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Potassium in PDB 1zho: The Structure of A Ribosomal Protein L1 in Complex with Mrna

Protein crystallography data

The structure of The Structure of A Ribosomal Protein L1 in Complex with Mrna, PDB code: 1zho was solved by N.Nevskaya, S.Tishchenko, S.Volchkov, V.Kljashtorny, E.Nikonova, O.Nikonov, A.Nikulin, C.Kohrer, W.Piendl, R.Zimmermann, P.Stockley, M.Garber, S.Nikonov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.06 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.600, 101.900, 119.600, 90.00, 93.66, 90.00
R / Rfree (%) 21.8 / 28.1

Potassium Binding Sites:

The binding sites of Potassium atom in the The Structure of A Ribosomal Protein L1 in Complex with Mrna (pdb code 1zho). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the The Structure of A Ribosomal Protein L1 in Complex with Mrna, PDB code: 1zho:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 1zho

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Potassium binding site 1 out of 4 in the The Structure of A Ribosomal Protein L1 in Complex with Mrna


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 A Ribosomal Protein L1 in Complex with Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K39

b:42.0
occ:1.00
O C:THR216 2.9 45.3 1.0
O2 D:U30 3.0 45.7 1.0
O C:THR217 3.1 43.3 1.0
O2' D:U30 3.3 38.8 1.0
OE2 C:GLU42 3.3 42.6 1.0
O4' D:U31 3.4 40.9 1.0
CD C:GLU42 3.6 44.9 1.0
C C:THR217 3.6 43.5 1.0
OE1 C:GLU42 3.7 48.7 1.0
CA C:THR217 3.8 42.9 1.0
C C:THR216 3.8 44.4 1.0
CG2 C:THR215 3.8 39.3 1.0
C2' D:U30 3.9 37.9 1.0
C1' D:U30 4.0 38.7 1.0
C1' D:U31 4.0 40.0 1.0
C2 D:U30 4.1 43.9 1.0
N C:THR217 4.2 44.1 1.0
N1 D:U31 4.4 39.6 1.0
N3 D:G10 4.4 39.9 1.0
OG1 C:THR215 4.5 40.8 1.0
C4' D:U31 4.6 40.6 1.0
N1 D:U30 4.6 41.4 1.0
CG C:GLU42 4.6 43.8 1.0
C2 D:A9 4.7 37.9 1.0
NE2 C:HIS44 4.7 45.7 1.0
O C:GLY219 4.7 46.3 1.0
N C:MSE218 4.7 44.9 1.0
C6 D:U31 4.7 37.9 1.0
CB C:THR215 4.8 41.0 1.0
C1' D:G10 4.9 37.9 1.0
N2 D:G10 4.9 42.2 1.0
C2 D:U31 4.9 39.7 1.0
C5' D:U31 4.9 38.3 1.0
O2' D:G10 4.9 36.9 1.0
N C:THR216 5.0 43.5 1.0

Potassium binding site 2 out of 4 in 1zho

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Potassium binding site 2 out of 4 in the The Structure of A Ribosomal Protein L1 in Complex with Mrna


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 A Ribosomal Protein L1 in Complex with Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K39

b:61.1
occ:1.00
O2' H:U30 2.6 42.2 1.0
O G:THR216 2.6 51.4 1.0
O2 H:U30 3.0 45.6 1.0
O G:THR217 3.0 50.6 1.0
O4' H:U31 3.2 45.0 1.0
C2' H:U30 3.4 41.8 1.0
OE1 G:GLU42 3.5 32.5 1.0
C G:THR217 3.5 51.0 1.0
C G:THR216 3.5 48.9 1.0
C1' H:U30 3.6 43.2 1.0
CA G:THR217 3.7 50.6 1.0
OE2 G:GLU42 3.8 32.1 1.0
OG1 G:THR215 3.8 46.4 1.0
CD G:GLU42 3.9 32.4 1.0
N G:THR217 4.0 49.7 1.0
C2 H:U30 4.0 45.7 1.0
C4' H:U31 4.2 44.2 1.0
CG2 G:THR215 4.2 45.4 1.0
C1' H:U31 4.2 45.6 1.0
C5' H:U31 4.2 44.3 1.0
N1 H:U30 4.3 45.2 1.0
O G:GLY219 4.4 51.9 1.0
N G:MSE218 4.5 53.0 1.0
N G:THR216 4.6 45.4 1.0
CB G:THR215 4.6 46.0 1.0
N1 H:U31 4.6 47.8 1.0
C6 H:U31 4.7 48.3 1.0
O4' H:U30 4.7 41.0 1.0
O5' H:U31 4.7 45.2 1.0
CA G:THR216 4.8 46.7 1.0
C3' H:U30 4.8 42.0 1.0
N3 H:G10 4.9 47.2 1.0
N2 H:G10 5.0 46.9 1.0

Potassium binding site 3 out of 4 in 1zho

Go back to Potassium Binding Sites List in 1zho
Potassium binding site 3 out of 4 in the The Structure of A Ribosomal Protein L1 in Complex with Mrna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of The Structure of A Ribosomal Protein L1 in Complex with Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K229

b:33.2
occ:1.00
O A:THR216 2.7 36.1 1.0
O2 B:U30 3.1 37.6 1.0
O2' B:U30 3.1 33.3 1.0
O A:THR217 3.2 38.1 1.0
O4' B:U31 3.3 30.0 1.0
OE2 A:GLU42 3.4 28.7 1.0
OE1 A:GLU42 3.5 34.1 1.0
CD A:GLU42 3.5 31.5 1.0
C A:THR216 3.7 34.1 1.0
C A:THR217 3.7 37.8 1.0
C2' B:U30 3.8 34.3 1.0
OG1 A:THR215 3.9 34.8 1.0
CA A:THR217 3.9 35.6 1.0
C1' B:U31 4.0 30.9 1.0
C1' B:U30 4.0 35.5 1.0
C2 B:U30 4.2 38.0 1.0
CG2 A:THR215 4.2 32.6 1.0
N A:THR217 4.3 34.9 1.0
N1 B:U31 4.4 32.8 1.0
C4' B:U31 4.4 30.8 1.0
CG A:GLU42 4.5 30.0 1.0
N3 B:G10 4.6 36.6 1.0
O A:GLY219 4.6 35.0 1.0
N1 B:U30 4.6 37.4 1.0
CB A:THR215 4.7 33.3 1.0
N A:MSE218 4.7 41.0 1.0
C6 B:U31 4.7 32.9 1.0
N2 B:G10 4.7 37.3 1.0
N A:THR216 4.8 32.2 1.0
C5' B:U31 4.8 31.8 1.0
C2 B:A9 4.9 29.6 1.0
NE2 A:HIS44 4.9 31.9 1.0
CA A:THR216 4.9 33.4 1.0

Potassium binding site 4 out of 4 in 1zho

Go back to Potassium Binding Sites List in 1zho
Potassium binding site 4 out of 4 in the The Structure of A Ribosomal Protein L1 in Complex with Mrna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of The Structure of A Ribosomal Protein L1 in Complex with Mrna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K229

b:66.4
occ:1.00
O2' F:U30 3.0 55.3 1.0
O E:THR216 3.1 58.3 1.0
O E:THR217 3.2 56.5 1.0
O4' F:U31 3.2 49.1 1.0
O2 F:U30 3.2 60.4 1.0
OE1 E:GLU42 3.4 42.9 1.0
OE2 E:GLU42 3.5 45.4 1.0
CD E:GLU42 3.5 44.4 1.0
C E:THR217 3.6 57.9 1.0
CA E:THR217 3.7 57.4 1.0
CG2 E:THR215 3.7 57.4 1.0
C E:THR216 3.8 57.5 1.0
C2' F:U30 3.8 52.6 1.0
C1' F:U30 3.9 54.0 1.0
C1' F:U31 4.0 50.2 1.0
N E:THR217 4.1 57.6 1.0
C2 F:U30 4.3 58.1 1.0
C4' F:U31 4.3 49.3 1.0
N1 F:U31 4.3 52.1 1.0
OG1 E:THR215 4.3 57.9 1.0
CG E:GLU42 4.4 43.9 1.0
C6 F:U31 4.4 51.9 1.0
C5' F:U31 4.5 50.0 1.0
N E:MSE218 4.6 58.9 1.0
N1 F:U30 4.7 56.7 1.0
CB E:THR215 4.7 57.0 1.0
N3 F:G10 4.8 59.5 1.0
O5' F:U31 4.8 51.8 1.0
C2 F:A9 4.9 51.4 1.0
N E:THR216 4.9 55.0 1.0
CA E:THR216 5.0 57.1 1.0

Reference:

N.Nevskaya, S.Tishchenko, S.Volchkov, V.Kljashtorny, E.Nikonova, O.Nikonov, A.Nikulin, C.Kohrer, W.Piendl, R.Zimmermann, P.Stockley, M.Garber, S.Nikonov. New Insights Into the Interaction of Ribosomal Protein L1 with Rna. J.Mol.Biol. V. 355 747 2006.
ISSN: ISSN 0022-2836
PubMed: 16330048
DOI: 10.1016/J.JMB.2005.10.084
Page generated: Mon Aug 12 05:53:51 2024

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