Magnesium in PDB 5id6: Structure of CPF1/Rna Complex

The structure of Structure of CPF1/Rna Complex, PDB code: 5id6 was solved by D.Dong, K.Ren, X.Qiu, J.Wang, Z.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.51 / 2.38
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	168.352, 83.011, 124.086, 90.00, 106.72, 90.00
R / Rfree (%)	20.2 / 26.1

The binding sites of Magnesium atom in the Structure of CPF1/Rna Complex (pdb code 5id6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of CPF1/Rna Complex, PDB code: 5id6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of CPF1/Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of CPF1/Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1301 b:53.3 occ:1.00 O A:THR716 2.3 57.9 1.0 OP2 G:A19 3.0 46.3 1.0 C A:THR716 3.4 51.1 1.0 CA A:PRO717 3.7 43.4 1.0 C A:PRO717 3.8 54.9 1.0 OD1 A:ASP708 3.8 67.7 1.0 N A:ASN718 3.8 42.9 1.0 N A:PRO717 4.0 47.3 1.0 OD1 A:ASN718 4.1 47.4 1.0 O A:PRO717 4.3 59.5 1.0 P G:A19 4.4 39.3 1.0 OP2 G:U18 4.5 51.7 1.0 CA A:THR716 4.6 52.6 1.0 CG A:ASN718 4.7 43.2 1.0 CG A:ASP708 4.7 63.6 1.0 CA A:ASN718 4.7 41.4 1.0 N A:THR716 4.8 58.4 1.0 OD2 A:ASP708 4.8 68.8 1.0 O5' G:A19 4.8 45.7 1.0 OP1 G:U18 4.8 44.4 1.0 N7 G:A19 4.9 39.8 1.0 C A:GLY715 4.9 64.7 1.0 OP2 G:G20 4.9 41.3 1.0 NZ A:LYS960 5.0 39.6 1.0

Magnesium binding site 2 out of 2 in the Structure of CPF1/Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of CPF1/Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg101 b:42.6 occ:1.00 O G:HOH204 2.0 41.0 1.0 O G:HOH201 2.0 40.1 1.0 O G:HOH203 2.0 35.3 1.0 O G:HOH205 2.0 45.7 1.0 O G:HOH206 2.0 49.4 1.0 O G:HOH202 2.1 37.4 1.0 OP2 G:A10 4.0 47.4 1.0 OP2 G:A4 4.1 43.6 1.0 O4 G:U5 4.2 41.0 1.0 OP2 G:U9 4.4 44.2 1.0 N7 G:A10 4.6 43.6 1.0 C5 G:C11 4.9 35.1 1.0

D.Dong, K.Ren, X.Qiu, J.Zheng, M.Guo, X.Guan, H.Liu, N.Li, B.Zhang, D.Yang, C.Ma, S.Wang, D.Wu, Y.Ma, S.Fan, J.Wang, N.Gao, Z.Huang. The Crystal Structure of CPF1 in Complex with Crispr Rna Nature V. 532 522 2016.
ISSN: ESSN 1476-4687
PubMed: 27096363
DOI: 10.1038/NATURE17944