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Magnesium in PDB 8p7b: Cryoem Structure of METTL6 Trna Serrs Complex in A 1:2:2 Stoichiometry

Enzymatic activity of Cryoem Structure of METTL6 Trna Serrs Complex in A 1:2:2 Stoichiometry

All present enzymatic activity of Cryoem Structure of METTL6 Trna Serrs Complex in A 1:2:2 Stoichiometry:
6.1.1.11;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryoem Structure of METTL6 Trna Serrs Complex in A 1:2:2 Stoichiometry (pdb code 8p7b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cryoem Structure of METTL6 Trna Serrs Complex in A 1:2:2 Stoichiometry, PDB code: 8p7b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8p7b

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Magnesium binding site 1 out of 6 in the Cryoem Structure of METTL6 Trna Serrs Complex in A 1:2:2 Stoichiometry


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structure of METTL6 Trna Serrs Complex in A 1:2:2 Stoichiometry within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg101

b:76.7
occ:1.00
 OP2 T:G9 2.0 77.7 1.0
OP2 T:4AC12 2.7 77.6 1.0
OP1 T:4AC12 2.9 77.6 1.0
P T:4AC12 3.2 77.6 1.0
P T:G9 3.3 77.7 1.0
OP1 T:G9 3.7 77.7 1.0
O3' T:C11 4.0 77.1 1.0
O5' T:G9 4.0 77.7 1.0
C3' T:C11 4.3 77.1 1.0
O5' T:C11 4.3 77.1 1.0
OP2 T:C11 4.4 77.1 1.0
OP1 T:U8 4.4 78.0 1.0
O3' T:U8 4.5 78.0 1.0
O5' T:4AC12 4.6 77.6 1.0
O6 T:G13 4.6 77.6 1.0
C3' T:U8 4.7 78.0 1.0
C5 T:4AC12 4.7 77.6 1.0
C6 T:4AC12 4.7 77.6 1.0
P T:C11 4.8 77.1 1.0
N7 T:G13 4.9 77.6 1.0
OP1 T:C11 5.0 77.1 1.0

Magnesium binding site 2 out of 6 in 8p7b

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Magnesium binding site 2 out of 6 in the Cryoem Structure of METTL6 Trna Serrs Complex in A 1:2:2 Stoichiometry


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem Structure of METTL6 Trna Serrs Complex in A 1:2:2 Stoichiometry within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg102

b:76.5
occ:1.00
 OP2 T:A22 3.8 81.0 1.0
CM7 T:4AC12 4.0 77.6 1.0
N7 T:G23 4.1 81.5 1.0
O6 T:G24 4.1 81.0 1.0
N7 T:G24 4.3 81.0 1.0
O6 T:G23 4.6 81.5 1.0
C8 T:G23 4.9 81.5 1.0
C6 T:G24 4.9 81.0 1.0
C5 T:G23 4.9 81.5 1.0
P T:A22 5.0 81.0 1.0

Magnesium binding site 3 out of 6 in 8p7b

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Magnesium binding site 3 out of 6 in the Cryoem Structure of METTL6 Trna Serrs Complex in A 1:2:2 Stoichiometry


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryoem Structure of METTL6 Trna Serrs Complex in A 1:2:2 Stoichiometry within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg103

b:83.9
occ:1.00
 OP1 T:5MC48 2.1 78.9 1.0
OP2 T:U50 2.9 85.3 1.0
P T:5MC48 3.6 78.9 1.0
P T:U50 4.1 85.3 1.0
O3' T:G47I 4.2 69.5 1.0
O5' T:U50 4.3 85.3 1.0
C5' T:5MC48 4.4 78.9 1.0
C5 T:U50 4.4 85.3 1.0
OP2 T:5MC48 4.4 78.9 1.0
O5' T:5MC48 4.5 78.9 1.0
OP1 T:G49 4.6 81.7 1.0
C6 T:U50 4.7 85.3 1.0
OP2 T:G51 4.7 91.5 1.0
C3' T:5MC48 4.8 78.9 1.0
N7 T:G51 4.8 91.5 1.0
O5' T:G49 4.9 81.7 1.0
OP1 T:U50 4.9 85.3 1.0

Magnesium binding site 4 out of 6 in 8p7b

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Magnesium binding site 4 out of 6 in the Cryoem Structure of METTL6 Trna Serrs Complex in A 1:2:2 Stoichiometry


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryoem Structure of METTL6 Trna Serrs Complex in A 1:2:2 Stoichiometry within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg101

b:75.9
occ:1.00
 OP2 R:4AC12 1.8 76.2 1.0
OP2 R:G9 2.3 73.7 1.0
P R:4AC12 3.1 76.2 1.0
P R:G9 3.4 73.7 1.0
OP1 R:4AC12 3.8 76.2 1.0
OP1 R:G9 3.8 73.7 1.0
O3' R:C11 3.9 74.7 1.0
OP1 R:U8 4.2 76.2 1.0
C3' R:C11 4.2 74.7 1.0
O5' R:4AC12 4.2 76.2 1.0
O5' R:C11 4.2 74.7 1.0
O5' R:G9 4.3 73.7 1.0
C5 R:4AC12 4.4 76.2 1.0
O6 R:G13 4.5 76.2 1.0
OP2 R:C11 4.5 74.7 1.0
O3' R:U8 4.7 76.2 1.0
P R:C11 4.8 74.7 1.0
C3' R:U8 4.8 76.2 1.0
N7 R:G13 4.9 76.2 1.0
OP1 R:C11 4.9 74.7 1.0
C6 R:4AC12 5.0 76.2 1.0

Magnesium binding site 5 out of 6 in 8p7b

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Magnesium binding site 5 out of 6 in the Cryoem Structure of METTL6 Trna Serrs Complex in A 1:2:2 Stoichiometry


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryoem Structure of METTL6 Trna Serrs Complex in A 1:2:2 Stoichiometry within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg102

b:70.7
occ:1.00
 N7 R:G23 4.0 79.6 1.0
OP2 R:A22 4.1 78.8 1.0
O6 R:G23 4.4 79.6 1.0
N7 R:G24 4.4 78.5 1.0
O6 R:G24 4.4 78.5 1.0
OP2 R:G23 4.6 79.6 1.0
OP1 R:A22 4.6 78.8 1.0
P R:A22 4.7 78.8 1.0
C5 R:G23 4.8 79.6 1.0
C8 R:G23 4.9 79.6 1.0
C6 R:G23 4.9 79.6 1.0
O5' R:A22 4.9 78.8 1.0

Magnesium binding site 6 out of 6 in 8p7b

Go back to Magnesium Binding Sites List in 8p7b
Magnesium binding site 6 out of 6 in the Cryoem Structure of METTL6 Trna Serrs Complex in A 1:2:2 Stoichiometry


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryoem Structure of METTL6 Trna Serrs Complex in A 1:2:2 Stoichiometry within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg103

b:83.1
occ:1.00
 OP1 R:5MC48 2.2 77.9 1.0
OP2 R:U50 3.2 85.5 1.0
P R:5MC48 3.6 77.9 1.0
O3' R:G47I 4.2 64.9 1.0
P R:U50 4.3 85.5 1.0
O5' R:U50 4.4 85.5 1.0
C5 R:U50 4.4 85.5 1.0
OP2 R:5MC48 4.4 77.9 1.0
OP2 R:G51 4.6 89.9 1.0
N7 R:G51 4.6 89.9 1.0
O5' R:5MC48 4.6 77.9 1.0
C5' R:5MC48 4.6 77.9 1.0
C6 R:U50 4.7 85.5 1.0
OP1 R:G49 4.7 82.5 1.0

Reference:

P.Throll, L.G.Dolce, P.R.Lastres, K.Arnold, L.Tengo, S.Basu, S.Kaiser, R.Schneider, E.Kowalinski. Structural Basis of the Cooperation Between the M3C-Rna-Methyltransferase METTL6 with Serrs Amino-Acyl-Synthetase For Trna Recognition To Be Published.
Page generated: Fri Aug 15 12:15:28 2025

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