Potassium in PDB 8tkb: Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp

Protein crystallography data

The structure of Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp, PDB code: 8tkb was solved by A.Jacewicz, S.Dantuluri, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.14 / 1.71
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.937, 43.665, 122.861, 90, 90, 90
R / Rfree (%) 18.5 / 20.9

Other elements in 8tkb:

The structure of Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp also contains other interesting chemical elements:

Sodium (Na) 1 atom
Chlorine (Cl) 7 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp (pdb code 8tkb). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp, PDB code: 8tkb:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 8tkb

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Potassium binding site 1 out of 4 in the Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K203

b:23.7
occ:0.41
 O A:GLY28 2.8 25.2 1.0
O A:LEU13 2.8 24.9 1.0
N A:ALA72 3.0 24.0 1.0
NE2 A:HIS76 3.1 25.6 1.0
CD2 A:HIS76 3.4 27.0 1.0
OH A:TYR78 3.5 26.0 1.0
CB A:ARG71 3.6 24.8 1.0
C A:LEU13 3.6 23.1 1.0
CB A:LEU13 3.6 22.5 1.0
CA A:ARG71 3.6 21.7 1.0
C A:GLY28 3.7 24.6 1.0
O A:ALA72 3.7 24.1 1.0
CB A:ALA72 3.8 23.4 1.0
C A:ARG71 3.8 27.5 1.0
CA A:ALA72 3.9 22.9 1.0
CA A:GLY28 3.9 24.6 1.0
CA A:LEU13 4.0 21.5 1.0
C A:ALA72 4.3 26.1 1.0
CE1 A:HIS76 4.3 23.4 1.0
CD2 A:LEU13 4.3 21.3 1.0
CG A:LEU13 4.5 23.7 1.0
N A:ARG14 4.6 23.7 1.0
CZ A:TYR78 4.7 26.5 1.0
CG A:HIS76 4.7 25.7 1.0
CG A:ARG71 4.7 25.4 1.0
N A:PHE29 4.9 24.8 1.0

Potassium binding site 2 out of 4 in 8tkb

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Potassium binding site 2 out of 4 in the Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K204

b:32.8
occ:0.49
 O1P A:AMP201 2.6 34.5 1.0
O A:HOH323 2.7 31.0 1.0
N A:HIS119 2.9 24.4 1.0
CE1 A:HIS95 3.4 31.6 1.0
O A:HOH312 3.5 32.6 1.0
O A:HOH374 3.6 43.1 1.0
CA A:VAL118 3.7 24.8 1.0
C A:VAL118 3.8 30.6 1.0
ND1 A:HIS119 3.8 33.5 1.0
P A:AMP201 3.8 30.2 1.0
CA A:HIS119 3.9 25.5 1.0
CG1 A:VAL118 3.9 30.1 1.0
CB A:HIS119 3.9 26.7 1.0
C5' A:AMP201 3.9 25.7 1.0
O A:HIS119 3.9 27.4 1.0
O5' A:AMP201 3.9 29.0 1.0
ND1 A:HIS95 4.1 25.4 1.0
CG A:HIS119 4.3 26.3 1.0
CB A:VAL118 4.3 29.6 1.0
C A:HIS119 4.4 28.2 1.0
C3' A:AMP201 4.4 32.0 1.0
NE2 A:HIS95 4.4 28.5 1.0
O A:TYR117 4.4 32.7 1.0
C2' A:AMP201 4.4 33.2 1.0
O2P A:AMP201 4.6 32.9 1.0
C4' A:AMP201 4.7 32.0 1.0
CG2 A:VAL118 4.8 33.8 1.0
N A:VAL118 4.8 27.8 1.0
CG2 A:ILE110 4.9 27.1 1.0
CE1 A:HIS119 5.0 36.0 1.0
O A:VAL118 5.0 29.7 1.0

Potassium binding site 3 out of 4 in 8tkb

Go back to Potassium Binding Sites List in 8tkb
Potassium binding site 3 out of 4 in the Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K205

b:32.1
occ:0.52
 O A:VAL55 2.9 24.7 1.0
N A:TYR63 2.9 25.1 1.0
O A:TYR63 2.9 25.0 1.0
C A:GLY61 3.4 28.2 1.0
N A:ARG62 3.4 22.1 1.0
CA A:TYR63 3.5 24.2 1.0
C A:TYR63 3.5 26.1 1.0
CA A:GLY61 3.5 25.4 1.0
CB A:TYR63 3.6 20.1 1.0
CB A:ASP58 3.6 23.9 1.0
O A:HOH319 3.6 35.4 1.0
C A:VAL55 3.7 23.0 1.0
CG1 A:VAL55 3.8 26.4 1.0
CA A:VAL55 3.9 22.1 1.0
C A:ARG62 4.0 28.8 1.0
O A:GLY61 4.0 26.2 1.0
CD2 A:TYR63 4.0 22.4 1.0
CG A:TYR63 4.2 20.4 1.0
CA A:ARG62 4.2 26.6 1.0
CG A:ASP58 4.2 30.6 1.0
OD1 A:ASP58 4.3 27.1 1.0
N A:GLY61 4.3 29.7 1.0
CB A:VAL55 4.5 23.0 1.0
CA A:ASP58 4.7 27.9 1.0
O A:ASP58 4.7 35.1 1.0
N A:ASP58 4.8 28.9 1.0
CB A:ARG62 4.8 24.0 1.0
N A:GLU64 4.8 24.8 1.0
NH2 A:ARG73 4.8 23.3 0.5
O A:ILE54 4.9 24.4 1.0
NE A:ARG73 4.9 29.3 0.5

Potassium binding site 4 out of 4 in 8tkb

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Potassium binding site 4 out of 4 in the Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K206

b:59.4
occ:0.89
 O A:HOH340 2.8 37.8 1.0
CB A:MET106 3.9 35.9 1.0
CG A:MET106 4.3 46.9 1.0
CA A:LYS103 4.6 30.1 1.0
O A:LYS103 4.8 36.8 1.0
CG A:LYS103 4.8 35.9 1.0
O A:HOH315 5.0 46.2 1.0

Reference:

A.Jacewicz, S.Dantuluri, S.Shuman. Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp To Be Published.
Page generated: Tue Aug 13 01:00:07 2024

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