Calcium in PDB 4ow3: Thermolysin Structure Determined By Free-Electron Laser

All present enzymatic activity of Thermolysin Structure Determined By Free-Electron Laser:
3.4.24.27;

The structure of Thermolysin Structure Determined By Free-Electron Laser, PDB code: 4ow3 was solved by J.Hattne, N.Echols, R.Tran, J.Kern, R.J.Gildea, A.S.Brewster, R.Alonso-Mori, C.Glockner, J.Hellmich, H.Laksmono, R.G.Sierra, B.Lassalle-Kaiser, A.Lampe, G.Han, S.Gul, D.Difiore, D.Milathianaki, A.R.Fry, A.Miahnahri, W.E.White, D.W.Schafer, M.M.Seibert, J.E.Koglin, D.Sokaras, T.-C.Weng, J.Sellberg, M.J.Latimer, P.Glatzel, P.H.Zwart, R.W.Grosse-Kunstleve, M.J.Bogan, M.Messerschmidt, G.J.Williams, S.Boutet, J.Messinger, A.Zouni, J.Yano, U.Bergmann, V.K.Yachandra, P.D.Adams, N.K.Sauter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.47 / 2.10
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.893, 92.893, 130.438, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 26.3

The structure of Thermolysin Structure Determined By Free-Electron Laser also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin Structure Determined By Free-Electron Laser (pdb code 4ow3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Thermolysin Structure Determined By Free-Electron Laser, PDB code: 4ow3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin Structure Determined By Free-Electron Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin Structure Determined By Free-Electron Laser within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:11.5 occ:1.00 O A:GLU187 2.3 8.5 1.0 OE1 A:GLU177 2.3 11.1 1.0 OE1 A:GLU190 2.6 10.4 1.0 O A:HOH611 2.6 12.3 1.0 OD2 A:ASP138 2.7 10.2 1.0 OD1 A:ASP185 2.8 11.7 1.0 OE2 A:GLU190 2.8 11.8 1.0 OE2 A:GLU177 2.9 11.7 1.0 CD A:GLU177 2.9 12.1 1.0 CD A:GLU190 3.0 12.3 1.0 C A:GLU187 3.3 11.8 1.0 HB3 A:ASP138 3.5 10.6 1.0 CG A:ASP138 3.5 9.5 1.0 HA A:ILE188 3.5 14.1 1.0 H A:GLU187 3.6 16.1 1.0 CG A:ASP185 3.7 15.8 1.0 H A:GLY189 3.8 11.7 1.0 CA A:CA405 3.9 15.5 1.0 HB2 A:GLU187 3.9 19.4 1.0 CB A:ASP138 3.9 8.8 1.0 OD2 A:ASP185 4.0 14.2 1.0 HB2 A:ASP138 4.1 10.6 1.0 N A:ILE188 4.1 10.8 1.0 N A:GLU187 4.2 13.4 1.0 HD13 A:ILE188 4.2 12.6 1.0 H A:GLU190 4.2 10.3 1.0 O A:ASP185 4.2 13.8 1.0 CA A:GLU187 4.2 13.2 1.0 CA A:ILE188 4.2 11.8 1.0 O A:HOH645 4.3 11.1 1.0 CG A:GLU177 4.4 10.3 1.0 H A:ASP185 4.4 18.0 1.0 N A:GLY189 4.4 9.7 1.0 OD1 A:ASP138 4.5 10.5 1.0 CG A:GLU190 4.5 10.5 1.0 CB A:GLU187 4.6 16.1 1.0 HB2 A:GLU177 4.6 12.2 1.0 C A:ASP185 4.7 11.4 1.0 HG3 A:GLU190 4.7 12.6 1.0 C A:ILE188 4.7 12.1 1.0 HB3 A:GLU177 4.8 12.2 1.0 HA A:THR174 4.8 12.3 1.0 HG3 A:GLU177 4.8 12.4 1.0 CB A:GLU177 4.9 10.2 1.0 HG2 A:GLU177 4.9 12.4 1.0 N A:ASP185 4.9 15.0 1.0 H A:ILE188 4.9 12.9 1.0 CB A:ASP185 5.0 13.8 1.0 HB3 A:GLU190 5.0 12.2 1.0 HG23 A:THR174 5.0 10.9 1.0

Calcium binding site 2 out of 4 in the Thermolysin Structure Determined By Free-Electron Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin Structure Determined By Free-Electron Laser within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:14.6 occ:0.95 O A:GLN61 2.2 12.4 1.0 O A:HOH570 2.4 11.9 1.0 OD1 A:ASP59 2.5 10.8 1.0 O A:HOH626 2.5 12.1 1.0 OD1 A:ASP57 2.6 12.4 1.0 O A:HOH653 2.6 12.9 1.0 OD2 A:ASP57 2.7 8.6 1.0 CG A:ASP57 3.0 12.5 1.0 CG A:ASP59 3.3 14.8 1.0 H A:GLN61 3.3 15.7 1.0 C A:GLN61 3.4 11.6 1.0 OD2 A:ASP59 3.5 16.9 1.0 H A:ASP59 3.6 16.8 1.0 HB2 A:GLN61 3.6 17.8 1.0 O A:HOH698 3.8 15.5 1.0 O A:HOH592 3.8 25.6 1.0 N A:GLN61 3.9 13.1 1.0 HA A:PHE62 4.0 14.8 1.0 CA A:GLN61 4.1 13.0 1.0 H A:ALA58 4.1 14.2 1.0 O A:HOH532 4.3 10.5 1.0 CB A:GLN61 4.3 14.8 1.0 N A:ASP59 4.4 14.0 1.0 H A:ASN60 4.5 14.7 1.0 N A:PHE62 4.5 11.4 1.0 CB A:ASP57 4.5 12.4 1.0 OD2 A:ASP67 4.6 12.5 1.0 CB A:ASP59 4.6 14.9 1.0 O A:HOH528 4.6 10.2 1.0 N A:ALA58 4.7 11.8 1.0 CA A:PHE62 4.7 12.4 1.0 N A:ASN60 4.7 12.3 1.0 HB3 A:GLN61 4.8 17.8 1.0 H A:PHE63 4.8 13.6 1.0 HB3 A:ALA58 4.8 14.2 1.0 HB2 A:ASP57 4.9 14.9 1.0 CA A:ASP59 4.9 14.4 1.0 HA A:ASP57 4.9 14.4 1.0 HB3 A:ASP57 4.9 14.9 1.0 O A:HOH566 5.0 15.0 1.0

Calcium binding site 3 out of 4 in the Thermolysin Structure Determined By Free-Electron Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin Structure Determined By Free-Electron Laser within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:17.8 occ:1.00 O A:TYR193 2.3 13.7 1.0 O A:THR194 2.3 17.7 1.0 OD1 A:ASP200 2.4 16.5 1.0 O A:HOH616 2.4 12.6 1.0 HB A:THR194 2.4 18.8 1.0 O A:ILE197 2.4 23.1 1.0 O A:HOH775 2.5 22.9 1.0 C A:THR194 3.2 17.2 1.0 CB A:THR194 3.3 15.7 1.0 C A:TYR193 3.3 12.6 1.0 CG A:ASP200 3.4 14.8 1.0 CA A:THR194 3.6 15.9 1.0 C A:ILE197 3.6 22.6 1.0 OD2 A:ASP200 3.7 14.0 1.0 HG22 A:THR194 3.7 30.5 1.0 H A:ASP200 3.8 21.9 1.0 N A:THR194 3.9 14.9 1.0 HA A:SER198 3.9 27.6 1.0 H A:ILE197 4.0 28.5 1.0 HB A:ILE197 4.0 29.8 1.0 CG2 A:THR194 4.0 25.4 1.0 HD2 A:TYR193 4.0 16.7 1.0 O A:HOH604 4.2 27.9 1.0 HG21 A:THR194 4.2 30.5 1.0 N A:PRO195 4.3 17.0 1.0 O A:ASP200 4.3 13.6 1.0 HB3 A:TYR193 4.3 14.9 1.0 HG1 A:THR194 4.3 20.8 1.0 OG1 A:THR194 4.3 17.4 1.0 HA A:PRO195 4.3 19.9 1.0 O A:GLU190 4.4 13.7 1.0 HA A:THR194 4.5 19.0 1.0 CA A:ILE197 4.5 22.1 1.0 N A:ILE197 4.5 23.7 1.0 CA A:TYR193 4.6 12.7 1.0 N A:SER198 4.6 28.2 1.0 N A:ASP200 4.6 18.2 1.0 CA A:SER198 4.6 23.0 1.0 H A:GLY199 4.6 23.5 1.0 C A:ASP200 4.7 15.2 1.0 CD2 A:TYR193 4.7 13.9 1.0 CB A:ASP200 4.7 14.4 1.0 CA A:PRO195 4.7 16.6 1.0 CB A:ILE197 4.7 24.8 1.0 H A:THR194 4.7 17.8 1.0 CB A:TYR193 4.8 12.4 1.0 O A:HOH671 4.8 26.9 1.0 HG23 A:THR194 4.9 30.5 1.0 H A:TYR193 4.9 14.0 1.0 CA A:ASP200 4.9 15.7 1.0 N A:GLY199 5.0 19.6 1.0

Calcium binding site 4 out of 4 in the Thermolysin Structure Determined By Free-Electron Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin Structure Determined By Free-Electron Laser within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:15.5 occ:1.00 OD2 A:ASP185 2.3 14.2 1.0 OE2 A:GLU190 2.4 11.8 1.0 OE2 A:GLU177 2.4 11.7 1.0 O A:HOH621 2.5 9.3 1.0 O A:HOH618 2.5 11.2 1.0 O A:ASN183 2.7 13.9 1.0 CD A:GLU177 3.2 12.1 1.0 CG A:ASP185 3.2 15.8 1.0 CD A:GLU190 3.3 12.3 1.0 HA A:PRO184 3.4 18.8 1.0 OE1 A:GLU177 3.7 11.1 1.0 HG3 A:GLU190 3.7 12.6 1.0 OD1 A:ASP185 3.7 11.7 1.0 C A:ASN183 3.8 20.5 1.0 CA A:CA402 3.9 11.5 1.0 CG A:GLU190 3.9 10.5 1.0 HG2 A:GLU190 4.0 12.6 1.0 CA A:PRO184 4.0 15.7 1.0 C A:PRO184 4.1 16.1 1.0 H A:ASP185 4.1 18.0 1.0 N A:ASP185 4.1 15.0 1.0 CG A:GLU177 4.2 10.3 1.0 HG2 A:GLU177 4.2 12.4 1.0 OD2 A:ASP191 4.2 14.2 1.0 OE1 A:GLU190 4.2 10.4 1.0 HG3 A:GLU177 4.2 12.4 1.0 OD1 A:ASP191 4.3 11.7 1.0 HB3 A:ASP185 4.3 16.5 1.0 CB A:ASP185 4.4 13.8 1.0 N A:PRO184 4.4 16.0 1.0 O A:HOH554 4.4 20.1 1.0 CG A:ASP191 4.6 13.8 1.0 O A:PRO184 4.7 17.4 1.0 CA A:ASP185 4.9 13.4 1.0 CA A:ASN183 5.0 20.0 1.0

J.Hattne, N.Echols, R.Tran, J.Kern, R.J.Gildea, A.S.Brewster, R.Alonso-Mori, C.Glockner, J.Hellmich, H.Laksmono, R.G.Sierra, B.Lassalle-Kaiser, A.Lampe, G.Han, S.Gul, D.Difiore, D.Milathianaki, A.R.Fry, A.Miahnahri, W.E.White, D.W.Schafer, M.M.Seibert, J.E.Koglin, D.Sokaras, T.C.Weng, J.Sellberg, M.J.Latimer, P.Glatzel, P.H.Zwart, R.W.Grosse-Kunstleve, M.J.Bogan, M.Messerschmidt, G.J.Williams, S.Boutet, J.Messinger, A.Zouni, J.Yano, U.Bergmann, V.K.Yachandra, P.D.Adams, N.K.Sauter. Accurate Macromolecular Structures Using Minimal Measurements From X-Ray Free-Electron Lasers. Nat.Methods V. 11 545 2014.
ISSN: ESSN 1548-7105
PubMed: 24633409
DOI: 10.1038/NMETH.2887