Magnesium in PDB 4jya: Crystal Structures of Pseudouridinilated Stop Codons with Asls

The structure of Crystal Structures of Pseudouridinilated Stop Codons with Asls, PDB code: 4jya was solved by I.S.Fernandez, C.L.Ng, A.C.Kelley, W.Guowei, Y.T.Yu, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.93 / 3.10
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	402.320, 402.320, 174.930, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 23.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structures of Pseudouridinilated Stop Codons with Asls (pdb code 4jya). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Crystal Structures of Pseudouridinilated Stop Codons with Asls, PDB code: 4jya:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in the Crystal Structures of Pseudouridinilated Stop Codons with Asls


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structures of Pseudouridinilated Stop Codons with Asls within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1601 b:49.2 occ:1.00 N3 A:C502 2.8 94.1 1.0 O6 A:G514 2.9 0.2 1.0 O2' X:A6 3.0 85.8 1.0 O2 A:C502 3.0 90.1 1.0 O L:PRO48 3.2 83.8 1.0 C2 A:C502 3.2 89.0 1.0 C1' X:A6 3.3 92.1 1.0 O4' X:A6 3.5 80.1 1.0 C6 A:G514 3.7 0.7 1.0 C L:PRO48 3.8 70.8 1.0 C2' X:A6 3.8 81.3 1.0 C4 A:C502 3.9 83.6 1.0 C4' X:A6 3.9 79.5 1.0 CA L:PRO48 4.1 64.8 1.0 N4 A:C502 4.1 91.5 1.0 C2 A:A1470 4.2 62.5 1.0 CB L:PRO48 4.3 58.8 1.0 C5 A:G514 4.4 0.4 1.0 N7 A:G514 4.5 0.6 1.0 N1 A:A1470 4.5 66.2 1.0 N1 A:C502 4.6 77.2 1.0 C3' X:A6 4.6 71.9 1.0 N9 X:A6 4.6 0.1 1.0 N1 A:G514 4.7 0.8 1.0 N L:ASN49 4.7 72.6 1.0 N3 A:A1470 4.7 65.5 1.0

Magnesium binding site 2 out of 14 in the Crystal Structures of Pseudouridinilated Stop Codons with Asls


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structures of Pseudouridinilated Stop Codons with Asls within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1602 b:48.1 occ:1.00 OP1 A:U1181 1.9 61.5 1.0 OP1 A:A942 2.2 90.1 1.0 P A:U1181 3.2 65.6 1.0 P A:A942 3.7 73.5 1.0 OP2 A:U1181 3.8 62.2 1.0 O3' A:G941 4.1 73.9 1.0 O5' A:U1181 4.1 64.4 1.0 OP1 A:G1180 4.2 78.1 1.0 C5' A:A942 4.3 59.9 1.0 O3' A:G1180 4.3 59.0 1.0 O5' A:A942 4.5 59.9 1.0 C5' A:G1180 4.5 59.6 1.0 OP2 A:A942 4.7 68.2 1.0 OP2 A:A943 5.0 48.8 1.0

Magnesium binding site 3 out of 14 in the Crystal Structures of Pseudouridinilated Stop Codons with Asls


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structures of Pseudouridinilated Stop Codons with Asls within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1603 b:60.0 occ:1.00 OP1 A:C1037 2.1 82.3 1.0 OP1 A:G1179 2.3 60.4 1.0 OP2 A:G1180 2.6 81.1 1.0 P A:C1037 3.6 80.0 1.0 P A:G1179 3.6 83.5 1.0 P A:G1180 3.7 74.6 1.0 C5' A:C1037 4.1 72.9 1.0 OP1 A:G1180 4.1 78.1 1.0 OP2 A:G1179 4.2 87.7 1.0 O5' A:C1037 4.2 75.7 1.0 O3' A:U1178 4.3 92.1 1.0 O3' A:G1179 4.3 64.2 1.0 OP1 Y:G34 4.5 69.3 1.0 O3' A:G1036 4.5 82.0 1.0 OP2 A:C1037 4.6 72.8 1.0 C3' A:U1178 4.6 89.0 1.0 C3' A:G1036 4.6 79.1 1.0 O2' A:U1178 4.8 92.9 1.0 O5' A:G1179 5.0 64.6 1.0 C3' A:G1179 5.0 57.5 1.0

Magnesium binding site 4 out of 14 in the Crystal Structures of Pseudouridinilated Stop Codons with Asls


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structures of Pseudouridinilated Stop Codons with Asls within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1604 b:57.0 occ:1.00 OP2 A:C1037 1.9 72.8 1.0 OP2 A:G1179 2.3 87.7 1.0 P A:C1037 3.4 80.0 1.0 O2' A:G1036 3.7 90.5 1.0 P A:G1179 3.8 83.5 1.0 N7 A:G1180 3.9 96.8 1.0 O5' A:C1037 4.1 75.7 1.0 O4 A:U1181 4.2 69.7 1.0 O5' A:G1179 4.2 64.6 1.0 OP1 A:C1037 4.3 82.3 1.0 O3' A:G1036 4.3 82.0 1.0 O3' A:U1178 4.4 92.1 1.0 C8 A:G1180 4.5 96.7 1.0 N7 A:G1179 4.7 86.9 1.0 OP1 A:G1179 4.8 60.4 1.0 C8 A:G1179 4.8 85.5 1.0 C2' A:G1036 4.9 80.8 1.0 C4 A:U1181 5.0 72.8 1.0 OP2 A:G1180 5.0 81.1 1.0 C5 A:G1180 5.0 98.7 1.0

Magnesium binding site 5 out of 14 in the Crystal Structures of Pseudouridinilated Stop Codons with Asls


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structures of Pseudouridinilated Stop Codons with Asls within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1605 b:42.7 occ:1.00 O4 A:U1181 2.8 69.7 1.0 O6 A:G1180 2.9 91.4 1.0 O6 A:G1041 3.0 74.8 1.0 N2 A:G1036 3.4 73.9 1.0 N4 A:C1042 3.4 88.3 1.0 OP2 A:G1040 3.7 77.1 1.0 C4 A:U1181 3.8 72.8 1.0 C6 A:G1180 3.9 97.8 1.0 C6 A:G1041 4.0 79.2 1.0 N3 A:U1181 4.1 74.9 1.0 N7 A:G1041 4.1 79.6 1.0 C2 A:G1036 4.2 79.3 1.0 N3 A:G1036 4.4 82.9 1.0 C5 A:G1041 4.4 81.0 1.0 C4 A:C1042 4.5 88.9 1.0 N1 A:G1180 4.7 96.7 1.0 C5 A:G1180 4.8 98.7 1.0 N7 A:G1040 4.9 0.8 1.0 N3 A:C1042 4.9 90.1 1.0

Magnesium binding site 6 out of 14 in the Crystal Structures of Pseudouridinilated Stop Codons with Asls


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structures of Pseudouridinilated Stop Codons with Asls within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1606 b:52.8 occ:1.00 OP1 A:A892 2.2 69.0 1.0 O2' A:U13 2.8 60.4 1.0 O3' A:U13 2.9 50.9 1.0 O3' A:C510 2.9 63.6 1.0 OP1 A:G511 3.2 65.7 1.0 P A:G511 3.3 62.0 1.0 O5' A:U14 3.4 57.5 1.0 C5' A:U14 3.5 53.2 1.0 OP2 A:G511 3.5 68.9 1.0 P A:A892 3.7 57.7 1.0 P A:U14 3.7 57.4 1.0 C2' A:U13 3.8 56.4 1.0 C3' A:U13 3.8 52.2 1.0 C3' A:C510 4.1 57.2 1.0 OP1 A:U14 4.2 57.3 1.0 C4' A:C510 4.2 53.2 1.0 C4' A:U13 4.3 54.2 1.0 C4' A:U14 4.3 52.8 1.0 O5' A:A892 4.4 54.3 1.0 OP2 A:A892 4.5 75.4 1.0 O3' A:A891 4.5 55.9 1.0 C5' A:C510 4.6 50.9 1.0 O2' A:C510 4.6 60.7 1.0 OP2 A:U15 4.8 56.6 1.0 O5' A:G511 4.9 52.5 1.0 C2' A:C510 4.9 52.5 1.0 C1' A:U13 5.0 55.1 1.0

Magnesium binding site 7 out of 14 in the Crystal Structures of Pseudouridinilated Stop Codons with Asls


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structures of Pseudouridinilated Stop Codons with Asls within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1607 b:46.8 occ:1.00 OP2 A:A17 3.7 56.2 1.0 OP2 A:G16 4.0 56.0 1.0 OP2 A:U15 4.2 56.6 1.0 OP1 A:U14 4.3 57.3 1.0 C5 A:U15 4.5 55.4 1.0 OP1 A:A17 4.5 64.8 1.0 P A:A17 4.6 63.1 1.0 C6 A:U15 4.7 51.9 1.0 O5' A:U15 4.9 50.0 1.0

Magnesium binding site 8 out of 14 in the Crystal Structures of Pseudouridinilated Stop Codons with Asls


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structures of Pseudouridinilated Stop Codons with Asls within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1608 b:52.3 occ:1.00 OP2 A:A893 3.6 63.7 1.0 OP2 A:G894 3.8 63.6 1.0 N7 A:G894 4.1 51.7 1.0 O2' A:U14 4.4 56.5 1.0 C8 A:G894 4.5 56.4 1.0 P A:A893 4.8 65.2 1.0 O5' A:A893 4.9 64.1 1.0

Magnesium binding site 9 out of 14 in the Crystal Structures of Pseudouridinilated Stop Codons with Asls


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structures of Pseudouridinilated Stop Codons with Asls within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1609 b:47.1 occ:1.00 OP2 A:A558 2.0 50.5 1.0 OP2 A:A556 2.5 62.4 1.0 OP2 A:A557 2.6 45.0 1.0 P A:A558 3.4 53.3 1.0 OP1 A:U555 3.6 47.7 1.0 P A:A556 3.7 60.9 1.0 P A:A557 4.1 49.4 1.0 O5' A:A558 4.1 46.3 1.0 OP2 A:U555 4.2 49.9 1.0 OP1 A:A556 4.2 80.6 1.0 OP1 A:A558 4.2 52.4 1.0 P A:U555 4.3 49.7 1.0 O5' A:A556 4.4 54.2 1.0 O3' A:A557 4.5 47.5 1.0 C5' A:A556 4.5 50.0 1.0 C2 A:A803 4.6 43.6 1.0 C3' A:A557 4.7 47.1 1.0 C5' A:U555 4.8 46.2 1.0 O5' A:U555 4.8 48.3 1.0 OP1 A:A557 4.9 59.7 1.0 O5' A:A557 4.9 45.2 1.0 C8 A:A558 4.9 59.9 1.0 O3' A:U555 5.0 49.6 1.0 N1 A:A803 5.0 37.8 1.0

Magnesium binding site 10 out of 14 in the Crystal Structures of Pseudouridinilated Stop Codons with Asls


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structures of Pseudouridinilated Stop Codons with Asls within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1610 b:44.0 occ:1.00 OP1 A:G22 2.1 53.5 1.0 P A:G22 3.6 52.5 1.0 O2' A:G551 3.9 51.9 1.0 N2 A:G551 4.0 69.8 1.0 N1 A:A557 4.0 60.8 1.0 N3 A:G551 4.0 59.7 1.0 N6 A:A557 4.2 60.0 1.0 N6 A:A547 4.3 73.2 1.0 O3' A:U21 4.3 48.3 1.0 O2' A:G552 4.3 47.7 1.0 C2 A:G551 4.5 61.7 1.0 O5' A:G22 4.6 52.6 1.0 C6 A:A557 4.6 58.6 1.0 OP2 A:G22 4.6 50.5 1.0 C2' A:G551 4.9 50.9 1.0 C1' A:G552 5.0 54.1 1.0

I.S.Fernandez, C.L.Ng, A.C.Kelley, G.Wu, Y.T.Yu, V.Ramakrishnan. Unusual Base Pairing During the Decoding of A Stop Codon By the Ribosome. Nature V. 500 107 2013.
ISSN: ISSN 0028-0836
PubMed: 23812587
DOI: 10.1038/NATURE12302