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Sodium in PDB 4f3y: X-Ray Crystal Structure of Dihydrodipicolinate Reductase From Burkholderia Thailandensis

Enzymatic activity of X-Ray Crystal Structure of Dihydrodipicolinate Reductase From Burkholderia Thailandensis

All present enzymatic activity of X-Ray Crystal Structure of Dihydrodipicolinate Reductase From Burkholderia Thailandensis:
1.3.1.26;

Protein crystallography data

The structure of X-Ray Crystal Structure of Dihydrodipicolinate Reductase From Burkholderia Thailandensis, PDB code: 4f3y was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural 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 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.740, 158.370, 70.440, 90.00, 130.00, 90.00
R / Rfree (%) 19 / 23.7

Other elements in 4f3y:

The structure of X-Ray Crystal Structure of Dihydrodipicolinate Reductase From Burkholderia Thailandensis also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Crystal Structure of Dihydrodipicolinate Reductase From Burkholderia Thailandensis (pdb code 4f3y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the X-Ray Crystal Structure of Dihydrodipicolinate Reductase From Burkholderia Thailandensis, PDB code: 4f3y:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4f3y

Go back to Sodium Binding Sites List in 4f3y
Sodium binding site 1 out of 3 in the X-Ray Crystal Structure of Dihydrodipicolinate Reductase From Burkholderia Thailandensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of Dihydrodipicolinate Reductase From Burkholderia Thailandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:36.4
occ:1.00
 O A:ALA29 2.3 32.3 1.0
O A:ALA26 2.3 38.5 1.0
O A:VAL23 2.5 30.8 1.0
O A:LEU24 2.6 40.6 1.0
O A:HOH518 2.6 40.3 1.0
C A:LEU24 3.2 37.8 1.0
C A:ALA29 3.5 31.2 1.0
C A:ALA26 3.5 38.8 1.0
CA A:LEU24 3.6 35.5 1.0
C A:VAL23 3.6 30.4 1.0
N A:ALA26 3.9 35.7 1.0
N A:ALA25 4.0 37.1 1.0
N A:LEU24 4.1 32.0 1.0
C A:ALA25 4.2 39.0 1.0
CA A:ALA26 4.2 37.0 1.0
N A:ALA29 4.3 31.1 1.0
CA A:ALA29 4.3 29.8 1.0
N A:THR30 4.4 30.8 1.0
CA A:THR30 4.5 31.8 1.0
CA A:ALA25 4.6 39.4 1.0
N A:PRO27 4.6 41.7 1.0
CB A:ALA29 4.6 27.9 1.0
CB A:ALA26 4.6 33.4 1.0
O A:ALA25 4.6 41.7 1.0
CA A:PRO27 4.8 42.9 1.0
C A:PRO27 4.9 41.6 1.0
CA A:VAL23 4.9 27.4 1.0
CG1 A:VAL23 4.9 25.5 1.0
CB A:LEU24 5.0 38.1 1.0

Sodium binding site 2 out of 3 in 4f3y

Go back to Sodium Binding Sites List in 4f3y
Sodium binding site 2 out of 3 in the X-Ray Crystal Structure of Dihydrodipicolinate Reductase From Burkholderia Thailandensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Crystal Structure of Dihydrodipicolinate Reductase From Burkholderia Thailandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:45.4
occ:1.00
 OG1 B:THR179 2.4 47.2 1.0
O B:ILE175 2.7 30.3 1.0
NH2 B:ARG181 3.1 41.6 1.0
CG2 B:THR179 3.3 45.8 1.0
CB B:THR179 3.3 48.4 1.0
N B:THR179 3.5 47.3 1.0
O B:ALA176 3.5 35.1 1.0
NE B:ARG181 3.6 43.4 1.0
C B:ILE175 3.7 29.9 1.0
CZ B:ARG181 3.8 43.9 1.0
CA B:ALA176 3.9 33.4 1.0
CA B:THR179 4.0 49.4 1.0
C B:ALA176 4.0 35.3 1.0
N B:ALA176 4.2 30.7 1.0
CG2 B:ILE175 4.4 26.1 1.0
C B:ALA178 4.4 46.4 1.0
CB B:ALA141 4.7 25.5 1.0
N B:ALA178 4.7 39.5 1.0
C B:THR179 4.8 51.1 1.0
CB B:ALA178 4.8 40.5 1.0
CA B:ILE175 4.8 27.8 1.0
CA B:ALA178 4.9 42.0 1.0
CD B:ARG181 4.9 45.0 1.0

Sodium binding site 3 out of 3 in 4f3y

Go back to Sodium Binding Sites List in 4f3y
Sodium binding site 3 out of 3 in the X-Ray Crystal Structure of Dihydrodipicolinate Reductase From Burkholderia Thailandensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Crystal Structure of Dihydrodipicolinate Reductase From Burkholderia Thailandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:25.8
occ:1.00
 O B:ALA29 2.3 25.2 1.0
O B:VAL23 2.3 20.7 1.0
O B:HOH458 2.4 25.5 1.0
O B:ALA26 2.4 26.9 1.0
O B:LEU24 2.6 31.2 1.0
C B:LEU24 3.1 29.0 1.0
C B:ALA29 3.4 24.3 1.0
CA B:LEU24 3.4 26.4 1.0
C B:VAL23 3.4 21.4 1.0
C B:ALA26 3.5 28.4 1.0
N B:ALA26 3.9 28.2 1.0
N B:LEU24 3.9 23.2 1.0
N B:ALA29 4.1 25.0 1.0
N B:ALA25 4.1 29.1 1.0
CA B:ALA29 4.1 23.3 1.0
CA B:ALA26 4.2 28.3 1.0
C B:ALA25 4.3 30.8 1.0
CB B:ALA29 4.3 21.4 1.0
N B:THR30 4.4 23.4 1.0
CB B:ALA26 4.5 25.8 1.0
N B:PRO27 4.6 30.4 1.0
CA B:THR30 4.6 24.8 1.0
CA B:PRO27 4.6 31.7 1.0
O B:HOH402 4.7 27.8 1.0
O B:HOH472 4.7 45.1 1.0
CA B:ALA25 4.7 30.8 1.0
CA B:VAL23 4.7 20.3 1.0
CB B:LEU24 4.8 28.2 1.0
C B:PRO27 4.8 31.2 1.0
O B:ALA25 4.9 32.3 1.0
CG1 B:VAL23 4.9 18.6 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: Tue Dec 15 06:39:37 2020

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