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Potassium 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:

Magnesium (Mg) 28 atoms
Zinc (Zn) 1 atom

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 10 binding sites of Potassium where determined in the Specific Features and Methylation Sites of A Plant Ribosome. 40S Head Ribosomal Subunit., PDB code: 7qiy:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 10 in 7qiy

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Potassium binding site 1 out of 10 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 Potassium with other atoms in the K 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:K1901

b:11.6
occ:1.00
 O5' 2:C1200 2.8 10.2 1.0
OP1 2:A1199 2.9 8.9 1.0
OP1 2:C1198 2.9 11.2 1.0
O4' 2:C1200 3.0 10.2 1.0
HD21 L:ASN79 3.4 11.0 1.0
OP1 2:C1200 3.4 10.2 1.0
O 2:HOH2154 3.5 17.8 1.0
O 2:HOH2137 3.6 10.8 1.0
H5'' 2:C1198 3.7 11.2 1.0
P 2:C1198 3.8 11.2 1.0
C4' 2:C1200 3.8 10.2 1.0
H4' 2:C1200 3.8 10.2 1.0
P 2:C1200 3.8 10.2 1.0
C5' 2:C1200 3.8 10.2 1.0
OP2 2:C1198 3.9 11.2 1.0
MG 2:MG1933 4.1 16.0 1.0
ND2 L:ASN79 4.1 11.0 1.0
P 2:A1199 4.1 8.9 1.0
H6 2:C1200 4.1 10.2 1.0
O5' 2:A1199 4.1 8.9 1.0
H1' 2:C1200 4.1 10.2 1.0
C1' 2:C1200 4.2 10.2 1.0
H5'' 2:C1200 4.2 10.2 1.0
H3' 2:A1199 4.2 8.9 1.0
O5' 2:C1198 4.3 11.2 1.0
C5' 2:C1198 4.5 11.2 1.0
HD22 L:ASN79 4.5 11.0 1.0
H5' 2:C1200 4.6 10.2 1.0
C6 2:C1200 4.7 10.2 1.0
H3' 2:C1198 4.8 11.2 1.0
N1 2:C1200 4.8 10.2 1.0
OP2 2:C1200 4.8 10.2 1.0
O3' 2:A1199 4.8 8.9 1.0
OD1 L:ASN79 4.9 11.0 1.0
CG L:ASN79 4.9 11.0 1.0
C3' 2:A1199 4.9 8.9 1.0
HO2' 2:C1200 5.0 10.2 0.0

Potassium binding site 2 out of 10 in 7qiy

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Potassium binding site 2 out of 10 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 Potassium with other atoms in the K 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:K1902

b:17.2
occ:1.00
 O6 2:G1281 2.8 13.4 1.0
O4 2:U1434 2.9 10.2 1.0
O6 2:G1433 3.1 10.0 1.0
H41 2:C1282 3.2 11.0 1.0
H22 2:G1276 3.3 11.7 1.0
H3 2:U1434 3.3 10.2 1.0
O 2:HOH2149 3.3 10.2 1.0
N2 2:G1276 3.6 11.7 1.0
N4 2:C1282 3.7 11.0 1.0
H42 2:C1282 3.7 11.0 1.0
C4 2:U1434 3.8 10.2 1.0
H21 2:G1276 3.8 11.7 1.0
C6 2:G1281 3.9 13.4 1.0
N3 2:U1434 3.9 10.2 1.0
C6 2:G1433 4.0 10.0 1.0
O 2:HOH2113 4.1 8.1 1.0
C2 2:G1276 4.2 11.7 1.0
OP2 2:G1280 4.3 15.7 1.0
N7 2:G1281 4.3 13.4 1.0
O 2:HOH2081 4.4 10.2 1.0
N3 2:G1276 4.5 11.7 1.0
C5 2:G1281 4.5 13.4 1.0
C4 2:C1282 4.6 11.0 1.0
H1 2:G1433 4.7 10.0 1.0
N1 2:G1433 4.8 10.0 1.0
C5 2:G1433 4.9 10.0 1.0
N3 2:C1282 5.0 11.0 1.0

Potassium binding site 3 out of 10 in 7qiy

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Potassium binding site 3 out of 10 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 Potassium with other atoms in the K 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:K1903

b:21.8
occ:1.00
 OP2 2:G1172 2.9 12.2 1.0
N7 2:G1173 3.0 10.3 1.0
OP2 2:U1171 3.0 11.1 1.0
N7 2:G1172 3.0 12.2 1.0
O6 2:G1173 3.1 10.3 1.0
H3' 2:U1171 3.3 11.1 1.0
H8 2:G1172 3.4 12.2 1.0
O5' 2:U1171 3.5 11.1 1.0
N7 2:G1579 3.5 12.7 1.0
C8 2:G1172 3.6 12.2 1.0
C5 2:G1173 3.7 10.3 1.0
C6 2:G1173 3.7 10.3 1.0
P 2:U1171 3.7 11.1 1.0
C8 2:G1579 4.0 12.7 1.0
H8 2:G1579 4.1 12.7 1.0
H6 2:U1171 4.1 11.1 1.0
C8 2:G1173 4.1 10.3 1.0
H5 2:U1171 4.1 11.1 1.0
P 2:G1172 4.2 12.2 1.0
C6 2:U1171 4.2 11.1 1.0
C5 2:G1579 4.3 12.7 1.0
C5 2:U1171 4.3 11.1 1.0
C3' 2:U1171 4.3 11.1 1.0
C5 2:G1172 4.3 12.2 1.0
OP1 2:U1171 4.3 11.1 1.0
H62 2:A1473 4.3 9.8 1.0
H8 2:G1173 4.4 10.3 1.0
O5' 2:G1172 4.4 12.2 1.0
O 2:HOH2097 4.4 9.1 1.0
C5' 2:U1171 4.6 11.1 1.0
O3' 2:U1171 4.7 11.1 1.0
O6 2:G1579 4.7 12.7 1.0
C6 2:G1579 4.8 12.7 1.0
O6 2:G1172 4.8 12.2 1.0
H5'' 2:U1171 4.8 11.1 1.0
N9 2:G1172 4.9 12.2 1.0
N1 2:U1171 4.9 11.1 1.0
H3' 2:G1170 4.9 11.8 1.0
N9 2:G1579 4.9 12.7 1.0
C6 2:G1172 5.0 12.2 1.0
C4 2:G1173 5.0 10.3 1.0
H2' 2:U1171 5.0 11.1 1.0
C4' 2:U1171 5.0 11.1 1.0

Potassium binding site 4 out of 10 in 7qiy

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Potassium binding site 4 out of 10 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 Potassium with other atoms in the K 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:K1904

b:12.0
occ:1.00
 O6 2:G1276 2.7 11.7 1.0
O4 2:U1438 2.9 15.0 1.0
O6 2:G1280 3.0 15.7 1.0
O 2:HOH2128 3.0 9.0 1.0
H1 2:G1280 3.3 15.7 1.0
H21 2:G1281 3.5 13.4 1.0
H5 2:U1438 3.5 15.0 1.0
H61 2:A1440 3.6 17.7 1.0
N2 2:G1281 3.7 13.4 1.0
H1 2:G1276 3.7 11.7 1.0
C6 2:G1276 3.7 11.7 1.0
H5' 2:C1435 3.8 11.7 1.0
C4 2:U1438 3.8 15.0 1.0
C6 2:G1280 3.9 15.7 1.0
N1 2:G1280 3.9 15.7 1.0
H2' 2:U1434 3.9 10.2 1.0
H22 2:G1281 3.9 13.4 1.0
N6 2:A1440 4.0 17.7 1.0
C5 2:U1438 4.0 15.0 1.0
H1 2:G1281 4.1 13.4 1.0
O2 2:U1434 4.1 10.2 1.0
C2 2:G1281 4.1 13.4 1.0
N1 2:G1276 4.1 11.7 1.0
O2' 2:U1434 4.3 10.2 1.0
H62 2:A1440 4.3 17.7 1.0
H4' 2:C1435 4.3 11.7 1.0
N1 2:G1281 4.3 13.4 1.0
N7 2:G1437 4.4 11.9 1.0
C2' 2:U1434 4.5 10.2 1.0
C5' 2:C1435 4.5 11.7 1.0
N7 2:A1440 4.6 17.7 1.0
C6 2:A1440 4.6 17.7 1.0
OP1 2:G1437 4.7 11.9 1.0
O4' 2:C1435 4.7 11.7 1.0
HO2' 2:U1434 4.7 10.2 0.0
H5'' 2:C1435 4.7 11.7 1.0
C4' 2:C1435 4.7 11.7 1.0
C5 2:A1440 4.8 17.7 1.0
O6 2:G1437 4.8 11.9 1.0
C2 2:U1434 4.9 10.2 1.0
N3 2:G1281 4.9 13.4 1.0

Potassium binding site 5 out of 10 in 7qiy

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Potassium binding site 5 out of 10 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 Potassium with other atoms in the K 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:K1905

b:19.5
occ:1.00
 O2 2:C1435 2.6 11.7 1.0
O4 2:U1275 2.9 13.2 1.0
O6 2:G1442 2.9 18.1 1.0
O6 2:OMG1274 3.1 15.8 1.0
HO2' 2:C1435 3.3 11.7 0.0
H3 2:U1275 3.4 13.2 1.0
C2 2:C1435 3.4 11.7 1.0
H3 2:U1441 3.4 17.2 1.0
H41 2:C1443 3.6 18.6 1.0
H1' 2:C1435 3.8 11.7 1.0
N3 2:U1441 3.8 17.2 1.0
C4 2:U1275 3.8 13.2 1.0
O4 2:U1441 3.9 17.2 1.0
C6 2:G1442 4.0 18.1 1.0
N3 2:U1275 4.0 13.2 1.0
C6 2:OMG1274 4.0 15.8 1.0
N3 2:C1435 4.0 11.7 1.0
N4 2:C1443 4.1 18.6 1.0
O2' 2:C1435 4.1 11.7 1.0
C4 2:U1441 4.1 17.2 1.0
N7 2:G1442 4.2 18.1 1.0
H42 2:C1443 4.2 18.6 1.0
N1 2:C1435 4.3 11.7 1.0
H61 2:A1278 4.4 16.2 1.0
C1' 2:C1435 4.4 11.7 1.0
C5 2:G1442 4.5 18.1 1.0
H62 2:A1278 4.5 16.2 1.0
HN1 2:OMG1274 4.5 15.8 1.0
C2 2:U1441 4.6 17.2 1.0
N6 2:A1278 4.7 16.2 1.0
N1 2:OMG1274 4.7 15.8 1.0
O2 2:U1441 4.8 17.2 1.0
C2' 2:C1435 4.9 11.7 1.0
C5 2:OMG1274 5.0 15.8 1.0

Potassium binding site 6 out of 10 in 7qiy

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Potassium binding site 6 out of 10 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 Potassium with other atoms in the K 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:K1906

b:58.9
occ:1.00
 O6 2:G1359 2.8 26.8 1.0
O6 2:G1358 2.9 28.9 1.0
O4 2:U1370 3.1 26.9 1.0
H61 2:A1360 3.5 28.2 1.0
H62 2:A1360 3.5 28.2 1.0
H41 2:C1371 3.6 26.8 1.0
H3 2:U1370 3.7 26.9 1.0
N6 2:A1360 3.7 28.2 1.0
C6 2:G1358 3.8 28.9 1.0
C6 2:G1359 3.9 26.8 1.0
O4 2:U1369 4.0 32.5 1.0
N4 2:C1371 4.1 26.8 1.0
C4 2:U1370 4.1 26.9 1.0
H42 2:C1371 4.2 26.8 1.0
N3 2:U1370 4.2 26.9 1.0
N7 2:G1359 4.3 26.8 1.0
H1 2:G1358 4.5 28.9 1.0
C5 2:G1359 4.5 26.8 1.0
N1 2:G1358 4.5 28.9 1.0
C5 2:G1358 4.6 28.9 1.0
C6 2:A1360 4.7 28.2 1.0
N7 2:G1358 4.8 28.9 1.0
C4 2:C1371 4.9 26.8 1.0

Potassium binding site 7 out of 10 in 7qiy

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Potassium binding site 7 out of 10 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 Potassium with other atoms in the K 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:K1907

b:44.9
occ:1.00
 O 2:HOH2095 2.7 9.5 1.0
O4 2:U1549 2.8 12.7 1.0
OP2 2:A1548 3.2 10.6 1.0
HO2' 2:G1547 3.2 10.9 0.0
O4 2:U1572 3.4 14.6 1.0
O2' 2:G1547 3.5 10.9 1.0
H61 2:A1550 3.6 13.9 1.0
H3 2:U1572 3.7 14.6 1.0
C4 2:U1549 3.8 12.7 1.0
H5 2:U1549 3.9 12.7 1.0
H62 2:A1550 4.0 13.9 1.0
N6 2:A1550 4.0 13.9 1.0
C5 2:U1549 4.3 12.7 1.0
C4 2:U1572 4.3 14.6 1.0
N3 2:U1572 4.3 14.6 1.0
N7 2:A1548 4.5 10.6 1.0
P 2:A1548 4.6 10.6 1.0
C2' 2:G1547 4.8 10.9 1.0
H8 2:A1548 4.9 10.6 1.0
O3' 2:G1547 5.0 10.9 1.0

Potassium binding site 8 out of 10 in 7qiy

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Potassium binding site 8 out of 10 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 Potassium with other atoms in the K 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
J:K201

b:28.6
occ:1.00
 O J:THR136 2.8 13.3 1.0
O J:THR139 2.8 14.2 1.0
O2' 2:C1463 3.1 12.3 1.0
HB J:THR136 3.1 13.3 1.0
HO2' 2:C1463 3.7 12.3 0.0
HA J:THR136 3.8 13.3 1.0
C J:THR136 3.8 13.3 1.0
O J:GLY140 3.8 16.8 1.0
HG2 J:ARG141 3.8 15.7 1.0
CB J:THR136 4.0 13.3 1.0
HA3 J:GLY140 4.0 16.8 1.0
C J:GLY140 4.0 16.8 1.0
C J:THR139 4.0 14.2 1.0
H2' 2:C1463 4.1 12.3 1.0
C2' 2:C1463 4.1 12.3 1.0
CA J:THR136 4.1 13.3 1.0
HG3 J:ARG141 4.2 15.7 1.0
HA J:ARG141 4.2 15.7 1.0
H3' 2:C1463 4.3 12.3 1.0
OP2 2:A1464 4.4 15.3 1.0
CA J:GLY140 4.4 16.8 1.0
N J:ARG141 4.5 15.7 1.0
CG J:ARG141 4.5 15.7 1.0
HG21 J:THR136 4.6 13.3 1.0
C3' 2:C1463 4.6 12.3 1.0
OP2 2:C1465 4.7 14.2 1.0
N J:GLY140 4.7 16.8 1.0
H J:THR139 4.8 14.2 1.0
O3' 2:C1463 4.8 12.3 1.0
CA J:ARG141 4.8 15.7 1.0
CG2 J:THR136 4.8 13.3 1.0
HE J:ARG141 4.9 15.7 1.0
H J:ARG141 4.9 15.7 1.0
N J:THR139 4.9 14.2 1.0
OG1 J:THR136 5.0 13.3 1.0

Potassium binding site 9 out of 10 in 7qiy

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Potassium binding site 9 out of 10 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 Potassium with other atoms in the K 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
K:K201

b:38.2
occ:1.00
 O K:GLY81 2.8 11.9 1.0
O K:ILE79 2.8 13.0 1.0
O 2:HOH2119 2.9 17.3 1.0
O4 2:U1485 3.1 13.2 1.0
O 2:HOH2152 3.2 18.6 1.0
HA K:TYR80 3.4 11.9 1.0
O2 2:PSU1484 3.6 12.7 1.0
OP1 2:A1530 3.7 10.4 1.0
C K:ILE79 3.8 13.0 1.0
C K:GLY81 3.9 11.9 1.0
C K:TYR80 4.0 11.9 1.0
CA K:TYR80 4.0 11.9 1.0
N K:GLY81 4.1 11.9 1.0
H K:GLY81 4.3 11.9 1.0
N K:TYR80 4.3 11.9 1.0
C4 2:U1485 4.3 13.2 1.0
O K:TYR80 4.5 11.9 1.0
HA2 K:GLY82 4.6 11.8 1.0
O K:ARG78 4.6 14.2 1.0
C2 2:PSU1484 4.7 12.7 1.0
CA K:GLY81 4.7 11.9 1.0
H3 2:U1485 4.7 13.2 1.0
HA3 K:GLY82 4.8 11.8 1.0
HA K:ILE79 4.8 13.0 1.0
N K:GLY82 4.9 11.8 1.0
P 2:A1530 4.9 10.4 1.0
CA K:GLY82 5.0 11.8 1.0
CA K:ILE79 5.0 13.0 1.0

Potassium binding site 10 out of 10 in 7qiy

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Potassium binding site 10 out of 10 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 Potassium with other atoms in the K 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
N:K101

b:11.2
occ:1.00
 OD1 N:ASN26 2.8 13.1 1.0
HB2 N:CYS39 2.8 12.7 1.0
O N:HIS28 2.9 10.4 1.0
O 2:HOH2060 2.9 7.8 1.0
HO2' 2:G1437 2.9 11.9 0.0
OE1 N:GLN41 3.0 10.9 1.0
H1' 2:G1437 3.2 11.9 1.0
HB2 N:HIS28 3.2 10.4 1.0
H4' 2:G1437 3.2 11.9 1.0
O4' 2:G1437 3.3 11.9 1.0
HB3 N:ASN26 3.3 13.1 1.0
CB N:CYS39 3.5 12.7 1.0
HB3 N:ALA29 3.5 11.1 1.0
CG N:ASN26 3.6 13.1 1.0
C1' 2:G1437 3.7 11.9 1.0
H N:HIS28 3.7 10.4 1.0
HB3 N:CYS39 3.7 12.7 1.0
SG N:CYS39 3.7 12.7 1.0
C N:HIS28 3.7 10.4 1.0
O2' 2:G1437 3.7 11.9 1.0
C4' 2:G1437 3.8 11.9 1.0
CB N:ASN26 4.0 13.1 1.0
CB N:HIS28 4.0 10.4 1.0
CD N:GLN41 4.1 10.9 1.0
HE21 N:GLN41 4.2 10.9 1.0
CA N:HIS28 4.2 10.4 1.0
C2' 2:G1437 4.3 11.9 1.0
N N:HIS28 4.3 10.4 1.0
HB2 N:ASN26 4.4 13.1 1.0
HB3 N:HIS28 4.4 10.4 1.0
CB N:ALA29 4.4 11.1 1.0
NE2 N:GLN41 4.5 10.9 1.0
H5' 2:G1437 4.5 11.9 1.0
HB2 N:GLN41 4.5 10.9 1.0
H N:GLN41 4.6 10.9 1.0
HB1 N:ALA29 4.6 11.1 1.0
HG2 N:ARG40 4.7 10.9 1.0
C3' 2:G1437 4.7 11.9 1.0
H N:ARG40 4.7 10.9 1.0
N N:ALA29 4.7 11.1 1.0
ND2 N:ASN26 4.7 13.1 1.0
C5' 2:G1437 4.8 11.9 1.0
CA N:CYS39 4.9 12.7 1.0
HD13 N:ILE30 4.9 13.0 1.0
N9 2:G1437 5.0 11.9 1.0
HD21 N:ASN26 5.0 13.1 1.0
HA N:CYS39 5.0 12.7 1.0
OP2 2:G1202 5.0 10.6 1.0
HD2 N:HIS28 5.0 10.4 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: Mon Aug 12 20:29:50 2024

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