Magnesium in PDB 6gtg: Transition State Structure of CPF1(CAS12A) I4 Conformation

All present enzymatic activity of Transition State Structure of CPF1(CAS12A) I4 Conformation:
3.1.21.1; 3.1.27.2;

The binding sites of Magnesium atom in the Transition State Structure of CPF1(CAS12A) I4 Conformation (pdb code 6gtg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Transition State Structure of CPF1(CAS12A) I4 Conformation, PDB code: 6gtg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Transition State Structure of CPF1(CAS12A) I4 Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Transition State Structure of CPF1(CAS12A) I4 Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1401 b:41.2 occ:1.00 O A:ARG800 2.1 42.8 1.0 C A:ARG800 2.7 42.8 1.0 O A:GLY799 3.1 42.8 1.0 C A:GLY799 3.1 42.8 1.0 N A:PRO801 3.3 30.5 1.0 N A:ARG800 3.3 42.8 1.0 OP1 B:U-5 3.3 38.2 1.0 CA A:PRO801 3.4 30.5 1.0 OP2 B:A-4 3.5 46.6 1.0 CA A:ARG800 3.5 42.8 1.0 OG A:SER797 3.6 38.5 1.0 OD1 A:ASP792 3.7 32.1 1.0 N A:GLY799 4.0 42.8 1.0 CA A:GLY799 4.0 42.8 1.0 OP2 B:U-5 4.0 38.2 1.0 P B:U-5 4.1 38.2 1.0 CG A:ASP792 4.4 32.1 1.0 CB A:PRO801 4.4 30.5 1.0 C A:PRO801 4.4 30.5 1.0 CD A:PRO801 4.5 30.5 1.0 O5' B:U-5 4.7 38.2 1.0 P B:A-4 4.7 46.6 1.0 CB A:ARG800 4.7 42.8 1.0 OD2 A:ASP792 4.8 32.1 1.0 O A:PRO801 4.9 30.5 1.0 CB A:SER797 4.9 38.5 1.0

Magnesium binding site 2 out of 4 in the Transition State Structure of CPF1(CAS12A) I4 Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Transition State Structure of CPF1(CAS12A) I4 Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1402 b:34.3 occ:1.00 O A:ASN270 3.1 40.8 1.0 OH A:TYR248 3.6 50.9 1.0 O A:SER67 3.6 39.8 1.0 O A:LEU66 3.8 29.6 1.0 CA A:SER67 3.9 39.8 1.0 CD1 A:ILE71 4.1 54.5 1.0 C A:SER67 4.2 39.8 1.0 C A:ASN270 4.2 40.8 1.0 CE2 A:TYR248 4.3 50.9 1.0 CA A:ASN271 4.4 34.1 1.0 CZ A:TYR248 4.4 50.9 1.0 CD1 A:LEU273 4.4 20.1 1.0 ND2 A:ASN271 4.5 34.1 1.0 CB A:SER67 4.6 39.8 1.0 C A:LEU66 4.7 29.6 1.0 N A:ASN271 4.8 34.1 1.0 N A:SER67 4.8 39.8 1.0

Magnesium binding site 3 out of 4 in the Transition State Structure of CPF1(CAS12A) I4 Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Transition State Structure of CPF1(CAS12A) I4 Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1403 b:22.8 occ:1.00 OD1 A:ASN802 3.3 26.0 1.0 NZ A:LYS1041 3.5 26.8 1.0 N7 B:G-3 3.5 35.6 1.0 C8 B:G-3 4.2 35.6 1.0 O A:PRO801 4.2 30.5 1.0 OP2 B:G-3 4.2 35.6 1.0 N7 B:A-4 4.2 46.6 1.0 O A:ARG800 4.2 42.8 1.0 CG A:ASN802 4.4 26.0 1.0 C A:PRO801 4.4 30.5 1.0 C8 B:A-4 4.5 46.6 1.0 CA A:ASN802 4.5 26.0 1.0 N A:ASN802 4.6 26.0 1.0 OP2 B:A-4 4.6 46.6 1.0 C5 B:G-3 4.7 35.6 1.0 C5 B:A-4 4.9 46.6 1.0 CE A:LYS1041 4.9 26.8 1.0 O6 B:G-3 5.0 35.6 1.0

Magnesium binding site 4 out of 4 in the Transition State Structure of CPF1(CAS12A) I4 Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Transition State Structure of CPF1(CAS12A) I4 Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:23.9 occ:1.00 N7 B:A-12 2.2 35.8 1.0 C8 B:A-12 2.7 35.8 1.0 OP2 B:A-12 3.4 35.8 1.0 C5 B:A-12 3.5 35.8 1.0 O4 B:U-17 3.7 44.5 1.0 C5 B:U-13 3.8 35.6 1.0 C6 B:U-13 4.0 35.6 1.0 N9 B:A-12 4.0 35.8 1.0 O5' B:A-12 4.2 35.8 1.0 C5 B:C-11 4.3 44.9 1.0 N6 B:A-12 4.3 35.8 1.0 C6 B:A-12 4.4 35.8 1.0 P B:A-12 4.4 35.8 1.0 C4 B:A-12 4.4 35.8 1.0 C4 B:U-13 4.5 35.6 1.0 C3' B:U-13 4.7 35.6 1.0 N1 B:U-13 4.7 35.6 1.0 C4 B:C-11 4.7 44.9 1.0 C6 B:C-11 4.7 44.9 1.0 C4 B:U-17 4.9 44.5 1.0 N4 B:C-11 4.9 44.9 1.0 O4 B:U-13 5.0 35.6 1.0 C2' B:U-13 5.0 35.6 1.0

S.Stella, P.Mesa, J.Thomsen, B.Paul, P.Alcon, S.B.Jensen, B.Saligram, M.E.Moses, N.S.Hatzakis, G.Montoya. Conformational Activation Promotes Crispr-CAS12A Catalysis and Resetting of the Endonuclease Activity. Cell V. 175 1856 2018.
ISSN: ISSN 1097-4172
PubMed: 30503205
DOI: 10.1016/J.CELL.2018.10.045