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Calcium in PDB 3upt: Crystal Structure of A Transketolase From Burkholderia Pseudomallei Bound to Tpp, Calcium and Ribose-5-Phosphate

Enzymatic activity of Crystal Structure of A Transketolase From Burkholderia Pseudomallei Bound to Tpp, Calcium and Ribose-5-Phosphate

All present enzymatic activity of Crystal Structure of A Transketolase From Burkholderia Pseudomallei Bound to Tpp, Calcium and Ribose-5-Phosphate:
2.2.1.1;

Protein crystallography data

The structure of Crystal Structure of A Transketolase From Burkholderia Pseudomallei Bound to Tpp, Calcium and Ribose-5-Phosphate, PDB code: 3upt was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 146.980, 146.980, 142.870, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 20

Other elements in 3upt:

The structure of Crystal Structure of A Transketolase From Burkholderia Pseudomallei Bound to Tpp, Calcium and Ribose-5-Phosphate also contains other interesting chemical elements:

Bromine (Br) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Transketolase From Burkholderia Pseudomallei Bound to Tpp, Calcium and Ribose-5-Phosphate (pdb code 3upt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of A Transketolase From Burkholderia Pseudomallei Bound to Tpp, Calcium and Ribose-5-Phosphate, PDB code: 3upt:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3upt

Go back to Calcium Binding Sites List in 3upt
Calcium binding site 1 out of 2 in the Crystal Structure of A Transketolase From Burkholderia Pseudomallei Bound to Tpp, Calcium and Ribose-5-Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Transketolase From Burkholderia Pseudomallei Bound to Tpp, Calcium and Ribose-5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca691

b:17.0
occ:1.00
 O A:HOH1158 2.2 11.1 1.0
O2A A:TPP692 2.2 20.4 1.0
O A:ILE207 2.2 19.7 1.0
O2B A:TPP692 2.3 17.9 1.0
OD2 A:ASP175 2.3 13.5 1.0
OD1 A:ASN205 2.5 16.1 1.0
CG A:ASP175 3.3 13.6 1.0
CG A:ASN205 3.4 16.6 1.0
PA A:TPP692 3.4 21.4 1.0
C A:ILE207 3.5 19.8 1.0
PB A:TPP692 3.5 19.5 1.0
ND2 A:ASN205 3.6 16.4 1.0
CB A:ASP175 3.7 13.4 1.0
O3A A:TPP692 3.7 20.8 1.0
N A:ASP175 4.0 13.3 1.0
N A:ILE207 4.1 19.4 1.0
O A:HOH1148 4.1 19.6 1.0
CA A:ILE207 4.3 20.3 1.0
O1B A:TPP692 4.3 21.5 1.0
O7 A:TPP692 4.4 22.2 1.0
N A:SER208 4.4 18.2 1.0
OD1 A:ASP175 4.4 13.7 1.0
CA A:ASP175 4.5 13.4 1.0
O1A A:TPP692 4.5 22.3 1.0
O A:ASP203 4.5 15.5 1.0
CA A:SER208 4.6 18.0 1.0
O3B A:TPP692 4.7 19.7 1.0
CB A:ASN205 4.8 16.9 1.0
N A:ASN205 4.8 16.8 1.0
CB A:ILE207 4.9 21.8 1.0
N A:GLY206 4.9 17.9 1.0

Calcium binding site 2 out of 2 in 3upt

Go back to Calcium Binding Sites List in 3upt
Calcium binding site 2 out of 2 in the Crystal Structure of A Transketolase From Burkholderia Pseudomallei Bound to Tpp, Calcium and Ribose-5-Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Transketolase From Burkholderia Pseudomallei Bound to Tpp, Calcium and Ribose-5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca691

b:14.6
occ:1.00
 O2A B:TPP692 2.1 19.9 1.0
O2B B:TPP692 2.2 18.8 1.0
O B:ILE207 2.3 15.4 1.0
O B:HOH959 2.3 15.9 1.0
OD2 B:ASP175 2.4 13.4 1.0
OD1 B:ASN205 2.4 15.4 1.0
CG B:ASN205 3.3 15.5 1.0
PA B:TPP692 3.3 20.3 1.0
CG B:ASP175 3.4 13.4 1.0
C B:ILE207 3.5 15.7 1.0
PB B:TPP692 3.5 18.8 1.0
ND2 B:ASN205 3.6 15.2 1.0
O3A B:TPP692 3.7 20.9 1.0
CB B:ASP175 3.8 13.2 1.0
N B:ASP175 4.1 13.7 1.0
N B:ILE207 4.1 16.8 1.0
O7 B:TPP692 4.2 21.7 1.0
CA B:ILE207 4.3 16.6 1.0
O1B B:TPP692 4.4 22.9 1.0
O B:HOH958 4.4 23.1 1.0
O B:ASP203 4.4 17.7 1.0
N B:SER208 4.4 15.3 1.0
O1A B:TPP692 4.5 20.5 1.0
O3B B:TPP692 4.5 20.4 1.0
OD1 B:ASP175 4.5 13.1 1.0
CA B:ASP175 4.6 13.6 1.0
CA B:SER208 4.6 14.3 1.0
CB B:ILE207 4.6 17.2 1.0
CB B:ASN205 4.7 15.6 1.0
N B:ASN205 4.8 16.6 1.0
N B:GLY206 5.0 16.8 1.0

Reference:

L.Baugh, L.A.Gallagher, R.Patrapuvich, M.C.Clifton, A.S.Gardberg, T.E.Edwards, B.Armour, D.W.Begley, S.H.Dieterich, D.M.Dranow, J.Abendroth, J.W.Fairman, D.Fox, B.L.Staker, I.Phan, A.Gillespie, R.Choi, S.Nakazawa-Hewitt, M.T.Nguyen, A.Napuli, L.Barrett, G.W.Buchko, R.Stacy, P.J.Myler, L.J.Stewart, C.Manoil, W.C.Van Voorhis. Combining Functional and Structural Genomics to Sample the Essential Burkholderia Structome. Plos One V. 8 53851 2013.
ISSN: ESSN 1932-6203
PubMed: 23382856
DOI: 10.1371/JOURNAL.PONE.0053851
Page generated: Sat Jul 13 20:15:23 2024

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