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Chlorine 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:

Sodium (Na) 7 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 7 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 5k4y

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl1403

b:34.5
occ:1.00
 OG A:SER1082 2.5 18.6 0.5
O A:HOH1503 2.8 21.1 1.0
NA A:NA1404 2.9 27.4 1.0
N A:ALA1185 3.0 19.9 1.0
N A:VAL1083 3.1 14.9 1.0
N A:SER1082 3.4 13.7 1.0
CA A:GLY1184 3.5 26.3 1.0
CG2 A:VAL1083 3.6 15.0 1.0
CB A:SER1082 3.6 15.8 0.5
CB A:SER1082 3.7 14.6 0.5
C A:GLY1184 3.7 22.1 1.0
CB A:VAL1083 3.8 14.5 1.0
CA A:SER1082 3.8 14.4 0.5
CA A:SER1082 3.8 13.8 0.5
CB A:ALA1185 3.9 22.3 1.0
C A:SER1082 4.0 14.2 1.0
CA A:ALA1185 4.1 22.3 1.0
CA A:VAL1083 4.1 14.1 1.0
C A:MET1081 4.2 11.9 1.0
CB A:MET1081 4.3 14.3 1.0
OG A:SER1082 4.5 15.4 0.5
O A:HOH1674 4.6 23.9 1.0
OXT A:ACT1402 4.7 19.7 1.0
N A:GLY1184 4.8 24.2 1.0
CA A:MET1081 4.9 11.2 1.0
N A:ARG1084 4.9 13.9 1.0
O A:MET1081 4.9 11.3 1.0

Chlorine binding site 2 out of 7 in 5k4y

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl2403

b:35.1
occ:1.00
 NA B:NA2404 2.7 30.3 1.0
N B:ALA2185 3.1 20.2 1.0
O B:HOH2510 3.1 19.4 1.0
OG B:SER2082 3.1 16.7 0.5
N B:VAL2083 3.2 16.0 1.0
CA B:GLY2184 3.3 23.9 1.0
N B:SER2082 3.5 12.4 1.0
C B:GLY2184 3.7 24.0 1.0
CG2 B:VAL2083 3.8 21.1 1.0
CB B:VAL2083 3.9 18.7 1.0
CB B:ALA2185 3.9 25.3 1.0
CB B:SER2082 4.0 13.8 0.5
CA B:SER2082 4.0 12.9 0.5
CA B:SER2082 4.0 13.7 0.5
C B:SER2082 4.1 15.2 1.0
CA B:VAL2083 4.1 16.3 1.0
CA B:ALA2185 4.1 26.2 1.0
CB B:SER2082 4.1 15.4 0.5
CB B:MET2081 4.2 15.2 1.0
C B:MET2081 4.2 12.5 1.0
O B:HOH2543 4.3 38.6 1.0
O B:HOH2671 4.5 24.3 1.0
N B:GLY2184 4.6 23.6 1.0
OG B:SER2082 4.7 12.1 0.5
CA B:MET2081 4.7 12.4 1.0
N B:ARG2084 4.8 14.5 1.0
OXT B:ACT2402 4.9 20.8 1.0
O B:MET2081 4.9 12.2 1.0
O B:GLY2184 5.0 24.2 1.0

Chlorine binding site 3 out of 7 in 5k4y

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl3403

b:21.1
occ:1.00
 NA C:NA3404 2.8 24.1 1.0
O C:HOH3642 3.2 14.7 1.0
N C:ALA3185 3.2 13.7 1.0
N C:VAL3083 3.5 14.1 1.0
N C:SER3082 3.6 11.8 1.0
CA C:GLY3184 3.6 15.2 1.0
CB C:MET3081 3.9 12.8 1.0
CG2 C:VAL3083 3.9 14.4 1.0
C C:GLY3184 3.9 13.9 1.0
CB C:ALA3185 4.0 15.7 1.0
CB C:VAL3083 4.0 14.7 1.0
CA C:ALA3185 4.2 14.6 1.0
C C:MET3081 4.2 11.6 1.0
CB C:SER3082 4.2 15.3 1.0
CA C:SER3082 4.2 13.6 1.0
O C:HOH3730 4.4 29.5 1.0
C C:SER3082 4.4 12.7 1.0
CA C:VAL3083 4.4 13.1 1.0
O C:HOH3696 4.4 25.8 1.0
CA C:MET3081 4.7 11.4 1.0
CE C:MET3081 4.7 19.3 1.0
OG C:SER3082 4.8 23.2 1.0
N C:GLY3184 4.9 15.8 1.0
O C:MET3081 4.9 10.6 1.0
N C:ARG3084 4.9 13.4 1.0
CH3 C:ACT3402 5.0 12.2 1.0

Chlorine binding site 4 out of 7 in 5k4y

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl4403

b:32.2
occ:1.00
 NA D:NA4405 2.7 29.1 1.0
O D:HOH4524 3.1 19.5 1.0
N D:ALA4185 3.2 17.7 1.0
CA D:GLY4184 3.4 19.3 1.0
OG D:SER4082 3.5 12.1 0.5
N D:VAL4083 3.5 14.2 1.0
N D:SER4082 3.6 12.3 1.0
C D:GLY4184 3.8 19.2 1.0
CG2 D:VAL4083 3.9 16.5 1.0
CB D:ALA4185 3.9 18.9 1.0
CB D:MET4081 3.9 12.2 1.0
CB D:VAL4083 4.0 17.3 1.0
CA D:ALA4185 4.2 20.4 1.0
C D:MET4081 4.2 12.4 1.0
CA D:SER4082 4.3 13.4 0.5
CB D:SER4082 4.3 13.7 0.5
CA D:SER4082 4.3 13.0 0.5
CA D:VAL4083 4.3 14.7 1.0
C D:SER4082 4.4 14.0 1.0
O D:HOH4662 4.4 26.2 1.0
CB D:SER4082 4.4 12.9 0.5
CA D:MET4081 4.6 11.7 1.0
N D:GLY4184 4.7 18.4 1.0
O D:HOH4503 4.8 43.5 1.0
N D:ARG4084 4.9 13.7 1.0
CE D:MET4081 4.9 19.1 1.0
O D:MET4081 4.9 11.7 1.0
OG D:SER4082 4.9 13.4 0.5
O D:GLY4183 5.0 15.0 0.5
OXT D:ACT4402 5.0 19.2 1.0

Chlorine binding site 5 out of 7 in 5k4y

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl4404

b:43.1
occ:1.00
 NA D:NA4406 2.6 31.3 1.0
O D:HOH4676 2.7 25.5 1.0
O D:GLY4184 2.8 17.9 1.0
O D:HOH4671 3.1 16.9 1.0
CG D:PRO4205 3.4 18.8 1.0
O D:HOH4538 3.6 27.6 1.0
O D:GLY4183 3.7 15.0 0.5
O D:GLY4183 3.7 20.2 0.5
CB D:ALA4273 3.7 15.0 1.0
C D:GLY4184 3.8 19.2 1.0
C D:GLY4183 3.9 16.1 0.5
O D:HOH4641 4.0 33.2 1.0
C D:GLY4183 4.1 19.9 0.5
CA D:GLY4183 4.2 15.5 0.5
CB D:PRO4205 4.3 17.6 1.0
CA D:ALA4185 4.5 20.4 1.0
N D:GLY4184 4.5 18.4 1.0
C D:ALA4185 4.6 20.9 1.0
N D:ALA4185 4.6 17.7 1.0
CD D:PRO4205 4.6 19.8 1.0
O D:ALA4185 4.6 24.9 1.0
N D:TYR4188 4.6 19.4 1.0
O D:HOH4720 4.7 22.6 1.0
CA D:GLY4184 4.7 19.3 1.0
O D:GLY4182 4.8 16.3 0.5
CA D:GLY4183 5.0 21.2 0.5

Chlorine binding site 6 out of 7 in 5k4y

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl5403

b:44.1
occ:1.00
 NA E:NA5404 2.9 32.2 1.0
N E:ALA5185 3.0 23.8 1.0
O E:HOH5512 3.0 22.3 1.0
OG E:SER5082 3.2 19.5 0.7
CA E:GLY5184 3.3 27.5 1.0
N E:VAL5083 3.5 13.5 1.0
N E:SER5082 3.6 13.0 1.0
C E:GLY5184 3.7 26.4 1.0
CB E:ALA5185 3.7 24.8 1.0
CA E:ALA5185 4.0 25.4 1.0
CG2 E:VAL5083 4.0 15.8 1.0
CB E:MET5081 4.0 14.4 1.0
O E:HOH5545 4.0 37.1 1.0
CB E:VAL5083 4.1 15.6 1.0
CA E:SER5082 4.2 13.3 0.7
C E:MET5081 4.3 11.6 1.0
CB E:SER5082 4.3 15.5 0.7
CA E:SER5082 4.3 12.3 0.3
CB E:SER5082 4.4 12.3 0.3
C E:SER5082 4.4 13.0 1.0
CA E:VAL5083 4.4 14.3 1.0
OG E:SER5082 4.6 12.0 0.3
N E:GLY5184 4.6 26.7 1.0
O E:ACT5402 4.7 19.8 1.0
CA E:MET5081 4.7 11.4 1.0
CE E:MET5081 4.8 21.3 1.0
OD1 E:ASP5187 4.8 46.2 1.0
O E:GLY5184 4.9 29.6 1.0

Chlorine binding site 7 out of 7 in 5k4y

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl6404

b:27.2
occ:1.00
 NA F:NA6405 2.7 27.8 1.0
O F:HOH6555 3.2 16.7 1.0
N F:ALA6185 3.2 15.1 1.0
CA F:GLY6184 3.5 16.0 1.0
OG F:SER6082 3.5 15.8 0.7
N F:VAL6083 3.6 16.6 1.0
N F:SER6082 3.7 12.6 1.0
CB F:MET6081 3.8 13.5 1.0
C F:GLY6184 3.9 14.4 1.0
CG2 F:VAL6083 4.0 17.6 1.0
CB F:ALA6185 4.0 16.6 1.0
CB F:VAL6083 4.0 18.1 1.0
O F:HOH6634 4.2 28.6 1.0
O F:HOH6699 4.2 33.6 1.0
C F:MET6081 4.2 12.9 1.0
CA F:ALA6185 4.2 16.3 1.0
CB F:SER6082 4.3 13.4 0.3
CA F:SER6082 4.3 13.3 0.3
CA F:SER6082 4.3 13.2 0.7
CA F:VAL6083 4.4 15.5 1.0
C F:SER6082 4.4 15.0 1.0
CB F:SER6082 4.5 14.0 0.7
CA F:MET6081 4.6 12.1 1.0
CE F:MET6081 4.6 17.8 1.0
N F:GLY6184 4.8 17.2 1.0
OG F:SER6082 4.9 13.0 0.3
O F:MET6081 4.9 13.7 1.0
N F:ARG6084 4.9 14.1 1.0
CH3 F:ACT6403 5.0 13.6 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: Fri Jul 26 10:26:33 2024

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