Atomistry » Potassium » PDB 1u1g-1w29 » 1vqn
Atomistry »
  Potassium »
    PDB 1u1g-1w29 »
      1vqn »

Potassium in PDB 1vqn: The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqn was solved by T.M.Schmeing, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.721, 298.782, 575.272, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 24.8

Other elements in 1vqn:

The structure of The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Strontium (Sr) 114 atoms
Magnesium (Mg) 94 atoms
Cadmium (Cd) 5 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 75 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1vqn). 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqn:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 1vqn

Go back to Potassium Binding Sites List in 1vqn
Potassium binding site 1 out of 2 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:K9001

b:74.5
occ:1.00
O6 0:G2482 2.8 37.5 1.0
O6 0:G2102 2.9 47.7 1.0
N7 0:G2482 3.0 38.1 1.0
O4' 0:C2536 3.0 40.0 1.0
O2 0:C2536 3.1 38.8 1.0
N7 0:G2102 3.4 46.7 1.0
C6 0:G2482 3.5 37.1 1.0
C1' 0:C2536 3.5 38.7 1.0
C5 0:G2482 3.5 38.6 1.0
C2 0:C2536 3.6 38.4 1.0
C6 0:G2102 3.6 45.6 1.0
N1 0:C2536 3.8 39.1 1.0
C5 0:G2102 3.8 45.1 1.0
C4' 0:C2536 3.8 40.8 1.0
N6 0:A2486 3.9 44.0 1.0
C8 0:G2482 4.2 38.8 1.0
O2 0:U2535 4.2 52.1 1.0
C5' 0:C2536 4.4 40.6 1.0
N3 0:C2536 4.5 39.7 1.0
C2 0:U2535 4.5 50.0 1.0
C8 0:G2102 4.6 46.4 1.0
C2' 0:U2535 4.6 47.1 1.0
OP1 0:U2539 4.7 55.0 1.0
C6 0:C2536 4.8 37.7 1.0
N1 0:G2482 4.8 39.4 1.0
N1 0:G2102 4.9 46.0 1.0
C4 0:G2482 4.9 38.7 1.0
N3 0:U2535 4.9 48.0 1.0
C2' 0:C2536 5.0 39.6 1.0
O2' 0:U2535 5.0 46.4 1.0
O5' 0:C2536 5.0 44.2 1.0

Potassium binding site 2 out of 2 in 1vqn

Go back to Potassium Binding Sites List in 1vqn
Potassium binding site 2 out of 2 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:K9002

b:88.3
occ:1.00
O4 0:U172 2.7 38.1 1.0
O M:HOH9324 2.9 37.2 1.0
CD M:ARG82 2.9 74.3 1.0
O 0:HOH9642 2.9 38.0 1.0
O 0:HOH9739 3.0 42.0 1.0
O4 0:U163 3.2 35.3 1.0
O 0:HOH5482 3.4 76.8 1.0
NE M:ARG82 3.4 73.8 1.0
OP2 0:C162 3.5 30.2 1.0
C4 0:U172 3.7 35.7 1.0
O 0:HOH8341 3.8 99.5 1.0
N3 0:U172 3.9 36.3 1.0
O 0:HOH9947 4.0 45.2 1.0
O 0:HOH8340 4.1 56.5 1.0
CG M:ARG82 4.2 78.0 1.0
C4 0:U163 4.3 34.7 1.0
N4 0:C171 4.4 40.0 1.0
CZ M:ARG82 4.5 76.1 1.0
OP2 0:A169 4.6 35.5 1.0
CB M:ARG82 4.6 80.3 1.0
O6 0:G164 4.7 33.1 1.0
P 0:C162 4.7 30.9 1.0
OP1 0:A169 4.8 38.1 1.0
C5 0:U163 4.9 34.2 1.0
NH1 M:ARG82 5.0 75.8 1.0

Reference:

T.M.Schmeing, K.S.Huang, S.A.Strobel, T.A.Steitz. An Induced-Fit Mechanism to Promote Peptide Bond Formation and Exclude Hydrolysis of Peptidyl-Trna. Nature V. 438 520 2005.
ISSN: ISSN 0028-0836
PubMed: 16306996
DOI: 10.1038/NATURE04152
Page generated: Sun Dec 13 23:03:51 2020

Last articles

Zn in 7L0B
Zn in 7KZZ
Zn in 7KZL
Zn in 7L3O
Zn in 7L52
Zn in 7L6T
Zn in 7KZ7
Zn in 7L6R
Zn in 7KKM
Zn in 7KKQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy