRO181 4.4 23.5 1.0
CB B:LEU184 4.4 24.1 1.0
OE2 B:GLU205 4.5 23.9 1.0
N B:PRO181 4.5 24.5 1.0
CA B:GLY180 4.5 22.6 1.0
O B:PRO181 4.5 27.5 1.0
N B:LEU185 4.5 18.1 1.0
N B:GLY183 4.6 24.5 1.0
CA B:ASP179 4.6 24.5 1.0
O B:ASP179 4.6 25.5 1.0
CB B:ASP179 4.6 22.9 1.0
CA B:GLY183 4.7 24.4 1.0
O B:GLY183 4.7 22.4 1.0
CA B:LEU185 4.7 18.8 1.0
O B:HOH547 4.8 36.4 1.0

Calcium binding site 6 out of 6 in 5bot

Go back to Calcium Binding Sites List in 5bot
Calcium binding site 6 out of 6 in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-Carbamoyl-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-Carbamoyl-1H-Indole-2- Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca306

b:17.5
occ:1.00
 O B:ASP162 2.3 15.4 1.0
O B:GLY196 2.4 19.6 1.0
O B:HOH422 2.4 16.4 1.0
O B:ASN194 2.4 20.6 1.0
O B:HOH453 2.5 17.8 1.0
OD1 B:ASP198 2.5 16.0 1.0
CG B:ASP198 3.5 18.1 1.0
C B:ASP162 3.5 16.0 1.0
C B:GLY196 3.5 20.4 1.0
C B:ASN194 3.6 22.6 1.0
C B:TYR195 3.9 21.6 1.0
OD2 B:ASP198 4.0 17.6 1.0
N B:GLY196 4.0 18.5 1.0
O B:TYR195 4.0 17.9 1.0
N B:ASP198 4.1 15.9 1.0
O B:ALA161 4.2 16.4 1.0
O B:HOH414 4.2 21.6 1.0
CA B:ASP162 4.3 16.6 1.0
CA B:GLY196 4.3 20.7 1.0
O B:GLY192 4.4 21.9 1.0
CA B:TYR195 4.4 18.3 1.0
N B:TYR195 4.4 19.7 1.0
O B:HOH571 4.4 33.1 1.0
N B:ILE163 4.5 13.1 1.0
N B:GLY197 4.5 18.0 1.0
N B:ASN194 4.5 22.2 1.0
CA B:ASN194 4.5 25.4 1.0
CB B:ASP198 4.6 16.1 1.0
CA B:ILE163 4.6 15.7 1.0
CA B:GLY197 4.6 18.4 1.0
N B:MET164 4.7 16.3 1.0
C B:GLY197 4.7 15.7 1.0
O B:HOH446 4.7 23.6 1.0
CA B:ASP198 4.7 15.8 1.0
C B:PRO193 4.8 26.9 1.0
CH2 B:TRP113 4.8 21.0 1.0
CG B:MET164 4.9 13.2 1.0
O B:PRO193 5.0 24.0 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: Sun Jul 14 16:54:33 2024

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