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Sodium in PDB 5lc1: L-Threonine Dehydrogenase From Trypanosoma Brucei with Nad and the Inhibitor Pyruvate Bound.

Enzymatic activity of L-Threonine Dehydrogenase From Trypanosoma Brucei with Nad and the Inhibitor Pyruvate Bound.

All present enzymatic activity of L-Threonine Dehydrogenase From Trypanosoma Brucei with Nad and the Inhibitor Pyruvate Bound.:
1.1.1.103;

Protein crystallography data

The structure of L-Threonine Dehydrogenase From Trypanosoma Brucei with Nad and the Inhibitor Pyruvate Bound., PDB code: 5lc1 was solved by P.T.Erskine, E.Adjogatse, S.P.Wood, J.B.Cooper, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 95.50 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 132.040, 276.490, 55.740, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 20.8

Sodium Binding Sites:

The binding sites of Sodium atom in the L-Threonine Dehydrogenase From Trypanosoma Brucei with Nad and the Inhibitor Pyruvate Bound. (pdb code 5lc1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the L-Threonine Dehydrogenase From Trypanosoma Brucei with Nad and the Inhibitor Pyruvate Bound., PDB code: 5lc1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5lc1

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Sodium binding site 1 out of 6 in the L-Threonine Dehydrogenase From Trypanosoma Brucei with Nad and the Inhibitor Pyruvate Bound.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of L-Threonine Dehydrogenase From Trypanosoma Brucei with Nad and the Inhibitor Pyruvate Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:29.2
occ:1.00
 O A:HOH603 2.2 22.0 1.0
OD1 A:ASP282 2.2 32.7 1.0
O A:SER211 2.3 16.1 1.0
OE2 A:GLU210 2.3 24.1 1.0
O A:HOH785 3.0 19.3 1.0
C A:SER211 3.4 15.2 1.0
CG A:ASP282 3.5 29.6 1.0
CD A:GLU210 3.5 19.8 1.0
N A:SER211 3.6 14.9 1.0
CE A:LYS129 4.0 40.6 1.0
NZ A:LYS129 4.0 41.2 1.0
CA A:SER211 4.0 15.9 1.0
CG A:GLU210 4.1 17.4 1.0
CA A:ASP282 4.1 19.9 1.0
CD2 A:LEU212 4.2 18.8 1.0
O A:PRO281 4.2 17.3 1.0
C A:GLU210 4.2 16.2 1.0
O A:TRP280 4.3 13.4 1.0
CB A:ASP282 4.3 23.4 1.0
OD2 A:ASP282 4.3 33.9 1.0
O A:ALA277 4.4 13.3 1.0
N A:ASP282 4.4 18.4 1.0
N A:LEU212 4.4 14.7 1.0
OE1 A:GLU210 4.5 17.8 1.0
C A:PRO281 4.5 17.2 1.0
CB A:SER211 4.5 16.1 1.0
CA A:GLU210 4.6 15.8 1.0
CG A:LEU212 4.7 17.5 1.0
CA A:LEU212 4.8 15.3 1.0
CB A:GLU210 4.9 17.5 1.0
O A:GLU210 4.9 16.3 1.0

Sodium binding site 2 out of 6 in 5lc1

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Sodium binding site 2 out of 6 in the L-Threonine Dehydrogenase From Trypanosoma Brucei with Nad and the Inhibitor Pyruvate Bound.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of L-Threonine Dehydrogenase From Trypanosoma Brucei with Nad and the Inhibitor Pyruvate Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na504

b:30.9
occ:1.00
 O B:HOH603 2.1 23.3 1.0
OD1 B:ASP282 2.2 33.6 1.0
O B:SER211 2.3 20.2 1.0
OE2 B:GLU210 2.3 23.1 1.0
C B:SER211 3.4 16.5 1.0
CG B:ASP282 3.5 31.2 1.0
CD B:GLU210 3.5 19.1 1.0
N B:SER211 3.5 14.5 1.0
NZ B:LYS129 3.7 39.9 1.0
CA B:SER211 3.9 16.1 1.0
CG B:GLU210 4.1 16.7 1.0
CE B:LYS129 4.1 40.0 1.0
C B:GLU210 4.2 13.9 1.0
CD2 B:LEU212 4.2 14.8 1.0
CA B:ASP282 4.2 18.9 1.0
O B:PRO281 4.3 16.9 1.0
OD2 B:ASP282 4.3 37.0 1.0
O B:TRP280 4.3 12.8 1.0
CB B:ASP282 4.4 23.1 1.0
OE1 B:GLU210 4.4 20.8 1.0
O B:ALA277 4.5 12.7 1.0
N B:ASP282 4.5 17.4 1.0
CB B:SER211 4.5 16.4 1.0
N B:LEU212 4.5 14.9 1.0
CA B:GLU210 4.5 14.3 1.0
C B:PRO281 4.6 16.8 1.0
CG B:LEU212 4.7 14.8 1.0
CA B:LEU212 4.8 14.3 1.0
CB B:GLU210 4.9 15.1 1.0
O B:GLU210 4.9 13.5 1.0

Sodium binding site 3 out of 6 in 5lc1

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Sodium binding site 3 out of 6 in the L-Threonine Dehydrogenase From Trypanosoma Brucei with Nad and the Inhibitor Pyruvate Bound.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of L-Threonine Dehydrogenase From Trypanosoma Brucei with Nad and the Inhibitor Pyruvate Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:21.3
occ:1.00
 OD1 C:ASP282 2.2 23.0 1.0
OE2 C:GLU210 2.3 23.4 1.0
O C:SER211 2.3 15.6 1.0
O C:HOH659 2.3 23.8 1.0
O C:HOH739 2.4 18.4 1.0
O C:HOH646 3.4 33.3 1.0
C C:SER211 3.4 14.7 1.0
CG C:ASP282 3.4 21.4 1.0
CD C:GLU210 3.5 20.0 1.0
N C:SER211 3.5 15.3 1.0
CA C:SER211 3.9 15.0 1.0
CA C:ASP282 4.1 16.3 1.0
C C:GLU210 4.2 15.4 1.0
CG C:GLU210 4.2 18.5 1.0
CB C:ASP282 4.2 18.4 1.0
OD2 C:ASP282 4.3 21.1 1.0
CD2 C:LEU212 4.3 14.8 1.0
O C:PRO281 4.4 15.1 1.0
NZ C:LYS129 4.4 33.9 1.0
OE1 C:GLU210 4.4 19.9 1.0
CB C:SER211 4.5 17.2 1.0
N C:LEU212 4.5 13.8 1.0
CA C:GLU210 4.5 15.6 1.0
N C:ASP282 4.5 16.2 1.0
O C:TRP280 4.6 14.5 1.0
O C:ALA277 4.7 16.6 1.0
O C:HOH803 4.7 32.3 1.0
C C:PRO281 4.7 15.4 1.0
CG C:LEU212 4.8 15.5 1.0
CA C:LEU212 4.9 13.4 1.0
CE C:LYS129 4.9 34.0 1.0
CB C:GLU210 5.0 16.2 1.0
O C:GLU210 5.0 15.9 1.0

Sodium binding site 4 out of 6 in 5lc1

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Sodium binding site 4 out of 6 in the L-Threonine Dehydrogenase From Trypanosoma Brucei with Nad and the Inhibitor Pyruvate Bound.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of L-Threonine Dehydrogenase From Trypanosoma Brucei with Nad and the Inhibitor Pyruvate Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:20.4
occ:1.00
 O D:HOH680 2.1 19.8 1.0
O D:SER211 2.3 15.7 1.0
OD1 D:ASP282 2.3 23.2 1.0
OE2 D:GLU210 2.3 21.3 1.0
O D:HOH758 2.5 13.3 1.0
O D:HOH616 3.2 35.3 1.0
C D:SER211 3.4 15.8 1.0
CG D:ASP282 3.4 22.4 1.0
CD D:GLU210 3.5 21.2 1.0
N D:SER211 3.5 16.4 1.0
NZ D:LYS129 3.9 42.2 1.0
CA D:SER211 4.0 16.4 1.0
CG D:GLU210 4.1 18.5 1.0
C D:GLU210 4.2 16.4 1.0
CD2 D:LEU212 4.2 16.8 1.0
CA D:ASP282 4.2 17.6 1.0
CB D:ASP282 4.3 19.2 1.0
OD2 D:ASP282 4.3 23.5 1.0
N D:LEU212 4.5 14.4 1.0
OE1 D:GLU210 4.5 20.8 1.0
O D:PRO281 4.5 14.4 1.0
CA D:GLU210 4.5 15.8 1.0
CB D:SER211 4.5 16.8 1.0
O D:TRP280 4.6 13.0 1.0
N D:ASP282 4.6 15.7 1.0
CG D:LEU212 4.6 17.8 1.0
O D:ALA277 4.7 15.5 1.0
CA D:LEU212 4.8 15.5 1.0
C D:PRO281 4.8 14.6 1.0
O D:HOH859 4.9 49.1 1.0
O D:GLU210 4.9 14.8 1.0
CB D:GLU210 5.0 16.6 1.0

Sodium binding site 5 out of 6 in 5lc1

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Sodium binding site 5 out of 6 in the L-Threonine Dehydrogenase From Trypanosoma Brucei with Nad and the Inhibitor Pyruvate Bound.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of L-Threonine Dehydrogenase From Trypanosoma Brucei with Nad and the Inhibitor Pyruvate Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na503

b:33.0
occ:1.00
 OE1 E:GLU210 2.3 29.5 1.0
O E:SER211 2.3 22.6 1.0
OD1 E:ASP282 2.5 38.1 1.0
O E:HOH650 2.9 35.9 1.0
CD E:GLU210 3.5 24.4 1.0
C E:SER211 3.6 16.9 1.0
CG E:ASP282 3.7 38.3 1.0
O E:TRP280 3.8 13.8 1.0
CD2 E:LEU212 3.9 22.9 1.0
O E:PRO281 3.9 18.0 1.0
O E:ALA277 4.0 17.1 1.0
N E:SER211 4.0 16.5 1.0
CA E:ASP282 4.1 23.6 1.0
N E:ASP282 4.1 19.5 1.0
C E:PRO281 4.2 19.3 1.0
CG E:GLU210 4.2 21.2 1.0
CA E:SER211 4.4 17.4 1.0
CB E:ASP282 4.5 28.5 1.0
C E:TRP280 4.6 16.4 1.0
OE2 E:GLU210 4.6 27.6 1.0
N E:LEU212 4.6 18.4 1.0
C E:GLU210 4.7 16.2 1.0
OD2 E:ASP282 4.7 50.4 1.0
CG E:LEU212 4.7 21.6 1.0
C E:ALA277 4.8 18.4 1.0
CA E:ASN278 4.9 19.9 1.0
CA E:LEU212 4.9 18.3 1.0
CB E:SER211 4.9 19.7 1.0

Sodium binding site 6 out of 6 in 5lc1

Go back to Sodium Binding Sites List in 5lc1
Sodium binding site 6 out of 6 in the L-Threonine Dehydrogenase From Trypanosoma Brucei with Nad and the Inhibitor Pyruvate Bound.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of L-Threonine Dehydrogenase From Trypanosoma Brucei with Nad and the Inhibitor Pyruvate Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na502

b:28.2
occ:1.00
 O F:HOH638 2.2 28.3 1.0
OD1 F:ASP282 2.3 23.5 1.0
OE2 F:GLU210 2.3 26.3 1.0
O F:SER211 2.3 20.5 1.0
O F:HOH762 2.4 22.6 1.0
O F:HOH602 3.3 34.5 1.0
C F:SER211 3.4 16.8 1.0
CG F:ASP282 3.4 21.9 1.0
CD F:GLU210 3.5 22.4 1.0
N F:SER211 3.5 17.3 1.0
NZ F:LYS129 3.7 35.5 1.0
CA F:SER211 3.9 17.7 1.0
CA F:ASP282 4.2 17.0 1.0
CG F:GLU210 4.2 21.1 1.0
C F:GLU210 4.2 17.4 1.0
CB F:ASP282 4.3 18.3 1.0
CD2 F:LEU212 4.3 18.2 1.0
OD2 F:ASP282 4.3 23.8 1.0
O F:PRO281 4.4 16.3 1.0
OE1 F:GLU210 4.4 22.7 1.0
CB F:SER211 4.4 19.4 1.0
O F:TRP280 4.5 17.5 1.0
N F:LEU212 4.5 14.8 1.0
CA F:GLU210 4.5 18.2 1.0
O F:HOH813 4.6 42.2 1.0
N F:ASP282 4.6 15.6 1.0
O F:ALA277 4.7 16.5 1.0
C F:PRO281 4.7 16.4 1.0
CA F:LEU212 4.9 15.1 1.0
O F:GLU210 5.0 19.6 1.0
CB F:GLU210 5.0 19.3 1.0
CG F:LEU212 5.0 17.8 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: Mon Oct 7 22:19:56 2024

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