Magnesium in PDB 1vqn: The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

The structure of The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqn 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 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.721, 298.782, 575.272, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.8

The structure of The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Strontium	(Sr)	114 atoms
Potassium	(K)	2 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	75 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 - 94;

Binding sites:

The binding sites of Magnesium atom in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1vqn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 94 binding sites of Magnesium where determined in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 94 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8001 b:22.4 occ:1.00 O 0:HOH9802 1.9 24.8 1.0 O 0:HOH4212 2.0 47.3 1.0 OP2 0:C2533 2.1 48.9 1.0 OP2 0:C2534 2.3 40.0 1.0 O 0:HOH8301 2.3 37.5 1.0 OP2 0:A2483 2.5 44.4 1.0 O2' 0:A2532 3.3 42.2 1.0 P 0:C2533 3.4 45.1 1.0 O3' 0:G2482 3.5 42.3 1.0 P 0:A2483 3.5 42.1 1.0 O3' 0:A2532 3.6 45.0 1.0 P 0:C2534 3.7 40.0 1.0 OP2 0:U2484 4.1 53.4 1.0 O 0:HOH7931 4.2 61.1 1.0 O 0:HOH4905 4.3 23.2 1.0 O3' 0:C2533 4.3 39.9 1.0 OP1 0:C2534 4.4 40.5 1.0 O5' 0:C2533 4.4 43.8 1.0 C2' 0:A2532 4.4 43.0 1.0 OP1 0:C2533 4.4 47.2 1.0 OP1 0:A2483 4.4 43.0 1.0 C3' 0:A2532 4.5 42.7 1.0 O2' 0:G2482 4.5 45.1 1.0 C3' 0:C2533 4.6 39.5 1.0 O5' 0:A2483 4.8 44.9 1.0 O5' 0:C2534 4.8 38.2 1.0 OP2 0:A2485 4.8 49.5 1.0 C3' 0:G2482 4.8 42.2 1.0 O 0:HOH6886 4.9 95.6 1.0 C5' 0:A2483 4.9 43.5 1.0

Magnesium binding site 2 out of 94 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8002 b:34.6 occ:1.00 O 0:HOH8280 1.9 39.0 1.0 OP1 0:A2483 2.0 43.0 1.0 OP1 0:C2534 2.2 40.5 1.0 O6 0:G627 2.5 40.3 1.0 O 0:HOH9884 2.5 59.4 1.0 OP2 0:U2535 3.1 41.5 1.0 O 0:HOH8279 3.1 75.7 1.0 O 0:HOH4905 3.3 23.2 1.0 P 0:A2483 3.4 42.1 1.0 C6 0:G627 3.6 38.6 1.0 P 0:C2534 3.6 40.0 1.0 O3' 0:G2482 3.9 42.3 1.0 C3' 0:G2482 3.9 42.2 1.0 P 0:U2535 4.1 41.5 1.0 N1 0:G627 4.1 38.2 1.0 OP1 0:U2535 4.2 42.4 1.0 O5' 0:C2534 4.2 38.2 1.0 OP2 0:A2483 4.3 44.4 1.0 OP2 0:C2534 4.3 40.0 1.0 C5' 0:C2534 4.3 39.5 1.0 O5' 0:A2483 4.4 44.9 1.0 O 0:HOH6406 4.4 65.5 1.0 O 0:HOH4978 4.5 54.0 1.0 O 0:HOH3727 4.6 52.5 1.0 O3' 0:C2533 4.6 39.9 1.0 O2 0:C2071 4.6 46.2 1.0 O2' 0:G2482 4.7 45.1 1.0 C5 0:G627 4.7 38.6 1.0 C2' 0:G2482 4.8 41.8 1.0 O3' 0:C2534 4.8 41.7 1.0 O5' 0:G2482 5.0 40.0 1.0 O2' 0:U625 5.0 37.0 1.0

Magnesium binding site 3 out of 94 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8003 b:35.0 occ:1.00 OP1 0:A2624 2.1 32.1 1.0 O 0:HOH4261 2.1 39.2 1.0 OP2 0:G877 2.1 30.9 1.0 O A:HOH9500 2.2 23.0 1.0 OP2 0:A876 2.2 35.0 1.0 O A:HOH9524 2.3 41.1 1.0 P 0:G877 3.3 32.6 1.0 P 0:A2624 3.5 28.6 1.0 P 0:A876 3.6 33.2 1.0 OP1 0:G877 3.7 39.0 1.0 OD1 A:ASN195 4.0 30.4 1.0 O5' 0:A876 4.1 29.4 1.0 O 0:HOH6792 4.1 44.8 1.0 O3' 0:G2623 4.1 32.0 1.0 O3' 0:A875 4.1 32.0 1.0 O3' 0:A876 4.2 33.3 1.0 OP2 0:A2624 4.3 38.5 1.0 O A:HOH9554 4.3 39.3 1.0 O A:ALA193 4.4 34.5 1.0 C5' 0:A876 4.4 30.3 1.0 O A:HOH9609 4.4 53.9 1.0 O5' 0:G877 4.5 33.5 1.0 O5' 0:A2624 4.6 36.4 1.0 C5' 0:A2624 4.7 33.0 1.0 C3' 0:A876 4.7 33.4 1.0 MG 0:MG8013 4.8 25.4 1.0 OP1 0:A876 4.8 36.5 1.0 O A:HOH9614 4.8 47.3 1.0 CG A:ASN195 4.8 27.3 1.0 O A:HOH9534 4.9 47.9 1.0

Magnesium binding site 4 out of 94 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8004 b:36.0 occ:1.00 OP1 0:A459 2.0 33.5 1.0 O 0:HOH4376 2.0 33.8 1.0 O 0:HOH9673 2.0 27.8 1.0 O 0:HOH3387 2.1 40.4 1.0 O6 0:G456 2.1 39.1 1.0 O 0:HOH8286 2.2 27.2 1.0 C6 0:G456 3.2 39.5 1.0 P 0:A459 3.4 35.2 1.0 C5 0:G456 4.0 39.2 1.0 N7 0:G456 4.1 38.7 1.0 OP2 0:A459 4.1 37.1 1.0 O5' 0:A459 4.1 34.9 1.0 O 0:HOH4114 4.2 44.7 1.0 C5' 0:A459 4.2 36.1 1.0 CE C:LYS85 4.3 30.9 1.0 O 0:HOH4298 4.3 45.8 1.0 N1 0:G456 4.3 41.5 1.0 NZ C:LYS85 4.4 35.0 1.0 N7 0:A455 4.4 39.6 1.0 OP1 0:A460 4.4 38.1 1.0 OP2 0:A455 4.4 31.5 1.0 O 0:HOH6485 4.5 83.0 1.0 O3' 0:G458 4.5 36.9 1.0 O 0:HOH9957 4.5 32.1 1.0 OP1 0:A477 4.6 39.8 1.0 O 0:HOH5950 4.8 48.5 1.0 CD C:LYS85 4.8 33.7 1.0 OP2 0:A477 5.0 36.5 1.0 C5' 0:U454 5.0 32.7 1.0 N6 0:A455 5.0 37.4 1.0

Magnesium binding site 5 out of 94 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8005 b:29.5 occ:1.00 OP2 0:A1839 2.0 34.8 1.0 OP1 0:U1838 2.0 32.3 1.0 O 0:HOH8302 2.1 30.8 1.0 O 0:HOH4208 2.1 26.4 1.0 OP1 0:A1836 2.1 31.9 1.0 O 0:HOH8303 2.2 32.6 1.0 P 0:A1839 3.4 33.0 1.0 P 0:U1838 3.5 30.6 1.0 P 0:A1836 3.6 32.1 1.0 O 0:HOH9635 3.9 29.7 1.0 O 0:HOH6044 4.1 34.7 1.0 O5' 0:A1839 4.1 35.2 1.0 O5' 0:U1838 4.2 34.7 1.0 O3' 0:U1838 4.2 34.4 1.0 O 0:HOH6101 4.3 46.3 1.0 O5' 0:A1836 4.3 36.5 1.0 O 0:HOH3134 4.3 51.8 1.0 OP2 0:U1838 4.3 33.1 1.0 C2' 0:U1835 4.3 33.0 1.0 C3' 0:G1837 4.3 36.1 1.0 C3' 0:U1838 4.4 31.9 1.0 C5' 0:U1838 4.4 31.5 1.0 OP2 0:A1836 4.4 35.5 1.0 O3' 0:G1837 4.4 33.2 1.0 OP1 0:A1839 4.4 35.0 1.0 O 0:HOH8375 4.5 38.8 1.0 O3' 0:U1835 4.5 32.1 1.0 O 0:HOH3257 4.5 35.3 1.0 OP2 0:G1837 4.6 34.6 1.0 C3' 0:U1835 4.6 32.2 1.0 N7 0:A1839 4.6 33.5 1.0 O2' 0:U1835 4.7 39.6 1.0 C8 0:A1839 4.7 33.7 1.0

Magnesium binding site 6 out of 94 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8008 b:16.0 occ:1.00 O 0:HOH8376 1.8 50.3 1.0 OP1 0:A2465 2.1 49.4 1.0 O 0:HOH4225 2.1 35.1 1.0 OP1 0:C2464 2.1 46.1 1.0 OP1 0:U919 2.3 35.2 1.0 O 0:HOH8295 2.5 33.1 1.0 P 0:C2464 3.4 44.1 1.0 P 0:A2465 3.5 48.2 1.0 P 0:U919 3.5 34.0 1.0 OP2 0:U919 3.9 35.7 1.0 O5' 0:C2464 4.0 46.6 1.0 OP2 0:C2464 4.0 47.9 1.0 O 0:HOH3169 4.1 46.2 1.0 O5' 0:A2465 4.1 49.3 1.0 OP2 0:A2465 4.1 51.7 1.0 C5' 0:C2464 4.2 45.9 1.0 O5' 0:U919 4.3 34.3 1.0 O 0:HOH3072 4.3 39.6 1.0 O 0:HOH3948 4.4 40.8 1.0 O 0:HOH6418 4.4 77.2 1.0 O 0:HOH3530 4.5 67.7 1.0 O3' 0:C2464 4.6 48.4 1.0 O3' 0:A2463 4.6 47.4 1.0 OP1 0:G2466 4.7 43.6 1.0 O3' 0:G918 4.8 36.2 1.0 C3' 0:A2465 4.8 44.3 1.0 C5' 0:U919 4.9 34.7 1.0 C3' 0:C2464 4.9 46.8 1.0 OP1 0:G2293 4.9 49.5 1.0 C5' 0:G2293 5.0 47.6 1.0 C2' 0:A2465 5.0 43.2 1.0 C5' 0:A2465 5.0 46.0 1.0

Magnesium binding site 7 out of 94 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8009 b:21.2 occ:1.00 O 0:HOH7886 2.0 60.9 1.0 OP1 0:G2611 2.2 43.6 1.0 O 0:HOH8296 2.5 47.2 1.0 O 0:HOH4332 2.5 54.9 1.0 NA 0:NA9158 2.5 66.0 1.0 O 0:HOH9958 2.5 39.7 1.0 OP1 0:A2612 2.6 37.9 1.0 O3' 0:U2610 3.3 41.6 1.0 P 0:G2611 3.4 41.6 1.0 P 0:A2612 3.9 35.5 1.0 O 0:HOH8312 4.0 64.8 1.0 OP1 0:G2094 4.1 32.8 1.0 C5' 0:G2611 4.1 35.4 1.0 O 0:HOH8297 4.2 50.9 1.0 O5' 0:G2611 4.2 37.8 1.0 O 0:HOH9929 4.3 11.2 1.0 OP2 0:A2612 4.4 39.4 1.0 OP2 0:G2094 4.4 28.9 1.0 C3' 0:U2610 4.5 37.8 1.0 O 0:HOH3090 4.5 34.0 1.0 OP2 0:G2611 4.6 41.7 1.0 C4' 0:U2610 4.6 38.2 1.0 O3' 0:G2611 4.7 36.2 1.0 O 0:HOH3107 4.7 53.4 1.0 C3' 0:G2611 4.7 32.3 1.0 P 0:G2094 4.8 29.1 1.0 OP2 0:G2093 4.8 34.7 1.0 C5' 0:U2610 4.8 35.1 1.0 O5' 0:A2612 5.0 39.3 1.0

Magnesium binding site 8 out of 94 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8012 b:39.6 occ:1.00 O 0:HOH3258 2.0 40.4 1.0 OP1 0:G28 2.1 42.2 1.0 O 0:HOH9665 2.2 47.3 1.0 O 0:HOH4243 2.4 37.8 1.0 O 0:HOH3830 2.5 55.3 1.0 O 0:HOH8377 2.6 61.4 1.0 P 0:G28 3.4 39.3 1.0 OP1 0:U1304 3.7 42.7 1.0 O3' 0:U27 4.0 38.3 1.0 OP2 0:G28 4.1 44.3 1.0 OP1 0:C1343 4.2 44.7 1.0 OP2 0:G1344 4.2 50.2 1.0 O 0:HOH4610 4.3 71.9 1.0 O 0:HOH3726 4.4 37.5 1.0 OP2 0:C1305 4.6 38.8 1.0 O5' 0:G28 4.7 41.5 1.0 OP1 0:C1305 4.7 38.1 1.0

Magnesium binding site 9 out of 94 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8013 b:25.4 occ:1.00 OP1 0:G877 2.1 39.0 1.0 OP1 0:G2623 2.2 36.6 1.0 O A:HOH9614 2.3 47.3 1.0 O 0:HOH4237 2.5 39.8 1.0 O 0:HOH4250 3.0 40.0 1.0 OP2 0:A2624 3.3 38.5 1.0 P 0:G877 3.5 32.6 1.0 P 0:G2623 3.6 34.3 1.0 O A:HOH9524 3.6 41.1 1.0 O 0:HOH8310 3.9 0.6 1.0 P 0:A2624 4.1 28.6 1.0 O5' 0:G2623 4.2 35.5 1.0 C5' 0:G2623 4.3 34.7 1.0 O3' 0:G2623 4.3 32.0 1.0 O5' 0:G877 4.3 33.5 1.0 OP1 0:A2624 4.3 32.1 1.0 OP2 0:G877 4.3 30.9 1.0 OP2 0:G2623 4.4 37.8 1.0 C5' 0:G877 4.4 31.6 1.0 O3' 0:A876 4.5 33.3 1.0 OD1 A:ASN195 4.5 30.4 1.0 O3' 0:A2622 4.6 33.7 1.0 O6 0:G885 4.7 34.3 1.0 OP2 0:C2475 4.7 40.2 1.0 MG 0:MG8003 4.8 35.0 1.0 C3' 0:G2623 4.9 33.4 1.0 O 0:HOH9861 4.9 42.3 1.0 O A:HOH9601 5.0 82.3 1.0

Magnesium binding site 10 out of 94 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8014 b:73.0 occ:1.00 OP2 0:G2537 2.8 43.0 1.0 O 0:HOH4211 2.8 63.1 1.0 O 0:HOH8277 2.9 53.0 1.0 O2' 0:A2101 3.0 50.9 1.0 O 0:HOH9659 3.1 58.1 1.0 O5' 0:G2102 3.2 53.6 1.0 O3' 0:A2101 3.2 52.5 1.0 O 0:HOH4254 3.6 56.1 1.0 O 0:HOH3436 3.6 39.2 1.0 P 0:G2102 3.8 53.7 1.0 C2' 0:A2101 4.0 49.7 1.0 OP2 0:G2102 4.1 56.2 1.0 P 0:G2537 4.1 43.3 1.0 C3' 0:A2101 4.1 50.8 1.0 C3' 0:G2102 4.3 47.9 1.0 C5' 0:G2102 4.4 48.9 1.0 O 0:HOH4750 4.4 0.3 1.0 C1' 0:A2101 4.5 48.1 1.0 OP1 0:A2103 4.6 52.4 1.0 O 0:HOH3114 4.6 36.3 1.0 N7 0:G2480 4.7 34.2 1.0 OP1 0:G2537 4.7 44.4 1.0 O C:HOH9123 4.7 75.6 1.0 C5' 0:G2537 4.7 45.3 1.0 C4' 0:G2102 4.9 49.4 1.0 N3 0:A2101 4.9 47.6 1.0 O5' 0:G2537 5.0 42.8 1.0 C8 0:G2480 5.0 34.3 1.0

T.M.Schmeing, K.S.Huang, S.A.Strobel, T.A.Steitz. An Induced-Fit Mechanism to Promote Peptide Bond Formation and Exclude Hydrolysis of Peptidyl-Trna. Nature V. 438 520 2005.
ISSN: ISSN 0028-0836
PubMed: 16306996
DOI: 10.1038/NATURE04152