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Bromine 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:

Calcium (Ca) 2 atoms

Bromine Binding Sites:

The binding sites of Bromine 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 Bromine atom.
In total 4 binding sites of Bromine 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 Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 3upt

Go back to Bromine Binding Sites List in 3upt
Bromine binding site 1 out of 4 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 Bromine with other atoms in the Br 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:Br695

b:92.7
occ:1.00
 N A:ALA301 3.3 23.7 1.0
CB A:ALA301 3.8 23.4 1.0
CA A:TRP300 3.8 24.3 1.0
C A:TRP300 4.1 23.2 1.0
CG1 A:VAL304 4.1 22.1 1.0
CD1 A:TRP300 4.1 24.7 1.0
CB A:TRP300 4.2 24.6 1.0
CA A:ALA301 4.2 23.2 1.0
CG2 A:VAL304 4.3 22.7 1.0
CB A:VAL304 4.3 23.1 1.0
CG A:TRP300 4.5 24.9 1.0
O A:THR299 4.8 28.3 1.0
N A:TRP300 4.9 25.9 1.0

Bromine binding site 2 out of 4 in 3upt

Go back to Bromine Binding Sites List in 3upt
Bromine binding site 2 out of 4 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 Bromine with other atoms in the Br 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
A:Br696

b:85.7
occ:1.00
 O A:HOH1009 3.5 20.6 1.0
CE A:LYS410 3.7 22.4 1.0
O A:HOH1008 3.8 26.2 1.0
CB A:LYS410 4.1 19.8 1.0
CB A:ALA411 4.2 17.2 1.0
N A:ALA411 4.6 17.7 1.0
NZ A:LYS410 4.7 23.7 1.0
CA A:ALA411 4.9 17.6 1.0
O A:HOH846 4.9 15.3 1.0
CD A:LYS410 4.9 22.3 1.0
CG A:LYS410 4.9 21.6 1.0
C A:LYS410 5.0 18.6 1.0

Bromine binding site 3 out of 4 in 3upt

Go back to Bromine Binding Sites List in 3upt
Bromine binding site 3 out of 4 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 Bromine with other atoms in the Br binding site number 3 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:Br693

b:51.7
occ:1.00
 O B:HOH853 3.3 23.7 1.0
N B:ASP212 3.3 17.8 1.0
CE1 B:HIS277 3.9 23.5 1.0
CB B:ASP212 3.9 22.7 1.0
OD1 B:ASN215 4.0 24.1 1.0
CA B:GLY211 4.0 15.7 1.0
O B:HOH882 4.1 24.2 1.0
O B:ASP210 4.1 14.8 1.0
C B:GLY211 4.2 16.6 1.0
CA B:ASP212 4.2 20.0 1.0
CG B:ASP212 4.3 26.5 1.0
CH2 B:TRP216 4.4 14.8 1.0
ND1 B:HIS277 4.5 23.9 1.0
OD2 B:ASP212 4.6 30.6 1.0
CZ3 B:TRP216 4.6 15.0 1.0
O B:ASP212 4.7 18.6 1.0
OD1 B:ASP212 4.7 27.8 1.0
NE2 B:HIS277 4.9 23.9 1.0
NH2 A:ARG416 4.9 18.0 1.0
C B:ASP212 4.9 18.9 1.0
C B:ASP210 4.9 14.8 1.0
N B:GLY211 5.0 14.6 1.0

Bromine binding site 4 out of 4 in 3upt

Go back to Bromine Binding Sites List in 3upt
Bromine binding site 4 out of 4 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 Bromine with other atoms in the Br binding site number 4 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:Br694

b:0.7
occ:1.00
 N B:LYS578 3.6 29.3 1.0
CD B:ARG577 3.8 30.0 1.0
CB B:LYS578 4.0 30.6 1.0
NE B:ARG577 4.0 29.1 1.0
CA B:ARG577 4.2 29.8 1.0
CG B:LYS578 4.3 33.8 1.0
CA B:LYS578 4.4 28.7 1.0
C B:ARG577 4.4 30.0 1.0
CG B:ARG577 4.4 29.0 1.0
CD B:LYS578 4.5 36.2 1.0
O B:ALA576 4.8 33.1 1.0
CB B:ARG577 4.9 29.1 1.0
O B:LYS578 4.9 27.8 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: Wed Jul 10 20:30:00 2024

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