Magnesium in PDB 6ai6: Crystal Structure of SPCAS9-Ng

The structure of Crystal Structure of SPCAS9-Ng, PDB code: 6ai6 was solved by H.Nishimasu, S.Hirano, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.17 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	177.377, 68.568, 187.968, 90.00, 111.51, 90.00
R / Rfree (%)	21.8 / 24.4

The structure of Crystal Structure of SPCAS9-Ng also contains other interesting chemical elements:

Potassium

(K)

10 atoms

The binding sites of Magnesium atom in the Crystal Structure of SPCAS9-Ng (pdb code 6ai6). 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 SPCAS9-Ng, PDB code: 6ai6:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of SPCAS9-Ng


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 SPCAS9-Ng within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1409 b:52.8 occ:1.00 O A:HOH1515 2.1 53.8 1.0 O B:HOH220 2.3 62.9 1.0 O B:HOH208 2.3 42.4 1.0 N7 B:G19 3.8 48.0 1.0 NH2 A:ARG71 4.3 61.5 1.0 CE1 A:TYR72 4.5 43.6 1.0 OH A:TYR72 4.6 44.7 1.0 O6 B:G19 4.6 47.6 1.0 C8 B:G19 4.7 50.3 1.0 CZ A:TYR72 4.8 44.3 1.0 C5 B:G19 4.8 50.8 1.0 NH1 A:ARG75 4.8 36.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of SPCAS9-Ng


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 SPCAS9-Ng within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:67.4 occ:1.00 O B:HOH219 2.1 67.5 1.0 OP1 B:U50 2.3 61.1 1.0 O B:HOH204 2.3 71.1 1.0 P B:U50 3.7 53.5 1.0 OP1 B:A52 3.9 52.9 1.0 O6 B:G62 4.1 58.0 1.0 O6 B:G53 4.1 51.8 1.0 N7 B:G53 4.2 52.2 1.0 OP2 B:A52 4.4 48.5 1.0 OP2 B:U50 4.4 53.1 1.0 O5' B:U50 4.4 50.9 1.0 O B:HOH217 4.5 48.8 1.0 P B:A52 4.7 46.3 1.0 O3' B:A49 4.7 47.4 1.0 C5' B:U50 4.7 49.8 1.0 NZ A:LYS1123 4.7 60.8 1.0 OP1 B:A51 4.8 38.6 1.0 C6 B:G53 4.8 51.8 1.0 N1 B:G62 4.9 53.9 1.0 C5 B:G53 4.9 52.1 1.0 C6 B:G62 4.9 54.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of SPCAS9-Ng


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 SPCAS9-Ng within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:59.7 occ:1.00 OP2 B:G21 3.5 53.6 1.0 O4 B:U22 3.7 46.4 1.0 N7 B:G21 4.2 50.4 1.0 K B:K101 4.4 77.7 1.0 NH1 A:ARG403 4.6 42.7 1.0 C4 B:U22 4.7 47.7 1.0 O B:HOH205 4.8 35.8 1.0 C8 B:G21 4.8 51.9 1.0 P B:G21 5.0 55.6 1.0

H.Nishimasu, X.Shi, S.Ishiguro, L.Gao, S.Hirano, S.Okazaki, T.Noda, O.O.Abudayyeh, J.S.Gootenberg, H.Mori, S.Oura, B.Holmes, M.Tanaka, M.Seki, H.Hirano, H.Aburatani, R.Ishitani, M.Ikawa, N.Yachie, F.Zhang, O.Nureki. Engineered Crispr-CAS9 Nuclease with Expanded Targeting Space Science V. 361 1259 2018.
ISSN: ESSN 1095-9203
PubMed: 30166441
DOI: 10.1126/SCIENCE.AAS9129