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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

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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

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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

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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

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