Magnesium in PDB 8cas: Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)

Enzymatic activity of Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)

All present enzymatic activity of Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial):
3.6.5.3;

Other elements in 8cas:

The structure of Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial) also contains other interesting chemical elements:

Iron (Fe) 8 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial) (pdb code 8cas). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial), PDB code: 8cas:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 8cas

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Magnesium binding site 1 out of 5 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)


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 48S Initiation Complex (Partial) within 5.0Å range:
probe atom residue distance (Å) B Occ
k:Mg702

b:88.2
occ:1.00
 O1G k:ATP703 2.2 104.1 1.0
O2B k:ATP703 2.3 104.1 1.0
O3G k:ATP703 2.4 104.1 1.0
PG k:ATP703 2.5 104.1 1.0
O3B k:ATP703 2.7 104.1 1.0
PB k:ATP703 2.9 104.1 1.0
O1B k:ATP703 3.4 104.1 1.0
O2G k:ATP703 4.0 104.1 1.0
O3A k:ATP703 4.3 104.1 1.0
CB k:THR392 4.4 80.7 1.0
CB k:GLN420 4.4 98.7 1.0
N k:GLY224 4.6 98.7 1.0

Magnesium binding site 2 out of 5 in 8cas

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Magnesium binding site 2 out of 5 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)


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 48S Initiation Complex (Partial) within 5.0Å range:
probe atom residue distance (Å) B Occ
k:Mg704

b:68.3
occ:1.00
 O3B k:ADP701 2.6 95.1 1.0
PB k:ADP701 3.9 95.1 1.0
CB k:ASP246 4.1 94.9 1.0
CB k:LYS116 4.2 104.9 1.0
CB k:SER117 4.2 104.1 1.0
N k:SER117 4.3 104.1 1.0
CB k:GLN171 4.3 91.9 1.0
O1B k:ADP701 4.4 95.1 1.0
CB k:VAL277 4.6 106.6 1.0
CA k:SER117 4.6 104.1 1.0
O2B k:ADP701 4.7 95.1 1.0
C k:LYS116 4.8 104.9 1.0
O2A k:ADP701 4.8 95.1 1.0
CA k:ASP246 4.8 94.9 1.0
N k:GLU247 5.0 94.8 1.0

Magnesium binding site 3 out of 5 in 8cas

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Magnesium binding site 3 out of 5 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)


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 48S Initiation Complex (Partial) within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1901

b:1.6
occ:1.00
 OP1 2:C449 3.1 20.9 1.0
O S:ARG30 3.2 0.0 1.0
OP2 2:U450 3.9 22.8 1.0
P 2:C449 4.2 20.9 1.0
CB S:THR81 4.2 1.0 1.0
OP1 2:U450 4.3 22.8 1.0
C S:ARG30 4.3 0.0 1.0
N S:SER32 4.3 1.0 1.0
CA S:SER32 4.4 1.0 1.0
CB S:SER32 4.4 1.0 1.0
P 2:U450 4.4 22.8 1.0
O5' 2:C449 4.4 20.9 1.0
C S:PRO31 4.6 0.1 1.0
C5' 2:C449 4.7 20.9 1.0
OP2 2:C449 4.7 20.9 1.0
CB S:ARG30 4.8 0.0 1.0
O3' 2:C449 4.8 20.9 1.0
O S:PRO31 4.9 0.1 1.0

Magnesium binding site 4 out of 5 in 8cas

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Magnesium binding site 4 out of 5 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)


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 48S Initiation Complex (Partial) within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1902

b:89.8
occ:1.00
 OP1 2:U1473 2.2 111.3 1.0
P 2:U1473 2.4 111.3 1.0
O3' 2:C1472 2.5 114.2 1.0
C3' 2:C1472 2.5 114.2 1.0
O2' 2:C1472 2.6 114.2 1.0
OP2 2:U1473 2.7 111.3 1.0
O C:LYS188 2.8 79.0 1.0
C2' 2:C1472 2.9 114.2 1.0
CA C:THR189 3.6 73.2 1.0
N C:ILE190 3.6 61.5 1.0
C C:LYS188 3.8 79.0 1.0
C C:THR189 3.9 73.2 1.0
O5' 2:U1473 4.0 111.3 1.0
C4' 2:C1472 4.0 114.2 1.0
N C:THR189 4.1 73.2 1.0
C1' 2:C1472 4.3 114.2 1.0
O C:ASN186 4.3 78.7 1.0
O C:ALA183 4.5 65.6 1.0
CA C:ILE190 4.6 61.5 1.0
C5' 2:C1472 4.7 114.2 1.0
CB C:THR189 4.7 73.2 1.0
CB C:ILE190 4.7 61.5 1.0
CB C:ALA183 4.7 65.6 1.0
O4' 2:C1472 4.8 114.2 1.0
O C:THR189 4.9 73.2 1.0
C5' 2:U1473 4.9 111.3 1.0

Magnesium binding site 5 out of 5 in 8cas

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Magnesium binding site 5 out of 5 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)


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 48S Initiation Complex (Partial) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg602

b:95.7
occ:1.00
 CA G:GLY141 3.6 152.8 1.0
N G:GLY141 3.6 152.8 1.0
OG1 G:THR137 3.7 170.2 1.0
CD G:LYS139 3.8 184.7 1.0
CB G:THR125 3.9 163.5 1.0
CE G:LYS139 3.9 184.7 1.0
OG1 G:THR125 3.9 163.5 1.0
O G:THR125 4.0 163.5 1.0
O G:LYS139 4.0 184.7 1.0
OG G:SER114 4.0 137.2 1.0
CG G:LYS139 4.1 184.7 1.0
CG G:ARG127 4.2 176.9 1.0
C G:LEU140 4.5 163.9 1.0
C G:LYS139 4.7 184.7 1.0
NZ G:LYS139 4.8 184.7 1.0
CG2 G:THR125 4.8 163.5 1.0
CB G:THR137 4.8 170.2 1.0
C G:THR125 4.8 163.5 1.0
CA G:THR125 5.0 163.5 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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