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Calcium in PDB 3wv2: Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydroquinazoline-2-Carboxamide

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydroquinazoline-2-Carboxamide, PDB code: 3wv2 was solved by H.Oki, Y.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.91 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 143.530, 35.719, 94.762, 90.00, 135.29, 90.00
R / Rfree (%) 17.1 / 24.1

Other elements in 3wv2:

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydroquinazoline-2-Carboxamide also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydroquinazoline-2-Carboxamide (pdb code 3wv2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydroquinazoline-2-Carboxamide, PDB code: 3wv2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3wv2

Go back to Calcium Binding Sites List in 3wv2
Calcium binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydroquinazoline-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydroquinazoline-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:16.9
occ:1.00
O A:GLY180 2.2 18.0 1.0
OE2 A:GLU205 2.3 16.4 1.0
OD2 A:ASP202 2.3 15.8 1.0
O A:LEU184 2.3 18.6 1.0
OD1 A:ASP179 2.3 20.5 1.0
O A:SER182 2.3 21.5 1.0
CG A:ASP202 3.4 14.4 1.0
C A:GLY180 3.5 18.4 1.0
C A:LEU184 3.5 17.6 1.0
C A:SER182 3.5 22.9 1.0
CD A:GLU205 3.5 16.0 1.0
CG A:ASP179 3.5 21.7 1.0
N A:SER182 3.9 21.6 1.0
N A:LEU184 3.9 17.9 1.0
C A:PRO181 4.0 21.7 1.0
OD2 A:ASP179 4.1 25.6 1.0
N A:GLY180 4.1 18.3 1.0
CB A:ASP202 4.1 14.0 1.0
C A:GLY183 4.2 19.4 1.0
CA A:LEU184 4.2 18.3 1.0
CA A:SER182 4.2 24.6 1.0
OD1 A:ASP202 4.3 14.2 1.0
O A:PRO181 4.3 22.9 1.0
C A:ASP179 4.3 18.9 1.0
CG A:GLU205 4.3 15.2 1.0
N A:ASP179 4.3 18.3 1.0
CA A:GLY180 4.4 18.6 1.0
OE1 A:GLU205 4.4 15.8 1.0
N A:PRO181 4.4 19.2 1.0
O A:HOH625 4.4 30.4 1.0
CA A:PRO181 4.4 20.0 1.0
N A:GLY183 4.5 20.4 1.0
N A:LEU185 4.5 16.7 1.0
O A:GLY183 4.6 19.4 1.0
CA A:GLY183 4.6 20.0 1.0
CB A:LEU184 4.6 19.4 1.0
CA A:ASP179 4.7 19.6 1.0
CB A:ASP179 4.7 21.8 1.0
O A:ASP179 4.8 21.9 1.0
CA A:LEU185 4.8 15.1 1.0

Calcium binding site 2 out of 4 in 3wv2

Go back to Calcium Binding Sites List in 3wv2
Calcium binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydroquinazoline-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydroquinazoline-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:23.4
occ:1.00
O A:GLY196 2.3 18.2 1.0
O A:ASN194 2.3 30.9 1.0
O A:ASP162 2.4 17.5 1.0
OD1 A:ASP198 2.4 15.4 1.0
O A:HOH693 2.4 10.8 1.0
O A:HOH695 2.5 13.5 1.0
CG A:ASP198 3.3 16.9 1.0
C A:GLY196 3.5 19.3 1.0
C A:ASN194 3.5 26.5 1.0
C A:ASP162 3.5 16.8 1.0
OD2 A:ASP198 3.7 15.8 1.0
O A:ALA161 4.0 17.2 1.0
C A:TYR195 4.0 23.6 1.0
N A:GLY196 4.0 22.6 1.0
N A:ASP198 4.1 15.8 1.0
O A:TYR195 4.2 21.6 1.0
CA A:GLY196 4.3 20.0 1.0
CA A:ASP162 4.3 17.8 1.0
CA A:TYR195 4.3 29.3 1.0
N A:TYR195 4.3 27.5 1.0
CA A:ASN194 4.4 30.4 1.0
N A:GLY197 4.4 18.0 1.0
N A:ASN194 4.4 27.3 1.0
O A:HOH694 4.5 18.2 1.0
N A:ILE163 4.5 16.9 1.0
O A:GLY192 4.5 24.6 1.0
N A:MET164 4.5 15.8 1.0
CB A:ASP198 4.5 15.0 1.0
CA A:GLY197 4.5 16.6 1.0
C A:GLY197 4.6 16.5 1.0
CA A:ILE163 4.6 16.5 1.0
CG A:MET164 4.7 17.4 1.0
O A:HOH659 4.7 42.7 1.0
CA A:ASP198 4.7 14.9 1.0
CH2 A:TRP113 4.8 26.0 1.0
C A:PRO193 4.9 26.6 1.0
C A:ALA161 4.9 18.5 1.0

Calcium binding site 3 out of 4 in 3wv2

Go back to Calcium Binding Sites List in 3wv2
Calcium binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydroquinazoline-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydroquinazoline-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:26.3
occ:1.00
O B:LEU184 2.2 28.0 1.0
OE2 B:GLU205 2.2 24.4 1.0
OD2 B:ASP202 2.3 21.7 1.0
O B:SER182 2.3 26.6 1.0
O B:GLY180 2.3 24.0 1.0
OD1 B:ASP179 2.5 27.9 1.0
CG B:ASP202 3.4 20.8 1.0
C B:LEU184 3.4 25.9 1.0
C B:SER182 3.4 25.1 1.0
CD B:GLU205 3.5 22.8 1.0
C B:GLY180 3.5 24.4 1.0
CG B:ASP179 3.6 26.5 1.0
N B:SER182 3.8 26.9 1.0
N B:LEU184 3.9 25.6 1.0
C B:PRO181 4.0 27.1 1.0
CB B:ASP202 4.0 19.2 1.0
N B:GLY180 4.0 22.9 1.0
CA B:SER182 4.1 27.0 1.0
CA B:LEU184 4.1 28.9 1.0
OD2 B:ASP179 4.2 27.5 1.0
C B:GLY183 4.2 26.3 1.0
N B:ASP179 4.2 24.8 1.0
C B:ASP179 4.3 23.3 1.0
O B:PRO181 4.3 27.6 1.0
OE1 B:GLU205 4.3 24.4 1.0
OD1 B:ASP202 4.3 22.0 1.0
CG B:GLU205 4.3 21.4 1.0
CA B:GLY180 4.4 23.9 1.0
CA B:PRO181 4.4 27.4 1.0
N B:LEU185 4.4 23.9 1.0
N B:GLY183 4.4 23.6 1.0
N B:PRO181 4.5 25.8 1.0
CB B:LEU184 4.6 30.5 1.0
CA B:ASP179 4.6 25.4 1.0
CA B:LEU185 4.6 24.4 1.0
CA B:GLY183 4.7 23.8 1.0
O B:GLY183 4.7 26.2 1.0
O B:HOH469 4.7 36.9 1.0
CB B:ASP179 4.7 26.6 1.0
O B:ASP179 4.8 22.7 1.0

Calcium binding site 4 out of 4 in 3wv2

Go back to Calcium Binding Sites List in 3wv2
Calcium binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydroquinazoline-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydroquinazoline-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:26.1
occ:1.00
O B:ASP162 2.2 24.5 1.0
O B:ASN194 2.3 35.2 1.0
O B:GLY196 2.3 29.2 1.0
O B:HOH470 2.4 23.6 1.0
OD1 B:ASP198 2.4 21.8 1.0
O B:HOH489 2.6 19.9 1.0
C B:ASP162 3.3 23.8 1.0
CG B:ASP198 3.4 22.1 1.0
C B:ASN194 3.5 34.9 1.0
C B:GLY196 3.5 30.9 1.0
O B:ALA161 3.8 24.4 1.0
OD2 B:ASP198 3.8 24.0 1.0
C B:TYR195 3.9 34.7 1.0
N B:GLY196 4.0 31.0 1.0
CA B:ASP162 4.1 24.4 1.0
O B:TYR195 4.1 31.2 1.0
N B:ASP198 4.2 22.1 1.0
CA B:GLY196 4.3 28.8 1.0
N B:ASN194 4.3 39.1 1.0
N B:ILE163 4.3 22.8 1.0
CA B:ASN194 4.3 39.8 1.0
N B:TYR195 4.4 34.1 1.0
CA B:TYR195 4.4 33.9 1.0
N B:GLY197 4.4 28.5 1.0
N B:MET164 4.5 18.6 1.0
O B:GLY192 4.5 37.4 1.0
CA B:ILE163 4.6 20.9 1.0
CB B:ASP198 4.6 20.9 1.0
CA B:GLY197 4.6 26.7 1.0
CG B:MET164 4.7 19.1 1.0
C B:GLY197 4.7 25.5 1.0
O B:HOH463 4.7 32.0 1.0
C B:PRO193 4.7 41.5 1.0
CA B:ASP198 4.7 21.4 1.0
C B:ALA161 4.7 24.0 1.0
N B:ASP162 4.9 22.7 1.0

Reference:

H.Nara, K.Sato, T.Naito, H.Mototani, H.Oki, Y.Yamamoto, H.Kuno, T.Santou, N.Kanzaki, J.Terauchi, O.Uchikawa, M.Kori. Thieno[2,3-D]Pyrimidine-2-Carboxamides Bearing A Carboxybenzene Group at 5-Position: Highly Potent, Selective, and Orally Available Mmp-13 Inhibitors Interacting with the S1 Binding Site Bioorg.Med.Chem. 2014.
ISSN: ESSN 1464-3391
PubMed: 25192810
DOI: 10.1016/J.BMC.2014.07.025
Page generated: Sat Dec 12 04:36:12 2020

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