Copper in PDB 7dwh: Complex Structure of Sam-Dependent Methyltransferase Ribozyme

The structure of Complex Structure of Sam-Dependent Methyltransferase Ribozyme, PDB code: 7dwh was solved by H.Y.Jiang, Y.Q.Gao, D.R.Chen, A.Murchie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.53 / 3.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.923, 77.305, 101.469, 90, 93.24, 90
R / Rfree (%)	20.9 / 25.8

The binding sites of Copper atom in the Complex Structure of Sam-Dependent Methyltransferase Ribozyme (pdb code 7dwh). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Complex Structure of Sam-Dependent Methyltransferase Ribozyme, PDB code: 7dwh:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the Complex Structure of Sam-Dependent Methyltransferase Ribozyme


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Complex Structure of Sam-Dependent Methyltransferase Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ X:Cu101 b:127.6 occ:1.00 N7 X:G40 2.3 106.8 1.0 O X:SAM102 2.4 115.5 1.0 N X:SAM102 2.4 102.7 1.0 O6 X:G40 2.9 100.5 1.0 C5 X:G40 3.1 97.6 1.0 C X:SAM102 3.2 110.5 1.0 C6 X:G40 3.3 95.7 1.0 CA X:SAM102 3.4 99.4 1.0 C8 X:G40 3.4 99.6 1.0 N7 X:G39 3.5 80.0 1.0 C5 X:G39 3.7 81.5 1.0 O6 X:G39 3.9 87.7 1.0 C6 X:G39 4.0 83.0 1.0 O6 X:G41 4.1 91.5 1.0 C8 X:G39 4.2 78.8 1.0 N7 X:G41 4.3 89.5 1.0 C4 X:G40 4.4 95.8 1.0 CB X:SAM102 4.4 85.5 1.0 OXT X:SAM102 4.4 114.1 1.0 N9 X:G40 4.5 93.7 1.0 C4 X:G39 4.5 78.2 1.0 C6 X:G41 4.6 91.5 1.0 C5 X:G41 4.7 87.1 1.0 OP2 X:G40 4.7 98.3 1.0 N1 X:G40 4.7 91.7 1.0 N9 X:G39 4.8 80.2 1.0 CG X:SAM102 4.8 76.8 1.0 N1 X:G39 4.9 75.9 1.0

Copper binding site 2 out of 2 in the Complex Structure of Sam-Dependent Methyltransferase Ribozyme


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Complex Structure of Sam-Dependent Methyltransferase Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ Y:Cu101 b:111.1 occ:1.00 O6 Y:G40 2.4 114.4 1.0 C6 Y:G40 3.3 110.7 1.0 N7 Y:G40 3.3 110.7 1.0 N7 Y:G39 3.4 117.9 1.0 C5 Y:G40 3.6 110.3 1.0 C5 Y:G39 4.1 119.0 1.0 O6 Y:G39 4.1 110.9 1.0 C8 Y:G39 4.2 116.9 1.0 C6 Y:G39 4.4 115.6 1.0 O6 Y:G41 4.5 96.3 1.0 C8 Y:G40 4.5 115.3 1.0 N1 Y:G40 4.6 106.5 1.0 OP2 Y:G39 4.7 113.5 1.0 O4 Y:U6 4.8 102.9 1.0 C4 Y:G40 5.0 110.6 1.0

H.Y.Jiang, Y.Q.Gao, L.Zhang, D.R.Chen, J.H.Gan, A.I.H.Murchie. The Identification and Characterization of A Selected Sam-Dependent Methyltransferase Ribozyme That Is Present in Natural Sequences Nat Catal V. 4 872 2021.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-021-00685-Z