Magnesium in PDB 7q7x: Crystal Structure of the Methyltransferase-Ribozyme 1 (with 1-Methyl- Adenosine)

The structure of Crystal Structure of the Methyltransferase-Ribozyme 1 (with 1-Methyl- Adenosine), PDB code: 7q7x 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)	42.94 / 2.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.037, 71.037, 82.748, 90, 90, 90
R / Rfree (%)	21.3 / 25.5

The binding sites of Magnesium atom in the Crystal Structure of the Methyltransferase-Ribozyme 1 (with 1-Methyl- Adenosine) (pdb code 7q7x). 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 (with 1-Methyl- Adenosine), PDB code: 7q7x:
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 (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 (with 1-Methyl- Adenosine) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:117.0 occ:1.00 OP2 B:G22 2.2 91.4 1.0 P B:G22 3.6 92.5 1.0 O5' B:G22 4.2 89.1 1.0 O5' B:A21 4.3 74.4 1.0 N7 B:G22 4.4 78.2 1.0 C3' B:A21 4.5 74.5 1.0 OP2 B:A21 4.5 76.8 1.0 C8 B:G22 4.5 80.2 1.0 O3' B:A21 4.5 81.7 1.0 OP1 B:G22 4.6 101.2 1.0 P B:A21 4.8 82.0 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of the Methyltransferase-Ribozyme 1 (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 (with 1-Methyl- Adenosine) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:104.3 occ:0.77 O B:HOH201 2.2 78.8 0.8 O B:HOH206 2.2 110.4 0.8 O B:HOH204 2.2 105.4 0.8 O B:HOH207 2.2 117.5 0.8 O C:HOH205 2.2 94.8 0.8 O B:HOH203 2.2 93.4 0.8 N7 B:G14 4.6 72.7 1.0 O6 B:G14 4.6 68.3 1.0 N4 B:C13 4.8 83.7 1.0 C5 B:C13 4.9 85.9 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of the Methyltransferase-Ribozyme 1 (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 (with 1-Methyl- Adenosine) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg102 b:81.1 occ:1.00 O2 C:C32 2.3 69.4 1.0 C2 C:C32 3.2 65.6 1.0 N3 C:C32 3.6 62.5 1.0 N4 B:C16 3.9 81.6 1.0 N6 C:A33 4.1 67.5 1.0 N7 C:A33 4.2 66.5 1.0 OP2 B:A15 4.3 75.4 1.0 N1 C:C32 4.4 71.0 1.0 N7 B:A15 4.5 77.7 1.0 C2' C:C32 4.7 80.5 1.0 C1' C:C32 4.8 74.4 1.0 C4 C:C32 4.9 56.2 1.0 O2' C:C32 4.9 82.8 1.0 C5 C:A33 4.9 65.5 1.0 C6 C:A33 4.9 66.3 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of the Methyltransferase-Ribozyme 1 (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 (with 1-Methyl- Adenosine) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg103 b:91.7 occ:1.00 O6 C:G48 2.1 97.2 1.0 O4 C:U47 2.2 88.8 1.0 C4 C:U47 3.2 81.5 1.0 C6 C:G48 3.2 95.2 1.0 C5 C:U47 3.8 87.7 1.0 C5 C:G48 4.1 92.3 1.0 N6 A:A3 4.1 84.8 1.0 N3 C:U47 4.2 82.3 1.0 N1 C:G48 4.2 90.0 1.0 N7 C:G48 4.2 94.3 1.0 N4 A:C2 4.5 100.0 1.0 O6 C:G46 4.5 82.9 1.0 C6 C:G46 5.0 82.4 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of the Methyltransferase-Ribozyme 1 (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 (with 1-Methyl- Adenosine) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg104 b:87.4 occ:0.72 O B:HOH202 2.2 83.8 0.7 O C:HOH203 2.2 66.9 0.7 O C:HOH201 2.2 75.9 0.7 O C:HOH204 2.2 94.7 0.7 O B:HOH205 2.2 80.9 0.7 O C:HOH202 2.2 72.1 0.7 O6 C:G29 3.8 68.6 1.0 O6 C:G28 4.1 68.6 1.0 O4 C:U27 4.4 65.4 1.0 OP1 B:C16 4.6 99.8 1.0 C5 C:U27 4.8 82.6 1.0 N7 C:G28 4.8 71.3 1.0 C4 C:U27 4.8 74.0 1.0 C6 C:G29 4.8 65.3 1.0 C6 C:G28 5.0 62.4 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