Calcium in PDB 6tj8: Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine Diphosphate

All present enzymatic activity of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine Diphosphate:
2.2.1.1;

The structure of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine Diphosphate, PDB code: 6tj8 was solved by F.Rabe Von Pappenheim, K.Tittmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.29 / 0.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.550, 101.910, 132.960, 90.00, 90.00, 90.00
R / Rfree (%)	9.5 / 10.6

The binding sites of Calcium atom in the Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine Diphosphate (pdb code 6tj8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine Diphosphate, PDB code: 6tj8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:5.2 occ:1.00 O13 A:NDQ701 2.1 7.6 0.5 O22 A:NDQ701 2.2 5.8 0.5 O A:ILE187 2.3 6.4 1.0 OD2 A:ASP155 2.3 6.4 1.0 O22 A:NDQ701 2.3 6.0 0.5 O13 A:NDQ701 2.4 5.5 0.5 OD1 A:ASN185 2.4 5.8 1.0 O A:HOH948 2.4 6.2 1.0 HD21 A:ASN185 3.0 7.2 1.0 HB2 A:ASP155 3.2 6.6 1.0 CG A:ASN185 3.3 5.6 1.0 H A:ASP155 3.3 6.0 1.0 H A:ILE187 3.3 7.2 1.0 P2 A:NDQ701 3.4 6.1 0.5 CG A:ASP155 3.4 5.6 1.0 P1 A:NDQ701 3.4 7.7 0.5 C A:ILE187 3.5 5.7 1.0 ND2 A:ASN185 3.5 6.0 1.0 P1 A:NDQ701 3.5 5.9 0.5 P2 A:NDQ701 3.6 7.0 0.5 O11 A:NDQ701 3.6 8.0 0.5 O11 A:NDQ701 3.7 6.9 0.5 CB A:ASP155 3.8 5.5 1.0 O23 A:NDQ701 3.8 8.2 0.5 N A:ILE187 4.0 6.0 1.0 HA A:SER188 4.0 7.6 1.0 O5G A:NDQ701 4.1 12.4 0.5 N A:ASP155 4.1 5.0 1.0 H A:ASN185 4.1 6.9 1.0 HB A:ILE187 4.2 8.2 1.0 CA A:ILE187 4.3 6.0 1.0 HD22 A:ASN185 4.3 7.2 1.0 O12 A:NDQ701 4.4 9.4 0.5 O A:HOH815 4.4 9.2 1.0 HB3 A:SER188 4.4 7.6 1.0 HD12 A:ILE247 4.4 8.7 1.0 OD1 A:ASP155 4.5 6.8 1.0 O A:ASP183 4.5 6.3 0.8 N A:SER188 4.5 6.1 1.0 O21 A:NDQ701 4.5 8.7 0.5 HB3 A:ASP155 4.5 6.6 1.0 O12 A:NDQ701 4.5 7.9 0.5 O A:ASP183 4.6 6.6 0.2 CA A:ASP155 4.6 5.1 1.0 HG11 A:VAL193 4.6 11.3 1.0 H A:GLY186 4.6 7.0 1.0 CA A:SER188 4.7 6.3 1.0 CB A:ASN185 4.7 5.9 1.0 O21 A:NDQ701 4.7 6.6 0.5 HG22 A:ILE187 4.7 9.9 1.0 O23 A:NDQ701 4.7 8.2 0.5 HA3 A:GLY154 4.7 6.4 1.0 CB A:ILE187 4.7 6.8 1.0 O5G A:NDQ701 4.7 8.1 0.5 N A:GLY186 4.9 5.8 1.0 H A:GLY156 4.9 6.1 1.0 N A:ASN185 4.9 5.8 1.0 C5B A:NDQ701 4.9 10.2 0.5

Calcium binding site 2 out of 2 in the Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:5.7 occ:1.00 O13 B:NDQ701 2.1 9.0 0.4 O21 B:NDQ701 2.3 5.3 0.4 O B:ILE187 2.3 6.8 1.0 OD2 B:ASP155 2.3 7.1 1.0 O22 B:NDQ701 2.3 7.7 0.6 O13 B:NDQ701 2.4 6.2 0.6 OD1 B:ASN185 2.4 6.0 1.0 O B:HOH935 2.4 6.5 1.0 HD21 B:ASN185 3.0 7.7 1.0 HB2 B:ASP155 3.2 7.0 1.0 CG B:ASN185 3.3 6.0 1.0 H B:ASP155 3.3 6.7 1.0 H B:ILE187 3.3 7.5 1.0 CG B:ASP155 3.3 6.2 1.0 P2 B:NDQ701 3.4 5.9 0.4 P1 B:NDQ701 3.4 8.3 0.4 C B:ILE187 3.5 6.2 1.0 ND2 B:ASN185 3.5 6.4 1.0 P1 B:NDQ701 3.5 6.3 0.6 P2 B:NDQ701 3.6 8.5 0.6 O11 B:NDQ701 3.7 7.7 0.4 O11 B:NDQ701 3.7 8.0 0.6 CB B:ASP155 3.8 5.8 1.0 O22 B:NDQ701 3.9 7.5 0.4 N B:ILE187 4.0 6.2 1.0 HA B:SER188 4.0 8.0 1.0 O5G B:NDQ701 4.1 13.7 0.4 N B:ASP155 4.1 5.6 1.0 H B:ASN185 4.1 7.4 1.0 HB B:ILE187 4.1 9.0 1.0 CA B:ILE187 4.3 6.4 1.0 HD22 B:ASN185 4.3 7.7 1.0 O12 B:NDQ701 4.3 10.3 0.6 O B:HOH816 4.4 9.9 1.0 HB3 B:SER188 4.4 8.2 1.0 HD12 B:ILE247 4.4 9.9 1.0 OD1 B:ASP155 4.4 7.5 1.0 O B:ASP183 4.5 7.0 1.0 N B:SER188 4.5 6.3 1.0 HB3 B:ASP155 4.5 7.0 1.0 O21 B:NDQ701 4.5 9.9 0.6 O12 B:NDQ701 4.5 8.1 0.4 CA B:ASP155 4.6 5.5 1.0 H B:GLY186 4.6 7.3 1.0 CB B:ASN185 4.7 6.2 1.0 CA B:SER188 4.7 6.6 1.0 HG22 B:ILE187 4.7 10.6 1.0 HG11 B:VAL193 4.7 11.4 1.0 O23 B:NDQ701 4.7 6.2 0.4 O23 B:NDQ701 4.7 9.8 0.6 CB B:ILE187 4.7 7.5 1.0 O5G B:NDQ701 4.7 8.1 0.6 HA3 B:GLY154 4.7 6.8 1.0 N B:GLY186 4.8 6.1 1.0 N B:ASN185 4.9 6.2 1.0 H B:GLY156 4.9 6.6 1.0 C5B B:NDQ701 4.9 10.3 0.6

F.Rabe Von Pappenheim, M.Aldeghi, B.Shome, T.Begley, B.L.De Groot, K.Tittmann. Structural Basis For Antibiotic Action of the B 1 Antivitamin 2'-Methoxy-Thiamine. Nat.Chem.Biol. V. 16 1237 2020.
ISSN: ESSN 1552-4469
PubMed: 32839604
DOI: 10.1038/S41589-020-0628-4