Magnesium in PDB 8cah: Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex

Other elements in 8cah:

The structure of Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex also contains other interesting chemical elements:

Iron (Fe) 8 atoms
Zinc (Zn) 2 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;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex (pdb code 8cah). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 80 binding sites of Magnesium where determined in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex, PDB code: 8cah:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 80 in 8cah

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Magnesium binding site 1 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex


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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1901

b:12.3
occ:1.00
 MG 2:MG1967 3.8 16.1 1.0
O6 2:G1294 4.0 21.4 1.0
N7 2:G1294 4.0 21.4 1.0
O6 2:G1295 4.1 21.4 1.0
N7 2:G1295 4.5 21.4 1.0
C6 2:G1294 4.5 21.4 1.0
C5 2:G1294 4.5 21.4 1.0
O4 2:U1302 4.7 21.4 1.0
N6 2:A1296 4.8 21.4 1.0
C6 2:G1295 4.9 21.4 1.0
C8 2:G1294 5.0 21.4 1.0

Magnesium binding site 2 out of 80 in 8cah

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Magnesium binding site 2 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex


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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range:

Magnesium binding site 3 out of 80 in 8cah

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Magnesium binding site 3 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex


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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1903

b:14.3
occ:1.00
 O6 2:G291 4.1 12.7 1.0
O4 2:U122 4.3 21.4 1.0
O6 2:G123 4.3 21.4 1.0
N6 2:A124 4.5 21.4 1.0
N7 2:G123 4.6 21.4 1.0
C4 2:U122 4.7 21.4 1.0
C5 2:U122 4.7 21.4 1.0

Magnesium binding site 4 out of 80 in 8cah

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Magnesium binding site 4 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex


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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1904

b:2.0
occ:1.00
 O6 2:G384 3.9 21.4 1.0
O4 2:U98 4.0 21.4 1.0
O6 2:G383 4.3 21.4 1.0
N4 2:C99 4.6 21.4 1.0
N6 2:A385 5.0 21.4 1.0
C6 2:G384 5.0 21.4 1.0

Magnesium binding site 5 out of 80 in 8cah

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Magnesium binding site 5 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex


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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1905

b:3.8
occ:1.00
 OP2 2:U101 2.1 21.4 1.0
OP2 2:C361 2.3 21.4 1.0
OP2 2:A100 2.5 21.4 1.0
P 2:U101 3.5 21.4 1.0
O4 2:U102 3.6 21.4 1.0
P 2:C361 3.6 21.4 1.0
P 2:A100 4.0 21.4 1.0
C3' 2:A360 4.0 21.4 1.0
O3' 2:A360 4.2 21.4 1.0
OP1 2:C361 4.3 21.4 1.0
OP1 2:U101 4.3 21.4 1.0
O5' 2:U101 4.3 21.4 1.0
C4 2:U102 4.4 21.4 1.0
OP2 2:A359 4.5 17.7 1.0
O3' 2:A100 4.5 21.4 1.0
O3' 2:C99 4.6 21.4 1.0
C5 2:U102 4.7 21.4 1.0
C3' 2:A100 4.7 21.4 1.0
OP1 2:A100 4.7 21.4 1.0
O5' 2:C361 4.8 21.4 1.0
C8 2:A360 4.8 21.4 1.0
C2' 2:A360 4.9 21.4 1.0
O5' 2:A100 4.9 21.4 1.0
C5' 2:A360 5.0 21.4 1.0

Magnesium binding site 6 out of 80 in 8cah

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Magnesium binding site 6 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex


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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1906

b:3.5
occ:1.00
 OP2 2:C424 2.1 21.4 1.0
P 2:C424 3.4 21.4 1.0
N7 2:G426 3.7 21.4 1.0
O5' 2:C424 3.9 21.4 1.0
OP1 2:C424 4.0 21.4 1.0
O4' 2:C424 4.0 21.4 1.0
C8 2:G426 4.2 21.4 1.0
C4' 2:C424 4.4 21.4 1.0
N1 2:A55 4.5 21.4 1.0
OP2 2:G403 4.6 21.4 1.0
O3' 2:G423 4.6 21.4 1.0
O4' 2:G403 4.7 21.4 1.0
C5 2:G426 4.7 21.4 1.0
N6 2:A55 4.7 21.4 1.0
OP1 2:G426 4.8 21.4 1.0
C5' 2:C424 4.8 21.4 1.0
C1' 2:C424 4.9 21.4 1.0

Magnesium binding site 7 out of 80 in 8cah

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Magnesium binding site 7 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex


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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1907

b:6.5
occ:1.00
 OP2 2:C49 2.2 21.4 1.0
P 2:C49 3.6 21.4 1.0
OP1 2:A425 3.8 21.4 1.0
N7 2:A425 3.8 21.4 1.0
C5' 2:G388 4.2 21.4 1.0
OP1 2:C49 4.2 21.4 1.0
C4' 2:G388 4.3 21.4 1.0
C8 2:A425 4.4 21.4 1.0
O5' 2:C49 4.4 21.4 1.0
O4' 2:G388 4.5 21.4 1.0
O3' 2:G48 4.6 21.4 1.0
C3' 2:G48 4.9 21.4 1.0
C5 2:A425 4.9 21.4 1.0

Magnesium binding site 8 out of 80 in 8cah

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Magnesium binding site 8 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex


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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1908

b:12.7
occ:1.00
 OP1 2:A100 2.3 21.4 1.0
OP1 2:C361 3.6 21.4 1.0
P 2:A100 3.7 21.4 1.0
C3' 2:C99 4.1 21.4 1.0
O3' 2:C99 4.2 21.4 1.0
OP2 2:A100 4.3 21.4 1.0
O2' 2:A43 4.4 21.4 1.0
C4' 2:U44 4.6 21.4 1.0
O4' 2:A378 4.6 21.4 1.0
C5' 2:U44 4.8 21.4 1.0
O5' 2:A100 4.8 21.4 1.0
P 2:C361 4.9 21.4 1.0

Magnesium binding site 9 out of 80 in 8cah

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Magnesium binding site 9 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex


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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1909

b:2.1
occ:1.00
 OP1 2:C402 3.2 21.4 1.0
OP2 2:C402 3.5 21.4 1.0
P 2:C402 3.8 21.4 1.0
OP2 2:G386 4.0 21.4 1.0
OP1 2:A400 4.1 21.4 1.0
O5' 2:A401 4.4 21.4 1.0
OP2 2:A387 4.4 21.4 1.0
C4' 2:A401 4.6 21.4 1.0
N7 2:G386 4.7 21.4 1.0
C8 2:G386 4.7 21.4 1.0
O3' 2:A401 4.7 21.4 1.0
N7 2:A387 4.8 21.4 1.0
NE S:ARG3 4.8 10.2 1.0
C5' 2:A401 4.9 21.4 1.0
C3' 2:A401 4.9 21.4 1.0
O5' 2:G386 4.9 21.4 1.0
CD S:ARG3 5.0 10.2 1.0

Magnesium binding site 10 out of 80 in 8cah

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Magnesium binding site 10 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex


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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1910

b:11.7
occ:1.00
 OP1 2:A401 2.1 21.4 1.0
P 2:A401 3.5 21.4 1.0
OP2 2:A401 4.1 21.4 1.0
O4' 2:C402 4.1 21.4 1.0
O6 2:G404 4.2 21.4 1.0
O2 2:C402 4.3 21.4 1.0
O5' 2:A401 4.3 21.4 1.0
OP1 2:A387 4.4 21.4 1.0
C3' 2:A401 4.4 21.4 1.0
O3' 2:A400 4.4 21.4 1.0
O6 2:G392 4.5 21.4 1.0
C1' 2:C402 4.5 21.4 1.0
N4 2:C405 4.5 21.4 1.0
C2' 2:A401 4.6 21.4 1.0
C2 2:C402 4.6 21.4 1.0
OP2 2:C402 4.6 21.4 1.0
O2' 2:A401 4.7 21.4 1.0
N1 2:C402 4.7 21.4 1.0
OP2 2:A387 4.8 21.4 1.0
P 2:A387 5.0 21.4 1.0

Reference:

K.Ikeuchi, N.Ivic, R.Buschauer, J.Cheng, T.Frohlich, Y.Matsuo, O.Berninghausen, T.Inada, T.Becker, R.Beckmann. Molecular Basis For Recognition and Deubiquitination of 40S Ribosomes By OTU2. Nat Commun V. 14 2730 2023.
ISSN: ESSN 2041-1723
PubMed: 37169754
DOI: 10.1038/S41467-023-38161-W
Page generated: Thu Jul 27 22:37:20 2023

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