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

Go back to Potassium Binding Sites List in 8tkb
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

Go back to Potassium Binding Sites List in 8tkb
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

Go back to Potassium Binding Sites List in 8tkb
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy