Atomistry » Calcium » PDB 5b4y-5bx5 » 5bot
Atomistry »
  Calcium »
    PDB 5b4y-5bx5 »
      5bot »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy