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Sodium in PDB 5k4y: Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Refined to 1.77 Angstroms

Enzymatic activity of Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Refined to 1.77 Angstroms

All present enzymatic activity of Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Refined to 1.77 Angstroms:
1.1.1.103;

Protein crystallography data

The structure of Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Refined to 1.77 Angstroms, PDB code: 5k4y 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) 39.60 / 1.77
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 133.451, 278.630, 56.270, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20.1

Other elements in 5k4y:

The structure of Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Refined to 1.77 Angstroms also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Refined to 1.77 Angstroms (pdb code 5k4y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Refined to 1.77 Angstroms, PDB code: 5k4y:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 5k4y

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Sodium binding site 1 out of 7 in the Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Refined to 1.77 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 Refined to 1.77 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1404

b:27.4
occ:1.00
 CL A:CL1403 2.9 34.5 1.0
N A:ARG1084 3.1 13.9 1.0
N A:VAL1083 3.4 14.9 1.0
CB A:ARG1084 3.6 14.0 1.0
O A:HOH1657 3.7 15.4 1.0
C A:MET1081 3.7 11.9 1.0
CB A:MET1081 3.9 14.3 1.0
N A:SER1082 3.9 13.7 1.0
CB A:VAL1083 3.9 14.5 1.0
CA A:GLY1184 3.9 26.3 1.0
CA A:VAL1083 3.9 14.1 1.0
CA A:ARG1084 4.0 13.2 1.0
O A:MET1081 4.0 11.3 1.0
C A:VAL1083 4.0 12.8 1.0
CA A:MET1081 4.1 11.2 1.0
C A:SER1082 4.3 14.2 1.0
N A:MET1081 4.5 11.4 1.0
CA A:SER1082 4.6 13.8 0.5
CA A:SER1082 4.6 14.4 0.5
N A:GLY1184 4.6 24.2 1.0
CG2 A:VAL1083 4.8 15.0 1.0
OG A:SER1082 4.8 18.6 0.5
CG1 A:VAL1083 4.9 17.9 1.0
O A:HOH1503 4.9 21.1 1.0
CG A:ARG1084 5.0 14.9 1.0
N A:GLY1085 5.0 10.0 1.0

Sodium binding site 2 out of 7 in 5k4y

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Sodium binding site 2 out of 7 in the Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Refined to 1.77 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 Refined to 1.77 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2404

b:30.3
occ:1.00
 CL B:CL2403 2.7 35.1 1.0
N B:ARG2084 3.1 14.5 1.0
CB B:ARG2084 3.5 16.0 1.0
N B:VAL2083 3.5 16.0 1.0
O B:HOH2641 3.6 15.6 1.0
C B:MET2081 3.8 12.5 1.0
CB B:VAL2083 3.9 18.7 1.0
CA B:ARG2084 3.9 16.0 1.0
CA B:VAL2083 3.9 16.3 1.0
CB B:MET2081 3.9 15.2 1.0
C B:VAL2083 4.0 15.4 1.0
N B:SER2082 4.0 12.4 1.0
O B:MET2081 4.0 12.2 1.0
CA B:MET2081 4.1 12.4 1.0
CA B:GLY2184 4.2 23.9 1.0
C B:SER2082 4.3 15.2 1.0
N B:MET2081 4.4 11.2 1.0
CA B:SER2082 4.7 12.9 0.5
CA B:SER2082 4.7 13.7 0.5
CG2 B:VAL2083 4.8 21.1 1.0
CG B:ARG2084 4.8 18.7 1.0
CG1 B:VAL2083 4.9 21.2 1.0
N B:GLY2184 4.9 23.6 1.0
N B:GLY2085 5.0 11.5 1.0

Sodium binding site 3 out of 7 in 5k4y

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Sodium binding site 3 out of 7 in the Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Refined to 1.77 Angstroms


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Refined to 1.77 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3404

b:24.1
occ:1.00
 O C:HOH3730 2.8 29.5 1.0
CL C:CL3403 2.8 21.1 1.0
N C:ARG3084 3.0 13.4 1.0
O C:HOH3647 3.1 14.8 1.0
CB C:ARG3084 3.5 15.4 1.0
N C:VAL3083 3.6 14.1 1.0
C C:MET3081 3.8 11.6 1.0
CB C:VAL3083 3.8 14.7 1.0
CA C:ARG3084 3.8 13.7 1.0
O C:MET3081 3.9 10.6 1.0
C C:VAL3083 4.0 13.0 1.0
CA C:VAL3083 4.0 13.1 1.0
CB C:MET3081 4.0 12.8 1.0
N C:SER3082 4.0 11.8 1.0
CA C:MET3081 4.2 11.4 1.0
N C:MET3081 4.3 10.8 1.0
C C:SER3082 4.4 12.7 1.0
CG2 C:VAL3083 4.7 14.4 1.0
CG1 C:VAL3083 4.8 16.9 1.0
CA C:SER3082 4.8 13.6 1.0
N C:GLY3085 4.8 11.4 1.0
CA C:GLY3184 4.9 15.2 1.0
CG C:ARG3084 4.9 18.8 1.0
C C:ARG3084 4.9 13.8 1.0

Sodium binding site 4 out of 7 in 5k4y

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Sodium binding site 4 out of 7 in the Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Refined to 1.77 Angstroms


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Refined to 1.77 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na4405

b:29.1
occ:1.00
 CL D:CL4403 2.7 32.2 1.0
N D:ARG4084 3.0 13.7 1.0
O D:HOH4634 3.2 13.3 1.0
CB D:ARG4084 3.4 16.2 1.0
N D:VAL4083 3.6 14.2 1.0
C D:MET4081 3.7 12.4 1.0
CA D:ARG4084 3.8 15.4 1.0
O D:MET4081 3.9 11.7 1.0
CB D:VAL4083 3.9 17.3 1.0
CB D:MET4081 3.9 12.2 1.0
N D:SER4082 3.9 12.3 1.0
C D:VAL4083 4.0 14.5 1.0
CA D:VAL4083 4.0 14.7 1.0
CA D:MET4081 4.0 11.7 1.0
N D:MET4081 4.2 11.0 1.0
C D:SER4082 4.4 14.0 1.0
CA D:GLY4184 4.6 19.3 1.0
CG D:ARG4084 4.7 19.4 1.0
CA D:SER4082 4.8 13.4 0.5
CG2 D:VAL4083 4.8 16.5 1.0
CA D:SER4082 4.8 13.0 0.5
N D:GLY4085 4.8 13.9 1.0
CG1 D:VAL4083 4.9 18.4 1.0
C D:ARG4084 4.9 14.6 1.0

Sodium binding site 5 out of 7 in 5k4y

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Sodium binding site 5 out of 7 in the Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Refined to 1.77 Angstroms


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Refined to 1.77 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na4406

b:31.3
occ:1.00
 CL D:CL4404 2.6 43.1 1.0
O D:ALA4185 3.0 24.9 1.0
N D:TYR4188 3.2 19.4 1.0
O D:GLY4184 3.3 17.9 1.0
C D:ALA4185 3.3 20.9 1.0
CB D:TYR4188 3.3 14.8 1.0
CG2 D:VAL4206 3.7 12.1 1.0
CD2 D:TYR4188 3.7 12.9 1.0
CA D:TYR4188 3.7 15.6 1.0
N D:ASP4187 3.8 28.5 1.0
O D:HOH4676 3.8 25.5 1.0
CB D:ALA4273 3.9 15.0 1.0
N D:THR4186 3.9 15.9 1.0
CG D:PRO4205 3.9 18.8 1.0
CG D:TYR4188 4.0 12.4 1.0
CA D:ALA4185 4.1 20.4 1.0
CA D:THR4186 4.1 18.3 1.0
C D:THR4186 4.1 23.6 1.0
C D:ASP4187 4.2 27.7 1.0
O D:HOH4538 4.2 27.6 1.0
C D:GLY4184 4.3 19.2 1.0
CA D:ASP4187 4.6 32.4 1.0
CD D:PRO4205 4.6 19.8 1.0
N D:ALA4185 4.7 17.7 1.0
CB D:VAL4206 4.8 11.0 1.0
CE2 D:TYR4188 4.9 12.5 1.0
O D:THR4186 4.9 19.4 1.0

Sodium binding site 6 out of 7 in 5k4y

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Sodium binding site 6 out of 7 in the Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Refined to 1.77 Angstroms


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Refined to 1.77 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na5404

b:32.2
occ:1.00
 CL E:CL5403 2.9 44.1 1.0
N E:ARG5084 3.1 11.7 1.0
O E:HOH5635 3.4 14.4 1.0
CB E:ARG5084 3.5 12.5 1.0
N E:VAL5083 3.6 13.5 1.0
C E:MET5081 3.7 11.6 1.0
CA E:ARG5084 3.9 12.3 1.0
CB E:VAL5083 3.9 15.6 1.0
O E:MET5081 3.9 10.9 1.0
CB E:MET5081 4.0 14.4 1.0
CA E:VAL5083 4.0 14.3 1.0
N E:SER5082 4.0 13.0 1.0
C E:VAL5083 4.0 11.7 1.0
CA E:MET5081 4.1 11.4 1.0
CA E:GLY5184 4.2 27.5 1.0
N E:MET5081 4.4 10.9 1.0
C E:SER5082 4.4 13.0 1.0
CA E:SER5082 4.8 13.3 0.7
CA E:SER5082 4.8 12.3 0.3
CG2 E:VAL5083 4.8 15.8 1.0
CG1 E:VAL5083 4.9 18.5 1.0
N E:GLY5184 4.9 26.7 1.0
CG E:ARG5084 4.9 14.1 1.0
N E:GLY5085 4.9 10.8 1.0
C E:ARG5084 5.0 12.8 1.0

Sodium binding site 7 out of 7 in 5k4y

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Sodium binding site 7 out of 7 in the Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Refined to 1.77 Angstroms


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Refined to 1.77 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na6405

b:27.8
occ:1.00
 CL F:CL6404 2.7 27.2 1.0
O F:HOH6699 2.8 33.6 1.0
N F:ARG6084 3.1 14.1 1.0
O F:HOH6630 3.2 14.8 1.0
CB F:ARG6084 3.5 18.2 1.0
N F:VAL6083 3.6 16.6 1.0
C F:MET6081 3.8 12.9 1.0
CB F:VAL6083 3.9 18.1 1.0
O F:MET6081 3.9 13.7 1.0
CA F:ARG6084 3.9 15.8 1.0
CB F:MET6081 4.0 13.5 1.0
CA F:VAL6083 4.0 15.5 1.0
C F:VAL6083 4.0 15.8 1.0
N F:SER6082 4.1 12.6 1.0
CA F:MET6081 4.1 12.1 1.0
N F:MET6081 4.3 11.5 1.0
C F:SER6082 4.4 15.0 1.0
CA F:GLY6184 4.7 16.0 1.0
CG2 F:VAL6083 4.7 17.6 1.0
CA F:SER6082 4.8 13.3 0.3
CA F:SER6082 4.8 13.2 0.7
CG1 F:VAL6083 4.9 20.9 1.0
N F:GLY6085 4.9 13.2 1.0
CG F:ARG6084 4.9 23.6 1.0
C F:ARG6084 5.0 15.7 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 22:02:42 2024

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