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Potassium in PDB 1vqp: The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqp 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 / 2.25
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.610, 298.189, 574.980, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 24.7

Other elements in 1vqp:

The structure of The Structure of the Transition State Analogue "Rap" 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 the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1vqp). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqp:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 1vqp

Go back to Potassium Binding Sites List in 1vqp
Potassium binding site 1 out of 3 in the The Structure of the Transition State Analogue "Rap" 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 the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:K9001

b:78.5
occ:1.00
O6 0:G2102 2.8 38.2 1.0
O6 0:G2482 2.8 37.5 1.0
N7 0:G2482 2.9 35.9 1.0
O4' 0:C2536 3.0 37.2 1.0
O2 0:C2536 3.1 38.7 1.0
N7 0:G2102 3.4 40.5 1.0
C1' 0:C2536 3.4 36.3 1.0
C6 0:G2482 3.4 35.0 1.0
C5 0:G2482 3.4 36.4 1.0
C2 0:C2536 3.5 38.1 1.0
C6 0:G2102 3.5 39.6 1.0
N1 0:C2536 3.6 37.2 1.0
C5 0:G2102 3.8 40.6 1.0
C4' 0:C2536 3.8 38.5 1.0
N6 0:A2486 4.0 41.0 1.0
C8 0:G2482 4.1 36.0 1.0
N3 0:C2536 4.3 38.9 1.0
C5' 0:C2536 4.4 37.2 1.0
O2 0:U2535 4.5 48.7 1.0
C8 0:G2102 4.5 42.7 1.0
C6 0:C2536 4.7 36.2 1.0
C2 0:U2535 4.7 43.1 1.0
OP1 0:U2539 4.7 48.3 1.0
C4 0:G2482 4.8 36.2 1.0
N1 0:G2482 4.8 34.6 1.0
C2' 0:U2535 4.8 41.8 1.0
N1 0:G2102 4.8 40.5 1.0
C2' 0:C2536 4.8 37.4 1.0
O5' 0:C2536 5.0 40.3 1.0

Potassium binding site 2 out of 3 in 1vqp

Go back to Potassium Binding Sites List in 1vqp
Potassium binding site 2 out of 3 in the The Structure of the Transition State Analogue "Rap" 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 the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:K9002

b:61.0
occ:1.00
O 0:HOH9642 2.8 29.2 1.0
O4 0:U172 2.8 32.5 1.0
O4 0:U163 2.9 30.3 1.0
O 0:HOH9737 3.0 37.9 1.0
O 0:HOH9773 3.1 31.0 1.0
CD M:ARG82 3.2 47.0 1.0
OP2 0:C162 3.2 25.8 1.0
O 0:HOH8369 3.3 46.9 1.0
O 0:HOH5510 3.3 55.2 1.0
C4 0:U172 3.7 33.2 1.0
N3 0:U172 3.9 33.8 1.0
O 0:HOH8368 3.9 36.0 1.0
O 0:HOH9950 3.9 36.5 1.0
NE M:ARG82 4.0 49.4 1.0
C4 0:U163 4.0 29.4 1.0
N4 0:C171 4.4 35.4 1.0
OP2 0:A169 4.4 28.1 1.0
CG M:ARG82 4.5 49.5 1.0
P 0:C162 4.5 28.2 1.0
C5 0:U163 4.6 28.8 1.0
O6 0:G164 4.6 34.0 1.0
CB M:ARG82 4.6 49.3 1.0
MG 0:MG8054 4.8 39.3 1.0
OP1 0:C162 4.8 28.1 1.0
OP1 0:A169 4.9 31.8 1.0
N3 0:C173 5.0 31.9 1.0
CZ M:ARG82 5.0 50.8 1.0

Potassium binding site 3 out of 3 in 1vqp

Go back to Potassium Binding Sites List in 1vqp
Potassium binding site 3 out of 3 in the The Structure of the Transition State Analogue "Rap" 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 3 of The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:K9003

b:80.3
occ:1.00
O2' 4:C175 2.7 42.2 1.0
O3' 0:C2104 2.9 41.3 1.0
O3' 4:C175 3.0 47.4 1.0
O2' 0:C2104 3.2 39.6 1.0
OP1 0:C2105 3.5 43.2 1.0
OP2 4:A176 3.6 50.0 1.0
C2' 4:C175 3.8 44.0 1.0
C3' 4:C175 3.8 45.1 1.0
P 0:C2105 3.8 41.5 1.0
C3' 0:C2104 3.9 40.8 1.0
P 4:A176 4.0 47.1 1.0
C4' 4:C175 4.1 45.7 1.0
C2' 0:C2104 4.1 39.8 1.0
C4' 0:C2104 4.1 41.3 1.0
O 0:HOH8310 4.3 75.0 1.0
C5' 0:C2105 4.5 38.9 1.0
N6 0:A2474 4.6 41.1 1.0
O5' 0:C2105 4.6 40.5 1.0
C1' 4:C175 4.7 44.2 1.0
O 4:HOH7915 4.8 49.2 1.0
C4' 4:A176 4.8 49.0 1.0
O4' 4:C175 4.9 46.9 1.0
O4' 4:A176 4.9 48.9 1.0
OP2 0:C2105 5.0 41.4 1.0

Reference:

T.M.Schmeing, K.S.Huang, D.E.Kitchen, S.A.Strobel, T.A.Steitz. Structural Insights Into the Roles of Water and the 2' Hydroxyl of the P Site Trna in the Peptidyl Transferase Reaction. Mol.Cell V. 20 437 2005.
ISSN: ISSN 1097-2765
PubMed: 16285925
DOI: 10.1016/J.MOLCEL.2005.09.006
Page generated: Sun Dec 13 23:04:20 2020

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