Atomistry » Magnesium » PDB 7qbm-7qpi » 7qiy
Atomistry »
  Magnesium »
    PDB 7qbm-7qpi »
      7qiy »

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

Go back to Magnesium Binding Sites List in 7qiy
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

Go back to Magnesium Binding Sites List in 7qiy
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

Go back to Magnesium Binding Sites List in 7qiy
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

Go back to Magnesium Binding Sites List in 7qiy
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

Go back to Magnesium Binding Sites List in 7qiy
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

Go back to Magnesium Binding Sites List in 7qiy
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

Go back to Magnesium Binding Sites List in 7qiy
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

Go back to Magnesium Binding Sites List in 7qiy
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

Go back to Magnesium Binding Sites List in 7qiy
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

Go back to Magnesium Binding Sites List in 7qiy
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy