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Potassium in PDB 2uxd: Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit.

Protein crystallography data

The structure of Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit., PDB code: 2uxd was solved by C.M.Dunham, M.Selmer, S.S.Phelps, A.C.Kelley, T.Suzuki, S.Joseph, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.38 / 3.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 401.903, 401.903, 174.435, 90.00, 90.00, 90.00
R / Rfree (%) 23.8 / 28.2

Other elements in 2uxd:

The structure of Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit. also contains other interesting chemical elements:

Magnesium (Mg) 70 atoms
Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit. (pdb code 2uxd). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit., PDB code: 2uxd:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 2uxd

Go back to Potassium Binding Sites List in 2uxd
Potassium binding site 1 out of 8 in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K3072

b:85.0
occ:0.91
 O4 A:U304 3.3 73.2 1.0
O6 A:G293 3.4 70.3 1.0
O6 A:G305 3.5 70.8 1.0
N6 A:A303 4.2 58.8 1.0
C6 A:G305 4.2 70.8 1.0
C4 A:U304 4.3 73.2 1.0
C6 A:G293 4.4 70.3 1.0
N7 A:G293 4.4 70.3 1.0
N1 A:G305 4.4 70.8 1.0
N3 A:U304 4.4 73.2 1.0
OP2 A:G292 4.5 63.2 1.0
O4 A:U294 4.6 72.3 1.0
C5 A:G293 4.8 70.3 1.0
OP1 A:G292 4.8 63.2 1.0

Potassium binding site 2 out of 8 in 2uxd

Go back to Potassium Binding Sites List in 2uxd
Potassium binding site 2 out of 8 in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K3073

b:85.0
occ:0.88
 OP1 A:G577 3.6 44.8 1.0
OP2 A:U813 3.7 50.5 1.0
N7 A:G577 4.0 44.8 1.0
OP1 A:U813 4.4 50.5 1.0
P A:U813 4.5 56.8 1.0
C8 A:G577 4.7 44.8 1.0

Potassium binding site 3 out of 8 in 2uxd

Go back to Potassium Binding Sites List in 2uxd
Potassium binding site 3 out of 8 in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K3074

b:85.0
occ:0.71
 O6 A:G297 3.5 64.9 1.0
O4 A:U296 4.5 65.9 1.0
C6 A:G297 4.7 64.9 1.0

Potassium binding site 4 out of 8 in 2uxd

Go back to Potassium Binding Sites List in 2uxd
Potassium binding site 4 out of 8 in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K3075

b:85.0
occ:0.67
 O6 A:G688 3.6 54.3 1.0
N7 A:G688 3.6 54.3 1.0
O6 A:G700 3.7 64.2 1.0
N1 A:G700 3.9 64.2 1.0
C6 A:G700 4.2 64.2 1.0
C6 A:G688 4.2 54.3 1.0
C5 A:G688 4.3 54.3 1.0
C8 A:G688 4.7 54.3 1.0
C2 A:G700 5.0 64.2 1.0

Potassium binding site 5 out of 8 in 2uxd

Go back to Potassium Binding Sites List in 2uxd
Potassium binding site 5 out of 8 in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K3076

b:85.0
occ:0.92
 N7 A:G247 3.4 62.3 1.0
O6 A:G247 3.9 62.3 1.0
C5 A:G247 4.2 62.3 1.0
N1 A:G278 4.3 72.9 1.0
C8 A:G247 4.3 62.3 1.0
C6 A:G247 4.4 62.3 1.0
N2 A:G278 4.4 72.9 1.0
C2 A:G278 4.9 72.9 1.0

Potassium binding site 6 out of 8 in 2uxd

Go back to Potassium Binding Sites List in 2uxd
Potassium binding site 6 out of 8 in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K3077

b:85.0
occ:0.58
 O4 A:U129 4.1 60.3 1.0
O6 A:G128 4.1 61.4 1.0
O6 A:G231 4.3 65.0 1.0
O6 A:G232 4.4 62.6 1.0
N4 A:C233 4.6 59.8 1.0
N7 A:G231 4.8 65.0 1.0
C6 A:G231 4.9 65.0 1.0
N7 A:G232 5.0 62.6 1.0

Potassium binding site 7 out of 8 in 2uxd

Go back to Potassium Binding Sites List in 2uxd
Potassium binding site 7 out of 8 in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K3078

b:85.0
occ:0.67
 N2 A:G168 4.2 0.2 1.0
C1' A:C169 4.4 91.9 1.0
O4' A:C169 4.5 91.9 1.0
O2 A:C169 4.5 92.1 1.0
O2' A:C169 4.9 91.9 1.0

Potassium binding site 8 out of 8 in 2uxd

Go back to Potassium Binding Sites List in 2uxd
Potassium binding site 8 out of 8 in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Cggg in the Context of the Thermus Thermophilus 30S Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K3079

b:85.0
occ:0.68
 O6 A:G494 3.7 0.9 1.0
O6 A:G492 3.7 0.7 1.0
N7 A:G491 4.5 1.0 1.0
C6 A:G494 4.5 0.9 1.0
OP2 A:A439 4.5 0.5 1.0
O6 A:G491 4.5 1.0 1.0
N7 A:G492 4.6 0.7 1.0
C6 A:G492 4.7 0.7 1.0

Reference:

C.M.Dunham, M.Selmer, S.S.Phelps, A.C.Kelley, T.Suzuki, S.Joseph, V.Ramakrishnan. Structures of Trnas with An Expanded Anticodon Loop in the Decoding Center of the 30S Ribosomal Subunit. Rna V. 13 817 2007.
ISSN: ISSN 1355-8382
PubMed: 17416634
DOI: 10.1261/RNA.367307
Page generated: Mon Aug 12 07:04:20 2024

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