Magnesium in PDB 4kvb: Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17

The structure of Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17, PDB code: 4kvb was solved by E.L.Murphy, G.Jogl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.91 / 4.20
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	397.316, 397.316, 215.505, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 25.8

The structure of Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17 also contains other interesting chemical elements:

Potassium	(K)	35 atoms
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 - 158;

Binding sites:

The binding sites of Magnesium atom in the Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17 (pdb code 4kvb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 158 binding sites of Magnesium where determined in the Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17, PDB code: 4kvb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 158 in the Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1601 b:1.0 occ:1.00 OP2 A:A702 2.2 0.9 1.0 P A:A702 2.5 0.8 1.0 OP1 A:A702 2.6 0.4 1.0 O3' A:C701 2.8 0.3 1.0 C1' A:C701 3.6 0.9 1.0 O2' A:C701 3.7 0.4 1.0 C3' A:C701 3.9 1.0 1.0 C2' A:C701 4.0 0.2 1.0 O2 A:C701 4.0 0.5 1.0 O4' A:C701 4.1 0.5 1.0 O5' A:A702 4.1 0.6 1.0 C4' A:C701 4.3 0.6 1.0 N1 A:C701 4.7 0.9 1.0 C2 A:C701 4.8 0.3 1.0 O6 A:G703 4.8 0.1 1.0 C5' A:A702 4.9 0.1 1.0

Magnesium binding site 2 out of 158 in the Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1657 b:75.6 occ:1.00 OP2 A:A621 4.1 0.7 1.0 N7 A:G617 4.1 0.9 1.0 N7 A:G616 4.2 0.5 1.0 OP1 A:A621 4.4 0.2 1.0 NH2 D:ARG141 4.4 0.8 1.0 C8 A:G616 4.5 0.9 1.0 P A:A621 4.6 0.3 1.0 C5 A:G616 4.6 0.2 1.0 OP2 A:G617 4.6 0.3 1.0 O3' A:C620 4.7 0.2 1.0 OP1 A:C620 4.7 0.1 1.0 C5' A:C620 4.8 0.6 1.0 C8 A:G617 4.8 0.4 1.0 C6 A:G616 5.0 0.1 1.0

Magnesium binding site 3 out of 158 in the Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1602 b:0.9 occ:1.00 O6 A:G158 2.7 0.4 1.0 O6 A:G157 3.0 0.1 1.0 O4 A:U164 3.7 0.6 1.0 C6 A:G158 3.7 0.1 1.0 C6 A:G157 3.9 0.2 1.0 N7 A:G157 4.2 0.8 1.0 N7 A:G158 4.3 0.8 1.0 O6 A:G159 4.4 0.5 1.0 C5 A:G158 4.4 0.9 1.0 C5 A:G157 4.4 0.2 1.0 N3 A:U164 4.4 0.2 1.0 N4 A:C163 4.4 0.1 1.0 O6 A:G156 4.5 0.2 1.0 C4 A:U164 4.5 0.4 1.0 N1 A:G158 4.9 1.0 1.0 C6 A:G156 5.0 0.8 1.0

Magnesium binding site 4 out of 158 in the Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1658 b:0.1 occ:1.00 OP2 A:G567 2.8 0.7 1.0 OP2 A:C564 3.4 0.0 1.0 OP2 A:U565 3.8 1.0 1.0 OP1 A:U565 4.1 0.9 1.0 P A:G567 4.3 0.7 1.0 P A:U565 4.3 0.3 1.0 O2' A:A563 4.3 0.5 1.0 O3' A:A563 4.4 0.8 1.0 P A:C564 4.5 0.9 1.0 NH2 L:ARG15 4.5 0.4 1.0 N7 A:G567 4.6 1.0 1.0 O3' A:C564 4.7 0.1 1.0 C5' A:C564 4.7 0.2 1.0 C2' A:A563 4.8 0.3 1.0 C8 A:G567 4.9 0.3 1.0 O5' A:G567 4.9 0.1 1.0 O3' A:G566 4.9 0.5 1.0 O L:PRO5 4.9 0.8 1.0 CD L:PRO5 5.0 0.1 1.0

Magnesium binding site 5 out of 158 in the Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1603 b:98.2 occ:1.00 N7 A:G258 4.6 0.8 1.0 OP2 A:G265 4.7 0.6 1.0 O6 A:G259 4.7 0.1 1.0 O6 A:G258 4.8 0.1 1.0 OP1 A:G265 4.8 0.2 1.0 O6 A:G260 4.9 0.9 1.0

Magnesium binding site 6 out of 158 in the Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1659 b:81.2 occ:1.00 OP2 A:U652 3.8 0.5 1.0 OP1 A:C651 3.9 0.5 1.0 OP2 A:U751 4.0 0.0 1.0 N7 A:G752 4.2 0.0 1.0 OP1 A:U751 4.7 0.1 1.0 P A:C651 4.7 0.1 1.0 OP2 A:C651 4.8 0.9 1.0 P A:U751 4.8 0.6 1.0 C8 A:G752 4.8 0.2 1.0 OP2 A:G752 5.0 0.3 1.0

Magnesium binding site 7 out of 158 in the Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1604 b:0.3 occ:1.00 MG A:MG1683 1.9 0.3 1.0 OP1 A:G1521 2.4 0.3 1.0 OP1 A:G1508 2.7 0.7 1.0 OP1 A:A1500 3.1 0.2 1.0 P A:G1521 3.7 0.9 1.0 P A:G1508 3.7 0.0 1.0 O3' A:A1499 4.0 0.5 1.0 MG A:MG1662 4.0 89.4 1.0 O5' A:G1508 4.0 0.6 1.0 OP2 A:G1521 4.1 0.6 1.0 P A:A1500 4.2 0.7 1.0 OP2 A:G1508 4.3 0.1 1.0 C5' A:G1508 4.4 0.4 1.0 C5' A:A1500 4.6 0.6 1.0 O5' A:G1521 4.7 0.6 1.0 O3' A:G1520 4.7 0.6 1.0 OP2 A:C1509 4.8 0.3 1.0 O5' A:A1500 5.0 0.2 1.0

Magnesium binding site 8 out of 158 in the Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1660 b:0.9 occ:1.00 OP2 A:C1234 2.7 0.4 1.0 OP1 A:C1234 3.4 0.7 1.0 P A:C1234 3.5 0.5 1.0 O5' A:C1234 4.6 0.5 1.0 OP1 A:U1351 4.7 1.0 1.0 O3' A:G1233 4.7 0.6 1.0

Magnesium binding site 9 out of 158 in the Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1605 b:92.8 occ:1.00 OP1 A:G730 2.8 0.5 1.0 P A:G730 3.9 0.1 1.0 OP2 A:G818 4.0 0.2 1.0 OP2 A:G731 4.0 0.3 1.0 OP2 A:G730 4.1 0.7 1.0 N7 A:G731 4.3 0.3 1.0 O5' A:G730 4.6 0.6 1.0 OP1 A:G818 4.7 0.6 1.0 P A:G818 4.8 0.6 1.0 C8 A:G731 4.9 0.0 1.0

Magnesium binding site 10 out of 158 in the Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Thermus Thermophilus HB27 30S Ribosomal Subunit Lacking Ribosomal Protein S17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1661 b:75.5 occ:1.00 N3 A:C980 3.3 0.3 1.0 O2 A:C980 3.6 0.7 1.0 C2 A:C980 3.9 0.8 1.0 O N:VAL18 4.0 0.8 1.0 C4 A:C980 4.3 0.4 1.0 O6 A:G1361 4.3 0.7 1.0 N4 A:C980 4.4 0.2 1.0 N4 A:C979 4.5 0.0 1.0 O N:ALA20 4.5 0.1 1.0 CB N:TYR21 4.7 0.5 1.0 N7 A:A1360 4.8 0.2 1.0

J.L.Connetti, E.L.Murphy, A.E.Dahlberg, S.T.Gregory, G.Jogl. Structural Robustness of the Ribosome Inferred From the X-Ray Crystal Structure of A 30S Ribosomal Subunit Lacking Ribosomal Protein S17 To Be Published.