Sodium in PDB 5b2p: Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam)

The structure of Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam), PDB code: 5b2p was solved by H.Hirano, H.Nishimasu, T.Nakane, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.26 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.611, 159.273, 96.674, 90.00, 106.86, 90.00
R / Rfree (%)	18 / 20.3

The structure of Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam) also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Calcium	(Ca)	17 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam) (pdb code 5b2p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam), PDB code: 5b2p:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1702 b:43.9 occ:1.00 O A:PHE647 2.3 29.6 1.0 O A:HOH2368 2.3 49.5 1.0 O A:HOH2031 2.3 51.8 1.0 OD1 A:ASP649 2.4 32.0 1.0 O A:HOH2189 2.5 48.6 1.0 O A:HOH2251 2.9 37.2 1.0 CG A:ASP649 3.3 32.6 1.0 C A:PHE647 3.5 28.9 1.0 OD2 A:ASP649 3.7 32.0 1.0 N A:ASP649 4.0 27.3 1.0 O A:HOH2202 4.0 39.6 1.0 N A:PHE647 4.1 27.7 1.0 O A:HOH2076 4.2 33.4 1.0 CA A:PHE647 4.3 29.0 1.0 O A:HOH1820 4.4 49.5 1.0 N A:ASP648 4.5 31.1 1.0 CB A:ASP649 4.5 28.3 1.0 CA A:ASP648 4.6 32.1 0.4 OD1 A:ASP650 4.6 38.3 1.0 CA A:ASP648 4.7 32.1 0.6 CA A:ASP649 4.7 30.6 1.0 CB A:PHE647 4.8 27.3 1.0 OE1 A:GLU631 4.8 38.2 1.0 C A:ASP648 4.8 29.4 1.0 CB A:ARG646 4.9 28.0 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1703 b:62.0 occ:1.00 O B:HOH529 2.3 41.0 1.0 O A:HOH2374 2.4 58.7 1.0 O B:HOH442 2.5 28.7 1.0 O B:HOH301 2.6 29.1 1.0 O B:HOH232 2.7 48.8 1.0 O B:HOH537 2.7 62.3 1.0 O B:HOH353 3.4 44.1 1.0 OD1 A:ASN1248 3.7 35.2 1.0 O B:HOH540 4.1 49.0 1.0 O B:ACT120 4.2 76.4 1.0 O B:HOH375 4.2 29.3 1.0 O A:HOH2281 4.3 27.0 1.0 O A:HOH2289 4.5 39.7 1.0 O B:HOH511 4.5 58.3 1.0 OP2 B:C26 4.6 22.0 1.0 O A:HOH2255 4.7 30.5 1.0 O A:HOH2407 4.7 44.1 1.0 O A:GLU1247 4.7 25.4 1.0 OP1 B:U25 4.8 21.1 1.0 OG1 A:THR1334 4.8 24.1 1.0 O B:HOH397 4.8 38.2 1.0 OP2 B:U25 4.8 22.5 1.0 O B:HOH281 4.8 43.8 1.0 CG A:ASN1248 4.9 32.9 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:27.7 occ:1.00 O4 B:U30 2.4 25.6 1.0 O B:HOH510 2.4 30.9 1.0 O B:HOH519 2.5 28.6 1.0 O B:HOH288 2.5 27.2 1.0 O4 B:U45 2.6 23.8 1.0 O6 B:G28 2.6 25.0 1.0 C6 B:G28 3.2 25.0 1.0 C4 B:U45 3.5 23.6 1.0 C4 B:U30 3.5 26.4 1.0 N3 B:U45 3.6 22.9 1.0 NA B:NA102 3.6 46.2 1.0 O B:HOH528 3.7 38.9 1.0 N1 B:G28 3.8 23.7 1.0 O B:HOH262 3.9 32.0 1.0 C5 B:G28 4.1 23.8 1.0 C5 B:U30 4.1 26.7 1.0 N4 B:C46 4.2 22.7 1.0 O6 B:G31 4.3 27.7 1.0 N4 B:C44 4.4 22.2 1.0 O B:HOH475 4.4 26.7 1.0 O B:HOH542 4.4 40.5 1.0 O B:HOH523 4.5 45.6 1.0 N3 B:C46 4.6 24.8 1.0 N7 B:G28 4.6 26.1 1.0 O B:HOH327 4.6 38.4 1.0 N3 B:U30 4.6 26.7 1.0 O B:HOH406 4.7 28.3 1.0 C4 B:C46 4.7 21.9 1.0 O B:HOH376 4.8 29.3 1.0 C5 B:U45 4.9 22.4 1.0 C2 B:U45 4.9 22.7 1.0 C2 B:G28 4.9 24.9 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:46.2 occ:1.00 O B:HOH475 2.2 26.7 1.0 O B:HOH510 2.3 30.9 1.0 O B:HOH514 2.3 36.6 1.0 O B:HOH262 2.4 32.0 1.0 O B:HOH541 2.5 41.1 1.0 O4 B:U45 2.6 23.8 1.0 O B:HOH539 2.6 48.0 1.0 O B:HOH524 3.2 49.2 1.0 NA B:NA101 3.6 27.7 1.0 C4 B:U45 3.7 23.6 1.0 O B:HOH342 3.8 27.5 1.0 O6 B:G28 4.0 25.0 1.0 O B:HOH327 4.2 38.4 1.0 C5 B:U45 4.2 22.4 1.0 N4 B:C44 4.3 22.2 1.0 O B:HOH469 4.4 38.2 1.0 O B:HOH316 4.6 47.2 1.0 O B:HOH542 4.6 40.5 1.0 N4 B:C46 4.7 22.7 1.0 O B:HOH324 4.7 26.5 1.0 O B:HOH433 4.7 29.1 1.0 O B:HOH540 4.7 49.0 1.0 O B:HOH329 4.8 32.1 1.0 C5 B:C44 4.8 24.4 1.0 O B:HOH288 4.8 27.2 1.0 N3 B:U45 4.9 22.9 1.0 C4 B:C44 5.0 23.7 1.0

H.Hirano, J.S.Gootenberg, T.Horii, O.O.Abudayyeh, M.Kimura, P.D.Hsu, T.Nakane, R.Ishitani, I.Hatada, F.Zhang, H.Nishimasu, O.Nureki. Structure and Engineering of Francisella Novicida CAS9 Cell V. 164 950 2016.
ISSN: ISSN 1097-4172
PubMed: 26875867
DOI: 10.1016/J.CELL.2016.01.039