Magnesium in PDB 1vq4: The Structure of the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

The structure of The Structure of the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vq4 was solved by T.M.Schmeing, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	212.998, 301.034, 575.272, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23

The structure of The Structure of the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Potassium	(K)	3 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 - 117;

Binding sites:

The binding sites of Magnesium atom in the The Structure of the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1vq4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 117 binding sites of Magnesium where determined in the The Structure of the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vq4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 117 in the The Structure of the Transition State Analogue "Daa" Bound to 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 The Structure of the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8001 b:38.2 occ:1.00 OP2 0:C2534 2.0 42.2 1.0 OP2 0:C2533 2.0 37.5 1.0 O 0:HOH7946 2.0 27.8 1.0 O 0:HOH3919 2.2 34.7 1.0 O 0:HOH9496 2.2 36.6 1.0 OP2 0:A2483 2.3 38.6 1.0 P 0:A2483 3.3 38.8 1.0 O3' 0:G2482 3.3 40.2 1.0 P 0:C2533 3.4 39.9 1.0 P 0:C2534 3.4 41.8 1.0 O3' 0:A2532 3.9 39.4 1.0 O 0:HOH9958 4.0 43.7 1.0 OP1 0:A2483 4.1 41.1 1.0 O 0:HOH4631 4.2 39.5 1.0 O3' 0:C2533 4.2 40.0 1.0 O2' 0:A2532 4.2 38.5 1.0 OP2 0:U2484 4.2 42.6 1.0 O2' 0:G2482 4.3 39.9 1.0 O 0:HOH7667 4.3 59.5 1.0 O5' 0:C2533 4.3 38.5 1.0 OP1 0:C2534 4.3 42.1 1.0 O5' 0:C2534 4.3 42.5 1.0 C3' 0:C2533 4.4 39.1 1.0 OP1 0:C2533 4.5 41.4 1.0 O 0:HOH6627 4.5 83.8 1.0 O5' 0:A2483 4.5 39.2 1.0 C3' 0:G2482 4.6 39.7 1.0 C5' 0:A2483 4.8 37.7 1.0 MG 0:MG8002 4.9 40.0 1.0 C2' 0:G2482 4.9 40.2 1.0 C3' 0:A2532 5.0 38.9 1.0 C5' 0:C2533 5.0 37.3 1.0

Magnesium binding site 2 out of 117 in the The Structure of the Transition State Analogue "Daa" Bound to 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 The Structure of the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8002 b:40.0 occ:1.00 O 0:HOH4631 2.0 39.5 1.0 OP1 0:A2483 2.0 41.1 1.0 O6 0:G627 2.1 35.8 1.0 O 0:HOH7924 2.1 42.2 1.0 OP1 0:C2534 2.1 42.1 1.0 O 0:HOH7925 2.2 40.9 1.0 C6 0:G627 3.2 34.3 1.0 P 0:A2483 3.3 38.8 1.0 P 0:C2534 3.4 41.8 1.0 OP2 0:A2483 3.7 38.6 1.0 O 0:HOH9580 3.8 27.4 1.0 OP2 0:C2534 3.8 42.2 1.0 N1 0:G627 3.9 33.3 1.0 O 0:HOH7316 3.9 61.9 1.0 O4 0:U626 3.9 36.5 1.0 O3' 0:C2533 4.2 40.0 1.0 O5' 0:A2483 4.2 39.2 1.0 O2' 0:U625 4.2 36.0 1.0 O3' 0:G2482 4.4 40.2 1.0 O 0:HOH6145 4.4 42.6 1.0 OP2 0:U2535 4.4 41.3 1.0 C5 0:U626 4.4 35.5 1.0 C5 0:G627 4.4 33.0 1.0 C4 0:U626 4.5 36.8 1.0 O 0:HOH3833 4.5 48.3 1.0 O5' 0:C2534 4.5 42.5 1.0 C3' 0:G2482 4.8 39.7 1.0 MG 0:MG8001 4.9 38.2 1.0 N7 0:G627 5.0 31.3 1.0 C5' 0:C2534 5.0 43.4 1.0

Magnesium binding site 3 out of 117 in the The Structure of the Transition State Analogue "Daa" Bound to 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 The Structure of the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8003 b:40.1 occ:1.00 OP1 0:A2624 1.9 31.0 1.0 O 0:HOH9341 2.1 28.3 1.0 OP2 0:G877 2.1 36.0 1.0 OP2 0:A876 2.1 34.2 1.0 O A:HOH9330 2.2 43.0 1.0 O 0:HOH3971 2.3 31.3 1.0 P 0:G877 3.3 36.1 1.0 P 0:A2624 3.4 33.6 1.0 P 0:A876 3.5 37.2 1.0 OP1 0:G877 3.8 36.2 1.0 O3' 0:G2623 3.9 34.1 1.0 O5' 0:A876 4.1 36.3 1.0 O3' 0:A875 4.1 34.1 1.0 O 0:HOH9340 4.1 30.8 1.0 O3' 0:A876 4.2 35.4 1.0 OD1 A:ASN195 4.2 38.4 1.0 C5' 0:A876 4.3 36.1 1.0 O 0:HOH7371 4.3 70.3 1.0 O5' 0:A2624 4.3 36.4 1.0 OP2 0:A2624 4.3 35.2 1.0 O 0:HOH6532 4.3 41.9 1.0 O A:ALA193 4.4 38.7 1.0 C5' 0:A2624 4.5 36.4 1.0 O5' 0:G877 4.5 35.5 1.0 O 0:HOH4774 4.6 38.8 1.0 C3' 0:A876 4.6 37.0 1.0 OP1 0:A876 4.7 36.1 1.0 O A:HOH9414 4.7 49.2 1.0 O A:HOH9420 4.8 30.5 1.0 O A:HOH9342 4.9 65.8 1.0

Magnesium binding site 4 out of 117 in the The Structure of the Transition State Analogue "Daa" Bound to 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 The Structure of the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8004 b:27.5 occ:1.00 OP1 0:A459 1.9 31.8 1.0 O6 0:G456 2.0 43.7 1.0 O 0:HOH4087 2.0 39.8 1.0 O 0:HOH7931 2.1 37.6 1.0 O 0:HOH9367 2.2 31.1 1.0 O 0:HOH3093 2.2 36.1 1.0 C6 0:G456 3.1 44.5 1.0 P 0:A459 3.2 36.7 1.0 C5 0:G456 3.8 42.8 1.0 N7 0:G456 3.8 41.6 1.0 OP2 0:A459 3.9 36.6 1.0 O5' 0:A459 4.0 36.1 1.0 CE C:LYS85 4.1 33.5 1.0 NZ C:LYS85 4.2 34.8 1.0 OP2 0:A455 4.2 35.4 1.0 N1 0:G456 4.3 46.5 1.0 C5' 0:A459 4.3 36.6 1.0 O3' 0:G458 4.4 37.5 1.0 N7 0:A455 4.5 43.5 1.0 O 0:HOH6224 4.5 58.9 1.0 O 0:HOH3819 4.5 58.6 1.0 O 0:HOH9653 4.6 46.4 1.0 CD C:LYS85 4.6 34.5 1.0 OP1 0:A460 4.7 38.6 1.0 O 0:HOH5682 4.7 49.5 1.0 O 0:HOH4007 4.7 48.6 1.0 OP1 0:A477 4.7 39.7 1.0 C5' 0:U454 4.9 37.5 1.0 O 0:HOH7932 5.0 29.1 1.0

Magnesium binding site 5 out of 117 in the The Structure of the Transition State Analogue "Daa" Bound to 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 The Structure of the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8005 b:37.8 occ:1.00 O 0:HOH7948 2.0 37.5 1.0 OP2 0:A1839 2.0 32.0 1.0 O 0:HOH3915 2.0 30.7 1.0 OP1 0:A1836 2.1 31.6 1.0 OP1 0:U1838 2.1 36.2 1.0 O 0:HOH7947 2.1 48.3 1.0 P 0:A1839 3.5 33.6 1.0 P 0:A1836 3.5 33.0 1.0 P 0:U1838 3.6 33.0 1.0 O 0:HOH9328 4.0 29.4 1.0 O 0:HOH5836 4.1 49.5 1.0 O5' 0:A1836 4.2 32.4 1.0 O5' 0:A1839 4.2 33.4 1.0 O 0:HOH5777 4.3 43.2 1.0 C2' 0:U1835 4.3 34.5 1.0 O5' 0:U1838 4.3 33.8 1.0 O3' 0:U1838 4.3 33.6 1.0 OP2 0:U1838 4.3 34.5 1.0 OP1 0:A1839 4.4 34.8 1.0 C3' 0:G1837 4.4 36.8 1.0 O 0:HOH9832 4.4 48.2 1.0 OP2 0:A1836 4.4 36.4 1.0 O3' 0:U1835 4.4 32.0 1.0 OP2 0:G1837 4.5 37.6 1.0 O3' 0:G1837 4.5 35.7 1.0 O 0:HOH9955 4.5 46.7 1.0 C3' 0:U1835 4.5 32.7 1.0 C5' 0:U1838 4.6 32.8 1.0 O 0:HOH8129 4.6 38.4 1.0 N7 0:A1839 4.6 34.0 1.0 C3' 0:U1838 4.6 34.1 1.0 O2' 0:U1835 4.6 33.9 1.0 C8 0:A1839 4.7 35.7 1.0

Magnesium binding site 6 out of 117 in the The Structure of the Transition State Analogue "Daa" Bound to 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 The Structure of the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8006 b:33.6 occ:1.00 OP2 0:C822 2.0 44.0 1.0 OP1 0:G854 2.1 40.7 1.0 O 0:HOH3921 2.1 34.7 1.0 OP2 0:U821 2.1 41.5 1.0 O 0:HOH3124 2.2 41.8 1.0 O 0:HOH4058 2.5 40.6 1.0 P 0:G854 3.3 41.0 1.0 P 0:C822 3.4 44.0 1.0 P 0:U821 3.5 40.8 1.0 O 0:HOH3511 3.8 53.9 1.0 O5' 0:G854 3.8 39.5 1.0 OP1 0:G856 3.9 45.8 1.0 O5' 0:U821 3.9 43.8 1.0 OP2 0:G854 4.0 38.2 1.0 O3' 0:U821 4.0 45.0 1.0 NA 0:NA9127 4.1 35.4 1.0 C3' 0:U821 4.1 43.0 1.0 OP1 0:C822 4.2 44.8 1.0 OP1 0:U855 4.2 42.2 1.0 C5' 0:G854 4.2 38.3 1.0 O3' 0:G820 4.3 41.0 1.0 O5' 0:C822 4.4 41.6 1.0 O 0:HOH5292 4.5 48.1 1.0 O3' 0:C853 4.6 41.0 1.0 OP1 0:U821 4.6 41.1 1.0

Magnesium binding site 7 out of 117 in the The Structure of the Transition State Analogue "Daa" Bound to 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 The Structure of the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8007 b:24.9 occ:1.00 OP2 0:U832 1.9 40.7 1.0 O 0:HOH7936 2.0 28.4 1.0 OP1 0:A1839 2.1 34.8 1.0 O 0:HOH3665 2.2 48.6 1.0 OP2 0:A1840 2.3 31.5 1.0 O 0:HOH9328 2.3 29.4 1.0 P 0:A1840 3.3 33.4 1.0 P 0:U832 3.4 38.3 1.0 P 0:A1839 3.5 33.6 1.0 OP1 0:A1840 3.6 31.6 1.0 O 0:HOH6605 3.6 47.8 1.0 O 0:HOH9419 4.0 61.7 1.0 O5' 0:U832 4.1 41.1 1.0 O3' 0:A1839 4.2 31.8 1.0 OP1 0:U832 4.2 39.2 1.0 O 0:HOH9955 4.3 46.7 1.0 OP2 0:A1839 4.3 32.0 1.0 O3' 0:U1838 4.3 33.6 1.0 OP2 0:G833 4.3 41.4 1.0 O3' 0:U831 4.4 40.1 1.0 O5' 0:A1839 4.5 33.4 1.0 O5' 0:A1840 4.6 33.6 1.0 O 0:HOH8158 4.7 58.5 1.0 C5' 0:U832 4.7 41.9 1.0 C3' 0:A1839 4.7 32.9 1.0 C5' 0:A1839 4.7 33.2 1.0 O 0:HOH8129 4.8 38.4 1.0 C3' 0:U831 4.9 41.0 1.0

Magnesium binding site 8 out of 117 in the The Structure of the Transition State Analogue "Daa" Bound to 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 The Structure of the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8008 b:37.3 occ:1.00 O 0:HOH8130 1.9 48.9 1.0 OP1 0:U919 1.9 34.7 1.0 O 0:HOH3934 2.1 40.3 1.0 O 0:HOH7940 2.2 50.7 1.0 OP1 0:C2464 2.2 38.3 1.0 OP1 0:A2465 2.2 38.2 1.0 P 0:U919 3.0 36.0 1.0 OP2 0:U919 3.4 35.8 1.0 P 0:A2465 3.6 40.8 1.0 P 0:C2464 3.6 38.8 1.0 O5' 0:U919 3.6 33.2 1.0 O 0:HOH9867 3.9 45.5 1.0 O 0:HOH6157 4.1 62.9 1.0 O5' 0:A2465 4.1 38.8 1.0 O5' 0:C2464 4.2 39.8 1.0 C5' 0:U919 4.2 32.1 1.0 O 0:HOH3655 4.2 35.2 1.0 OP2 0:A2465 4.2 39.3 1.0 C5' 0:C2464 4.3 39.8 1.0 O 0:HOH9769 4.3 40.0 1.0 O3' 0:G918 4.3 36.6 1.0 OP2 0:C2464 4.4 40.4 1.0 OP1 0:G2466 4.4 41.7 1.0 O 0:HOH6592 4.5 51.7 1.0 C3' 0:A2465 4.5 37.4 1.0 O3' 0:A2463 4.6 41.2 1.0 O3' 0:C2464 4.8 39.8 1.0 C2' 0:A2465 4.8 38.4 1.0 O 0:HOH3239 4.8 47.8 1.0 C5' 0:A2465 4.8 36.2 1.0

Magnesium binding site 9 out of 117 in the The Structure of the Transition State Analogue "Daa" Bound to 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 The Structure of the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8009 b:35.2 occ:1.00 O 0:HOH7623 1.9 32.2 1.0 O 0:HOH7942 2.1 36.2 1.0 O 0:HOH4043 2.1 26.3 1.0 OP1 0:A2612 2.1 30.8 1.0 OP1 0:G2611 2.2 32.5 1.0 O 0:HOH7941 2.3 34.7 1.0 P 0:G2611 3.4 31.4 1.0 O3' 0:U2610 3.4 31.9 1.0 NA 0:NA9158 3.4 84.2 1.0 P 0:A2612 3.6 33.6 1.0 OP2 0:G2093 3.8 32.7 1.0 OP2 0:G2094 3.9 28.9 1.0 O 0:HOH9654 4.0 52.3 1.0 OP1 0:G2094 4.0 31.0 1.0 O 0:HOH9787 4.1 33.6 1.0 C5' 0:G2611 4.3 30.3 1.0 O5' 0:G2611 4.3 30.7 1.0 O 0:HOH9624 4.3 31.6 1.0 OP2 0:A2612 4.4 36.7 1.0 P 0:G2094 4.4 30.7 1.0 O5' 0:A2612 4.5 36.4 1.0 O3' 0:G2611 4.5 31.4 1.0 OP2 0:G2611 4.5 33.5 1.0 C3' 0:U2610 4.7 33.1 1.0 C3' 0:G2611 4.8 29.1 1.0 O 0:HOH7957 4.9 48.0 1.0 C4' 0:U2610 4.9 33.9 1.0 O3' 0:G2093 4.9 30.5 1.0

Magnesium binding site 10 out of 117 in the The Structure of the Transition State Analogue "Daa" Bound to 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 The Structure of the Transition State Analogue "Daa" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8010 b:29.8 occ:1.00 O B:HOH9326 1.8 48.2 1.0 O 0:HOH4143 1.9 39.3 1.0 OP1 0:G836 2.0 29.6 1.0 OP1 0:U2615 2.1 33.1 1.0 OE1 B:GLN230 2.4 34.8 1.0 O 0:HOH9682 2.5 36.3 1.0 P 0:G836 3.4 34.8 1.0 CD B:GLN230 3.5 34.9 1.0 P 0:U2615 3.6 36.4 1.0 O B:HOH9439 3.8 44.5 1.0 CB B:GLN230 4.0 35.9 1.0 CG B:GLN230 4.1 33.8 1.0 OP2 0:G836 4.2 34.2 1.0 C5' 0:G836 4.2 33.6 1.0 O 0:HOH5337 4.2 61.5 1.0 O5' 0:G836 4.2 33.6 1.0 O 0:HOH9523 4.2 39.7 1.0 OP2 0:U2615 4.3 35.6 1.0 O 0:HOH4299 4.4 44.6 1.0 O3' 0:C2614 4.4 36.0 1.0 O3' 0:U835 4.5 33.2 1.0 C3' 0:U835 4.5 30.7 1.0 O5' 0:U2615 4.5 37.7 1.0 CA B:GLN230 4.6 36.0 1.0 O B:GLN230 4.6 37.9 1.0 NE2 B:GLN230 4.6 36.4 1.0 OP2 0:G2616 4.9 35.5 1.0 C5' 0:U835 5.0 34.7 1.0

T.M.Schmeing, K.S.Huang, D.E.Kitchen, S.A.Strobel, T.A.Steitz. Structural Insights Into the Roles of Water and the 2' Hydroxyl of the P Site Trna in the Peptidyl Transferase Reaction. Mol.Cell V. 20 437 2005.
ISSN: ISSN 1097-2765
PubMed: 16285925
DOI: 10.1016/J.MOLCEL.2005.09.006