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Calcium in PDB 2r8p: Transketolase From E. Coli in Complex with Substrate D-Fructose-6- Phosphate

Enzymatic activity of Transketolase From E. Coli in Complex with Substrate D-Fructose-6- Phosphate

All present enzymatic activity of Transketolase From E. Coli in Complex with Substrate D-Fructose-6- Phosphate:
2.2.1.1;

Protein crystallography data

The structure of Transketolase From E. Coli in Complex with Substrate D-Fructose-6- Phosphate, PDB code: 2r8p was solved by G.Wille, P.Asztalos, M.S.Weiss, K.Tittmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.87 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.214, 101.863, 133.345, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 18

Calcium Binding Sites:

The binding sites of Calcium atom in the Transketolase From E. Coli in Complex with Substrate D-Fructose-6- Phosphate (pdb code 2r8p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Transketolase From E. Coli in Complex with Substrate D-Fructose-6- Phosphate, PDB code: 2r8p:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2r8p

Go back to Calcium Binding Sites List in 2r8p
Calcium binding site 1 out of 2 in the Transketolase From E. Coli in Complex with Substrate D-Fructose-6- Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Transketolase From E. Coli in Complex with Substrate D-Fructose-6- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca670

b:5.2
occ:1.00
O1A A:T6F671 2.2 7.2 1.0
O A:ILE187 2.3 4.8 1.0
O2B A:T6F671 2.3 7.6 1.0
OD2 A:ASP155 2.3 5.0 1.0
OD1 A:ASN185 2.4 5.9 1.0
O A:HOH677 2.5 3.6 1.0
CG A:ASN185 3.3 5.8 1.0
CG A:ASP155 3.4 4.6 1.0
PA A:T6F671 3.4 10.3 1.0
C A:ILE187 3.5 5.4 1.0
ND2 A:ASN185 3.5 5.2 1.0
PB A:T6F671 3.5 8.8 1.0
O3A A:T6F671 3.7 9.8 1.0
CB A:ASP155 3.8 3.8 1.0
N A:ILE187 4.0 5.0 1.0
N A:ASP155 4.1 4.3 1.0
CA A:ILE187 4.3 5.7 1.0
O7 A:T6F671 4.3 13.6 1.0
O3B A:T6F671 4.4 11.6 1.0
O A:HOH736 4.5 6.5 1.0
OD1 A:ASP155 4.5 5.0 1.0
N A:SER188 4.5 5.5 1.0
O2A A:T6F671 4.5 12.8 1.0
O A:ASP183 4.5 4.7 1.0
CA A:ASP155 4.6 4.3 1.0
O1B A:T6F671 4.6 12.6 1.0
CA A:SER188 4.7 4.9 1.0
CB A:ASN185 4.7 5.2 1.0
CB A:ILE187 4.7 5.9 1.0
N A:GLY186 4.8 5.2 1.0
N A:ASN185 4.9 4.7 1.0

Calcium binding site 2 out of 2 in 2r8p

Go back to Calcium Binding Sites List in 2r8p
Calcium binding site 2 out of 2 in the Transketolase From E. Coli in Complex with Substrate D-Fructose-6- Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Transketolase From E. Coli in Complex with Substrate D-Fructose-6- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca670

b:5.6
occ:1.00
O1A B:T6F671 2.2 8.1 1.0
O B:ILE187 2.2 6.2 1.0
O2B B:T6F671 2.3 7.9 1.0
OD2 B:ASP155 2.3 5.7 1.0
OD1 B:ASN185 2.4 5.8 1.0
O B:HOH703 2.5 4.7 1.0
CG B:ASN185 3.3 4.8 1.0
CG B:ASP155 3.4 6.0 1.0
C B:ILE187 3.4 6.2 1.0
PA B:T6F671 3.5 10.3 1.0
ND2 B:ASN185 3.5 4.3 1.0
PB B:T6F671 3.5 10.2 1.0
O3A B:T6F671 3.8 11.1 1.0
CB B:ASP155 3.8 4.7 1.0
N B:ILE187 4.0 5.8 1.0
N B:ASP155 4.1 4.6 1.0
CA B:ILE187 4.2 6.4 1.0
O7 B:T6F671 4.4 14.1 1.0
N B:SER188 4.4 6.0 1.0
OD1 B:ASP155 4.5 6.3 1.0
O B:HOH722 4.5 8.3 1.0
O3B B:T6F671 4.5 12.6 1.0
O2A B:T6F671 4.5 13.1 1.0
O B:ASP183 4.6 5.4 1.0
O1B B:T6F671 4.6 14.2 1.0
CA B:ASP155 4.6 4.8 1.0
CA B:SER188 4.6 5.9 1.0
CB B:ASN185 4.7 5.5 1.0
CB B:ILE187 4.7 6.6 1.0
N B:GLY186 4.8 5.9 1.0
N B:ASN185 4.9 5.2 1.0

Reference:

P.Asztalos, C.Parthier, R.Golbik, M.Kleinschmidt, G.Hubner, M.S.Weiss, R.Friedemann, G.Wille, K.Tittmann. Strain and Near Attack Conformers in Enzymic Thiamin Catalysis: X-Ray Crystallographic Snapshots of Bacterial Transketolase in Covalent Complex with Donor Ketoses Xylulose 5-Phosphate and Fructose 6-Phosphate, and in Noncovalent Complex with Acceptor Aldose Ribose 5-Phosphate. Biochemistry V. 46 12037 2007.
ISSN: ISSN 0006-2960
PubMed: 17914867
DOI: 10.1021/BI700844M
Page generated: Sat Dec 12 03:51:49 2020

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