Magnesium in PDB 2vqf: Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding

The structure of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding, PDB code: 2vqf was solved by S.Kurata, A.Weixlbaumer, T.Ohtsuki, T.Shimazaki, T.Wada, Y.Kirino, K.Takai, K.Watanabe, V.Ramakrishnan, T.Suzuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.92 / 2.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	402.481, 402.481, 175.969, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 25.8

The structure of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding also contains other interesting chemical elements:

Potassium	(K)	73 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; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 130; Page 14, Binding sites: 131 - 140; Page 15, Binding sites: 141 - 150; Page 16, Binding sites: 151 - 160; Page 17, Binding sites: 161 - 170; Page 18, Binding sites: 171 - 180; Page 19, Binding sites: 181 - 190; Page 20, Binding sites: 191 - 200; Page 21, Binding sites: 201 - 210; Page 22, Binding sites: 211 - 214;

Binding sites:

The binding sites of Magnesium atom in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding (pdb code 2vqf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 214 binding sites of Magnesium where determined in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding, PDB code: 2vqf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 214 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1602 b:0.9 occ:1.00 O6 A:G157 2.1 1.0 1.0 O6 A:G158 2.6 0.2 1.0 C6 A:G157 2.8 0.8 1.0 N7 A:G158 3.3 0.2 1.0 C6 A:G158 3.3 0.5 1.0 C5 A:G157 3.4 0.1 1.0 N7 A:G157 3.5 0.9 1.0 C5 A:G158 3.6 0.4 1.0 N1 A:G157 3.9 0.3 1.0 N3 A:U164 4.2 0.5 1.0 O4 A:U164 4.3 0.0 1.0 C8 A:G158 4.5 0.9 1.0 N1 A:G158 4.6 0.4 1.0 O6 A:G156 4.6 0.6 1.0 C4 A:G157 4.6 0.7 1.0 O6 A:G159 4.7 1.0 1.0 C8 A:G157 4.7 0.8 1.0 C4 A:U164 4.7 0.5 1.0 N4 A:C163 4.9 0.4 1.0 C4 A:G158 4.9 0.2 1.0 N4 A:C165 5.0 0.7 1.0

Magnesium binding site 2 out of 214 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1603 b:0.4 occ:1.00 OP2 A:G265 4.0 64.0 1.0 O6 A:G259 4.1 77.8 1.0 K A:K1813 4.2 0.3 1.0 O6 A:G260 4.5 79.3 1.0 OP1 A:G265 4.5 62.5 1.0 N7 A:G258 4.5 78.9 1.0 O6 A:G258 4.7 74.9 1.0 P A:G265 4.7 63.5 1.0 OP2 A:G266 4.9 66.1 1.0

Magnesium binding site 3 out of 214 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1604 b:47.4 occ:1.00 O6 A:G285 2.1 54.5 1.0 K A:K1836 2.5 0.3 1.0 C6 A:G285 2.9 53.3 1.0 N7 A:G285 3.0 53.2 1.0 MG A:MG1696 3.3 0.8 1.0 C5 A:G285 3.3 52.9 1.0 O6 A:G284 3.6 53.9 1.0 O6 A:G286 3.8 50.3 1.0 N4 A:C241 4.0 44.4 1.0 C6 A:G284 4.0 51.4 1.0 N1 A:G285 4.2 52.4 1.0 C8 A:G285 4.3 54.7 1.0 N7 A:G284 4.3 50.7 1.0 C5 A:G284 4.3 51.5 1.0 N7 A:G286 4.4 48.3 1.0 C6 A:G286 4.4 49.7 1.0 N4 A:C242 4.6 46.4 1.0 C4 A:G285 4.6 53.9 1.0 C5 A:G286 4.7 48.4 1.0 N1 A:G284 4.9 50.3 1.0 N4 A:C240 5.0 55.9 1.0

Magnesium binding site 4 out of 214 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1605 b:0.1 occ:1.00 OP2 A:G731 3.9 61.3 1.0 OP1 A:C1527 4.0 52.0 1.0 OP1 A:G730 4.1 56.6 1.0 N7 A:G731 4.3 54.8 1.0 C8 A:G731 4.8 54.1 1.0

Magnesium binding site 5 out of 214 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1606 b:82.9 occ:1.00 O2 A:C519 2.6 86.5 1.0 O4' A:A520 3.1 82.7 1.0 O2' A:C519 3.3 83.5 1.0 C2 A:C519 3.8 86.6 1.0 C1' A:A520 3.9 82.9 1.0 C2' A:C519 4.1 83.5 1.0 C4' A:A520 4.1 82.9 1.0 O2' A:U516 4.3 99.1 1.0 O3' A:U516 4.4 98.1 1.0 C1' A:C519 4.5 83.8 1.0 C5' A:A520 4.5 82.6 1.0 OP1 A:G517 4.6 97.8 1.0 N9 A:A520 4.6 82.8 1.0 N3 A:C519 4.7 86.8 1.0 N1 A:C519 4.7 85.4 1.0

Magnesium binding site 6 out of 214 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1607 b:0.7 occ:1.00 O6 A:G799 3.8 54.6 1.0 N7 A:G799 3.9 57.8 1.0 O6 A:G800 4.0 54.0 1.0 O6 A:G798 4.1 52.1 1.0 N7 A:G798 4.4 51.7 1.0 C6 A:G800 4.5 55.0 1.0 OP2 A:A781 4.5 60.4 1.0 C6 A:G799 4.6 56.0 1.0 C5 A:G799 4.6 56.5 1.0 N1 A:G800 4.7 53.2 1.0 C6 A:G798 4.8 51.0 1.0 C5 A:G798 4.9 50.0 1.0

Magnesium binding site 7 out of 214 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1608 b:95.2 occ:1.00 OP2 A:G21 4.1 59.5 1.0 N7 A:G21 4.3 62.4 1.0 OP2 A:U20 4.5 56.4 1.0 OP1 A:U561 4.6 62.5 1.0 O E:GLY124 4.8 59.8 1.0 C8 A:G21 4.9 61.1 1.0

Magnesium binding site 8 out of 214 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1609 b:67.3 occ:1.00 O2' A:G854 2.2 59.6 1.0 O3' A:G854 2.8 58.6 1.0 OP2 A:G725 2.9 70.2 1.0 C2' A:G854 3.2 60.0 1.0 C3' A:G854 3.3 58.5 1.0 C4' A:G854 3.3 58.6 1.0 OP1 A:G724 3.3 95.0 1.0 OP1 A:G855 3.9 59.0 1.0 P A:G855 3.9 59.7 1.0 C1' A:G854 4.0 60.4 1.0 O4' A:G854 4.0 59.8 1.0 P A:G725 4.2 71.5 1.0 O5' A:G855 4.3 60.5 1.0 P A:G724 4.5 93.7 1.0 C5' A:G854 4.5 59.5 1.0 OP1 A:G725 4.6 74.8 1.0 OP2 A:G724 4.7 93.8 1.0

Magnesium binding site 9 out of 214 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1610 b:0.2 occ:1.00 N7 A:G758 3.4 62.1 1.0 N7 A:G581 3.6 54.0 1.0 OP2 A:G758 3.9 56.6 1.0 O6 A:G581 4.0 55.4 1.0 C8 A:G758 4.1 62.1 1.0 OP2 A:U580 4.1 62.6 1.0 OP2 A:U757 4.3 58.7 1.0 C5 A:G581 4.5 53.7 1.0 C5 A:G758 4.5 59.9 1.0 C8 A:G581 4.6 56.2 1.0 C6 A:G581 4.6 52.5 1.0 O6 A:G758 4.7 61.6 1.0 OP2 A:G581 4.8 61.0 1.0 O5' A:U757 4.9 58.1 1.0 P A:U757 5.0 58.1 1.0 C6 A:G758 5.0 59.5 1.0

Magnesium binding site 10 out of 214 in the Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U-G Wobble Pairing During Decoding within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1611 b:0.4 occ:1.00 OP1 A:G438 3.6 99.9 1.0 OP2 A:G438 3.8 0.3 1.0 P A:G438 4.2 0.6 1.0 OP2 A:G492 4.2 0.3 1.0 O6 A:G494 4.9 0.8 1.0

S.Kurata, A.Weixlbaumer, T.Ohtsuki, T.Shimazaki, T.Wada, Y.Kirino, K.Takai, K.Watanabe, V.Ramakrishnan, T.Suzuki. Modified Uridines with C5-Methylene Substituents at the First Position of the Trna Anticodon Stabilize U.G Wobble Pairing During Decoding. J.Biol.Chem. V. 283 18801 2008.
ISSN: ISSN 0021-9258
PubMed: 18456657
DOI: 10.1074/JBC.M800233200