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Calcium in PDB 6tj9: Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate

Enzymatic activity of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate

All present enzymatic activity of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate:
2.2.1.1;

Protein crystallography data

The structure of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate, PDB code: 6tj9 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) 47.66 / 0.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.760, 102.080, 133.130, 90.00, 90.00, 90.00
R / Rfree (%) 9.9 / 11

Other elements in 6tj9:

The structure of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate (pdb code 6tj9). 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 and Substrate Xylulose 5-Phosphate, PDB code: 6tj9:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6tj9

Go back to Calcium Binding Sites List in 6tj9
Calcium binding site 1 out of 2 in the Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate


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 and Substrate Xylulose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:5.1
occ:1.00
 O13 A:NDQ702 2.1 7.1 0.3
O22 A:NDQ702 2.2 6.2 0.7
O A:ILE187 2.3 6.3 1.0
OD2 A:ASP155 2.3 6.5 1.0
O13 A:NDQ702 2.4 6.1 0.7
OD1 A:ASN185 2.4 5.5 1.0
O A:HOH924 2.4 6.1 1.0
O22 A:NDQ702 2.4 6.0 0.3
HD21 A:ASN185 3.0 7.3 1.0
HB2 A:ASP155 3.2 6.8 1.0
CG A:ASN185 3.3 5.5 1.0
H A:ASP155 3.3 6.0 1.0
H A:ILE187 3.3 6.9 1.0
P1 A:NDQ702 3.4 6.6 0.3
CG A:ASP155 3.4 5.4 1.0
P2 A:NDQ702 3.4 6.4 0.7
C A:ILE187 3.5 5.6 1.0
ND2 A:ASN185 3.5 6.0 1.0
P1 A:NDQ702 3.5 6.1 0.7
P2 A:NDQ702 3.6 6.8 0.3
O11 A:NDQ702 3.7 7.5 0.3
O11 A:NDQ702 3.7 8.5 0.7
CB A:ASP155 3.8 5.7 1.0
O5G A:NDQ702 4.0 10.7 0.3
O23 A:NDQ702 4.0 8.4 0.7
N A:ILE187 4.0 5.7 1.0
HA A:SER188 4.1 7.1 1.0
N A:ASP155 4.1 5.0 1.0
HB A:ILE187 4.1 8.1 1.0
H A:ASN185 4.1 6.9 1.0
CA A:ILE187 4.3 5.8 1.0
HD22 A:ASN185 4.3 7.3 1.0
O A:HOH808 4.4 9.8 1.0
O12 A:NDQ702 4.4 11.0 0.7
HB3 A:SER188 4.4 7.4 1.0
O A:ASP183 4.4 6.5 1.0
OD1 A:ASP155 4.5 6.9 1.0
O21 A:NDQ702 4.5 8.4 0.3
N A:SER188 4.5 5.6 1.0
HD12 A:ILE247 4.5 9.0 1.0
O12 A:NDQ702 4.5 6.8 0.3
HB3 A:ASP155 4.6 6.8 1.0
CA A:ASP155 4.6 4.9 1.0
HG22 A:ILE187 4.6 9.6 1.0
H A:GLY186 4.6 6.8 1.0
CB A:ASN185 4.7 5.8 1.0
CA A:SER188 4.7 5.9 1.0
HG11 A:VAL193 4.7 10.5 1.0
O21 A:NDQ702 4.7 8.1 0.7
CB A:ILE187 4.7 6.7 1.0
HA3 A:GLY154 4.7 6.5 1.0
O5G A:NDQ702 4.7 10.0 0.7
O23 A:NDQ702 4.8 7.4 0.3
C5B A:NDQ702 4.8 12.4 0.7
N A:GLY186 4.8 5.7 1.0
N A:ASN185 4.9 5.7 1.0
H A:GLY156 4.9 6.0 1.0

Calcium binding site 2 out of 2 in 6tj9

Go back to Calcium Binding Sites List in 6tj9
Calcium binding site 2 out of 2 in the Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate


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 and Substrate Xylulose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:5.5
occ:1.00
 O12 B:NDQ701 2.1 8.6 0.3
O22 B:NDQ701 2.3 7.0 0.7
O B:ILE187 2.3 6.5 1.0
OD2 B:ASP155 2.3 6.8 1.0
O22 B:NDQ701 2.3 5.6 0.3
O13 B:NDQ701 2.4 6.9 0.7
OD1 B:ASN185 2.4 5.9 1.0
O B:HOH933 2.4 6.7 1.0
HD21 B:ASN185 3.0 7.3 1.0
HB2 B:ASP155 3.2 6.8 1.0
CG B:ASN185 3.3 5.7 1.0
H B:ASP155 3.3 6.5 1.0
H B:ILE187 3.3 7.0 1.0
CG B:ASP155 3.4 6.0 1.0
P1 B:NDQ701 3.4 7.8 0.3
P2 B:NDQ701 3.5 6.9 0.7
C B:ILE187 3.5 5.8 1.0
ND2 B:ASN185 3.5 6.1 1.0
P1 B:NDQ701 3.5 6.4 0.7
P2 B:NDQ701 3.6 6.8 0.3
O11 B:NDQ701 3.7 7.5 0.3
O11 B:NDQ701 3.7 8.9 0.7
CB B:ASP155 3.8 5.7 1.0
O5G B:NDQ701 3.9 11.7 0.3
N B:ILE187 4.0 5.8 1.0
HA B:SER188 4.1 7.3 1.0
O23 B:NDQ701 4.1 8.5 0.7
HB B:ILE187 4.1 8.5 1.0
H B:ASN185 4.1 7.2 1.0
N B:ASP155 4.1 5.4 1.0
CA B:ILE187 4.3 6.1 1.0
HD22 B:ASN185 4.3 7.3 1.0
O12 B:NDQ701 4.4 11.5 0.7
O B:HOH801 4.4 10.6 1.0
O B:ASP183 4.4 6.7 0.7
HB3 B:SER188 4.4 7.6 1.0
OD1 B:ASP155 4.5 7.2 1.0
O21 B:NDQ701 4.5 8.7 0.3
N B:SER188 4.5 5.8 1.0
HD12 B:ILE247 4.5 9.5 1.0
O B:ASP183 4.5 7.3 0.3
HB3 B:ASP155 4.5 6.8 1.0
O13 B:NDQ701 4.6 6.8 0.3
CA B:ASP155 4.6 5.3 1.0
HG22 B:ILE187 4.6 10.2 1.0
H B:GLY186 4.6 7.0 1.0
CB B:ASN185 4.7 6.3 1.0
CB B:ILE187 4.7 7.1 1.0
HG11 B:VAL193 4.7 10.7 1.0
CA B:SER188 4.7 6.0 1.0
O21 B:NDQ701 4.7 8.7 0.7
O5G B:NDQ701 4.7 10.8 0.7
O23 B:NDQ701 4.7 7.6 0.3
HA3 B:GLY154 4.7 7.0 1.0
C5B B:NDQ701 4.8 13.3 0.7
N B:GLY186 4.9 5.8 1.0
N B:ASN185 4.9 6.0 1.0
H B:GLY156 4.9 6.5 1.0
C B:ASN185 5.0 6.2 1.0

Reference:

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
Page generated: Tue Jul 16 15:19:46 2024

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