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Magnesium in PDB 8y2o: The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah)

Enzymatic activity of The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah)

All present enzymatic activity of The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah):
2.1.1.205;

Other elements in 8y2o:

The structure of The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah) also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah) (pdb code 8y2o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah), PDB code: 8y2o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8y2o

Go back to Magnesium Binding Sites List in 8y2o
Magnesium binding site 1 out of 7 in the The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:41.8
occ:1.00
 O4 C:U27 3.6 50.7 1.0
OP2 C:C25 3.8 52.8 1.0
N7 C:G26 3.9 49.7 1.0
C5 C:C25 4.3 52.8 1.0
O6 C:G26 4.4 49.7 1.0
N6 C:A43 4.5 42.1 1.0
C4 C:U27 4.6 50.7 1.0
C8 C:G26 4.8 49.7 1.0
C5 C:G26 4.8 49.7 1.0
C6 C:C25 4.8 52.8 1.0
OP2 C:G26 4.9 49.7 1.0

Magnesium binding site 2 out of 7 in 8y2o

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Magnesium binding site 2 out of 7 in the The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg102

b:42.6
occ:1.00
 OP2 C:G45 3.3 42.0 1.0
OP2 C:A44 3.7 41.7 1.0
OD2 A:ASP405 3.8 46.9 1.0
OD1 A:ASP405 3.9 46.9 1.0
N7 C:G45 4.0 42.0 1.0
CG A:ASP405 4.3 46.9 1.0
O5' C:A44 4.3 41.7 1.0
C8 C:G45 4.5 42.0 1.0
P C:A44 4.5 41.7 1.0
P C:G45 4.8 42.0 1.0
C8 C:A44 4.9 41.7 1.0
OP1 C:A44 4.9 41.7 1.0

Magnesium binding site 3 out of 7 in 8y2o

Go back to Magnesium Binding Sites List in 8y2o
Magnesium binding site 3 out of 7 in the The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg103

b:61.8
occ:1.00
 O2' C:A58 4.3 57.5 1.0
O6 C:G53 4.3 65.0 1.0
N7 C:G53 4.4 65.0 1.0
O4 C:U54 4.5 60.8 1.0
C2' C:A58 4.5 57.5 1.0
OP1 C:A58 4.6 57.5 1.0

Magnesium binding site 4 out of 7 in 8y2o

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Magnesium binding site 4 out of 7 in the The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg104

b:60.2
occ:1.00
 OP2 C:G57 3.7 56.9 1.0
OP2 C:C56 3.8 55.2 1.0
OP2 C:U55 3.8 58.4 1.0
C5 C:U55 4.0 58.4 1.0
C6 C:U55 4.3 58.4 1.0
O5' C:U55 4.6 58.4 1.0
OP1 C:G57 4.6 56.9 1.0
P C:G57 4.6 56.9 1.0
P C:U55 4.8 58.4 1.0

Magnesium binding site 5 out of 7 in 8y2o

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Magnesium binding site 5 out of 7 in the The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg105

b:59.3
occ:1.00
 O6 C:G70 4.0 70.7 1.0
O6 C:G71 4.2 84.0 1.0
N7 C:G70 4.4 70.7 1.0
C6 C:G70 4.8 70.7 1.0
C5 C:G70 4.9 70.7 1.0

Magnesium binding site 6 out of 7 in 8y2o

Go back to Magnesium Binding Sites List in 8y2o
Magnesium binding site 6 out of 7 in the The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg106

b:62.3
occ:1.00
 N7 C:G15 2.8 62.8 1.0
C8 C:G15 3.5 62.8 1.0
C5 C:G15 3.9 62.8 1.0
O4 C:U8 4.1 53.0 1.0
O6 C:G15 4.2 62.8 1.0
C4 C:U8 4.2 53.0 1.0
OP1 C:A7 4.4 54.3 1.0
C6 C:G15 4.5 62.8 1.0
N3 C:U8 4.6 53.0 1.0
C5 C:U8 4.6 53.0 1.0
OP2 C:G15 4.8 62.8 1.0
N9 C:G15 4.8 62.8 1.0
OP2 C:A14 4.8 61.8 1.0
N7 C:A14 5.0 61.8 1.0
C8 C:A14 5.0 61.8 1.0

Magnesium binding site 7 out of 7 in 8y2o

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Magnesium binding site 7 out of 7 in the The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Cryo-Em Structure of Human Trna Methyltransferase FTSJ1-Thada with Substrate Trna and S-Adenosyl Homocysteine (Sah) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg107

b:62.3
occ:1.00
 C5 C:A35 3.1 85.3 1.0
CA A:GLY1107 3.1 77.1 1.0
C6 C:A35 3.2 85.3 1.0
N7 C:A35 3.4 85.3 1.0
CB A:TRP1054 3.5 63.5 1.0
N6 C:A35 3.6 85.3 1.0
C4 C:A35 3.6 85.3 1.0
N A:GLY1107 3.7 77.1 1.0
N1 C:A35 3.8 85.3 1.0
C8 C:A35 3.9 85.3 1.0
CD1 A:ILE967 4.0 69.3 1.0
CG A:TRP1054 4.0 63.5 1.0
NH2 A:ARG1106 4.0 79.5 1.0
N9 C:A35 4.1 85.3 1.0
C2 C:A35 4.1 85.3 1.0
N3 C:A35 4.1 85.3 1.0
CD2 A:TRP1054 4.2 63.5 1.0
CE3 A:TRP1054 4.3 63.5 1.0
CD1 A:LEU1111 4.3 59.0 1.0
C A:GLY1107 4.5 77.1 1.0
NE A:ARG1106 4.5 79.5 1.0
CG1 A:ILE967 4.6 69.3 1.0
CD2 A:HIS1105 4.7 79.7 1.0
CZ A:ARG1106 4.7 79.5 1.0
C A:ARG1106 4.8 79.5 1.0
CA A:TRP1054 4.8 63.5 1.0
CD1 A:TRP1054 4.9 63.5 1.0
CG A:LEU1111 4.9 59.0 1.0
N A:ALA1108 5.0 74.5 1.0

Reference:

K.Ishiguro, A.Fujimura, M.Shirouzu. Structural Insights Into Trna Recognition of the Human FTSJ1-Thada Complex. Commun Biol V. 8 893 2025.
ISSN: ESSN 2399-3642
PubMed: 40483304
DOI: 10.1038/S42003-025-08278-3
Page generated: Fri Aug 15 21:18:13 2025

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