Magnesium in PDB 5nfv: Crystal Structure of Catalytically Inactive FNCAS12 Mutant Bound to An R-Loop Structure Containing A Pre-Crrna Mimic and Full-Length Dna Target

The structure of Crystal Structure of Catalytically Inactive FNCAS12 Mutant Bound to An R-Loop Structure Containing A Pre-Crrna Mimic and Full-Length Dna Target, PDB code: 5nfv was solved by D.C.Swarts, J.Van Der Oost, M.Jinek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.57 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.421, 143.703, 84.628, 90.00, 94.16, 90.00
R / Rfree (%)	20.5 / 23.8

The binding sites of Magnesium atom in the Crystal Structure of Catalytically Inactive FNCAS12 Mutant Bound to An R-Loop Structure Containing A Pre-Crrna Mimic and Full-Length Dna Target (pdb code 5nfv). 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 Catalytically Inactive FNCAS12 Mutant Bound to An R-Loop Structure Containing A Pre-Crrna Mimic and Full-Length Dna Target, PDB code: 5nfv:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Catalytically Inactive FNCAS12 Mutant Bound to An R-Loop Structure Containing A Pre-Crrna Mimic and Full-Length Dna Target


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 Catalytically Inactive FNCAS12 Mutant Bound to An R-Loop Structure Containing A Pre-Crrna Mimic and Full-Length Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1401 b:38.5 occ:1.00 O A:HOH1511 2.1 48.8 1.0 O A:ARG800 2.1 50.5 1.0 O B:HOH215 2.1 41.7 1.0 O B:HOH208 2.1 40.6 1.0 O B:HOH216 2.2 41.8 1.0 OP2 B:A-3 2.2 48.3 1.0 C A:ARG800 3.3 47.3 1.0 P B:A-3 3.6 53.7 1.0 OD1 A:ASP792 3.9 50.1 1.0 OP2 B:U-4 4.0 53.4 1.0 O B:HOH207 4.0 46.9 1.0 N A:ARG800 4.1 50.1 1.0 CA A:PRO801 4.2 43.3 1.0 OP1 B:U-4 4.2 62.0 1.0 N A:PRO801 4.2 45.4 1.0 O A:HOH1503 4.2 46.4 1.0 O A:HOH1509 4.2 42.1 1.0 CA A:ARG800 4.2 46.3 1.0 O5' B:A-3 4.2 53.7 1.0 C A:GLY799 4.3 56.4 1.0 P B:U-4 4.4 53.1 1.0 C A:PRO801 4.5 45.5 1.0 OD1 A:ASN802 4.5 52.5 1.0 OP1 B:A-3 4.5 46.0 1.0 O5' B:U-4 4.5 56.8 1.0 O A:GLY799 4.5 62.8 1.0 O3' B:U-4 4.6 48.3 1.0 C3' B:U-4 4.7 51.1 1.0 CB A:ARG800 4.8 45.6 1.0 N A:ASN802 4.8 43.0 1.0 OP2 B:G-2 4.8 46.4 1.0 CA A:GLY799 4.8 57.1 1.0 O A:PRO801 4.9 48.9 1.0 CG A:ASP792 4.9 47.7 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Catalytically Inactive FNCAS12 Mutant Bound to An R-Loop Structure Containing A Pre-Crrna Mimic and Full-Length Dna Target


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 Catalytically Inactive FNCAS12 Mutant Bound to An R-Loop Structure Containing A Pre-Crrna Mimic and Full-Length Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1402 b:60.6 occ:1.00 OH A:TYR248 2.4 73.8 1.0 O A:SER67 2.5 74.8 1.0 O A:VAL69 2.6 78.2 1.0 O A:ASN270 2.6 65.5 1.0 O A:LEU66 3.2 70.0 1.0 CZ A:TYR248 3.3 72.5 1.0 C A:SER67 3.4 72.9 1.0 C A:ASN270 3.8 59.7 1.0 C A:VAL69 3.8 74.5 1.0 CA A:SER67 3.9 68.1 1.0 CE2 A:TYR248 3.9 72.5 1.0 CE1 A:TYR248 4.1 70.2 1.0 CD1 A:LEU273 4.1 57.1 1.0 N A:VAL69 4.2 69.1 1.0 CB A:ASN270 4.2 54.6 1.0 C A:LEU66 4.3 64.3 1.0 CA A:ASN270 4.5 55.9 1.0 N A:SER68 4.5 71.3 1.0 C A:SER68 4.5 68.6 1.0 CA A:VAL69 4.5 70.2 1.0 N A:SER67 4.6 62.8 1.0 N A:ASN271 4.8 60.2 1.0 CG A:LEU273 4.8 55.7 1.0 N A:CYS70 4.9 72.8 1.0 OD1 A:ASN270 4.9 61.2 1.0 CA A:SER68 4.9 70.6 1.0 O A:SER68 5.0 64.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Catalytically Inactive FNCAS12 Mutant Bound to An R-Loop Structure Containing A Pre-Crrna Mimic and Full-Length Dna Target


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 Catalytically Inactive FNCAS12 Mutant Bound to An R-Loop Structure Containing A Pre-Crrna Mimic and Full-Length Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:48.7 occ:1.00 O B:HOH219 2.1 57.9 1.0 O B:HOH212 2.1 73.9 1.0 O B:HOH217 2.2 45.4 1.0 O B:HOH214 2.2 43.9 1.0 O B:HOH202 2.2 45.8 1.0 O B:HOH211 2.2 48.2 1.0 OP2 B:A-11 4.0 48.8 1.0 O4 B:U-16 4.1 46.4 1.0 O B:HOH204 4.2 37.2 1.0 OP2 B:A-17 4.2 77.0 1.0 O B:HOH205 4.5 51.4 1.0 OP2 B:U-12 4.5 55.0 1.0 N7 B:A-11 4.5 55.4 1.0 C5 B:C-10 4.6 59.3 1.0 C8 B:A-11 5.0 52.4 1.0

D.C.Swarts, J.Van Der Oost, M.Jinek. Structural Basis For Guide Rna Processing and Seed-Dependent Dna Targeting By Crispr-CAS12A. Mol. Cell V. 66 221 2017.
ISSN: ISSN 1097-4164
PubMed: 28431230
DOI: 10.1016/J.MOLCEL.2017.03.016