Magnesium in PDB 6prv: 58NT Rna L11-Binding Domain From E. Coli 23S Rrna

The structure of 58NT Rna L11-Binding Domain From E. Coli 23S Rrna, PDB code: 6prv was solved by G.L.Conn, M.S.Dunstan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.36 / 2.71
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.610, 73.610, 130.280, 90.00, 100.96, 90.00
R / Rfree (%)	20.4 / 26

The structure of 58NT Rna L11-Binding Domain From E. Coli 23S Rrna also contains other interesting chemical elements:

Potassium

(K)

3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Magnesium atom in the 58NT Rna L11-Binding Domain From E. Coli 23S Rrna (pdb code 6prv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 22 binding sites of Magnesium where determined in the 58NT Rna L11-Binding Domain From E. Coli 23S Rrna, PDB code: 6prv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 22 in the 58NT Rna L11-Binding Domain From E. Coli 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 58NT Rna L11-Binding Domain From E. Coli 23S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1201 b:68.0 occ:1.00 O4 A:U1094 1.8 95.5 1.0 OP2 A:A1073 2.2 73.8 1.0 C4 A:U1094 3.0 56.3 1.0 O6 A:G1093 3.5 79.1 1.0 P A:A1073 3.6 63.6 1.0 N3 A:U1094 3.6 52.8 1.0 OP2 A:U1097 3.8 63.0 1.0 OP1 A:A1096 4.0 53.4 1.0 C5 A:U1094 4.1 60.5 1.0 OP1 A:A1073 4.2 65.4 1.0 C6 A:G1093 4.2 61.5 1.0 O3' A:C1072 4.5 67.8 1.0 N1 A:G1093 4.6 67.5 1.0 C3' A:C1072 4.6 63.8 1.0 O5' A:A1073 4.6 54.1 1.0 O5' A:A1096 4.7 52.8 1.0 C2 A:A1069 4.8 61.2 1.0 P A:A1096 4.8 79.2 1.0 P A:U1097 4.9 61.9 1.0 C2' A:C1072 4.9 65.3 1.0 OP1 A:U1097 5.0 66.1 1.0 N3 A:A1069 5.0 53.7 1.0 C5' A:A1096 5.0 64.2 1.0 C2 A:U1094 5.0 61.3 1.0

Magnesium binding site 2 out of 22 in the 58NT Rna L11-Binding Domain From E. Coli 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 58NT Rna L11-Binding Domain From E. Coli 23S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1202 b:63.5 occ:1.00 OP2 A:A1070 2.1 82.2 1.0 OP1 A:C1072 2.5 70.2 1.0 P A:A1070 3.2 54.3 1.0 OP1 A:A1070 3.6 54.5 1.0 P A:C1072 3.6 73.8 1.0 OP1 A:G1062 3.8 75.9 1.0 O5' A:A1070 4.0 54.1 1.0 O3' A:G1071 4.0 73.7 1.0 O6 A:G1062 4.0 57.1 1.0 N7 A:G1062 4.2 64.0 1.0 O6 A:G1063 4.2 76.3 1.0 OP2 A:C1072 4.2 84.8 1.0 O6 A:G1074 4.3 86.2 1.0 C5' A:A1070 4.4 53.9 1.0 K A:K1210 4.4 84.7 1.0 O3' A:A1069 4.5 0.0 1.0 C6 A:G1062 4.6 57.4 1.0 C5 A:G1062 4.7 55.7 1.0 N4 A:C1064 4.9 72.2 1.0 O5' A:C1072 4.9 68.3 1.0 N4 A:C1075 5.0 55.6 1.0

Magnesium binding site 3 out of 22 in the 58NT Rna L11-Binding Domain From E. Coli 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 58NT Rna L11-Binding Domain From E. Coli 23S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1203 b:90.1 occ:1.00 OP2 A:C1102 3.7 61.1 1.0 O6 A:G1056 3.8 53.6 1.0 OP1 A:C1102 3.9 78.6 1.0 N7 A:A1054 3.9 60.0 1.0 O6 A:G1055 4.3 72.0 1.0 N6 A:A1054 4.4 54.7 1.0 P A:C1102 4.4 79.4 1.0 C6 A:G1056 4.4 53.8 1.0 N7 A:G1055 4.5 56.7 1.0 N1 A:G1056 4.6 60.9 1.0 C5 A:A1054 4.7 54.4 1.0 C8 A:A1054 4.8 60.6 1.0 C6 A:A1054 4.9 61.5 1.0

Magnesium binding site 4 out of 22 in the 58NT Rna L11-Binding Domain From E. Coli 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 58NT Rna L11-Binding Domain From E. Coli 23S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1204 b:73.3 occ:1.00 OP2 A:G1087 2.9 89.7 1.0 O2' A:A1086 3.0 76.2 1.0 N7 A:G1087 3.0 74.5 1.0 C2' A:A1086 3.4 68.9 1.0 N7 A:A1057 3.5 77.0 1.0 C8 A:G1087 3.7 59.4 1.0 O3' A:A1086 4.1 63.0 1.0 P A:G1087 4.1 80.4 1.0 C5 A:G1087 4.1 55.1 1.0 C3' A:A1086 4.2 74.7 1.0 OP2 A:A1057 4.3 71.0 1.0 N6 A:A1057 4.3 86.6 1.0 C8 A:A1057 4.4 70.0 1.0 N6 A:A1089 4.5 56.6 1.0 O6 A:G1087 4.5 81.2 1.0 C5 A:A1057 4.5 69.1 1.0 O2' A:G1056 4.5 0.6 1.0 O5' A:G1087 4.6 58.1 1.0 C1' A:A1086 4.7 84.5 1.0 C6 A:G1087 4.7 58.3 1.0 O3' A:G1056 4.8 95.9 1.0 C6 A:A1089 4.8 67.9 1.0 C6 A:A1057 4.9 68.1 1.0 N1 A:A1103 4.9 61.4 1.0 C5 A:A1089 5.0 54.6 1.0 N7 A:A1089 5.0 61.7 1.0

Magnesium binding site 5 out of 22 in the 58NT Rna L11-Binding Domain From E. Coli 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 58NT Rna L11-Binding Domain From E. Coli 23S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1205 b:92.8 occ:1.00 OP1 A:A1069 3.4 75.7 1.0 OP2 A:A1069 3.7 74.7 1.0 P A:A1069 3.8 69.4 1.0 O4 A:U1065 4.2 91.8 1.0 O5' A:A1069 4.2 87.0 1.0 O4 A:U1066 4.5 95.6 1.0 O2 A:U1061 4.6 92.1 1.0

Magnesium binding site 6 out of 22 in the 58NT Rna L11-Binding Domain From E. Coli 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 58NT Rna L11-Binding Domain From E. Coli 23S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1206 b:88.6 occ:1.00 OP1 C:U1081 2.3 0.0 1.0 OP1 A:G1059 2.6 93.2 1.0 OP2 A:U1060 2.7 73.9 1.0 P C:U1081 3.6 0.1 1.0 O5' C:U1081 4.0 90.0 1.0 P A:G1059 4.0 64.9 1.0 OP2 C:U1082 4.1 0.9 1.0 P A:U1060 4.1 80.2 1.0 C5' C:U1081 4.2 92.0 1.0 OP2 C:U1081 4.5 0.6 1.0 OP1 A:U1061 4.5 81.8 1.0 C5' A:G1059 4.5 66.4 1.0 O5' A:G1059 4.6 62.0 1.0 OP2 A:G1059 4.7 54.1 1.0 O3' C:A1080 4.7 99.7 1.0 OP1 A:U1060 4.8 68.5 1.0 C5' A:U1060 4.8 59.0 1.0 O5' A:U1060 4.8 88.7 1.0 P C:U1082 4.9 0.6 1.0 OP1 C:U1082 4.9 0.4 1.0 C3' A:U1060 5.0 71.5 1.0

Magnesium binding site 7 out of 22 in the 58NT Rna L11-Binding Domain From E. Coli 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 58NT Rna L11-Binding Domain From E. Coli 23S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1207 b:91.4 occ:0.50 OP1 A:C1052 2.3 0.9 1.0 P A:C1052 3.6 82.1 1.0 O5' A:C1052 4.0 78.5 1.0 C5' A:C1052 4.1 79.3 1.0 O3' A:GTP1051 4.4 86.8 1.0 OP2 A:C1052 4.4 92.4 1.0

Magnesium binding site 8 out of 22 in the 58NT Rna L11-Binding Domain From E. Coli 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 58NT Rna L11-Binding Domain From E. Coli 23S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1208 b:84.0 occ:1.00 OP2 A:G1099 4.3 73.0 1.0 N7 A:G1071 4.4 59.3 1.0 O6 A:G1071 4.6 92.3 1.0

Magnesium binding site 9 out of 22 in the 58NT Rna L11-Binding Domain From E. Coli 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of 58NT Rna L11-Binding Domain From E. Coli 23S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1209 b:92.0 occ:1.00 O2 A:U1060 3.1 90.7 1.0 N7 A:G1059 3.5 55.2 1.0 O6 A:G1059 3.6 60.1 1.0 O2' A:U1060 3.7 71.0 1.0 O4 A:U1058 3.8 97.2 1.0 C2 A:U1060 4.0 83.3 1.0 C4 A:U1058 4.0 65.0 1.0 C5 A:G1059 4.2 55.5 1.0 C6 A:G1059 4.2 60.1 1.0 C8 A:A1088 4.4 80.4 1.0 C5 A:U1058 4.4 54.8 1.0 C8 A:G1059 4.6 55.1 1.0 N3 A:U1058 4.6 55.3 1.0 N3 A:U1060 4.7 73.5 1.0 N1 A:U1060 4.8 69.8 1.0 C2' A:U1060 4.8 69.8 1.0 C1' A:U1060 4.8 56.4 1.0 N7 A:A1088 4.9 91.4 1.0

Magnesium binding site 10 out of 22 in the 58NT Rna L11-Binding Domain From E. Coli 23S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of 58NT Rna L11-Binding Domain From E. Coli 23S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1201 b:69.0 occ:1.00 OP2 B:A1073 1.9 90.1 1.0 O4 B:U1094 2.0 95.9 1.0 O B:HOH1302 2.6 70.0 1.0 O6 B:G1093 3.2 74.6 1.0 C4 B:U1094 3.2 88.3 1.0 P B:A1073 3.3 81.6 1.0 O3' B:C1072 3.8 73.2 1.0 C3' B:C1072 3.8 69.0 1.0 C2' B:C1072 4.0 69.2 1.0 C6 B:G1093 4.1 68.5 1.0 C5 B:U1094 4.1 84.5 1.0 N3 B:U1094 4.2 66.9 1.0 O5' B:A1073 4.3 84.0 1.0 C5' B:A1073 4.4 72.3 1.0 OP1 B:A1073 4.4 75.7 1.0 N1 B:G1093 4.7 75.6 1.0 OP1 B:A1096 4.7 88.0 1.0 OP2 B:U1097 4.7 71.0 1.0 O2' B:C1072 4.8 69.9 1.0 C2 B:A1069 5.0 81.5 1.0

R.Welty, M.Rau, S.Pabit, M.S.Dunstan, G.L.Conn, L.Pollack, K.B.Hall. Ribosomal Protein L11 Selectively Stabilizes A Tertiary Structure of the Gtpase Center Rrna Domain. J.Mol.Biol. 2019.
ISSN: ESSN 1089-8638
PubMed: 31874150
DOI: 10.1016/J.JMB.2019.12.010