Magnesium in PDB 5br8: Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin

The structure of Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin, PDB code: 5br8 was solved by R.G.Sierra, C.Gati, H.Laksmono, E.H.Dao, S.Gul, F.Fuller, J.Kern, R.Chatterjee, M.Ibrahim, A.Brewster, I.D.Young, T.Michels-Clark, A.Aquila, L.Mengning, M.S.Hunter, J.E.Koglin, S.Boutet, E.A.Junco, B.Hayes, M.J.Bogan, C.Y.Hampton, E.V.Puglisi, N.K.Sauter, C.A.Stan, A.Zouni, J.Yano, V.K.Yachandra, S.M.Soltis, J.D.Puglisi, H.Demirci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.84 / 3.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.300, 401.300, 176.400, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.4

The structure of Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin also contains other interesting chemical elements:

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 - 220; Page 23, Binding sites: 221 - 230; Page 24, Binding sites: 231 - 240; Page 25, Binding sites: 241 - 250; Page 26, Binding sites: 251 - 260; Page 27, Binding sites: 261 - 270; Page 28, Binding sites: 271 - 280; Page 29, Binding sites: 281 - 287;

Binding sites:

The binding sites of Magnesium atom in the Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin (pdb code 5br8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 287 binding sites of Magnesium where determined in the Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin, PDB code: 5br8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 287 in the Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1607 b:0.8 occ:1.00 O A:HOH2019 2.1 42.0 1.0 O A:HOH2182 2.1 60.7 1.0 O A:HOH2170 2.1 74.4 1.0 O A:HOH1993 2.1 53.5 1.0 N7 A:G376 3.4 82.8 1.0 O6 A:G377 3.6 75.5 1.0 N7 A:G377 3.9 0.0 1.0 O6 A:G376 3.9 76.7 1.0 C5 A:G376 4.0 81.1 1.0 C6 A:G376 4.2 78.8 1.0 C8 A:G376 4.2 79.3 1.0 C6 A:G377 4.4 81.6 1.0 C5 A:G377 4.6 94.2 1.0 O4 A:U375 4.7 0.8 1.0 C5 A:U375 4.8 0.3 1.0 C4 A:U375 4.8 0.2 1.0

Magnesium binding site 2 out of 287 in the Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1608 b:94.4 occ:1.00 O A:HOH2093 2.1 55.6 1.0 O O:HOH101 2.1 0.2 1.0 O A:HOH2123 2.1 88.8 1.0 N7 A:G650 3.3 99.5 1.0 O6 A:G650 3.5 0.1 1.0 N7 A:G649 3.8 0.3 1.0 OP2 A:A753 3.9 83.2 1.0 C5 A:G650 4.1 96.8 1.0 C6 A:G650 4.1 97.5 1.0 O6 A:G649 4.2 0.9 1.0 C8 A:G650 4.4 1.0 1.0 C5 A:G649 4.4 99.3 1.0 C6 A:G649 4.6 97.3 1.0 C8 A:G649 4.6 0.1 1.0 P A:A753 4.9 82.7 1.0

Magnesium binding site 3 out of 287 in the Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1609 b:0.2 occ:1.00 O A:HOH1985 2.1 89.5 1.0 O A:HOH1930 2.1 41.0 1.0 O A:HOH2059 2.1 82.0 1.0 O6 A:G752 3.2 0.2 1.0 OP2 A:G750 3.2 0.4 1.0 C6 A:G752 4.3 96.0 1.0 P A:G750 4.5 0.7 1.0 OP2 A:A653 4.5 80.3 1.0 OP2 A:C749 4.6 1.0 1.0 N1 A:G752 4.6 89.4 1.0 OP1 A:C749 4.8 0.6 1.0 N7 A:G750 4.9 0.1 1.0 OP1 A:G750 4.9 0.1 1.0

Magnesium binding site 4 out of 287 in the Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1610 b:0.9 occ:1.00 O A:HOH1910 2.1 0.4 1.0 O A:HOH1902 2.1 21.7 1.0 O A:HOH1991 2.1 89.7 1.0 OP2 A:G117 3.0 62.6 1.0 O5' A:A288 3.0 78.4 1.0 OP2 A:A288 3.3 81.3 1.0 OP2 A:G289 3.3 66.1 1.0 OP1 A:A116 3.5 62.8 1.0 P A:A288 3.6 75.2 1.0 C3' A:A288 3.6 61.7 1.0 OP1 A:A288 4.0 61.7 1.0 O3' A:A288 4.0 61.8 1.0 C5' A:A288 4.0 73.7 1.0 P A:G289 4.0 71.9 1.0 C8 A:A288 4.1 75.1 1.0 P A:G117 4.3 73.3 1.0 C4' A:A288 4.3 65.3 1.0 OP1 A:G289 4.5 62.3 1.0 C2' A:A288 4.6 61.6 1.0 P A:A116 4.7 72.5 1.0 N7 A:A288 4.7 79.2 1.0 N9 A:A288 4.8 70.1 1.0 O4' A:A288 4.9 66.2 1.0 OP2 A:A116 4.9 81.8 1.0 O4 A:U118 4.9 73.8 1.0 O3' A:A116 5.0 70.7 1.0 OP1 A:G117 5.0 86.2 1.0

Magnesium binding site 5 out of 287 in the Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1611 b:0.5 occ:1.00 O A:HOH1981 2.1 93.5 1.0 O A:HOH2000 2.1 77.2 1.0 O A:HOH1994 2.1 60.5 1.0 OP2 A:U49 2.8 91.7 1.0 OP2 A:C48 2.8 74.9 1.0 O5' A:C48 3.2 77.3 1.0 P A:C48 3.6 81.5 1.0 OP1 A:G115 4.1 75.5 1.0 OP1 A:A51 4.1 87.2 1.0 P A:U49 4.2 87.0 1.0 O3' A:C47 4.2 72.4 1.0 C5' A:C48 4.5 77.2 1.0 O5' A:U49 4.5 93.3 1.0 C4' A:C48 4.7 83.3 1.0 C3' A:C48 4.9 79.0 1.0 OP1 A:C48 4.9 76.0 1.0 O62 A:PAR1603 5.0 79.8 1.0

Magnesium binding site 6 out of 287 in the Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1612 b:0.9 occ:1.00 O A:HOH2041 2.1 74.7 1.0 O A:HOH2026 2.1 67.8 1.0 O A:HOH2120 2.1 77.4 1.0 OP2 A:G752 3.9 0.4 1.0 N7 A:G752 4.0 87.9 1.0 OP1 A:C651 4.3 99.8 1.0 C8 A:G752 4.3 82.3 1.0 OP2 A:C651 4.6 0.3 1.0 OP2 A:U751 4.8 88.3 1.0 OP1 A:U751 4.8 91.4 1.0 P A:C651 4.8 0.2 1.0 OP2 A:U652 4.9 95.0 1.0

Magnesium binding site 7 out of 287 in the Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1613 b:97.7 occ:1.00 O A:HOH2064 2.1 32.2 1.0 O A:HOH2186 2.1 57.9 1.0 O K:HOH201 2.1 53.3 1.0 O6 A:G800 3.4 82.3 1.0 OP2 A:A781 3.7 80.2 1.0 O6 A:G799 3.8 71.6 1.0 C6 A:G800 4.0 83.1 1.0 N1 A:G800 4.2 83.4 1.0 N7 A:G799 4.3 80.7 1.0 OP1 A:A781 4.7 82.2 1.0 C6 A:G799 4.7 76.9 1.0 P A:A781 4.7 77.8 1.0 C5 A:G799 4.9 77.1 1.0 O6 A:G798 4.9 70.5 1.0 O A:HOH1967 5.0 70.3 1.0

Magnesium binding site 8 out of 287 in the Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1614 b:84.1 occ:1.00 O2' A:C795 3.0 84.9 1.0 O2 A:U1506 3.1 73.6 1.0 O3' A:C795 3.2 70.7 1.0 O4' A:U1506 3.5 76.6 1.0 OP1 A:C796 3.7 74.6 1.0 C1' A:U1506 3.9 80.8 1.0 C2 A:U1506 4.0 78.0 1.0 C2' A:C795 4.1 76.6 1.0 P A:C796 4.2 83.0 1.0 C3' A:C795 4.2 69.8 1.0 C4' A:U1506 4.4 72.0 1.0 N1 A:U1506 4.5 83.3 1.0 O3' A:U1506 4.7 74.2 1.0 C5' A:C796 4.8 73.0 1.0 C4' A:C795 4.8 66.8 1.0 O5' A:C796 5.0 67.8 1.0

Magnesium binding site 9 out of 287 in the Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1615 b:51.3 occ:1.00 O A:HOH1922 2.1 30.9 1.0 OP1 A:G1508 2.7 81.6 1.0 OP1 A:A1500 2.8 66.6 1.0 OP1 A:G1505 2.9 79.9 1.0 O2' A:U1506 3.0 87.0 1.0 O5' A:G1505 3.5 77.1 1.0 C2' A:U1506 3.5 81.9 1.0 C5' A:G1505 3.5 77.8 1.0 O3' A:A1507 3.5 72.6 1.0 MG A:MG1773 3.6 48.9 1.0 P A:G1508 3.6 78.5 1.0 P A:G1505 3.8 67.3 1.0 P A:A1500 4.1 75.8 1.0 C6 A:U1506 4.2 87.4 1.0 C3' A:U1506 4.5 74.3 1.0 OP1 A:G1504 4.5 95.9 1.0 OP2 A:G1508 4.5 77.2 1.0 OP2 A:A1500 4.5 67.4 1.0 C1' A:U1506 4.7 80.8 1.0 O3' A:A1499 4.7 75.1 1.0 N1 A:U1506 4.8 83.3 1.0 C3' A:A1507 4.8 71.9 1.0 C4' A:G1505 4.8 78.7 1.0 O3' A:G1504 4.8 69.6 1.0 C5 A:U1506 4.9 87.6 1.0 O5' A:G1508 4.9 71.0 1.0 C3' A:G1504 4.9 67.0 1.0 OP2 A:G1505 4.9 67.3 1.0

Magnesium binding site 10 out of 287 in the Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1616 b:0.6 occ:1.00 O A:HOH1980 2.1 0.1 1.0 O A:HOH2192 2.1 81.7 1.0 O A:HOH2168 2.1 77.8 1.0 O A:HOH2126 2.1 55.9 1.0 O A:HOH2037 2.1 74.3 1.0 O6 A:G1526 3.5 90.5 1.0 N7 A:G1525 3.9 76.5 1.0 O6 A:G1525 4.0 76.4 1.0 C6 A:G1526 4.5 79.3 1.0 N7 A:G1526 4.5 91.6 1.0 C5 A:G1525 4.6 68.1 1.0 C6 A:G1525 4.6 67.7 1.0 C5 A:G1526 4.9 67.4 1.0 N4 A:C1524 4.9 67.7 1.0 C8 A:G1525 4.9 71.5 1.0 N4 A:C1509 4.9 79.9 1.0

R.G.Sierra, C.Gati, H.Laksmono, E.H.Dao, S.Gul, F.Fuller, J.Kern, R.Chatterjee, M.Ibrahim, A.Brewster, I.D.Young, T.Michels-Clark, A.Aquila, L.Mengning, M.S.Hunter, J.E.Koglin, S.Boutet, E.A.Junco, B.Hayes, M.J.Bogan, C.Y.Hampton, E.V.Puglisi, N.K.Sauter, C.A.Stan, A.Zouni, J.Yano, V.K.Yachandra, S.M.Soltis, J.D.Puglisi, H.Demirci. Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin To Be Published.