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Sodium in PDB 5k4w: Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Bound to Nadh and L-Threonine Refined to 1.72 Angstroms

Enzymatic activity of Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Bound to Nadh and L-Threonine Refined to 1.72 Angstroms

All present enzymatic activity of Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Bound to Nadh and L-Threonine Refined to 1.72 Angstroms:
1.1.1.103;

Protein crystallography data

The structure of Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Bound to Nadh and L-Threonine Refined to 1.72 Angstroms, PDB code: 5k4w was solved by E.A.Adjogatse, P.T.Erskine, J.B.Cooper, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.14 / 1.72
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 83.450, 136.120, 55.690, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 19.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Bound to Nadh and L-Threonine Refined to 1.72 Angstroms (pdb code 5k4w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Bound to Nadh and L-Threonine Refined to 1.72 Angstroms, PDB code: 5k4w:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5k4w

Go back to Sodium Binding Sites List in 5k4w
Sodium binding site 1 out of 2 in the Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Bound to Nadh and L-Threonine Refined to 1.72 Angstroms


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Bound to Nadh and L-Threonine Refined to 1.72 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1404

b:27.9
occ:1.00
O A:TRP1280 2.8 22.3 1.0
OE2 A:GLU1210 2.8 28.1 1.0
OD1 A:ASP1282 2.9 35.8 1.0
O A:ALA1277 2.9 22.5 1.0
O A:SER1211 3.1 20.9 1.0
O A:PRO1281 3.2 21.8 1.0
CD2 A:LEU1212 3.4 22.0 1.0
C A:TRP1280 3.6 20.8 1.0
C A:PRO1281 3.7 22.4 1.0
CD A:GLU1210 4.0 27.5 1.0
N A:ASP1282 4.1 22.8 1.0
C A:ALA1277 4.1 23.5 1.0
CG A:ASP1282 4.1 37.2 1.0
CA A:ASP1282 4.2 25.0 1.0
C A:SER1211 4.3 20.3 1.0
N A:TRP1280 4.3 19.8 1.0
CG A:LEU1212 4.4 23.3 1.0
CB A:TRP1280 4.4 19.1 1.0
CA A:TRP1280 4.4 19.6 1.0
N A:PRO1281 4.5 20.5 1.0
CE A:LYS1129 4.5 45.5 1.0
CA A:ASN1278 4.5 24.6 1.0
CG A:GLU1210 4.5 25.2 1.0
O A:HOH1633 4.5 27.2 1.0
O A:ASN1278 4.6 27.5 1.0
CA A:PRO1281 4.6 20.8 1.0
C A:ASN1278 4.6 25.4 1.0
N A:ASN1278 4.7 22.1 1.0
CB A:ASP1282 4.8 28.7 1.0
CA A:LEU1212 4.9 19.0 1.0
N A:SER1211 4.9 22.3 1.0
OD2 A:ASP1282 5.0 43.9 1.0

Sodium binding site 2 out of 2 in 5k4w

Go back to Sodium Binding Sites List in 5k4w
Sodium binding site 2 out of 2 in the Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Bound to Nadh and L-Threonine Refined to 1.72 Angstroms


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Bound to Nadh and L-Threonine Refined to 1.72 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1405

b:32.0
occ:1.00
O C:TRP1280 2.7 26.2 1.0
OE2 C:GLU1210 2.8 33.6 1.0
O C:ALA1277 2.9 21.9 1.0
OD1 C:ASP1282 3.1 38.9 1.0
O C:SER1211 3.2 24.2 1.0
O C:PRO1281 3.5 25.3 1.0
CD2 C:LEU1212 3.5 28.8 1.0
C C:TRP1280 3.6 28.1 1.0
NZ C:LYS1129 3.7 65.5 1.0
C C:PRO1281 3.9 25.7 1.0
C C:ALA1277 4.0 23.3 1.0
CD C:GLU1210 4.0 30.3 1.0
CE C:LYS1129 4.2 59.7 1.0
CG C:ASP1282 4.2 37.0 1.0
N C:TRP1280 4.3 25.4 1.0
O C:ASN1278 4.3 31.1 1.0
CA C:TRP1280 4.3 24.2 1.0
CA C:ASN1278 4.3 26.4 1.0
O C:HOH1537 4.4 36.7 1.0
N C:ASP1282 4.4 28.8 1.0
CB C:TRP1280 4.4 22.2 1.0
CA C:ASP1282 4.4 31.7 1.0
C C:SER1211 4.4 23.6 1.0
C C:ASN1278 4.4 27.9 1.0
N C:PRO1281 4.5 26.0 1.0
CG C:LEU1212 4.5 28.7 1.0
N C:ASN1278 4.6 24.9 1.0
CG C:GLU1210 4.6 27.4 1.0
CD C:LYS1129 4.7 59.6 1.0
CA C:PRO1281 4.7 27.5 1.0
CB C:ASP1282 4.9 33.1 1.0
CA C:LEU1212 4.9 21.6 1.0
OE1 C:GLU1210 5.0 33.5 1.0

Reference:

E.Adjogatse, P.Erskine, S.A.Wells, J.M.Kelly, J.D.Wilden, A.W.E.Chan, D.Selwood, A.Coker, S.Wood, J.B.Cooper. Structure and Function of L-Threonine-3-Dehydrogenase From the Parasitic Protozoan Trypanosoma Brucei Revealed By X-Ray Crystallography and Geometric Simulations. Acta Crystallogr D Struct V. 74 861 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30198897
DOI: 10.1107/S2059798318009208
Page generated: Tue Dec 15 11:09:53 2020

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