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Magnesium in PDB 7qiy: Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit.

Enzymatic activity of Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit.

All present enzymatic activity of Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit.:
2.7.11.24;

Other elements in 7qiy:

The structure of Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit. also contains other interesting chemical elements:

Potassium (K) 10 atoms
Zinc (Zn) 1 atom

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Magnesium atom in the Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit. (pdb code 7qiy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 28 binding sites of Magnesium where determined in the Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit., PDB code: 7qiy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 28 in 7qiy

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Magnesium binding site 1 out of 28 in the Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1909

b:12.6
occ:1.00
 O 2:HOH2003 1.7 7.4 1.0
O 2:HOH2014 2.0 6.8 1.0
O 2:HOH2026 2.0 14.6 1.0
O H:HOH201 2.1 10.7 1.0
OP2 2:A1163 2.2 9.9 1.0
OP1 2:U1584 2.3 12.0 1.0
O3' 2:C1162 3.3 13.5 1.0
P 2:A1163 3.3 9.9 1.0
P 2:U1584 3.4 12.0 1.0
OP2 2:C1585 3.4 4.7 1.0
H5'' 2:U1584 3.5 12.0 1.0
O5' 2:U1584 3.7 12.0 1.0
H5' 2:A1163 3.8 9.9 1.0
OH H:TYR146 4.0 18.6 1.0
OP2 2:U1584 4.1 12.0 1.0
HE2 H:TYR146 4.1 18.6 1.0
C5' 2:U1584 4.1 12.0 1.0
OP1 2:A1163 4.2 9.9 1.0
H3' 2:U1584 4.3 12.0 1.0
P 2:C1585 4.4 4.7 1.0
O5' 2:A1163 4.5 9.9 1.0
HH H:TYR146 4.5 18.6 0.0
C5' 2:A1163 4.6 9.9 1.0
C3' 2:C1162 4.6 13.5 1.0
O3' 2:U1584 4.7 12.0 1.0
O3' 2:U1583 4.7 12.9 1.0
H5' 2:U1584 4.8 12.0 1.0
CE2 H:TYR146 4.8 18.6 1.0
H4' 2:C1162 4.8 13.5 1.0
OP1 2:C1585 4.8 4.7 1.0
C3' 2:U1584 4.9 12.0 1.0
OP1 2:C1164 4.9 8.9 1.0
CZ H:TYR146 4.9 18.6 1.0
O2' 2:C1162 4.9 13.5 1.0

Magnesium binding site 2 out of 28 in 7qiy

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Magnesium binding site 2 out of 28 in the Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1910

b:12.2
occ:1.00
 O 2:HOH2009 1.9 12.7 1.0
O 2:HOH2032 2.0 9.9 1.0
O 2:HOH2132 2.1 8.0 1.0
O 2:HOH2147 2.2 12.4 1.0
OP2 2:C1165 2.2 8.8 1.0
P 2:C1165 3.4 8.8 1.0
O5' 2:C1165 3.8 8.8 1.0
H61 2:A1166 3.8 8.2 1.0
N7 2:G1167 3.8 6.3 1.0
OP1 2:C1165 3.9 8.8 1.0
O6 2:G1167 4.1 6.3 1.0
N7 2:A1166 4.2 8.2 1.0
O 2:HOH2072 4.2 7.9 1.0
OP2 2:A1166 4.4 8.2 1.0
O 2:HOH2101 4.5 9.1 1.0
H6 2:C1165 4.5 8.8 1.0
H3' 2:C1164 4.5 8.9 1.0
H5 2:C1165 4.5 8.8 1.0
N6 2:A1166 4.6 8.2 1.0
H3' 2:C1165 4.6 8.8 1.0
C5 2:G1167 4.7 6.3 1.0
O3' 2:C1164 4.7 8.9 1.0
C6 2:G1167 4.7 6.3 1.0
C8 2:G1167 4.9 6.3 1.0
H8 2:G1167 5.0 6.3 1.0
C6 2:C1165 5.0 8.8 1.0
C5 2:C1165 5.0 8.8 1.0

Magnesium binding site 3 out of 28 in 7qiy

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Magnesium binding site 3 out of 28 in the Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1911

b:9.2
occ:1.00
 O 2:HOH2163 1.7 17.7 1.0
OP1 2:U1171 2.1 11.1 1.0
O 2:HOH2139 2.2 10.7 1.0
O 2:HOH2130 2.2 11.8 1.0
O 2:HOH2125 2.3 18.7 1.0
H61 2:A1473 3.3 9.8 1.0
O 2:HOH2161 3.4 13.0 1.0
P 2:U1171 3.4 11.1 1.0
O3' 2:G1170 3.7 11.8 1.0
O4 2:U1472 3.7 8.4 1.0
H5'' 2:U1171 4.1 11.1 1.0
N6 2:A1473 4.2 9.8 1.0
H5 2:U1472 4.4 8.4 1.0
OP2 2:U1171 4.4 11.1 1.0
N7 2:A1473 4.5 9.8 1.0
O5' 2:U1171 4.5 11.1 1.0
H5' 2:U1171 4.5 11.1 1.0
H62 2:A1473 4.5 9.8 1.0
C4 2:U1472 4.6 8.4 1.0
C5' 2:U1171 4.6 11.1 1.0
C5 2:U1472 4.8 8.4 1.0

Magnesium binding site 4 out of 28 in 7qiy

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Magnesium binding site 4 out of 28 in the Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1912

b:7.5
occ:1.00
 OP2 2:G1173 2.0 10.3 1.0
O 2:HOH2055 2.0 5.0 1.0
O 2:HOH2114 2.1 6.4 1.0
O 2:HOH2073 2.1 11.7 1.0
O 2:HOH2097 2.1 9.1 1.0
OP1 2:G1172 2.3 12.2 1.0
P 2:G1172 3.2 12.2 1.0
P 2:G1173 3.4 10.3 1.0
OP2 2:G1172 3.5 12.2 1.0
H5'' 2:G1172 3.6 12.2 1.0
O5' 2:G1172 3.7 12.2 1.0
O5' 2:G1173 4.0 10.3 1.0
OP1 2:G1173 4.1 10.3 1.0
C5' 2:G1172 4.1 12.2 1.0
H3' 2:G1172 4.2 12.2 1.0
N7 2:A1174 4.2 8.2 1.0
H61 2:A1174 4.2 8.2 1.0
O 2:HOH2082 4.3 6.8 1.0
OP2 2:A1174 4.4 8.2 1.0
O3' 2:G1172 4.5 12.2 1.0
O3' 2:U1171 4.6 11.1 1.0
H3' 2:G1173 4.7 10.3 1.0
C3' 2:G1172 4.7 12.2 1.0
O6 2:G1470 4.7 7.9 1.0
H5' 2:G1172 4.8 12.2 1.0
N7 2:G1173 4.9 10.3 1.0
H8 2:A1174 4.9 8.2 1.0
C8 2:A1174 5.0 8.2 1.0
N6 2:A1174 5.0 8.2 1.0

Magnesium binding site 5 out of 28 in 7qiy

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Magnesium binding site 5 out of 28 in the Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1913

b:18.6
occ:1.00
 O 2:HOH2112 2.0 13.6 1.0
OP1 2:U1285 2.0 15.8 1.0
O 2:HOH2001 2.1 14.2 1.0
O 2:HOH2078 2.1 12.4 1.0
O 2:HOH2046 2.2 15.4 1.0
P 2:U1285 3.4 15.8 1.0
OP1 2:A1196 3.7 13.1 1.0
O3' 2:U1284 3.7 11.2 1.0
N7 2:A1196 4.1 13.1 1.0
O2 2:C1162 4.1 13.5 1.0
H5'' 2:U1285 4.2 15.8 1.0
H2' 2:C1195 4.2 15.2 1.0
H8 2:A1196 4.2 13.1 1.0
OP1 2:U1287 4.3 25.4 1.0
N3 2:C1162 4.4 13.5 1.0
OP2 2:U1285 4.4 15.8 1.0
O5' 2:U1285 4.4 15.8 1.0
H5' 2:U1285 4.4 15.8 1.0
C8 2:A1196 4.5 13.1 1.0
C5' 2:U1285 4.6 15.8 1.0
OP2 2:U1287 4.6 25.4 1.0
H3' 2:C1286 4.7 20.1 1.0
C2 2:C1162 4.7 13.5 1.0
O2' 2:C1195 4.9 15.2 1.0
H61 2:A1196 4.9 13.1 1.0
P 2:U1287 4.9 25.4 1.0
C2' 2:C1195 5.0 15.2 1.0
H5'' 2:U1284 5.0 11.2 1.0

Magnesium binding site 6 out of 28 in 7qiy

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Magnesium binding site 6 out of 28 in the Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1914

b:6.7
occ:1.00
 OP1 2:G1204 2.1 11.6 1.0
O 2:HOH2104 2.1 8.0 1.0
O 2:HOH2058 2.1 7.2 1.0
O 2:HOH2088 2.1 8.4 1.0
O 2:HOH2151 2.2 8.2 1.0
O 2:HOH2045 2.2 7.6 1.0
P 2:G1204 3.4 11.6 1.0
H62 2:A1605 3.7 10.6 1.0
O5' 2:G1204 3.7 11.6 1.0
O 2:HOH2037 3.8 21.8 1.0
HO2' 2:C1607 3.9 9.5 0.0
H3' 2:G1203 3.9 9.7 1.0
O 2:HOH2103 4.2 10.1 1.0
H1' 2:C1607 4.2 9.5 1.0
N1 2:A1605 4.3 10.6 1.0
OP2 2:G1204 4.4 11.6 1.0
O2' 2:G1202 4.4 10.6 1.0
O3' 2:G1203 4.4 9.7 1.0
O2 2:C1607 4.4 9.5 1.0
O2' 2:C1607 4.5 9.5 1.0
OP2 2:G1201 4.5 11.3 1.0
H1' 2:A1199 4.5 8.9 1.0
N6 2:A1605 4.5 10.6 1.0
N3 2:A1199 4.6 8.9 1.0
C3' 2:G1203 4.6 9.7 1.0
HO2' 2:G1202 4.7 10.6 0.0
H2 2:A1199 4.8 8.9 1.0
C6 2:A1605 5.0 10.6 1.0
O4' 2:G1204 5.0 11.6 1.0

Magnesium binding site 7 out of 28 in 7qiy

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Magnesium binding site 7 out of 28 in the Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1915

b:9.9
occ:1.00
 OP2 2:A1206 2.0 12.4 1.0
O 2:HOH2047 2.0 18.2 1.0
O 2:HOH2021 2.0 16.6 1.0
O 2:HOH2068 2.1 18.3 1.0
OP1 2:A1205 2.2 9.3 1.0
P 2:A1206 3.2 12.4 1.0
P 2:A1205 3.4 9.3 1.0
H5'' 2:A1205 3.5 9.3 1.0
OP1 2:A1206 3.6 12.4 1.0
O2 2:C1604 3.7 14.2 1.0
OP2 2:A1205 3.8 9.3 1.0
H3' 2:A1205 3.9 9.3 1.0
H2' 2:G1204 4.0 11.6 1.0
O3' 2:A1205 4.3 9.3 1.0
O5' 2:A1206 4.3 12.4 1.0
C5' 2:A1205 4.3 9.3 1.0
H5' 2:A1206 4.3 12.4 1.0
O5' 2:A1205 4.4 9.3 1.0
C2 2:C1604 4.4 14.2 1.0
C3' 2:A1205 4.5 9.3 1.0
N3 2:C1604 4.5 14.2 1.0
O3' 2:G1204 4.6 11.6 1.0
C2' 2:G1204 4.7 11.6 1.0
C5' 2:A1206 4.8 12.4 1.0
O2' 2:G1204 4.9 11.6 1.0
H3' 2:G1204 4.9 11.6 1.0
H2 2:A1205 4.9 9.3 1.0
HO2' 2:U1565 5.0 14.2 0.0
C4' 2:A1205 5.0 9.3 1.0

Magnesium binding site 8 out of 28 in 7qiy

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Magnesium binding site 8 out of 28 in the Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1916

b:10.1
occ:1.00
 O 2:HOH2044 2.0 8.1 1.0
O4 2:U1209 2.1 10.7 1.0
OP2 2:C1208 2.1 11.3 1.0
O6 2:G1459 2.1 8.5 1.0
OP1 2:A1207 2.2 13.6 1.0
O 2:HOH2089 2.3 8.5 1.0
C4 2:U1209 3.0 10.7 1.0
H5 2:U1209 3.1 10.7 1.0
C6 2:G1459 3.3 8.5 1.0
H5'' 2:A1207 3.3 13.6 1.0
C5 2:U1209 3.4 10.7 1.0
P 2:C1208 3.5 11.3 1.0
P 2:A1207 3.5 13.6 1.0
H41 2:C1460 3.5 8.3 1.0
N4 2:C1460 3.8 8.3 1.0
O5' 2:A1207 3.9 13.6 1.0
H42 2:C1460 4.0 8.3 1.0
O4 2:PSU1210 4.1 7.7 1.0
H1 2:G1459 4.1 8.5 1.0
C5' 2:A1207 4.1 13.6 1.0
OP1 2:C1208 4.1 11.3 1.0
OP2 2:A1207 4.2 13.6 1.0
N1 2:G1459 4.2 8.5 1.0
HO2' 2:A1205 4.2 9.3 0.0
N3 2:U1209 4.2 10.7 1.0
O 2:HOH2090 4.3 9.9 1.0
H3' 2:A1207 4.3 13.6 1.0
HN3 2:PSU1210 4.3 7.7 1.0
H5 2:C1208 4.3 11.3 1.0
C5 2:G1459 4.3 8.5 1.0
O6 2:G1458 4.3 10.3 1.0
H3 2:U1209 4.4 10.7 1.0
O3' 2:A1207 4.4 13.6 1.0
O5' 2:C1208 4.4 11.3 1.0
C4 2:PSU1210 4.6 7.7 1.0
C4 2:C1460 4.6 8.3 1.0
N7 2:G1459 4.6 8.5 1.0
O 2:HOH2056 4.6 12.4 1.0
N3 2:PSU1210 4.7 7.7 1.0
C3' 2:A1207 4.7 13.6 1.0
O3' 2:A1206 4.7 12.4 1.0
H5' 2:A1207 4.7 13.6 1.0
C6 2:U1209 4.8 10.7 1.0
N3 2:C1460 4.9 8.3 1.0
H6 2:C1208 4.9 11.3 1.0
C4' 2:A1207 4.9 13.6 1.0
O2' 2:A1205 5.0 9.3 1.0
O2' 2:PSU1210 5.0 7.7 1.0

Magnesium binding site 9 out of 28 in 7qiy

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Magnesium binding site 9 out of 28 in the Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1917

b:10.7
occ:1.00
 OP1 2:C1208 1.9 11.3 1.0
O 2:HOH2049 2.0 10.5 1.0
O 2:HOH2029 2.1 16.2 1.0
O 2:HOH2056 2.1 12.4 1.0
O 2:HOH2093 2.2 13.4 1.0
P 2:C1208 3.4 11.3 1.0
H5'' 2:C1208 3.6 11.3 1.0
O 2:HOH2085 4.0 7.3 1.0
O5' 2:C1208 4.1 11.3 1.0
H5 2:U1456 4.1 20.6 1.0
O4 2:U1456 4.1 20.6 1.0
O3' 2:A1207 4.2 13.6 1.0
O6 2:G1457 4.2 13.7 1.0
C5' 2:C1208 4.2 11.3 1.0
H5' 2:C1208 4.2 11.3 1.0
OP2 2:C1208 4.4 11.3 1.0
O 2:HOH2089 4.5 8.5 1.0
O 2:HOH2090 4.6 9.9 1.0
OP2 2:U1209 4.6 10.7 1.0
O6 2:G1458 4.7 10.3 1.0
C5 2:U1456 4.7 20.6 1.0
C4 2:U1456 4.8 20.6 1.0
O 2:HOH2044 4.8 8.1 1.0
H42 2:C1455 4.9 23.6 1.0
H42 2:C1212 4.9 8.4 1.0
N7 2:G1457 4.9 13.7 1.0
H41 2:C1212 4.9 8.4 1.0

Magnesium binding site 10 out of 28 in 7qiy

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Magnesium binding site 10 out of 28 in the Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1918

b:22.2
occ:1.00
 O 2:HOH2133 2.0 21.9 1.0
O 2:HOH2018 2.0 16.1 1.0
O 2:HOH2013 2.1 10.3 1.0
OP2 2:OMU1272 2.1 13.3 1.0
O 2:HOH2004 2.2 12.1 1.0
OP2 2:U1436 3.1 11.1 1.0
P 2:OMU1272 3.3 13.3 1.0
H5'' 2:OMU1272 3.6 13.3 1.0
O5' 2:OMU1272 3.7 13.3 1.0
OP1 2:OMU1272 4.0 13.3 1.0
OP1 2:U1438 4.1 15.0 1.0
C5' 2:OMU1272 4.1 13.3 1.0
H3' 2:G1271 4.3 23.4 1.0
H5' 2:U1436 4.4 11.1 1.0
H5' 2:OMU1272 4.4 13.3 1.0
P 2:U1436 4.6 11.1 1.0
O3' 2:G1271 4.6 23.4 1.0
OP2 2:G1439 4.7 26.5 1.0
H6 2:OMU1272 4.8 13.3 1.0
H5'' 2:U1436 4.8 11.1 1.0
OP1 2:G1439 4.8 26.5 1.0
C3' 2:G1271 5.0 23.4 1.0
C5' 2:U1436 5.0 11.1 1.0

Reference:

P.Cottilli, Y.Itoh, Y.Nobe, A.S.Petrov, P.Lison, M.Taoka, A.Amunts. Cryo-Em Structure and Rrna Modification Sites of A Plant Ribosome. Plant Commun. V. 3 00342 2022.
ISSN: ISSN 2590-3462
PubMed: 35643637
DOI: 10.1016/J.XPLC.2022.100342
Page generated: Thu Oct 3 05:08:58 2024

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