Magnesium in PDB 7q7z: Crystal Structure of the Methyltransferase-Ribozyme 1 (with 1- Benzylamine-Adenosine)

The structure of Crystal Structure of the Methyltransferase-Ribozyme 1 (with 1- Benzylamine-Adenosine), PDB code: 7q7z 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)	44.54 / 3.26
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	117.861, 117.861, 83.275, 90, 90, 90
R / Rfree (%)	21 / 26.5

The binding sites of Magnesium atom in the Crystal Structure of the Methyltransferase-Ribozyme 1 (with 1- Benzylamine-Adenosine) (pdb code 7q7z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Methyltransferase-Ribozyme 1 (with 1- Benzylamine-Adenosine), PDB code: 7q7z:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Methyltransferase-Ribozyme 1 (with 1- Benzylamine-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- Benzylamine-Adenosine) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:142.1 occ:1.00 O B:HOH202 2.2 136.9 1.0 O B:HOH201 2.2 159.6 1.0 O C:HOH201 2.2 139.5 1.0 O E:HOH101 2.2 157.1 1.0 O F:HOH201 2.2 161.2 1.0 O F:HOH202 2.2 124.6 1.0 O4' B:A15 4.1 133.4 1.0 O2' F:A39 4.2 106.4 1.0 N6 C:A39 4.4 125.4 1.0 C1' B:A15 4.5 130.1 1.0 N1 C:A39 4.5 126.9 1.0 O2' B:A15 4.6 131.7 1.0 C4' B:A15 4.7 152.6 1.0 N1 E:A15 4.8 119.5 1.0 O2 C:C40 4.9 119.5 1.0 C6 C:A39 5.0 113.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Methyltransferase-Ribozyme 1 (with 1- Benzylamine-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- Benzylamine-Adenosine) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg102 b:112.0 occ:1.00 O2 C:C32 2.5 141.4 1.0 C2 C:C32 3.5 136.5 1.0 N7 B:A15 3.6 145.4 1.0 N3 C:C32 3.8 128.8 1.0 N6 B:A15 4.2 148.4 1.0 N6 C:A33 4.2 127.1 1.0 N7 C:A33 4.5 137.1 1.0 OP2 B:A15 4.5 121.0 1.0 C5 B:A15 4.6 142.1 1.0 C8 B:A15 4.6 137.6 1.0 O2' B:G14 4.6 115.7 1.0 N1 C:C32 4.7 121.1 1.0 C2' B:G14 4.8 93.8 1.0 C6 B:A15 4.8 139.5 1.0 C2' C:C32 5.0 144.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Methyltransferase-Ribozyme 1 (with 1- Benzylamine-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- Benzylamine-Adenosine) within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg102 b:120.0 occ:1.00 O2 F:C32 2.3 138.6 1.0 C2 F:C32 3.1 146.2 1.0 N3 F:C32 3.4 136.9 1.0 N6 F:A33 3.7 144.2 1.0 OP2 E:A15 3.9 130.8 1.0 N7 F:A33 4.0 135.5 1.0 N4 E:C16 4.1 150.3 1.0 N7 E:A15 4.3 126.1 1.0 N1 F:C32 4.3 138.0 1.0 C6 F:A33 4.6 145.3 1.0 C4 F:C32 4.6 126.5 1.0 C5 F:A33 4.6 132.7 1.0 C2' F:C32 4.7 130.6 1.0 C1' F:C32 4.8 136.8 1.0 O2' E:G14 4.9 131.3 1.0 C8 E:A15 5.0 123.7 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