Atomistry » Calcium » PDB 5uw6-5vlh » 5uwm
Atomistry »
  Calcium »
    PDB 5uw6-5vlh »
      5uwm »

Calcium in PDB 5uwm: Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A

Protein crystallography data

The structure of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A, PDB code: 5uwm was solved by A.B.Taylor, X.Cao, P.J.Hart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.77 / 1.62
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 140.073, 140.073, 46.860, 90.00, 90.00, 120.00
R / Rfree (%) 12.9 / 17.8

Other elements in 5uwm:

The structure of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A (pdb code 5uwm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A, PDB code: 5uwm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5uwm

Go back to Calcium Binding Sites List in 5uwm
Calcium binding site 1 out of 6 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:17.0
occ:1.00
 OE2 A:GLU205 2.2 21.4 1.0
O A:GLY180 2.3 18.2 1.0
O A:LEU184 2.3 17.2 1.0
OD2 A:ASP202 2.3 16.0 1.0
OD1 A:ASP179 2.4 16.5 1.0
O A:SER182 2.4 18.6 1.0
CD A:GLU205 3.5 20.9 1.0
CG A:ASP202 3.5 14.3 1.0
C A:LEU184 3.5 17.1 1.0
C A:GLY180 3.5 19.4 1.0
CG A:ASP179 3.5 15.7 1.0
C A:SER182 3.5 19.5 1.0
N A:SER182 3.8 19.6 1.0
N A:LEU184 3.9 16.3 1.0
C A:PRO181 4.0 20.0 1.0
OD2 A:ASP179 4.1 17.1 1.0
N A:GLY180 4.1 16.2 1.0
CA A:LEU184 4.1 13.5 1.0
C A:GLY183 4.2 16.8 1.0
CB A:ASP202 4.3 13.2 1.0
CA A:SER182 4.3 20.8 1.0
C A:ASP179 4.3 18.7 1.0
CG A:GLU205 4.3 17.7 1.0
OD1 A:ASP202 4.3 17.1 1.0
OE1 A:GLU205 4.3 22.6 1.0
CA A:PRO181 4.4 19.6 1.0
N A:ASP179 4.4 18.2 1.0
N A:PRO181 4.4 20.0 1.0
CA A:GLY180 4.4 15.4 1.0
CB A:LEU184 4.5 15.4 1.0
N A:GLY183 4.5 20.1 1.0
N A:LEU185 4.6 15.0 1.0
O A:PRO181 4.6 21.7 1.0
CA A:GLY183 4.6 20.8 1.0
CA A:ASP179 4.7 16.4 1.0
O A:GLY183 4.7 20.7 1.0
CB A:ASP179 4.7 15.8 1.0
O A:ASP179 4.7 21.3 1.0
CA A:LEU185 4.9 12.0 1.0
O A:HOH494 4.9 20.5 1.0

Calcium binding site 2 out of 6 in 5uwm

Go back to Calcium Binding Sites List in 5uwm
Calcium binding site 2 out of 6 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:21.1
occ:1.00
 O A:HOH525 2.3 20.3 1.0
O A:GLU205 2.4 16.1 1.0
OD1 A:ASP203 2.4 18.9 1.0
OD2 A:ASP128 2.4 21.0 1.0
O A:ASP203 2.5 20.1 1.0
O A:HOH498 2.5 20.7 1.0
OD1 A:ASP128 2.7 22.3 1.0
CG A:ASP128 2.9 19.9 1.0
C A:ASP203 3.4 16.4 1.0
CG A:ASP203 3.5 16.0 1.0
C A:GLU205 3.5 17.1 1.0
CA A:ASP203 3.8 16.6 1.0
OG1 A:THR126 4.0 15.8 1.0
CB A:ASP203 4.0 16.9 1.0
CA A:THR206 4.1 17.4 1.0
N A:THR206 4.3 17.0 1.0
CD1 A:TRP207 4.3 15.8 1.0
N A:GLU205 4.4 16.4 1.0
CB A:ASP128 4.4 16.9 1.0
N A:ASP204 4.5 15.0 1.0
OD2 A:ASP203 4.5 20.2 1.0
CA A:GLU205 4.6 16.7 1.0
C A:ASP204 4.6 14.7 1.0
N A:TRP207 4.7 16.4 1.0
CD A:PRO127 4.7 16.2 1.0
O A:HOH436 4.7 38.1 1.0
CA A:ASP204 4.8 16.0 1.0
NE1 A:TRP207 4.8 15.8 1.0
OG1 A:THR206 4.9 21.2 1.0
C A:THR206 5.0 17.6 1.0

Calcium binding site 3 out of 6 in 5uwm

Go back to Calcium Binding Sites List in 5uwm
Calcium binding site 3 out of 6 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:20.7
occ:1.00
 O A:GLY196 2.3 20.2 1.0
O A:ASN194 2.4 24.1 1.0
O A:HOH434 2.4 20.8 1.0
O A:ASP162 2.4 20.2 1.0
O A:HOH418 2.4 18.9 1.0
OD1 A:ASP198 2.4 20.9 1.0
CG A:ASP198 3.4 18.9 1.0
C A:GLY196 3.5 17.5 1.0
C A:ASN194 3.6 23.3 1.0
C A:ASP162 3.6 17.8 1.0
OD2 A:ASP198 3.8 19.5 1.0
C A:TYR195 3.9 19.9 1.0
N A:GLY196 3.9 19.5 1.0
O A:TYR195 4.0 18.4 1.0
N A:ASP198 4.2 18.9 1.0
O A:ALA161 4.2 21.8 1.0
O A:HOH456 4.2 27.6 1.0
CA A:GLY196 4.2 21.1 1.0
CA A:TYR195 4.3 18.2 1.0
CA A:ASP162 4.4 15.8 1.0
O A:GLY192 4.4 28.7 1.0
N A:TYR195 4.4 21.6 1.0
N A:ASN194 4.4 25.9 1.0
N A:GLY197 4.4 18.8 1.0
CA A:ASN194 4.5 26.0 1.0
N A:ILE163 4.5 18.6 1.0
CB A:ASP198 4.6 17.0 1.0
CA A:GLY197 4.6 18.2 1.0
C A:GLY197 4.6 18.1 1.0
N A:MET164 4.7 16.4 1.0
C A:PRO193 4.7 24.6 1.0
CA A:ILE163 4.7 18.8 1.0
O A:HOH443 4.7 22.3 1.0
CA A:ASP198 4.8 16.2 1.0
CG A:MET164 4.8 18.7 1.0
O A:PRO193 4.9 27.6 1.0

Calcium binding site 4 out of 6 in 5uwm

Go back to Calcium Binding Sites List in 5uwm
Calcium binding site 4 out of 6 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:16.1
occ:1.00
 OE2 B:GLU205 2.2 20.3 1.0
O B:LEU184 2.3 16.5 1.0
OD1 B:ASP179 2.3 16.6 1.0
O B:GLY180 2.3 17.5 1.0
OD2 B:ASP202 2.3 16.3 1.0
O B:SER182 2.3 20.8 1.0
CG B:ASP202 3.4 15.3 1.0
C B:LEU184 3.5 15.9 1.0
CG B:ASP179 3.5 16.7 1.0
C B:SER182 3.5 19.5 1.0
CD B:GLU205 3.5 18.0 1.0
C B:GLY180 3.6 17.5 1.0
N B:SER182 3.8 20.6 1.0
N B:LEU184 3.9 15.5 1.0
C B:PRO181 4.0 19.7 1.0
OD2 B:ASP179 4.0 19.7 1.0
CB B:ASP202 4.1 13.1 1.0
CA B:LEU184 4.2 15.5 1.0
CA B:SER182 4.2 23.2 1.0
N B:GLY180 4.2 19.7 1.0
C B:GLY183 4.2 18.7 1.0
OE1 B:GLU205 4.3 20.3 1.0
C B:ASP179 4.3 16.0 1.0
N B:ASP179 4.3 16.4 1.0
OD1 B:ASP202 4.3 17.9 1.0
CG B:GLU205 4.4 14.9 1.0
CA B:PRO181 4.4 22.4 1.0
N B:PRO181 4.4 22.7 1.0
N B:GLY183 4.5 19.9 1.0
CA B:GLY180 4.5 19.7 1.0
N B:LEU185 4.5 14.6 1.0
O B:PRO181 4.5 21.0 1.0
CA B:GLY183 4.6 20.2 1.0
CB B:LEU184 4.6 17.3 1.0
CA B:ASP179 4.7 16.3 1.0
CB B:ASP179 4.7 16.1 1.0
CA B:LEU185 4.7 13.1 1.0
O B:GLY183 4.8 19.6 1.0
O B:ASP179 4.8 18.3 1.0

Calcium binding site 5 out of 6 in 5uwm

Go back to Calcium Binding Sites List in 5uwm
Calcium binding site 5 out of 6 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:18.0
occ:1.00
 O B:HOH492 2.3 17.2 1.0
O B:GLU205 2.4 16.0 1.0
O B:ASP203 2.4 21.5 1.0
OD2 B:ASP128 2.4 17.1 1.0
OD1 B:ASP203 2.5 17.1 1.0
O B:HOH496 2.5 20.5 1.0
OD1 B:ASP128 2.7 19.0 1.0
CG B:ASP128 2.9 17.5 1.0
C B:ASP203 3.3 17.2 1.0
C B:GLU205 3.5 17.3 1.0
CG B:ASP203 3.5 15.9 1.0
CA B:ASP203 3.8 16.6 1.0
CB B:ASP203 4.0 16.8 1.0
OG1 B:THR126 4.0 15.1 1.0
CA B:THR206 4.1 18.4 1.0
N B:THR206 4.2 16.4 1.0
CD1 B:TRP207 4.3 15.9 1.0
O B:HOH404 4.4 39.9 1.0
N B:GLU205 4.4 16.0 1.0
CB B:ASP128 4.4 12.7 1.0
N B:ASP204 4.5 15.8 1.0
OD2 B:ASP203 4.6 17.8 1.0
C B:ASP204 4.6 17.1 1.0
CA B:GLU205 4.6 15.9 1.0
CA B:ASP204 4.7 16.2 1.0
N B:TRP207 4.8 15.2 1.0
CD B:PRO127 4.8 13.4 1.0
NE1 B:TRP207 4.8 15.7 1.0
OG1 B:THR206 4.9 19.6 1.0

Calcium binding site 6 out of 6 in 5uwm

Go back to Calcium Binding Sites List in 5uwm
Calcium binding site 6 out of 6 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:21.4
occ:1.00
 O B:GLY196 2.3 20.4 1.0
O B:ASN194 2.3 24.7 1.0
O B:ASP162 2.4 20.8 1.0
O B:HOH431 2.5 21.0 1.0
OD1 B:ASP198 2.5 18.6 1.0
O B:HOH418 2.5 20.4 1.0
CG B:ASP198 3.5 17.9 1.0
C B:GLY196 3.5 19.9 1.0
C B:ASP162 3.5 19.4 1.0
C B:ASN194 3.5 20.2 1.0
OD2 B:ASP198 3.9 18.8 1.0
C B:TYR195 3.9 20.4 1.0
N B:GLY196 4.0 20.5 1.0
O B:ALA161 4.1 21.6 1.0
O B:TYR195 4.1 20.2 1.0
N B:ASP198 4.2 17.9 1.0
CA B:GLY196 4.3 18.8 1.0
O B:HOH455 4.3 28.2 1.0
CA B:ASP162 4.3 20.4 1.0
CA B:TYR195 4.4 20.4 1.0
O B:GLY192 4.4 25.8 1.0
N B:ASN194 4.4 27.7 1.0
O B:HOH519 4.4 41.6 1.0
N B:TYR195 4.4 20.3 1.0
CA B:ASN194 4.4 24.4 1.0
N B:GLY197 4.5 19.4 1.0
N B:ILE163 4.5 17.3 1.0
CB B:ASP198 4.6 15.3 1.0
CA B:GLY197 4.7 19.2 1.0
N B:MET164 4.7 17.4 1.0
C B:GLY197 4.7 17.8 1.0
CA B:ILE163 4.7 16.7 1.0
C B:PRO193 4.7 27.6 1.0
O B:HOH433 4.7 25.8 1.0
CA B:ASP198 4.8 17.0 1.0
CG B:MET164 4.8 17.7 1.0
CH2 B:TRP113 4.9 24.9 1.0
O B:PRO193 4.9 25.9 1.0

Reference:

J.Y.Choi, R.Fuerst, A.M.Knapinska, A.B.Taylor, L.Smith, X.Cao, P.J.Hart, G.B.Fields, W.R.Roush. Structure-Based Design and Synthesis of Potent and Selective Matrix Metalloproteinase 13 Inhibitors. J. Med. Chem. V. 60 5816 2017.
ISSN: ISSN 1520-4804
PubMed: 28653849
DOI: 10.1021/ACS.JMEDCHEM.7B00514
Page generated: Mon Jul 15 12:15:21 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