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Potassium in PDB 1vq6: The Structure of C-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of The Structure of C-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vq6 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 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 212.050, 300.187, 573.987, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 23.3

Other elements in 1vq6:

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

Magnesium (Mg) 117 atoms
Cadmium (Cd) 5 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 86 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the The Structure of C-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1vq6). 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 C-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vq6:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 1vq6

Go back to Potassium Binding Sites List in 1vq6
Potassium binding site 1 out of 2 in the The Structure of C-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 C-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:70.4
occ:1.00
O6 0:G2482 2.6 46.1 1.0
O6 0:G2102 2.6 44.2 1.0
N7 0:G2482 3.1 45.0 1.0
O2 0:C2536 3.1 40.4 1.0
C6 0:G2482 3.3 45.5 1.0
O4' 0:C2536 3.3 44.2 1.0
N7 0:G2102 3.4 47.1 1.0
C6 0:G2102 3.4 45.5 1.0
C5 0:G2482 3.5 46.5 1.0
C2 0:C2536 3.6 41.1 1.0
C1' 0:C2536 3.7 43.8 1.0
C5 0:G2102 3.7 47.0 1.0
N1 0:C2536 3.9 42.5 1.0
N6 0:A2486 3.9 46.5 1.0
C4' 0:C2536 4.2 41.8 1.0
O2 0:U2535 4.3 54.2 1.0
C8 0:G2482 4.3 45.6 1.0
N3 0:C2536 4.5 41.1 1.0
C8 0:G2102 4.6 49.1 1.0
C2 0:U2535 4.6 51.6 1.0
N1 0:G2482 4.6 46.5 1.0
OP1 0:U2539 4.7 48.5 1.0
N1 0:G2102 4.7 44.4 1.0
C2' 0:U2535 4.7 50.0 1.0
C5' 0:C2536 4.7 42.6 1.0
C4 0:G2482 4.8 46.8 1.0
N3 0:U2535 4.9 51.5 1.0
C6 0:C2536 5.0 42.9 1.0

Potassium binding site 2 out of 2 in 1vq6

Go back to Potassium Binding Sites List in 1vq6
Potassium binding site 2 out of 2 in the The Structure of C-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 C-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:47.5
occ:1.00
O 0:HOH9335 2.8 30.3 1.0
O4 0:U163 2.9 37.7 1.0
O 0:HOH9435 2.9 32.3 1.0
O4 0:U172 3.0 43.7 1.0
O 0:HOH9470 3.0 27.4 1.0
O 0:HOH5207 3.0 59.5 1.0
OP2 0:C162 3.2 32.8 1.0
O 0:HOH7998 3.5 32.6 1.0
CD M:ARG82 3.7 38.3 1.0
C4 0:U172 3.8 44.1 1.0
N3 0:U172 3.9 43.6 1.0
C4 0:U163 4.0 37.1 1.0
O 0:HOH9647 4.0 42.0 1.0
O 0:HOH7997 4.1 42.7 1.0
N4 0:C171 4.3 43.1 1.0
O6 0:G164 4.4 40.5 1.0
P 0:C162 4.4 31.4 1.0
OP2 0:A169 4.5 36.1 1.0
C5 0:U163 4.5 39.6 1.0
NE M:ARG82 4.6 39.2 1.0
OP1 0:C162 4.8 34.6 1.0
CG M:ARG82 4.8 39.0 1.0
CB M:ARG82 4.8 37.7 1.0
N3 0:C173 4.9 35.7 1.0
OP1 0:A169 4.9 36.3 1.0
MG 0:MG8054 4.9 35.5 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 23:03:09 2020

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