Magnesium in PDB 7r4x: Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map

Enzymatic activity of Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map

All present enzymatic activity of Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map:
4.2.99.18;

Other elements in 7r4x:

The structure of Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map also contains other interesting chemical elements:

Zinc (Zn) 3 atoms
Potassium (K) 82 atoms

Magnesium Binding Sites:

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 Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map (pdb code 7r4x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 88 binding sites of Magnesium where determined in the Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map, PDB code: 7r4x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 88 in 7r4x

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Magnesium binding site 1 out of 88 in the Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1977

b:16.9
occ:1.00
 OP2 2:A1082 1.9 13.1 1.0
O 2:HOH3023 2.0 20.1 1.0
O 2:HOH2998 2.1 17.4 1.0
O 2:HOH4090 2.2 13.7 1.0
O 2:HOH4735 2.2 19.3 1.0
O 2:HOH2630 2.4 15.9 1.0
P 2:A1082 3.2 13.1 1.0
OP1 2:A1082 3.9 13.1 1.0
O 2:HOH3606 4.0 19.2 1.0
OP2 2:G673 4.0 11.6 1.0
C5' 2:A1082 4.1 13.1 1.0
O 2:HOH3022 4.1 16.9 1.0
O5' 2:A1082 4.1 13.1 1.0
OP1 2:G673 4.3 11.6 1.0
O 2:HOH5191 4.3 22.4 1.0
O3' 2:PSU1081 4.4 12.9 1.0
O 2:HOH2117 4.4 20.4 1.0
N7 2:A1084 4.4 10.2 1.0
OP1 2:A1083 4.4 20.6 1.0
MG 2:MG2055 4.5 20.9 1.0
OP2 2:A1083 4.7 20.6 1.0
N6 2:A1084 4.7 10.2 1.0
P 2:G673 4.7 11.6 1.0
C3' 2:PSU1081 4.8 12.9 1.0
C5' 2:PSU1081 4.8 12.9 1.0

Magnesium binding site 2 out of 88 in 7r4x

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Magnesium binding site 2 out of 88 in the Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1978

b:17.6
occ:1.00
 OP2 2:C472 1.9 14.1 1.0
O 2:HOH3321 2.0 14.5 1.0
O 2:HOH3494 2.1 17.5 1.0
O 2:HOH2619 2.1 17.3 1.0
O 2:HOH3979 2.3 16.0 1.0
O 2:HOH2576 2.3 13.9 1.0
P 2:C472 3.3 14.1 1.0
O5' 2:C472 3.7 14.1 1.0
O 2:HOH3368 4.0 21.0 1.0
O 2:HOH3608 4.1 16.9 1.0
N7 2:G474 4.1 9.9 1.0
O4' 2:C472 4.1 14.1 1.0
O4' 2:G451 4.1 11.9 1.0
N1 2:A54 4.2 12.6 1.0
OP1 2:C472 4.2 14.1 1.0
O3' 2:G471 4.3 20.2 1.0
OP2 2:G451 4.3 11.9 1.0
O 2:HOH2388 4.4 17.4 1.0
N6 2:A54 4.5 12.6 1.0
O 2:HOH5069 4.5 15.3 1.0
C8 2:G474 4.6 9.9 1.0
O 2:HOH4262 4.6 18.2 1.0
C3' 2:G471 4.7 20.2 1.0
C4' 2:C472 4.7 14.1 1.0
OP1 2:G474 4.7 9.9 1.0
C5' 2:C472 4.8 14.1 1.0
C6 2:A54 4.8 12.6 1.0

Magnesium binding site 3 out of 88 in 7r4x

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Magnesium binding site 3 out of 88 in the Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1979

b:15.1
occ:1.00
 O 2:HOH2268 1.9 14.9 1.0
O 2:HOH3782 2.0 11.4 1.0
O6 2:G1387 2.0 11.7 1.0
OP2 2:G1385 2.0 9.5 1.0
O 2:HOH4309 2.3 17.8 1.0
C6 2:G1387 3.0 11.7 1.0
P 2:G1385 3.2 9.5 1.0
O5' 2:G1385 3.7 9.5 1.0
OP1 2:G1385 3.8 9.5 1.0
C5 2:G1387 3.8 11.7 1.0
O 2:HOH3231 3.8 14.5 1.0
N1 2:G1387 3.9 11.7 1.0
OG D:SER160 4.0 13.6 1.0
N7 2:G1387 4.1 11.7 1.0
N7 2:A1386 4.2 11.6 1.0
N1 2:A1388 4.2 12.4 1.0
OP2 2:A1386 4.3 11.6 1.0
C6 2:A1388 4.4 12.4 1.0
O3' 2:C1384 4.5 11.0 1.0
O 2:HOH4862 4.5 22.4 1.0
N6 2:A1388 4.6 12.4 1.0
C2 2:A1388 4.7 12.4 1.0
O D:HOH306 4.8 19.6 1.0
N6 2:A1386 4.8 11.6 1.0
C5' 2:G1385 5.0 9.5 1.0
O 2:HOH3290 5.0 15.4 1.0

Magnesium binding site 4 out of 88 in 7r4x

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Magnesium binding site 4 out of 88 in the Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1980

b:22.3
occ:1.00
 OP2 2:C1443 2.0 25.0 1.0
O 2:HOH3672 2.1 26.3 1.0
O 2:HOH3177 2.1 24.0 1.0
OP2 2:OMU1442 2.1 25.3 1.0
O 2:HOH4602 2.2 23.1 1.0
O 2:HOH2131 2.5 23.9 1.0
P 2:C1443 3.3 25.0 1.0
P 2:OMU1442 3.5 25.3 1.0
O3' 2:U1441 3.8 29.7 1.0
OP1 2:C1443 3.8 25.0 1.0
O4 2:U1444 4.0 24.8 1.0
O2 2:PSU1445 4.1 24.4 1.0
O 2:HOH5155 4.1 27.3 1.0
O 2:HOH2856 4.1 24.5 1.0
O5' 2:OMU1442 4.2 25.3 1.0
O 2:HOH2149 4.2 23.9 1.0
O3' 2:OMU1442 4.3 25.3 1.0
O5' 2:C1443 4.4 25.0 1.0
O 2:HOH4169 4.4 26.5 1.0
O 2:HOH5067 4.5 25.5 1.0
N6 2:A1401 4.5 27.8 1.0
C5' 2:OMU1442 4.6 25.3 1.0
C3' 2:OMU1442 4.6 25.3 1.0
O2' 2:U1441 4.6 29.7 1.0
C5 2:U1444 4.6 24.8 1.0
OP1 2:OMU1442 4.7 25.3 1.0
C4 2:U1444 4.7 24.8 1.0
O 2:HOH4291 5.0 25.3 1.0

Magnesium binding site 5 out of 88 in 7r4x

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Magnesium binding site 5 out of 88 in the Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1981

b:14.3
occ:1.00
 OP2 2:G1491 1.8 14.8 1.0
O 2:HOH3820 2.0 19.6 1.0
OP1 2:OMG1490 2.0 16.5 1.0
OP1 2:C1331 2.1 19.4 1.0
O 2:HOH2993 2.2 23.1 1.0
O 2:HOH3640 2.4 22.3 1.0
P 2:G1491 3.0 14.8 1.0
P 2:C1331 3.4 19.4 1.0
P 2:OMG1490 3.4 16.5 1.0
OP1 2:G1491 3.5 14.8 1.0
O 2:HOH3257 3.6 15.5 1.0
O3' 2:OMG1490 3.7 16.5 1.0
OP2 2:C1331 3.9 19.4 1.0
O 2:HOH3226 4.0 21.9 1.0
O2' 2:A1489 4.0 22.8 1.0
C3' 2:OMG1490 4.1 16.5 1.0
C5' 2:OMG1490 4.1 16.5 1.0
OP2 2:OMG1490 4.1 16.5 1.0
O5' 2:OMG1490 4.3 16.5 1.0
O5' 2:G1491 4.3 14.8 1.0
O5' 2:C1331 4.3 19.4 1.0
O 2:HOH2889 4.4 21.0 1.0
O3' 2:A1489 4.5 22.8 1.0
O3' 2:G1330 4.5 17.2 1.0
MG 2:MG2046 4.6 18.3 1.0
O 2:HOH3693 4.6 23.0 1.0
C4' 2:OMG1490 4.7 16.5 1.0
C3' 2:A1489 4.7 22.8 1.0
C3' 2:G1330 4.8 17.2 1.0
C2' 2:A1489 4.8 22.8 1.0
O2' 2:G1330 4.9 17.2 1.0
O 2:HOH2353 4.9 20.8 1.0

Magnesium binding site 6 out of 88 in 7r4x

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Magnesium binding site 6 out of 88 in the Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1982

b:24.5
occ:1.00
 O 2:HOH3369 1.9 20.3 1.0
OP1 2:U1519 2.2 21.7 1.0
O 2:HOH3185 2.2 20.7 1.0
O 2:HOH2133 2.3 18.5 1.0
O 2:HOH4782 2.4 20.9 1.0
O 2:HOH4736 2.4 19.4 1.0
P 2:U1519 3.3 21.7 1.0
OP2 2:U1519 3.6 21.7 1.0
OP1 2:G1233 4.0 18.3 1.0
O 2:HOH4827 4.1 19.3 1.0
N2 2:G1257 4.2 18.7 1.0
O 2:HOH5028 4.2 21.4 1.0
O3' 2:C1518 4.2 18.6 1.0
OP2 2:C1234 4.3 19.4 1.0
N7 2:A1259 4.4 20.2 1.0
O2' 2:C1518 4.4 18.6 1.0
N6 2:A1259 4.5 20.2 1.0
O5' 2:U1519 4.5 21.7 1.0
O 2:HOH3633 4.6 22.0 1.0
C2' 2:C1518 4.6 18.6 1.0
O 2:HOH2241 4.6 24.1 1.0
O 2:HOH2106 4.8 18.6 1.0
C3' 2:C1518 4.8 18.6 1.0
O 2:HOH2903 4.9 20.0 1.0
C5' 2:U1519 4.9 21.7 1.0
O2 2:PSU1244 5.0 20.3 1.0
O5' 2:G1233 5.0 18.3 1.0
OP1 2:C1234 5.0 19.4 1.0

Magnesium binding site 7 out of 88 in 7r4x

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Magnesium binding site 7 out of 88 in the Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1983

b:21.3
occ:1.00
 O 2:HOH2711 2.0 19.8 1.0
OP2 2:OMU1326 2.0 20.0 1.0
O 2:HOH3531 2.1 22.3 1.0
O 2:HOH3093 2.3 23.9 1.0
O 2:HOH4723 2.4 22.1 1.0
O 2:HOH2515 2.5 19.6 1.0
P 2:OMU1326 3.4 20.0 1.0
OP2 2:U1494 3.7 19.1 1.0
K 2:K1929 3.8 33.0 1.0
O5' 2:OMU1326 4.0 20.0 1.0
O 2:HOH5156 4.2 21.2 1.0
C5' 2:OMU1326 4.3 20.0 1.0
O 2:HOH2287 4.3 22.5 1.0
OP1 2:OMU1326 4.3 20.0 1.0
OP2 2:G1497 4.5 23.6 1.0
O3' 2:G1325 4.5 22.2 1.0
OP1 2:G1497 4.6 23.6 1.0
C3' 2:G1325 4.6 22.2 1.0
OP1 2:U1496 4.7 19.4 1.0
OP2 2:G1325 4.8 22.2 1.0
O5' 2:G1325 4.8 22.2 1.0
O 2:HOH3614 4.9 21.1 1.0

Magnesium binding site 8 out of 88 in 7r4x

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Magnesium binding site 8 out of 88 in the Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1984

b:20.2
occ:1.00
 OP2 2:U1511 2.0 20.4 1.0
O 2:HOH2678 2.0 20.7 1.0
O 2:HOH4513 2.1 20.3 1.0
O 2:HOH2444 2.2 20.2 1.0
OP1 2:G1510 2.3 24.5 1.0
O 2:HOH3933 2.7 22.3 1.0
P 2:G1510 3.4 24.5 1.0
P 2:U1511 3.4 20.4 1.0
OP2 2:G1510 3.6 24.5 1.0
O 2:HOH2307 4.0 22.3 1.0
OP1 2:G1327 4.0 22.0 1.0
O 2:HOH3742 4.0 23.0 1.0
OP1 2:A1265 4.1 18.9 1.0
O5' 2:A1265 4.1 18.9 1.0
O 2:HOH4102 4.2 24.3 1.0
CM2 2:OMU1326 4.2 20.0 1.0
O5' 2:G1510 4.2 24.5 1.0
OP1 2:U1511 4.2 20.4 1.0
O5' 2:U1511 4.3 20.4 1.0
O 2:HOH2355 4.3 20.5 1.0
O3' 2:G1510 4.3 24.5 1.0
O 2:HOH2562 4.4 24.1 1.0
P 2:A1265 4.6 18.9 1.0
O3' 2:U1509 4.6 26.8 1.0
C5' 2:G1510 4.6 24.5 1.0
C3' 2:G1510 4.7 24.5 1.0
O 2:HOH2483 4.7 20.6 1.0
O2' 2:G1325 4.8 22.2 1.0

Magnesium binding site 9 out of 88 in 7r4x

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Magnesium binding site 9 out of 88 in the Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1985

b:19.7
occ:1.00
 OP2 2:OMG509 2.0 10.5 1.0
O 2:HOH4934 2.0 20.1 1.0
OP2 2:A508 2.1 11.7 1.0
O 2:HOH4798 2.2 17.2 1.0
O 2:HOH4116 2.3 20.4 1.0
O 2:HOH4344 2.4 13.8 1.0
P 2:A508 3.4 11.7 1.0
P 2:OMG509 3.4 10.5 1.0
O5' 2:A508 3.9 11.7 1.0
O 2:HOH3889 3.9 21.4 1.0
O3' 2:G507 3.9 12.1 1.0
O 2:HOH2434 4.1 18.8 1.0
OP1 2:OMG509 4.1 10.5 1.0
O 2:HOH2748 4.1 20.3 1.0
C5' 2:C475 4.1 12.6 1.0
O 2:HOH3795 4.2 17.6 1.0
O J:HOH201 4.2 17.9 1.0
O5' 2:OMG509 4.2 10.5 1.0
O 2:HOH4338 4.3 15.1 1.0
O3' 2:A508 4.4 11.7 1.0
C4' 2:C475 4.4 12.6 1.0
OP1 2:A508 4.6 11.7 1.0
C5' 2:A508 4.6 11.7 1.0
C3' 2:A508 4.8 11.7 1.0
N7 2:OMG509 4.9 10.5 1.0
O2' 2:G95 5.0 9.8 1.0

Magnesium binding site 10 out of 88 in 7r4x

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Magnesium binding site 10 out of 88 in the Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit - Full Map within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1986

b:23.3
occ:1.00
 O 2:HOH5132 2.0 23.4 1.0
OP1 2:A2M99 2.0 14.3 1.0
O 2:HOH2412 2.1 20.6 1.0
O 2:HOH3675 2.2 21.0 1.0
O 2:HOH4069 2.3 20.2 1.0
O 2:HOH2199 2.6 17.9 1.0
O 2:HOH4232 3.0 21.2 1.0
P 2:A2M99 3.5 14.3 1.0
O 2:HOH3620 3.7 18.3 1.0
O 2:HOH3603 3.9 24.2 1.0
OP2 2:A2M99 4.2 14.3 1.0
C3' 2:C98 4.2 12.4 1.0
O3' 2:C98 4.3 12.4 1.0
OP1 2:C409 4.3 12.2 1.0
OP2 2:U44 4.3 18.1 1.0
C5' 2:U43 4.3 16.4 1.0
C4' 2:U43 4.4 16.4 1.0
O2' 2:A42 4.4 14.8 1.0
O5' 2:A2M99 4.5 14.3 1.0
O 2:HOH5148 4.7 21.9 1.0
OP2 2:C409 4.8 12.2 1.0
O4' 2:U43 4.9 16.4 1.0
O 2:HOH3087 5.0 21.1 1.0

Reference:

S.Pellegrino, K.C.Dent, T.Spikes, A.J.Warren. Cryo-Em Reconstruction of the Human 40S Ribosomal Subunit at 2.15 Angstroms Resolution To Be Published.
Page generated: Thu Apr 6 21:31:40 2023

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