Magnesium in PDB 6okk: Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit

Other elements in 6okk:

The structure of Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit also contains other interesting chemical elements:

Zinc (Zn) 1 atom

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 - 67;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit (pdb code 6okk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 67 binding sites of Magnesium where determined in the Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit, PDB code: 6okk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 67 in 6okk

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Magnesium binding site 1 out of 67 in the Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2101

b:71.6
occ:1.00
OP2 A:A1930 2.1 93.5 1.0
P A:A1930 3.3 94.0 1.0
OP1 A:G10 3.4 88.6 1.0
O5' A:A1930 3.6 87.8 1.0
OP1 A:A1930 4.0 95.0 1.0
OP2 A:C1929 4.1 93.4 1.0
O3' A:U9 4.5 86.6 1.0
OP1 A:C1929 4.5 90.0 1.0
P A:G10 4.6 86.7 1.0
O3' A:C1929 4.6 82.8 1.0
P A:C1929 4.6 89.8 1.0
C8 A:A1930 4.7 67.9 1.0
O5' A:C1929 4.8 82.6 1.0
C5' A:A1930 4.8 89.0 1.0
C3' A:C1929 4.9 76.2 1.0

Magnesium binding site 2 out of 67 in 6okk

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Magnesium binding site 2 out of 67 in the Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2102

b:37.2
occ:1.00
OP1 A:G16 1.9 58.0 1.0
P A:G16 3.4 55.3 1.0
O2 A:C621 4.0 44.3 1.0
OP2 A:G16 4.0 60.6 1.0
O6 A:G617 4.1 49.9 1.0
N1 A:A627 4.2 71.7 1.0
O2' A:C621 4.3 66.2 1.0
O3' A:U15 4.3 51.6 1.0
O5' A:G16 4.3 52.8 1.0
OP2 A:U615 4.3 81.6 1.0
N6 A:A627 4.5 74.9 1.0
N2 A:G1208 4.5 52.1 1.0
C5' A:G16 4.6 53.2 1.0
O4' A:A622 4.8 67.4 1.0
C6 A:A627 4.9 70.1 1.0
C5' A:U615 4.9 69.4 1.0
C2' A:C621 4.9 65.4 1.0

Magnesium binding site 3 out of 67 in 6okk

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Magnesium binding site 3 out of 67 in the Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2103

b:51.3
occ:1.00
OP1 A:A102 2.1 72.1 1.0
P A:A102 3.4 67.5 1.0
OP1 A:C367 3.5 58.4 1.0
OP2 A:A102 3.9 71.1 1.0
O3' A:C101 4.3 65.7 1.0
C3' A:C101 4.4 63.5 1.0
O5' A:A102 4.5 68.8 1.0
C4' A:U44 4.7 82.0 1.0
P A:C367 4.7 58.7 1.0
C5' A:U44 4.8 80.8 1.0
O2' A:A43 4.9 71.0 1.0
C5' A:A102 4.9 76.8 1.0

Magnesium binding site 4 out of 67 in 6okk

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Magnesium binding site 4 out of 67 in the Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2104

b:50.8
occ:1.00
OP2 A:U103 1.9 81.2 1.0
OP2 A:C367 2.1 57.5 1.0
OP2 A:A102 2.5 71.1 1.0
P A:U103 3.3 79.2 1.0
P A:C367 3.3 58.7 1.0
O4 A:U104 3.7 59.8 1.0
C3' A:A366 3.7 70.5 1.0
O3' A:A366 3.7 64.6 1.0
P A:A102 4.0 67.5 1.0
O5' A:U103 4.0 82.0 1.0
OP1 A:C367 4.1 58.4 1.0
OP1 A:U103 4.2 84.9 1.0
O3' A:A102 4.2 79.2 1.0
C2' A:A366 4.4 70.5 1.0
C8 A:A366 4.4 63.2 1.0
C4 A:U104 4.5 58.6 1.0
OP2 A:A365 4.5 0.6 1.0
O3' A:C101 4.5 65.7 1.0
O5' A:C367 4.5 58.6 1.0
C3' A:A102 4.6 78.5 1.0
C5 A:U104 4.7 60.1 1.0
N7 A:A366 4.9 63.7 1.0
OP1 A:A102 4.9 72.1 1.0
O5' A:A365 4.9 0.5 1.0
N9 A:A366 4.9 62.5 1.0
C5' A:C367 4.9 57.2 1.0
O5' A:A102 4.9 68.8 1.0
C4' A:A366 5.0 76.0 1.0

Magnesium binding site 5 out of 67 in 6okk

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Magnesium binding site 5 out of 67 in the Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2105

b:55.7
occ:1.00
OP2 A:C49 2.2 93.6 1.0
OP1 A:A431 3.3 82.6 1.0
P A:C49 3.6 91.9 1.0
N7 A:A431 4.0 67.4 1.0
OP1 A:C49 4.3 92.5 1.0
O5' A:C49 4.4 90.0 1.0
C8 A:A431 4.5 67.4 1.0
C5' A:G394 4.5 81.7 1.0
O3' A:C430 4.6 78.6 1.0
P A:A431 4.6 83.1 1.0
C4' A:G394 4.6 81.2 1.0
O3' A:G48 4.6 93.3 1.0
O4' A:G394 4.6 83.2 1.0
C3' A:G48 4.9 94.9 1.0
C5 A:C49 4.9 83.0 1.0

Magnesium binding site 6 out of 67 in 6okk

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Magnesium binding site 6 out of 67 in the Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2106

b:46.3
occ:1.00
O4 A:U454 2.5 78.8 1.0
OP2 A:A452 3.3 81.0 1.0
C4 A:U454 3.5 71.3 1.0
N6 A:A464 3.9 65.2 1.0
C5 A:U454 4.0 69.9 1.0
O2' A:C450 4.2 86.1 1.0
O4 A:U453 4.2 58.8 1.0
P A:A452 4.6 81.9 1.0
C5 A:U453 4.6 60.1 1.0
N3 A:U454 4.7 66.0 1.0
C4 A:U453 4.8 58.8 1.0
O6 A:G463 4.9 56.6 1.0
N4 A:C455 5.0 61.4 1.0

Magnesium binding site 7 out of 67 in 6okk

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Magnesium binding site 7 out of 67 in the Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2107

b:63.0
occ:1.00
OP1 A:A459 2.2 0.6 1.0
OP1 A:A60 3.1 0.3 1.0
P A:A459 3.5 0.1 1.0
O3' A:A60 3.7 0.1 1.0
OP2 A:A62 3.8 0.3 1.0
OP2 A:A459 4.0 94.8 1.0
C3' A:A60 4.2 0.4 1.0
OP1 A:G460 4.2 0.0 1.0
O3' A:A458 4.2 0.8 1.0
N7 A:A62 4.4 0.2 1.0
P A:A60 4.5 0.5 1.0
C5' A:A60 4.6 0.1 1.0
C5' A:A61 4.7 0.9 1.0
O5' A:A459 4.7 0.1 1.0
C8 A:A62 4.7 0.5 1.0
C5' A:A459 4.9 0.2 1.0
C4' A:A60 5.0 0.1 1.0

Magnesium binding site 8 out of 67 in 6okk

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Magnesium binding site 8 out of 67 in the Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2108

b:69.8
occ:1.00
OP2 A:A87 2.8 0.3 1.0
N7 A:A88 4.2 68.6 1.0
P A:A87 4.2 0.1 1.0
N7 A:G59 4.2 81.7 1.0
N7 A:A87 4.7 83.9 1.0
O5' A:A87 4.7 0.6 1.0
O6 A:G59 4.8 80.1 1.0
N6 A:A88 4.8 72.5 1.0
C8 A:A87 4.8 86.3 1.0
OP1 A:A87 4.9 0.1 1.0
O5' A:A86 5.0 0.7 1.0

Magnesium binding site 9 out of 67 in 6okk

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Magnesium binding site 9 out of 67 in the Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2109

b:53.7
occ:1.00
OP2 A:G97 2.3 77.5 1.0
P A:G97 3.5 76.4 1.0
O5' A:G97 4.0 76.6 1.0
OP1 A:C96 4.1 69.5 1.0
N7 A:G97 4.2 87.0 1.0
OP1 A:G97 4.2 74.3 1.0
N7 A:G98 4.3 62.6 1.0
O6 A:G98 4.4 68.7 1.0
C8 A:G97 4.5 84.0 1.0
O5' A:C96 4.5 67.9 1.0
OP2 A:C96 4.5 68.0 1.0
P A:C96 4.6 66.3 1.0
O3' A:C96 4.8 71.5 1.0
N4 A:C99 5.0 47.2 1.0

Magnesium binding site 10 out of 67 in 6okk

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Magnesium binding site 10 out of 67 in the Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine, Small Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2110

b:40.0
occ:1.00
O6 A:G390 3.9 44.1 1.0
O6 A:G389 4.3 43.6 1.0
O4 A:U100 4.5 40.1 1.0
N4 A:C101 4.5 57.8 1.0
N7 A:G389 4.6 41.6 1.0
N4 A:C388 4.9 52.4 1.0
OP1 A:U386 4.9 89.0 1.0
C6 A:G390 5.0 44.5 1.0

Reference:

W.Wong, S.H.W.Schere. Cryo-Em Structure of the Plasmodium Falciparum 80S Ribosome Bound to the Anti-Protozoan Drug Emetine. To Be Published.
Page generated: Mon Dec 14 23:43:46 2020

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