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Potassium in PDB 3cma: The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cma was solved by M.Simonovic, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.79 / 2.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.316, 297.905, 573.138, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 24.5

Other elements in 3cma:

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

Strontium (Sr) 107 atoms
Magnesium (Mg) 93 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 Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 3cma). 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 Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cma:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 3cma

Go back to Potassium Binding Sites List in 3cma
Potassium binding site 1 out of 2 in the The Structure of Cca 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 Cca 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:K8401

b:66.1
occ:1.00
O6 0:G2102 3.2 41.5 1.0
O6 0:G2482 3.2 28.9 1.0
O4' 0:C2536 3.3 34.2 1.0
N7 0:G2102 3.4 42.5 1.0
N7 0:G2482 3.4 29.3 1.0
O2 0:C2536 3.5 30.4 1.0
O2 0:U2535 3.9 38.5 1.0
C6 0:G2102 3.9 42.4 1.0
C4' 0:C2536 3.9 34.3 1.0
C1' 0:C2536 3.9 33.3 1.0
C6 0:G2482 4.0 28.2 1.0
C5 0:G2102 4.0 42.6 1.0
C5 0:G2482 4.1 29.3 1.0
N6 0:A2486 4.1 36.9 1.0
C2 0:C2536 4.1 30.6 1.0
OP1 0:U2539 4.2 44.7 1.0
N1 0:C2536 4.4 31.8 1.0
C5' 0:C2536 4.4 35.2 1.0
C2 0:U2535 4.4 39.5 1.0
C8 0:G2102 4.6 41.4 1.0
C8 0:G2482 4.6 29.6 1.0
C2' 0:U2535 4.7 42.1 1.0
N3 0:U2535 4.8 39.5 1.0
O4' 0:A2538 5.0 47.1 1.0
O2' 0:U2535 5.0 41.1 1.0

Potassium binding site 2 out of 2 in 3cma

Go back to Potassium Binding Sites List in 3cma
Potassium binding site 2 out of 2 in the The Structure of Cca 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 Cca 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:K8402

b:81.4
occ:1.00
O4 0:U172 3.2 34.7 1.0
O4 0:U163 3.2 34.6 1.0
O 0:HOH2936 3.3 24.0 1.0
OP2 0:C162 3.3 23.9 1.0
O 0:HOH3065 3.3 27.5 1.0
CD M:ARG82 3.5 57.2 1.0
O M:HOH8898 3.5 53.6 1.0
O 0:HOH3031 3.5 48.0 1.0
O 0:HOH9613 3.8 61.1 1.0
O 0:HOH9612 3.9 35.4 1.0
NE M:ARG82 4.2 56.9 1.0
O 0:HOH3241 4.2 78.0 1.0
C4 0:U172 4.2 32.7 1.0
C4 0:U163 4.2 32.8 1.0
N3 0:U172 4.4 31.3 1.0
P 0:C162 4.5 20.6 1.0
OP1 0:A169 4.6 21.1 1.0
C5 0:U163 4.6 32.1 1.0
CG M:ARG82 4.7 58.9 1.0
N4 0:C171 4.7 30.4 1.0
OP2 0:A169 4.7 22.0 1.0
CB M:ARG82 4.8 59.9 1.0
OP1 0:C162 4.8 22.3 1.0
O6 0:G164 5.0 19.5 1.0

Reference:

M.Simonovic, T.A.Steitz. Peptidyl-Cca Deacylation on the Ribosome Promoted By Induced Fit and the O3'-Hydroxyl Group of A76 of the Unacylated A-Site Trna. Rna V. 14 2372 2008.
ISSN: ISSN 1355-8382
PubMed: 18818369
DOI: 10.1261/RNA.1118908
Page generated: Sun Dec 13 23:17:10 2020

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