Magnesium 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.

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

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:

Potassium	(K)	8 atoms
Zinc	(Zn)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70;

Binding sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 70 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 70 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 Magnesium with other atoms in the Mg 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:Mg3002 b:85.0 occ:0.75 N7 A:G867 3.5 60.2 1.0 OP2 A:C866 3.7 64.3 1.0 OP2 A:G867 3.7 60.2 1.0 OP1 A:C866 4.0 64.3 1.0 C8 A:G867 4.1 60.2 1.0 P A:C866 4.3 63.8 1.0 O5' A:C866 4.7 63.8 1.0 C5 A:G867 4.7 60.2 1.0

Magnesium binding site 2 out of 70 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 Magnesium with other atoms in the Mg 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:Mg3003 b:85.0 occ:1.00 OP2 A:A1110 2.1 85.7 1.0 O2 A:C1189 2.8 97.3 1.0 P A:A1110 3.3 89.3 1.0 OP1 A:A1110 3.7 85.7 1.0 C2 A:C1189 4.0 97.3 1.0 O5' A:A1110 4.1 89.3 1.0 OP2 A:C1109 4.1 0.9 1.0 OP1 A:C1109 4.3 0.9 1.0 CD2 C:HIS176 4.3 0.1 1.0 N3 A:C1189 4.5 97.3 1.0 O3' A:C1109 4.6 66.5 1.0 N6 A:A1188 4.6 74.9 1.0 P A:C1109 4.6 66.5 1.0 N7 A:A1110 4.7 85.7 1.0 C8 A:A1110 4.9 85.7 1.0

Magnesium binding site 3 out of 70 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 Magnesium with other atoms in the Mg 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:Mg3004 b:85.0 occ:1.00 O6 A:G126 3.0 67.1 1.0 N7 A:G126 3.4 67.1 1.0 C6 A:G126 3.7 67.1 1.0 O6 A:G127 3.8 61.6 1.0 C5 A:G126 3.8 67.1 1.0 O4 A:U125 3.9 53.1 1.0 N7 A:G127 4.3 61.6 1.0 C4 A:U125 4.3 53.1 1.0 C8 A:G126 4.5 67.1 1.0 C6 A:G127 4.5 61.6 1.0 C5 A:U125 4.6 53.1 1.0 C5 A:G127 4.7 61.6 1.0 N1 A:G126 5.0 67.1 1.0

Magnesium binding site 4 out of 70 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 Magnesium with other atoms in the Mg 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:Mg3005 b:85.0 occ:0.94 OP1 A:C624 3.3 89.5 1.0 OP1 A:G610 3.7 69.9 1.0 O3' A:A609 3.7 63.9 1.0 O2' A:A609 3.9 63.9 1.0 OP2 A:G625 4.2 77.2 1.0 P A:G610 4.4 80.9 1.0 P A:C624 4.4 74.4 1.0 O5' A:C624 4.7 74.4 1.0 C3' A:A609 4.8 63.9 1.0 O3' A:C624 4.8 74.4 1.0 OP2 A:C624 4.8 89.5 1.0 C5' A:G610 4.9 80.9 1.0 C5' A:C624 4.9 74.4 1.0 P A:G625 4.9 69.2 1.0 C2' A:A609 4.9 63.9 1.0

Magnesium binding site 5 out of 70 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 Magnesium with other atoms in the Mg 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:Mg3006 b:85.0 occ:1.00 OP2 A:C970 2.1 92.6 1.0 P A:C970 2.9 78.6 1.0 OP1 A:C970 3.0 92.6 1.0 O3' A:A969 3.7 68.1 1.0 O5' A:A969 3.8 68.1 1.0 OP2 A:A969 3.8 82.4 1.0 O5' A:C970 4.3 78.6 1.0 C5' A:A968 4.4 0.6 1.0 P A:A969 4.5 68.1 1.0 C3' A:A969 4.5 68.1 1.0 C5' A:A969 4.9 68.1 1.0 C4' A:A968 5.0 0.6 1.0

Magnesium binding site 6 out of 70 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 Magnesium with other atoms in the Mg 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:Mg3007 b:85.0 occ:1.00 N7 A:G391 3.9 92.8 1.0 OP2 A:G391 4.1 92.8 1.0 OP2 A:C390 4.2 74.4 1.0 C5 A:C390 4.3 74.4 1.0 N7 A:G392 4.3 98.0 1.0 C6 A:C390 4.7 74.4 1.0 O6 A:G391 4.7 92.8 1.0 C8 A:G391 4.7 92.8 1.0 C5 A:G391 4.8 92.8 1.0 O6 A:G392 4.9 98.0 1.0 O5' A:C390 5.0 73.8 1.0

Magnesium binding site 7 out of 70 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 Magnesium with other atoms in the Mg 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:Mg3008 b:85.0 occ:1.00 OP1 A:G1361 1.3 93.2 1.0 P A:G1361 1.6 96.6 1.0 OP2 A:G1361 2.1 93.2 1.0 O3' A:A1360 2.4 0.7 1.0 O5' A:G1361 3.2 96.6 1.0 C3' A:A1360 3.7 0.7 1.0 C5' A:G1361 4.0 96.6 1.0 O2' A:C1359 4.2 0.6 1.0 C2' A:C1359 4.4 0.6 1.0 C4' A:A1360 4.6 0.7 1.0 O2 A:C1359 4.7 88.5 1.0 C2' A:A1360 4.7 0.7 1.0 O2' A:A1360 4.8 0.7 1.0 C5' A:A1360 4.9 0.7 1.0

Magnesium binding site 8 out of 70 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 Magnesium with other atoms in the Mg 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:Mg3009 b:85.0 occ:1.00 N1 A:C1362 0.8 0.5 1.0 C2 A:C1362 0.9 0.9 1.0 C6 A:C1362 1.5 0.7 1.0 N3 A:C1362 1.6 0.8 1.0 C4 A:C1362 2.0 0.9 1.0 C5 A:C1362 2.0 0.6 1.0 O2 A:C1362 2.1 0.8 1.0 C1' A:C1362 2.2 0.3 1.0 C2' A:C1362 2.9 99.2 1.0 O4' A:C1362 3.2 99.9 1.0 N4 A:C1362 3.4 0.1 1.0 C2 A:G976 3.4 0.8 1.0 N2 A:G976 3.5 0.8 1.0 N3 A:G976 3.5 0.8 1.0 O2' A:C1362 3.6 0.3 1.0 C5 A:G1361 3.8 93.2 1.0 C6 A:G1361 3.9 93.2 1.0 N1 A:G976 4.0 0.8 1.0 C3' A:C1362 4.1 98.2 1.0 N7 A:G1361 4.1 93.2 1.0 C4 A:G976 4.1 0.8 1.0 O6 A:G1361 4.2 93.2 1.0 C4 A:G1361 4.2 93.2 1.0 C4' A:C1362 4.3 98.4 1.0 N1 A:G1361 4.4 93.2 1.0 C8 A:G1361 4.5 93.2 1.0 N9 A:G1361 4.6 93.2 1.0 C6 A:G976 4.6 0.8 1.0 C5 A:G976 4.7 0.8 1.0 N3 A:G1361 4.8 93.2 1.0 C2 A:G1361 4.8 93.2 1.0 N9 A:G976 4.9 0.8 1.0

Magnesium binding site 9 out of 70 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 Magnesium with other atoms in the Mg binding site number 9 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:Mg3010 b:85.0 occ:1.00 OP1 A:C1352 2.8 93.0 1.0 NZ V:LYS3 3.0 0.5 1.0 OP2 A:A1236 4.0 66.9 1.0 OP1 A:A1236 4.1 66.9 1.0 P A:C1352 4.2 75.1 1.0 CE V:LYS3 4.4 0.5 1.0 P A:A1236 4.6 79.0 1.0 O3' A:U1351 4.6 75.3 1.0 CG V:LYS3 4.8 0.5 1.0 CD V:LYS3 4.9 0.5 1.0 NH1 V:ARG10 4.9 0.1 1.0 OP2 A:C1352 5.0 93.0 1.0

Magnesium binding site 10 out of 70 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 Magnesium with other atoms in the Mg binding site number 10 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:Mg3011 b:85.0 occ:1.00 OP1 A:G944 1.9 76.2 1.0 OP2 A:G945 2.2 70.0 1.0 P A:G944 3.0 71.0 1.0 OP2 A:G944 3.4 76.2 1.0 P A:G945 3.5 67.2 1.0 O5' A:G944 3.7 71.0 1.0 OP1 A:G945 3.9 70.0 1.0 C5' A:G944 4.2 71.0 1.0 N7 A:A946 4.2 52.2 1.0 O3' A:U943 4.4 71.9 1.0 O5' A:G945 4.5 67.2 1.0 O3' A:G944 4.6 71.0 1.0 OP2 A:A946 4.6 52.2 1.0 C3' A:G944 4.8 71.0 1.0 C8 A:A946 4.9 52.2 1.0 O6 A:G947 5.0 63.2 1.0 O6 A:G1233 5.0 71.9 1.0

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