Magnesium in PDB 7q81: Crystal Structure of the Methyltransferase-Ribozyme 1, 2'- Selenomethyl-Uridine Modified (with 1-Methyl-Adenosine)

The structure of Crystal Structure of the Methyltransferase-Ribozyme 1, 2'- Selenomethyl-Uridine Modified (with 1-Methyl-Adenosine), PDB code: 7q81 was solved by M.Mieczkowski, C.Hoebartner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.07 / 2.85
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.085, 71.085, 83.561, 90, 90, 90
R / Rfree (%)	18.8 / 21.4

The binding sites of Magnesium atom in the Crystal Structure of the Methyltransferase-Ribozyme 1, 2'- Selenomethyl-Uridine Modified (with 1-Methyl-Adenosine) (pdb code 7q81). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of the Methyltransferase-Ribozyme 1, 2'- Selenomethyl-Uridine Modified (with 1-Methyl-Adenosine), PDB code: 7q81:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of the Methyltransferase-Ribozyme 1, 2'- Selenomethyl-Uridine Modified (with 1-Methyl-Adenosine)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Methyltransferase-Ribozyme 1, 2'- Selenomethyl-Uridine Modified (with 1-Methyl-Adenosine) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:169.1 occ:1.00 O B:HOH209 2.2 169.0 1.0 O B:HOH203 2.2 118.0 1.0 O B:HOH210 2.2 184.6 1.0 O B:HOH205 2.2 135.8 1.0 O C:HOH207 2.2 131.9 1.0 O B:HOH208 2.2 145.7 1.0 C5 B:C13 4.8 97.5 1.0 OP2 B:C13 4.8 127.3 1.0 N4 B:C13 4.9 87.7 1.0 N7 B:G14 4.9 96.7 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of the Methyltransferase-Ribozyme 1, 2'- Selenomethyl-Uridine Modified (with 1-Methyl-Adenosine)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Methyltransferase-Ribozyme 1, 2'- Selenomethyl-Uridine Modified (with 1-Methyl-Adenosine) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:168.8 occ:1.00 O C:HOH208 2.2 179.7 1.0 O B:HOH204 2.2 128.9 1.0 O C:HOH205 2.2 159.2 1.0 O B:HOH201 2.2 180.5 1.0 O C:HOH206 2.2 147.0 1.0 O C:HOH203 2.2 144.0 1.0 O4 B:U9 4.2 145.8 1.0 O6 B:G10 4.6 142.7 1.0 O2' C:A33 4.7 111.1 1.0 OP2 C:A34 4.8 143.0 1.0 C4 B:U9 4.8 141.1 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of the Methyltransferase-Ribozyme 1, 2'- Selenomethyl-Uridine Modified (with 1-Methyl-Adenosine)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Methyltransferase-Ribozyme 1, 2'- Selenomethyl-Uridine Modified (with 1-Methyl-Adenosine) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg102 b:90.3 occ:1.00 O2 C:C32 2.4 95.7 1.0 C2 C:C32 3.3 89.2 1.0 N3 C:C32 3.6 96.0 1.0 N4 B:C16 3.8 113.0 1.0 OP2 B:A15 4.1 82.3 1.0 N7 B:A15 4.2 98.7 1.0 N7 C:A33 4.5 97.5 1.0 N1 C:C32 4.5 86.8 1.0 N6 C:A33 4.5 84.7 1.0 C2' C:C32 4.9 113.1 1.0 C4 B:C16 4.9 87.1 1.0 O2' B:G14 4.9 115.6 1.0 C4 C:C32 4.9 72.0 1.0 C1' C:C32 4.9 92.0 1.0 N6 B:A15 5.0 101.3 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of the Methyltransferase-Ribozyme 1, 2'- Selenomethyl-Uridine Modified (with 1-Methyl-Adenosine)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Methyltransferase-Ribozyme 1, 2'- Selenomethyl-Uridine Modified (with 1-Methyl-Adenosine) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg103 b:111.2 occ:1.00 O6 C:G48 2.6 116.7 1.0 O4 C:U47 2.6 111.1 1.0 C4 C:U47 3.6 111.5 1.0 C6 C:G48 3.7 117.4 1.0 C5 C:U47 4.1 125.3 1.0 C5 C:G48 4.5 114.2 1.0 N7 C:G48 4.6 127.6 1.0 N4 A:C2 4.6 104.3 1.0 N6 A:A3 4.6 115.4 1.0 N3 C:U47 4.7 106.7 1.0 N1 C:G48 4.7 112.5 1.0 O6 C:G46 5.0 119.9 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of the Methyltransferase-Ribozyme 1, 2'- Selenomethyl-Uridine Modified (with 1-Methyl-Adenosine)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Methyltransferase-Ribozyme 1, 2'- Selenomethyl-Uridine Modified (with 1-Methyl-Adenosine) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg104 b:161.5 occ:1.00 O C:HOH201 2.2 111.2 1.0 O C:HOH202 2.2 115.2 1.0 O B:HOH207 2.2 118.6 1.0 O B:HOH206 2.2 133.3 1.0 O C:HOH204 2.2 105.7 1.0 O B:HOH202 2.2 130.9 1.0 O6 C:G29 4.2 101.0 1.0 OP1 B:C16 4.2 101.2 1.0 O6 C:G28 4.4 99.2 1.0 O4 C:U27 4.5 87.6 1.0 C5 C:U27 5.0 102.7 1.0 C4 C:U27 5.0 84.8 1.0

C.P.M.Scheitl, M.Mieczkowski, H.Schindelin, C.Hobartner. Structure and Mechanism of the Methyltransferase Ribozyme MTR1. Nat.Chem.Biol. V. 18 547 2022.
ISSN: ESSN 1552-4469
PubMed: 35301481
DOI: 10.1038/S41589-022-00976-X