Calcium in PDB 4m65: In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand

The structure of In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand, PDB code: 4m65 was solved by X.Yin, A.Scalia, L.Leroy, C.M.Cuttitta, G.M.Polizzo, D.L.Ericson, C.G.Roessler, O.Campos, R.Agarwal, M.Allaire, A.M.Orville, R.Jackimowicz, M.Y.Ma, R.M.Sweet, A.S.Soares, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.59 / 1.60
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.831, 92.831, 129.171, 90.00, 90.00, 120.00
R / Rfree (%)	13 / 15.9

The structure of In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand (pdb code 4m65). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand, PDB code: 4m65:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:11.3 occ:1.00 OD2 A:ASP138 2.3 11.6 1.0 O A:GLU187 2.4 11.5 1.0 OE1 A:GLU177 2.4 11.4 1.0 O A:HOH505 2.4 12.3 1.0 OD1 A:ASP185 2.4 11.5 1.0 OE1 A:GLU190 2.5 11.4 1.0 OE2 A:GLU190 2.6 12.8 1.0 OE2 A:GLU177 2.8 12.5 1.0 CD A:GLU190 2.8 10.0 1.0 CD A:GLU177 2.9 12.0 1.0 C A:GLU187 3.4 12.0 1.0 CG A:ASP138 3.4 14.7 1.0 CG A:ASP185 3.4 12.4 1.0 CA A:CA402 3.8 13.6 1.0 OD2 A:ASP185 3.8 13.3 1.0 CB A:ASP138 4.0 11.8 1.0 O A:ASP185 4.2 12.8 1.0 N A:GLU187 4.2 13.4 1.0 O A:HOH716 4.2 29.4 1.0 N A:ILE188 4.3 12.7 1.0 CA A:GLU187 4.3 14.3 1.0 OD1 A:ASP138 4.3 13.2 1.0 CA A:ILE188 4.3 11.8 1.0 CG A:GLU190 4.3 12.9 1.0 CG A:GLU177 4.4 11.5 1.0 N A:GLY189 4.4 11.1 1.0 O A:HOH549 4.4 16.6 1.0 C A:ASP185 4.5 13.4 1.0 CB A:ASP185 4.7 14.4 1.0 CB A:GLU187 4.7 17.0 1.0 N A:ASP185 4.8 14.0 1.0 C A:ILE188 4.8 11.8 1.0 O A:HOH701 4.9 13.8 1.0 CB A:GLU177 4.9 10.6 1.0 CA A:ASP185 4.9 13.1 1.0 N A:GLU190 5.0 11.0 1.0

Calcium binding site 2 out of 5 in the In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:13.6 occ:1.00 OD2 A:ASP185 2.3 13.3 1.0 O A:ASN183 2.3 15.8 1.0 O A:HOH701 2.3 13.8 1.0 OE2 A:GLU190 2.3 12.8 1.0 OE2 A:GLU177 2.4 12.5 1.0 O A:HOH591 2.4 16.8 1.0 CG A:ASP185 3.1 12.4 1.0 CD A:GLU177 3.3 12.0 1.0 CD A:GLU190 3.3 10.0 1.0 C A:ASN183 3.4 13.6 1.0 OD1 A:ASP185 3.7 11.5 1.0 CG A:GLU190 3.8 12.9 1.0 OE1 A:GLU177 3.8 11.4 1.0 CA A:CA401 3.8 11.3 1.0 O A:LYS182 4.0 19.9 1.0 O A:HOH638 4.1 29.9 1.0 CA A:PRO184 4.2 12.9 1.0 CB A:ASN183 4.2 17.2 1.0 OD1 A:ASP191 4.2 17.8 1.0 N A:ASP185 4.2 14.0 1.0 OD2 A:ASP191 4.2 20.6 1.0 CG A:GLU177 4.2 11.5 1.0 C A:PRO184 4.2 14.7 1.0 N A:PRO184 4.3 14.6 1.0 CB A:ASP185 4.3 14.4 1.0 OE1 A:GLU190 4.3 11.4 1.0 O1 A:EDO415 4.4 57.5 1.0 CA A:ASN183 4.4 17.0 1.0 O A:HOH716 4.5 29.4 1.0 CG A:ASP191 4.5 18.9 1.0 CA A:ASP185 4.9 13.1 1.0 O A:PRO184 4.9 16.3 1.0 C A:LYS182 5.0 18.9 1.0

Calcium binding site 3 out of 5 in the In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:11.9 occ:1.00 O A:GLN61 2.3 11.8 1.0 O A:HOH636 2.3 16.6 1.0 OD1 A:ASP57 2.3 11.3 1.0 OD1 A:ASP59 2.4 13.0 1.0 O A:HOH513 2.4 15.9 1.0 O A:HOH521 2.5 14.6 1.0 OD2 A:ASP57 2.6 11.3 1.0 CG A:ASP57 2.8 11.6 1.0 CG A:ASP59 3.4 16.7 1.0 C A:GLN61 3.4 10.2 1.0 OD2 A:ASP59 3.8 17.1 1.0 O A:HOH517 3.9 18.2 1.0 N A:GLN61 4.0 10.8 1.0 CA A:GLN61 4.2 11.2 1.0 N A:ASP59 4.3 12.0 1.0 CB A:ASP57 4.4 10.8 1.0 CB A:GLN61 4.4 14.2 1.0 O A:HOH503 4.4 14.6 1.0 O A:HOH545 4.4 36.6 1.0 N A:PHE62 4.5 10.3 1.0 CB A:ASP59 4.6 13.4 1.0 O A:HOH650 4.6 39.4 1.0 O A:HOH511 4.6 12.6 1.0 OD2 A:ASP67 4.6 11.7 1.0 N A:ASN60 4.7 10.2 1.0 CA A:ASP59 4.7 12.5 1.0 N A:ALA58 4.8 11.4 1.0 CA A:PHE62 4.8 9.7 1.0 O A:HOH594 4.8 30.2 1.0 C A:ASP59 4.9 11.2 1.0

Calcium binding site 4 out of 5 in the In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:13.6 occ:1.00 O A:ILE197 2.3 15.7 1.0 O A:TYR193 2.3 12.1 1.0 O A:HOH552 2.4 13.1 1.0 OD1 A:ASP200 2.4 13.6 1.0 O1 A:EDO416 2.5 19.7 1.0 OG1 A:THR194 2.5 16.0 1.0 O A:THR194 2.5 15.1 1.0 C A:THR194 3.3 16.1 1.0 C A:TYR193 3.3 13.6 1.0 CG A:ASP200 3.4 12.4 1.0 C A:ILE197 3.5 21.1 1.0 C1 A:EDO416 3.5 22.2 1.0 CB A:THR194 3.5 14.2 1.0 CA A:THR194 3.7 14.1 1.0 N A:THR194 3.9 13.8 1.0 OD2 A:ASP200 3.9 15.0 1.0 CB A:ILE197 4.1 21.7 1.0 CA A:ILE197 4.1 20.4 1.0 N A:ILE197 4.2 21.4 1.0 N A:PRO195 4.3 15.5 1.0 C2 A:EDO416 4.4 21.2 1.0 O A:ASP200 4.5 18.2 1.0 N A:SER198 4.5 18.9 1.0 CA A:TYR193 4.5 14.6 1.0 O A:GLU190 4.6 13.0 1.0 N A:ASP200 4.7 15.8 1.0 CA A:SER198 4.7 21.0 1.0 CB A:TYR193 4.7 14.0 1.0 CG2 A:ILE197 4.7 20.9 1.0 CA A:PRO195 4.7 18.6 1.0 O A:HOH858 4.7 52.1 1.0 CD2 A:TYR193 4.7 15.8 1.0 CG2 A:THR194 4.7 14.2 1.0 CB A:ASP200 4.8 14.9 1.0 C A:ASP200 4.9 15.3 1.0 O A:HOH823 5.0 39.1 1.0 N A:GLY199 5.0 19.8 1.0 C A:SER198 5.0 18.9 1.0

Calcium binding site 5 out of 5 in the In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:17.2 occ:0.60 O A:HOH925 2.2 14.4 1.0 O A:HOH931 2.4 35.1 1.0 O A:HOH832 2.4 32.4 1.0 O A:HOH926 2.5 28.7 1.0 O A:HOH927 2.5 29.2 1.0 O A:HOH928 2.5 22.9 1.0 O A:TYR211 2.6 21.5 1.0 C A:TYR211 3.8 18.9 1.0 O A:HOH938 3.9 44.1 1.0 O A:HOH667 3.9 41.2 1.0 CB A:TYR211 4.0 15.4 1.0 O A:HOH851 4.1 56.9 1.0 OD1 A:ASP213 4.3 14.9 1.0 CA A:TYR211 4.4 15.5 1.0 O A:LEU202 4.4 12.9 1.0 OD2 A:ASP213 4.5 13.4 1.0 CG A:ASP213 4.7 13.8 1.0 N A:GLY212 4.9 17.8 1.0 O A:HOH542 4.9 26.8 1.0

X.Yin, A.Scalia, L.Leroy, C.M.Cuttitta, G.M.Polizzo, D.L.Ericson, C.G.Roessler, O.Campos, R.Agarwal, M.Allaire, A.M.Orville, R.Jackimowicz, M.Y.Ma, R.M.Sweet, A.S.Soares. Hitting the Target: Fragment Screening with Acoustic in Situ Co-Crystallization of Proteins Plus Fragment Libraries on Pin-Mounted Data-Collection Micromeshes Acta Crystallogr.,Sect.D V. D70 1177.
ISSN: ISSN 0907-4449