Atomistry » Potassium » PDB 2qyo-2vxy » 2vpl
Atomistry »
  Potassium »
    PDB 2qyo-2vxy »
      2vpl »

Potassium in PDB 2vpl: The Structure of the Complex Between the First Domain of L1 Protein From Thermus Thermophilus and Mrna From Methanococcus Jannaschii

Protein crystallography data

The structure of The Structure of the Complex Between the First Domain of L1 Protein From Thermus Thermophilus and Mrna From Methanococcus Jannaschii, PDB code: 2vpl was solved by V.Kljashtorny, S.Tishchenko, N.Nevskaya, S.Nikonov, M.Garber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.100, 144.350, 56.160, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 27.4

Potassium Binding Sites:

The binding sites of Potassium atom in the The Structure of the Complex Between the First Domain of L1 Protein From Thermus Thermophilus and Mrna From Methanococcus Jannaschii (pdb code 2vpl). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the The Structure of the Complex Between the First Domain of L1 Protein From Thermus Thermophilus and Mrna From Methanococcus Jannaschii, PDB code: 2vpl:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 2vpl

Go back to Potassium Binding Sites List in 2vpl
Potassium binding site 1 out of 2 in the The Structure of the Complex Between the First Domain of L1 Protein From Thermus Thermophilus and Mrna From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of The Structure of the Complex Between the First Domain of L1 Protein From Thermus Thermophilus and Mrna From Methanococcus Jannaschii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1229

b:33.9
occ:0.85
O2 B:U41 2.5 33.0 1.0
O A:THR216 2.8 41.2 1.0
OE1 A:GLU42 2.9 36.5 1.0
OE2 A:GLU42 3.0 59.7 1.0
O2' B:U41 3.0 29.8 1.0
O A:THR217 3.1 28.0 1.0
O4' B:U42 3.3 46.6 1.0
CD A:GLU42 3.3 42.7 1.0
C2' B:U41 3.5 40.8 1.0
C2 B:U41 3.6 46.2 1.0
C1' B:U41 3.8 36.9 1.0
C A:THR217 3.8 26.0 1.0
C A:THR216 3.9 34.6 1.0
C1' B:U42 3.9 31.4 1.0
CG2 A:THR215 4.0 35.3 1.0
CA A:THR217 4.0 23.3 1.0
OG1 A:THR215 4.1 31.6 1.0
N1 B:U41 4.2 25.4 1.0
C4' B:U42 4.4 17.4 1.0
N A:THR217 4.4 28.2 1.0
N1 B:U42 4.4 28.1 1.0
N3 B:G10 4.6 18.4 1.0
C6 B:U42 4.7 18.9 1.0
O A:GLY219 4.7 45.8 1.0
N3 B:U41 4.7 19.8 1.0
CB A:THR215 4.7 35.5 1.0
C2 B:A9 4.7 31.3 1.0
CG A:GLU42 4.8 31.8 1.0
C5' B:U42 4.8 17.9 1.0
N A:MET218 4.8 34.1 1.0
N2 B:G10 5.0 25.9 1.0

Potassium binding site 2 out of 2 in 2vpl

Go back to Potassium Binding Sites List in 2vpl
Potassium binding site 2 out of 2 in the The Structure of the Complex Between the First Domain of L1 Protein From Thermus Thermophilus and Mrna From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of The Structure of the Complex Between the First Domain of L1 Protein From Thermus Thermophilus and Mrna From Methanococcus Jannaschii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1229

b:42.4
occ:0.70
O C:THR216 2.8 29.0 1.0
O2 D:U41 2.8 32.7 1.0
OE2 C:GLU42 2.9 49.9 1.0
O2' D:U41 2.9 35.5 1.0
OE1 C:GLU42 3.2 38.8 1.0
O C:THR217 3.3 35.7 1.0
O4' D:U42 3.3 58.6 1.0
CD C:GLU42 3.3 41.2 1.0
C2' D:U41 3.6 29.4 1.0
C C:THR216 3.8 37.2 1.0
C C:THR217 3.8 34.6 1.0
OG1 C:THR215 3.9 47.1 1.0
C1' D:U42 3.9 33.8 1.0
CA C:THR217 3.9 29.2 1.0
C2 D:U41 3.9 36.0 1.0
C1' D:U41 3.9 27.6 1.0
CG2 C:THR215 4.0 43.1 1.0
N C:THR217 4.3 41.8 1.0
C4' D:U42 4.4 37.0 1.0
N1 D:U41 4.4 28.1 1.0
N1 D:U42 4.5 37.7 1.0
CB C:THR215 4.6 39.5 1.0
N3 D:G10 4.7 27.4 1.0
O C:GLY219 4.7 36.1 1.0
CG C:GLU42 4.8 28.8 1.0
N C:MET218 4.8 30.9 1.0
C6 D:U42 4.8 29.4 1.0
N C:THR216 4.9 24.4 1.0
C5' D:U42 4.9 34.7 1.0
C2 D:A9 5.0 37.2 1.0

Reference:

S.Tishchenko, V.Kljashtorny, O.Kostareva, N.Nevskaya, A.Nikulin, P.Gulak, W.Piendl, M.Garber, S.Nikonov. Domain II of Thermus Thermophilus Ribosomal Protein L1 Hinders Recognition of Its Mrna. J. Mol. Biol. V. 383 301 2008.
ISSN: ESSN 1089-8638
PubMed: 18778715
DOI: 10.1016/J.JMB.2008.08.058
Page generated: Sun Dec 13 23:12:47 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy