Atomistry » Calcium » PDB 6t72-6to1 » 6tj9
Atomistry »
  Calcium »
    PDB 6t72-6to1 »
      6tj9 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy