Magnesium in PDB 1qvf: Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui

The structure of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1qvf was solved by T.M.Schmeing, P.B.Moore, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	213.522, 300.817, 574.861, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.9

The structure of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	86 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 - 119;

Binding sites:

The binding sites of Magnesium atom in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1qvf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 119 binding sites of Magnesium where determined in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1qvf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 119 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8001 b:43.7 occ:1.00 O 0:HOH7229 1.7 22.8 1.0 OP2 0:C2534 2.0 38.9 1.0 O 0:HOH8699 2.0 60.4 1.0 O 0:HOH3135 2.1 34.9 1.0 OP2 0:A2483 2.1 36.7 1.0 OP2 0:C2533 2.2 31.8 1.0 P 0:A2483 3.2 37.0 1.0 O3' 0:G2482 3.3 37.2 1.0 P 0:C2534 3.5 39.1 1.0 P 0:C2533 3.6 33.6 1.0 O2' 0:G2482 3.8 40.9 1.0 O 0:HOH9163 3.9 55.3 1.0 O2' 0:A2532 4.0 35.8 1.0 OP1 0:A2483 4.1 39.6 1.0 O3' 0:A2532 4.1 35.2 1.0 O3' 0:C2533 4.2 36.3 1.0 OP2 0:U2484 4.2 46.0 1.0 OP1 0:C2534 4.3 36.6 1.0 O 0:HOH3832 4.3 45.4 1.0 O5' 0:C2533 4.4 35.8 1.0 O5' 0:C2534 4.4 38.1 1.0 O5' 0:A2483 4.4 38.0 1.0 C3' 0:C2533 4.4 36.6 1.0 C5' 0:A2483 4.5 38.7 1.0 C3' 0:G2482 4.5 37.7 1.0 O 0:HOH5855 4.6 54.6 1.0 O 0:HOH6944 4.6 46.4 1.0 C2' 0:G2482 4.6 38.1 1.0 OP1 0:C2533 4.7 37.7 1.0 C5 0:C2534 4.7 45.9 1.0 MG 0:MG8002 4.9 43.7 1.0

Magnesium binding site 2 out of 119 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8002 b:43.7 occ:1.00 O6 0:G627 1.9 33.1 1.0 O 0:HOH3832 2.0 45.4 1.0 O 0:HOH7209 2.0 21.5 1.0 O 0:HOH7210 2.0 29.6 1.0 OP1 0:A2483 2.1 39.6 1.0 OP1 0:C2534 2.2 36.6 1.0 C6 0:G627 3.1 32.7 1.0 P 0:A2483 3.2 37.0 1.0 P 0:C2534 3.5 39.1 1.0 OP2 0:A2483 3.6 36.7 1.0 O4 0:U626 3.8 42.4 1.0 N1 0:G627 3.8 32.8 1.0 OP2 0:C2534 4.0 38.9 1.0 O 0:HOH6576 4.1 48.5 1.0 O3' 0:C2533 4.1 36.3 1.0 O5' 0:A2483 4.2 38.0 1.0 O 0:HOH5360 4.2 45.5 1.0 O2' 0:U625 4.2 34.5 1.0 O 0:HOH8783 4.2 14.0 1.0 C5 0:G627 4.3 32.4 1.0 C4 0:U626 4.4 40.4 1.0 C5 0:U626 4.4 39.9 1.0 O3' 0:G2482 4.4 37.2 1.0 OP2 0:U2535 4.4 41.8 1.0 O 0:HOH3047 4.7 49.4 1.0 O5' 0:C2534 4.7 38.1 1.0 N7 0:G627 4.8 34.3 1.0 MG 0:MG8001 4.9 43.7 1.0 C3' 0:G2482 4.9 37.7 1.0

Magnesium binding site 3 out of 119 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8003 b:26.8 occ:1.00 OP1 0:A2624 1.9 38.8 1.0 O 0:HOH3181 2.0 69.4 1.0 OP2 0:A876 2.1 39.0 1.0 OP2 0:G877 2.1 34.7 1.0 O A:HOH8511 2.1 44.3 1.0 O A:HOH8532 2.6 30.1 1.0 P 0:A2624 3.3 39.9 1.0 P 0:G877 3.3 35.3 1.0 P 0:A876 3.4 39.8 1.0 O3' 0:G2623 3.8 40.9 1.0 OP1 0:G877 3.8 34.5 1.0 O5' 0:A876 3.9 37.9 1.0 O 0:HOH5759 4.0 88.5 1.0 O3' 0:A875 4.1 38.8 1.0 C5' 0:A876 4.1 36.2 1.0 O3' 0:A876 4.1 34.6 1.0 O 0:HOH6633 4.2 94.6 1.0 OP2 0:A2624 4.2 39.4 1.0 O A:ALA193 4.3 37.3 1.0 O5' 0:A2624 4.3 42.0 1.0 O A:HOH8565 4.3 51.6 1.0 O 0:HOH8540 4.4 31.8 1.0 OD1 A:ASN195 4.4 38.6 1.0 O A:HOH8621 4.5 57.6 1.0 C5' 0:A2624 4.5 43.2 1.0 O5' 0:G877 4.5 37.6 1.0 C3' 0:A876 4.6 35.2 1.0 OP1 0:A876 4.6 38.0 1.0 C4' 0:A876 4.9 36.0 1.0 O A:HOH8544 5.0 64.8 1.0

Magnesium binding site 4 out of 119 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8004 b:60.7 occ:1.00 O 0:HOH8566 1.8 19.8 1.0 OP1 0:A459 1.8 35.6 1.0 O 0:HOH9298 1.9 25.8 1.0 O6 0:G456 1.9 42.8 1.0 O 0:HOH3296 2.1 28.1 1.0 O 0:HOH7216 2.3 17.4 1.0 C6 0:G456 3.1 42.9 1.0 P 0:A459 3.1 37.0 1.0 O5' 0:A459 3.7 37.7 1.0 C5 0:G456 3.9 41.3 1.0 OP2 0:A459 3.9 39.0 1.0 N7 0:G456 3.9 38.7 1.0 C5' 0:A459 4.1 37.6 1.0 O 0:HOH8855 4.2 42.3 1.0 O 0:HOH5446 4.2 44.2 1.0 N1 0:G456 4.2 43.9 1.0 CE C:LYS85 4.2 33.2 1.0 O3' 0:G458 4.3 38.8 1.0 OP2 0:A455 4.4 34.6 1.0 O 0:HOH3219 4.4 28.2 1.0 NZ C:LYS85 4.5 32.0 1.0 O 0:HOH3033 4.5 44.6 1.0 OP1 0:A460 4.5 42.8 1.0 OP1 0:A477 4.6 35.7 1.0 N7 0:A455 4.6 41.4 1.0 O 0:HOH4885 4.7 36.0 1.0 CD C:LYS85 4.8 33.3 1.0 O 0:HOH7217 5.0 36.0 1.0

Magnesium binding site 5 out of 119 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8005 b:66.5 occ:1.00 O 0:HOH7230 1.9 17.7 1.0 O 0:HOH7231 1.9 26.9 1.0 OP2 0:A1839 2.0 31.1 1.0 OP1 0:U1838 2.0 38.0 1.0 OP1 0:A1836 2.1 36.8 1.0 O 0:HOH3131 2.2 25.5 1.0 P 0:U1838 3.4 37.6 1.0 P 0:A1839 3.4 33.8 1.0 P 0:A1836 3.5 37.1 1.0 O 0:HOH5041 3.8 56.3 1.0 O 0:HOH8527 4.0 30.3 1.0 O 0:HOH4983 4.0 40.1 1.0 OP2 0:U1838 4.1 38.5 1.0 O5' 0:A1836 4.2 37.7 1.0 O3' 0:U1838 4.2 34.3 1.0 O5' 0:U1838 4.2 33.9 1.0 C2' 0:U1835 4.3 37.4 1.0 O5' 0:A1839 4.3 33.0 1.0 O 0:HOH9159 4.3 38.7 1.0 C3' 0:G1837 4.3 43.5 1.0 O3' 0:G1837 4.3 39.3 1.0 OP1 0:A1839 4.3 34.8 1.0 OP2 0:A1836 4.4 38.5 1.0 O3' 0:U1835 4.4 35.6 1.0 OP2 0:G1837 4.4 45.0 1.0 O 0:HOH7303 4.4 46.4 1.0 C3' 0:U1835 4.5 36.8 1.0 C3' 0:U1838 4.5 30.9 1.0 C5' 0:U1838 4.6 29.9 1.0 N7 0:A1839 4.6 33.6 1.0 O2' 0:U1835 4.6 38.6 1.0 O 0:HOH9033 4.7 29.6 1.0 C8 0:A1839 4.7 33.9 1.0

Magnesium binding site 6 out of 119 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8006 b:57.2 occ:1.00 O 0:HOH9329 1.7 53.5 1.0 OP2 0:C822 1.8 47.1 1.0 O 0:HOH3268 2.0 43.0 1.0 OP1 0:G854 2.1 38.5 1.0 OP2 0:U821 2.1 46.8 1.0 O 0:HOH3137 2.3 18.9 1.0 P 0:C822 3.2 48.6 1.0 P 0:G854 3.3 40.5 1.0 P 0:U821 3.5 47.0 1.0 OP1 0:G856 3.9 49.6 1.0 O3' 0:U821 3.9 49.3 1.0 O5' 0:U821 3.9 48.5 1.0 O5' 0:G854 3.9 40.1 1.0 C3' 0:U821 4.0 47.7 1.0 OP2 0:G854 4.0 38.3 1.0 OP1 0:C822 4.0 49.1 1.0 NA 0:NA8327 4.1 44.4 1.0 O 0:HOH9720 4.1 47.9 1.0 O5' 0:C822 4.2 49.4 1.0 OP1 0:U855 4.2 44.7 1.0 C5' 0:G854 4.3 41.2 1.0 O3' 0:G820 4.3 45.8 1.0 O 0:HOH4488 4.4 33.4 1.0 O3' 0:C853 4.5 40.6 1.0 OP1 0:U821 4.6 46.0 1.0 C5 0:C822 4.8 45.5 1.0 O 0:HOH9252 4.9 61.5 1.0 C5' 0:U821 5.0 48.7 1.0 C4' 0:U821 5.0 47.7 1.0 O 0:HOH8830 5.0 0.2 1.0

Magnesium binding site 7 out of 119 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8007 b:26.0 occ:1.00 O 0:HOH9876 1.9 39.6 1.0 OP2 0:U832 2.0 45.6 1.0 O 0:HOH7221 2.0 32.6 1.0 OP1 0:A1839 2.1 34.8 1.0 O 0:HOH8527 2.3 30.3 1.0 OP2 0:A1840 2.4 35.3 1.0 P 0:U832 3.4 45.2 1.0 P 0:A1839 3.4 33.8 1.0 P 0:A1840 3.6 37.9 1.0 O 0:HOH8623 3.7 30.8 1.0 O 0:HOH5834 3.8 64.8 1.0 O 0:HOH9159 3.8 38.7 1.0 OP1 0:A1840 4.0 36.6 1.0 OP2 0:A1839 4.0 31.1 1.0 O5' 0:U832 4.2 43.2 1.0 OP1 0:U832 4.2 43.6 1.0 O3' 0:U1838 4.2 34.3 1.0 O3' 0:A1839 4.3 34.4 1.0 O3' 0:U831 4.4 42.3 1.0 O 0:HOH7303 4.4 46.4 1.0 O5' 0:A1839 4.5 33.0 1.0 O 0:HOH7333 4.5 34.8 1.0 C3' 0:A1839 4.7 34.6 1.0 C5' 0:A1839 4.7 33.3 1.0 OP2 0:G833 4.8 42.0 1.0 C5' 0:U832 4.8 42.9 1.0 O5' 0:A1840 4.8 37.2 1.0 C3' 0:U831 4.9 42.4 1.0 O 0:HOH7230 4.9 17.7 1.0

Magnesium binding site 8 out of 119 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8008 b:45.3 occ:1.00 O 0:HOH7304 1.9 57.2 1.0 OP1 0:C2464 2.0 41.6 1.0 O 0:HOH3147 2.0 26.3 1.0 OP1 0:A2465 2.0 44.0 1.0 O 0:HOH7224 2.0 33.8 1.0 OP1 0:U919 2.2 34.2 1.0 P 0:U919 3.2 35.5 1.0 P 0:C2464 3.4 42.5 1.0 P 0:A2465 3.4 43.2 1.0 OP2 0:U919 3.7 35.4 1.0 O5' 0:U919 3.8 33.2 1.0 O5' 0:C2464 3.9 44.5 1.0 O 0:HOH9866 3.9 41.2 1.0 C5' 0:C2464 3.9 44.7 1.0 O 0:HOH8969 4.0 52.9 1.0 O5' 0:A2465 4.0 41.9 1.0 O 0:HOH5373 4.2 91.8 1.0 OP2 0:A2465 4.2 41.5 1.0 OP2 0:C2464 4.2 42.6 1.0 OP1 0:G2466 4.3 40.9 1.0 C5' 0:U919 4.3 33.4 1.0 O3' 0:A2463 4.4 45.0 1.0 C3' 0:A2465 4.5 42.1 1.0 O 0:HOH9441 4.5 88.9 1.0 O 0:HOH9068 4.6 32.5 1.0 O3' 0:C2464 4.6 44.1 1.0 O3' 0:G918 4.6 36.1 1.0 C5' 0:A2465 4.7 40.4 1.0 C3' 0:C2464 4.9 43.6 1.0 C4' 0:C2464 4.9 44.4 1.0

Magnesium binding site 9 out of 119 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8009 b:18.2 occ:1.00 O 0:HOH6898 1.8 41.4 1.0 OP1 0:A2612 1.9 29.4 1.0 O 0:HOH7225 2.1 29.4 1.0 O 0:HOH3253 2.1 12.5 1.0 OP1 0:G2611 2.3 33.2 1.0 P 0:A2612 3.3 30.1 1.0 NA 0:NA8358 3.5 91.2 1.0 P 0:G2611 3.5 32.4 1.0 OP2 0:G2093 3.7 38.9 1.0 O3' 0:U2610 3.7 31.6 1.0 O 0:HOH8856 3.8 20.8 1.0 OP2 0:G2094 3.9 31.4 1.0 OP2 0:A2612 4.0 31.9 1.0 OP1 0:G2094 4.1 31.3 1.0 O5' 0:A2612 4.2 33.4 1.0 O 0:HOH8988 4.2 44.0 1.0 O 0:HOH8827 4.3 30.6 1.0 O3' 0:G2611 4.3 31.9 1.0 C5' 0:G2611 4.4 32.2 1.0 O5' 0:G2611 4.4 31.6 1.0 P 0:G2094 4.4 31.7 1.0 OP2 0:G2611 4.7 34.7 1.0 C3' 0:G2611 4.7 32.7 1.0 O 0:HOH8648 4.9 34.0 1.0 O 0:HOH7240 4.9 65.8 1.0 O3' 0:G2093 5.0 33.1 1.0 C3' 0:U2610 5.0 34.9 1.0

Magnesium binding site 10 out of 119 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8010 b:34.3 occ:1.00 O B:HOH8525 1.8 42.6 1.0 OP1 0:G836 1.8 34.2 1.0 O 0:HOH3352 2.0 43.8 1.0 OE1 B:GLN230 2.0 29.3 1.0 O 0:HOH8884 2.3 44.3 1.0 OP1 0:U2615 2.3 34.7 1.0 CD B:GLN230 3.2 30.7 1.0 P 0:G836 3.3 34.1 1.0 P 0:U2615 3.8 36.3 1.0 C5' 0:G836 3.8 30.9 1.0 CG B:GLN230 3.9 31.2 1.0 CB B:GLN230 4.0 33.3 1.0 O5' 0:G836 4.0 30.7 1.0 O 0:HOH4533 4.1 77.6 1.0 OP2 0:G836 4.2 35.3 1.0 O3' 0:U835 4.2 33.8 1.0 C3' 0:U835 4.2 34.6 1.0 NE2 B:GLN230 4.3 27.4 1.0 CA B:GLN230 4.4 36.1 1.0 O 0:HOH3503 4.4 45.4 1.0 O 0:HOH6300 4.4 52.0 1.0 O 0:HOH8727 4.5 65.4 1.0 OP2 0:U2615 4.5 38.3 1.0 O B:GLN230 4.6 36.8 1.0 O3' 0:C2614 4.6 36.0 1.0 O5' 0:U2615 4.6 37.1 1.0 C5' 0:U835 4.7 36.0 1.0 OP2 0:G2616 4.8 31.1 1.0 C B:GLN230 5.0 37.3 1.0

T.M.Schmeing, P.B.Moore, T.A.Steitz. Structures of Deacylated Trna Mimics Bound to the E Site of the Large Ribosomal Subunit Rna V. 9 1345 2003.
ISSN: ISSN 1355-8382
PubMed: 14561884
DOI: 10.1261/RNA.5120503