Calcium in PDB 6rjc: E.Coli Transketolase Apoenzyme

All present enzymatic activity of E.Coli Transketolase Apoenzyme:
2.2.1.1;

The structure of E.Coli Transketolase Apoenzyme, PDB code: 6rjc 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)	80.95 / 1.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.905, 102.048, 132.933, 90.00, 90.00, 90.00
R / Rfree (%)	10.4 / 12.3

The structure of E.Coli Transketolase Apoenzyme also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the E.Coli Transketolase Apoenzyme (pdb code 6rjc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the E.Coli Transketolase Apoenzyme, PDB code: 6rjc:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the E.Coli Transketolase Apoenzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of E.Coli Transketolase Apoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:10.2 occ:0.58 HO1 A:EDO713 1.8 17.8 0.6 HO2 A:EDO714 1.8 16.1 0.6 O2 A:EDO714 2.3 13.4 0.6 H22 A:EDO714 2.3 25.1 0.4 O A:ILE187 2.3 13.5 1.0 O A:HOH1018 2.3 11.8 1.0 OD2 A:ASP155 2.4 18.8 1.0 O1 A:EDO713 2.4 14.8 0.6 OD1 A:ASN185 2.4 13.0 1.0 H21 A:EDO714 2.9 25.1 0.4 HD21 A:ASN185 3.0 14.9 1.0 C2 A:EDO714 3.0 20.9 0.4 HO2 A:EDO714 3.2 23.1 0.4 CG A:ASN185 3.3 11.1 1.0 HB2 A:ASP155 3.3 12.3 1.0 H A:ASP155 3.3 9.1 1.0 C2 A:EDO714 3.4 18.9 0.6 H A:ILE187 3.4 13.7 1.0 CG A:ASP155 3.4 17.3 1.0 H22 A:EDO714 3.4 22.7 0.6 ND2 A:ASN185 3.4 12.4 1.0 C A:ILE187 3.5 12.0 1.0 C1 A:EDO713 3.5 17.6 0.6 H12 A:EDO713 3.6 21.1 0.6 O2 A:EDO714 3.6 19.2 0.4 CB A:ASP155 3.9 10.3 1.0 H11 A:EDO713 3.9 21.1 0.6 H21 A:EDO714 3.9 22.7 0.6 HA A:SER188 4.1 14.9 1.0 N A:ILE187 4.1 11.4 1.0 HB A:ILE187 4.1 15.3 1.0 N A:ASP155 4.2 7.6 1.0 H A:ASN185 4.2 11.6 1.0 O1 A:EDO714 4.2 25.6 0.6 HD22 A:ASN185 4.3 14.9 1.0 O A:HOH804 4.3 14.6 0.9 CA A:ILE187 4.3 11.7 1.0 C1 A:EDO714 4.3 23.3 0.4 O1 A:EDO714 4.4 28.5 0.4 HB3 A:SER188 4.4 14.8 1.0 OD1 A:ASP155 4.5 18.6 1.0 C1 A:EDO714 4.5 19.2 0.6 O A:ASP183 4.5 9.7 1.0 N A:SER188 4.5 11.9 1.0 HD12 A:ILE247 4.6 13.1 1.0 HB3 A:ASP155 4.6 12.3 1.0 CA A:ASP155 4.7 8.3 1.0 HG22 A:ILE187 4.7 16.9 1.0 HA3 A:GLY154 4.7 9.6 1.0 HG11 A:VAL193 4.7 17.4 1.0 CB A:ASN185 4.7 10.8 1.0 CA A:SER188 4.7 12.4 1.0 CB A:ILE187 4.7 12.8 1.0 H A:GLY186 4.7 13.3 1.0 C2 A:EDO713 4.8 17.1 0.6 H12 A:EDO714 4.8 28.0 0.4 O2 A:EDO713 4.8 25.7 0.6 H12 A:EDO714 4.9 23.0 0.6 H A:GLY156 4.9 9.0 1.0 N A:GLY186 4.9 11.1 1.0 N A:ASN185 5.0 9.7 1.0

Calcium binding site 2 out of 2 in the E.Coli Transketolase Apoenzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of E.Coli Transketolase Apoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:9.8 occ:0.38 O B:HOH939 2.3 13.3 1.0 O B:ILE187 2.3 16.2 1.0 OD2 B:ASP155 2.4 20.9 1.0 O B:HOH1376 2.5 20.0 0.4 OD1 B:ASN185 2.5 15.5 1.0 O B:HOH1406 2.7 29.9 1.0 HD21 B:ASN185 2.9 17.9 1.0 CG B:ASN185 3.3 14.0 1.0 HB2 B:ASP155 3.3 13.0 1.0 H B:ASP155 3.3 10.0 1.0 H B:ILE187 3.4 16.7 1.0 ND2 B:ASN185 3.4 14.9 1.0 CG B:ASP155 3.4 15.9 1.0 C B:ILE187 3.5 14.5 1.0 CB B:ASP155 3.9 10.8 1.0 N B:ILE187 4.1 13.9 1.0 HA B:SER188 4.1 16.7 1.0 N B:ASP155 4.2 8.3 1.0 HB B:ILE187 4.2 18.1 1.0 HD22 B:ASN185 4.2 17.9 1.0 H B:ASN185 4.3 13.1 1.0 O B:HOH825 4.3 18.5 1.0 CA B:ILE187 4.3 13.9 1.0 O B:HOH1376 4.4 21.1 0.6 HB3 B:SER188 4.5 16.9 1.0 OD1 B:ASP155 4.5 18.6 1.0 O B:ASP183 4.5 10.5 1.0 HD12 B:ILE247 4.5 13.8 1.0 N B:SER188 4.5 14.0 1.0 HB3 B:ASP155 4.6 13.0 1.0 CA B:ASP155 4.7 8.0 1.0 HA3 B:GLY154 4.7 10.1 1.0 CB B:ASN185 4.7 13.0 1.0 O B:HOH1354 4.7 19.9 1.0 CA B:SER188 4.7 13.9 1.0 H B:GLY186 4.7 14.9 1.0 HG22 B:ILE187 4.8 20.7 1.0 HG11 B:VAL193 4.8 20.2 1.0 CB B:ILE187 4.8 15.1 1.0 H B:GLY156 4.9 9.2 1.0 N B:GLY186 5.0 12.4 1.0

S.Dai, L.M.Funk, F.R.Von Pappenheim, V.Sautner, M.Paulikat, B.Schroder, J.Uranga, R.A.Mata, K.Tittmann. Low-Barrier Hydrogen Bonds in Enzyme Cooperativity. Nature V. 573 609 2019.
ISSN: ESSN 1476-4687
PubMed: 31534226
DOI: 10.1038/S41586-019-1581-9