Magnesium in PDB 9bkd: The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit

All present enzymatic activity of The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit:
4.2.99.18;

The structure of The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit also contains other interesting chemical elements:

Potassium	(K)	19 atoms
Zinc	(Zn)	3 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 - 88;

Binding sites:

The binding sites of Magnesium atom in the The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit (pdb code 9bkd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 88 binding sites of Magnesium where determined in the The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit, PDB code: 9bkd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 88 in the The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit


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 Human PDCD4 Bound to the 40S Small Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1901 b:49.2 occ:1.00 OP1 A:A1589 2.1 58.2 1.0 O d:GLY80 2.7 53.5 1.0 P A:A1589 3.3 57.6 1.0 OP1 A:A1588 3.7 58.8 1.0 O d:ILE78 3.8 64.4 1.0 OP2 A:A1589 3.9 49.2 1.0 O4 A:U1543 3.9 66.0 1.0 C d:GLY80 3.9 54.1 1.0 O3' A:A1588 3.9 56.2 1.0 O5' A:A1589 4.5 52.3 1.0 N d:GLY80 4.5 58.5 1.0 C d:ILE78 4.7 65.2 1.0 CA d:GLY80 4.8 55.5 1.0 O d:LYS77 4.8 66.9 1.0 P A:A1588 4.8 64.2 1.0 N4 A:C1542 4.8 73.8 1.0 N d:GLY81 4.8 54.6 1.0 CE1 d:PHE92 4.8 49.7 1.0 CA d:GLY81 4.9 53.6 1.0 OP2 A:A1588 4.9 56.4 1.0 C4 A:U1543 5.0 67.4 1.0 C d:TYR79 5.0 60.3 1.0

Magnesium binding site 2 out of 88 in the The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit


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 Human PDCD4 Bound to the 40S Small Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1919 b:35.4 occ:1.00 OP2 A:A1217 1.9 46.1 1.0 OP1 A:U1643 2.2 47.1 1.0 P A:A1217 3.1 42.5 1.0 P A:U1643 3.4 43.9 1.0 O5' A:A1217 3.5 48.0 1.0 O3' A:C1216 3.6 45.4 1.0 OH Y:TYR145 3.9 47.2 1.0 OP2 A:U1643 4.0 46.8 1.0 O5' A:U1643 4.0 47.4 1.0 OP2 A:C1644 4.1 39.2 1.0 OP1 A:A1217 4.4 35.3 1.0 C5' A:U1643 4.6 47.8 1.0 O3' A:U1642 4.6 64.1 1.0 O3' A:A1217 4.7 41.5 1.0 CZ Y:TYR145 4.7 48.9 1.0 C5' A:A1217 4.8 41.5 1.0 OP1 A:C1218 4.8 40.9 1.0 CE1 Y:TYR145 4.8 43.9 1.0

Magnesium binding site 3 out of 88 in the The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit


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 Human PDCD4 Bound to the 40S Small Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1920 b:47.1 occ:1.00 OP2 A:JMH1219 2.1 56.7 1.0 P A:JMH1219 3.2 57.1 1.0 OP1 A:JMH1219 3.8 50.8 1.0 O5' A:JMH1219 3.9 55.4 1.0 O6 A:G1221 4.2 48.6 1.0 N7 A:G1221 4.3 51.3 1.0 O3' A:C1218 4.6 52.0 1.0 N7 A:A1220 4.8 55.0 1.0 OP2 A:A1220 4.9 54.7 1.0

Magnesium binding site 4 out of 88 in the The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit


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 Human PDCD4 Bound to the 40S Small Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1921 b:42.6 occ:1.00 OP1 A:U1225 2.4 56.5 1.0 P A:U1225 3.5 63.0 1.0 O3' A:G1224 3.6 57.6 1.0 O4 A:U1530 4.2 58.0 1.0 N6 A:A1531 4.4 65.1 1.0 OP2 A:U1225 4.5 60.5 1.0 N7 A:A1531 4.6 63.0 1.0 O5' A:U1225 4.6 58.0 1.0 C5' A:U1225 4.7 55.2 1.0 C4 A:U1530 4.9 55.1 1.0

Magnesium binding site 5 out of 88 in the The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit


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 Human PDCD4 Bound to the 40S Small Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1922 b:43.5 occ:1.00 OP2 A:G1227 2.0 64.3 1.0 OP1 A:G1226 2.1 67.0 1.0 P A:G1226 3.0 57.6 1.0 OP2 A:G1226 3.4 64.1 1.0 P A:G1227 3.4 65.4 1.0 O5' A:G1226 3.4 56.1 1.0 C5' A:G1226 3.8 57.0 1.0 O5' A:G1227 3.9 68.5 1.0 N7 A:A1228 4.2 62.5 1.0 O3' A:G1226 4.4 63.7 1.0 OP1 A:G1227 4.4 67.5 1.0 O3' A:U1225 4.4 60.8 1.0 C3' A:G1226 4.5 61.9 1.0 OP2 A:A1228 4.6 65.6 1.0 C4' A:G1226 4.7 59.7 1.0 N7 A:G1227 4.8 66.0 1.0 C8 A:A1228 4.9 66.7 1.0 N6 A:A1228 5.0 60.4 1.0

Magnesium binding site 6 out of 88 in the The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit


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 Human PDCD4 Bound to the 40S Small Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1923 b:41.5 occ:1.00 OP1 A:U1340 1.9 45.1 1.0 P A:U1340 3.2 31.6 1.0 O3' A:U1339 3.4 28.1 1.0 N7 A:A1250 3.8 33.6 1.0 OP1 A:A1250 4.0 40.7 1.0 C5' A:U1340 4.0 29.7 1.0 O5' A:U1340 4.0 30.8 1.0 O2 A:C1216 4.3 46.3 1.0 OP2 A:U1340 4.3 36.0 1.0 C8 A:A1250 4.4 33.5 1.0 N3 A:C1216 4.4 46.1 1.0 O2' A:C1249 4.7 42.6 1.0 C2' A:C1249 4.8 39.4 1.0 C2 A:C1216 4.8 45.0 1.0 C3' A:U1339 4.8 27.7 1.0 C5 A:A1250 4.9 30.6 1.0

Magnesium binding site 7 out of 88 in the The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit


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 Human PDCD4 Bound to the 40S Small Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1924 b:36.6 occ:1.00 OP1 A:A1253 3.0 49.0 1.0 OP1 A:C1254 3.1 36.4 1.0 OP2 A:A1253 3.8 43.4 1.0 P A:A1253 3.9 41.9 1.0 O2' A:C1527 4.1 48.3 1.0 P A:C1254 4.3 38.3 1.0 O5' A:C1254 4.4 27.7 1.0 C3' A:A1253 4.6 36.4 1.0 O4' A:C1527 4.7 43.5 1.0 C4' A:C1527 4.8 42.4 1.0 O5' A:A1253 4.8 36.6 1.0 OP2 A:C1252 4.9 34.0 1.0 CE h:LYS75 4.9 30.5 1.0 C1' A:C1527 4.9 43.9 1.0

Magnesium binding site 8 out of 88 in the The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit


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 Human PDCD4 Bound to the 40S Small Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1925 b:35.3 occ:1.00 OP1 A:A1258 2.2 50.1 1.0 P A:A1258 3.3 39.4 1.0 OP2 A:A1258 3.6 41.0 1.0 O3' A:G1257 4.1 33.3 1.0 OP2 A:G1255 4.2 41.2 1.0 C3' A:G1257 4.3 38.6 1.0 O2' A:G1256 4.5 38.7 1.0 N6 A:A1664 4.5 40.5 1.0 N3 A:A1253 4.5 36.7 1.0 O2 A:C1666 4.6 39.9 1.0 OP2 A:G1257 4.6 43.6 1.0 O5' A:A1258 4.6 43.3 1.0 N1 A:A1664 4.7 36.0 1.0 O2' A:C1666 4.7 31.9 1.0 O3' A:G1256 4.9 39.4 1.0 C2 A:A1253 4.9 40.8 1.0 O5' A:G1257 5.0 35.8 1.0

Magnesium binding site 9 out of 88 in the The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit


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 Human PDCD4 Bound to the 40S Small Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1926 b:35.6 occ:1.00 OP2 A:A1260 2.0 58.8 1.0 OP1 A:A1259 2.3 46.9 1.0 P A:A1260 3.3 55.3 1.0 P A:A1259 3.4 55.3 1.0 OP2 A:A1259 3.6 45.7 1.0 OP1 A:A1260 3.8 53.6 1.0 O3' A:A1259 4.2 43.7 1.0 O5' A:A1260 4.3 53.7 1.0 C3' A:A1259 4.4 43.2 1.0 O5' A:A1259 4.5 43.7 1.0 O3' A:A1258 4.5 46.8 1.0 C5' A:A1259 4.6 43.0 1.0 C5' A:A1260 4.7 53.8 1.0 N3 A:A1259 4.7 45.4 1.0 N1 A:A1663 4.8 48.2 1.0 O2' A:A1258 4.8 46.7 1.0 C2 A:A1663 4.9 47.6 1.0 C2' A:A1258 4.9 42.8 1.0 C2 A:A1259 4.9 44.2 1.0

Magnesium binding site 10 out of 88 in the The Structure of Human PDCD4 Bound to the 40S Small Ribosomal Subunit


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 Human PDCD4 Bound to the 40S Small Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1927 b:43.1 occ:1.00 OP1 A:C1262 2.6 54.6 1.0 P A:C1262 4.0 56.5 1.0 C5' A:C1262 4.2 53.4 1.0 O6 A:G1515 4.3 58.6 1.0 N7 A:G1514 4.5 62.0 1.0 O5' A:C1262 4.5 53.4 1.0 O3' A:C1261 4.6 57.3 1.0 N7 A:G1515 4.7 56.8 1.0 C5 A:C1513 4.9 60.5 1.0 N4 A:C1513 4.9 65.8 1.0 O6 A:G1514 5.0 64.8 1.0

J.Brito Querido, M.Sokabe, I.Diaz-Lopez, Y.Gordiyenko, P.Zuber, Y.Du, L.Albacete-Albacete, V.Ramakrishnan, C.S.Fraser. Human Tumor Suppressor Protein PDCD4 Binds at the Mrna Entry Channel in the 40S Small Ribosomal Subunit. Nat Commun V. 15 6633 2024.
ISSN: ESSN 2041-1723
PubMed: 39117603
DOI: 10.1038/S41467-024-50672-8