Sodium in PDB 5b2q: Crystal Structure of Francisella Novicida CAS9 Rha in Complex with Sgrna and Target Dna (Tgg Pam)

The structure of Crystal Structure of Francisella Novicida CAS9 Rha in Complex with Sgrna and Target Dna (Tgg Pam), PDB code: 5b2q 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)	46.29 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.562, 158.977, 96.738, 90.00, 106.88, 90.00
R / Rfree (%)	18.3 / 20.6

The structure of Crystal Structure of Francisella Novicida CAS9 Rha in Complex with Sgrna and Target Dna (Tgg 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 Rha in Complex with Sgrna and Target Dna (Tgg Pam) (pdb code 5b2q). 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 Rha in Complex with Sgrna and Target Dna (Tgg Pam), PDB code: 5b2q:
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 Rha in Complex with Sgrna and Target Dna (Tgg 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 Rha in Complex with Sgrna and Target Dna (Tgg Pam) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1702 b:47.5 occ:1.00 O A:PHE647 2.3 29.1 1.0 O A:HOH2338 2.3 60.4 1.0 O A:HOH1850 2.4 53.5 1.0 OD1 A:ASP649 2.5 31.5 1.0 O A:HOH2206 2.6 49.1 1.0 O A:HOH2200 2.9 36.3 1.0 CG A:ASP649 3.4 34.5 1.0 C A:PHE647 3.5 27.1 1.0 OD2 A:ASP649 3.8 34.8 1.0 O A:HOH2190 4.0 42.9 1.0 N A:ASP649 4.1 27.5 1.0 O A:HOH2026 4.1 29.4 1.0 N A:PHE647 4.1 27.9 1.0 CA A:PHE647 4.4 29.8 1.0 O A:HOH1815 4.4 52.5 1.0 N A:ASP648 4.5 31.5 1.0 CB A:ASP649 4.6 26.8 1.0 OD1 A:ASP650 4.6 41.5 1.0 CA A:ASP648 4.7 31.6 0.4 CA A:ASP648 4.7 31.9 0.6 OE1 A:GLU631 4.8 40.7 1.0 CA A:ASP649 4.8 32.8 1.0 CB A:PHE647 4.9 30.3 1.0 CB A:ARG646 4.9 25.7 1.0 C A:ASP648 4.9 27.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Francisella Novicida CAS9 Rha in Complex with Sgrna and Target Dna (Tgg 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 Rha in Complex with Sgrna and Target Dna (Tgg Pam) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1703 b:63.1 occ:1.00 O A:HOH2003 2.3 43.0 1.0 O A:HOH2323 2.3 53.1 1.0 O A:HOH1975 2.5 27.6 1.0 O B:HOH534 2.5 67.4 1.0 O A:HOH2369 2.6 39.5 1.0 OD1 A:ASN1248 2.9 36.3 1.0 O B:HOH421 3.1 26.8 1.0 O B:HOH388 3.3 53.1 1.0 O A:ACT1728 3.8 84.9 1.0 CG A:ASN1248 4.0 36.2 1.0 O B:HOH498 4.1 52.0 1.0 O A:GLU1247 4.4 26.5 1.0 C A:ACT1728 4.4 84.4 1.0 O A:HOH2216 4.5 29.9 1.0 O A:HOH2058 4.6 39.1 1.0 O B:HOH228 4.6 45.5 1.0 O B:HOH352 4.6 27.1 1.0 CB A:ASN1248 4.7 27.4 1.0 OP1 B:U25 4.8 18.1 1.0 O B:HOH528 4.8 46.9 1.0 O A:HOH2227 4.8 28.3 1.0 OG1 A:THR1334 4.9 22.5 1.0 OP2 B:U25 4.9 20.6 1.0 CA A:ASN1248 4.9 22.8 1.0 OXT A:ACT1728 5.0 82.7 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Francisella Novicida CAS9 Rha in Complex with Sgrna and Target Dna (Tgg 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 Rha in Complex with Sgrna and Target Dna (Tgg Pam) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:28.1 occ:1.00 O B:HOH475 2.3 27.6 1.0 O B:HOH334 2.4 29.9 1.0 O B:HOH515 2.5 28.2 1.0 O4 B:U30 2.5 27.1 1.0 O4 B:U45 2.6 24.1 1.0 O6 B:G28 2.6 23.0 1.0 C6 B:G28 3.3 23.9 1.0 C4 B:U45 3.5 22.9 1.0 NA B:NA102 3.6 59.7 1.0 C4 B:U30 3.6 25.7 1.0 N3 B:U45 3.7 21.1 1.0 O B:HOH527 3.7 41.1 1.0 O B:HOH260 3.9 32.1 1.0 N1 B:G28 3.9 23.2 1.0 C5 B:G28 4.1 23.3 1.0 C5 B:U30 4.2 25.8 1.0 O B:HOH525 4.2 37.8 1.0 N4 B:C46 4.3 22.8 1.0 O B:HOH474 4.3 24.1 1.0 O6 B:G31 4.4 27.5 1.0 N4 B:C44 4.4 20.5 1.0 O2 B:EDO118 4.4 45.3 1.0 O B:HOH509 4.5 49.5 1.0 N7 B:G28 4.5 27.5 1.0 N3 B:C46 4.6 23.8 1.0 O B:HOH350 4.7 28.6 1.0 N3 B:U30 4.8 27.9 1.0 C4 B:C46 4.8 23.5 1.0 O B:HOH356 4.8 30.2 1.0 C5 B:U45 4.9 21.2 1.0 C2 B:U45 5.0 22.5 1.0 C2 B:G28 5.0 24.2 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Francisella Novicida CAS9 Rha in Complex with Sgrna and Target Dna (Tgg 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 Rha in Complex with Sgrna and Target Dna (Tgg Pam) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:59.7 occ:1.00 O B:HOH474 2.3 24.1 1.0 O B:HOH260 2.4 32.1 1.0 O B:HOH514 2.4 43.6 1.0 O B:HOH475 2.5 27.6 1.0 O4 B:U45 2.5 24.1 1.0 O B:HOH279 2.6 54.8 1.0 O B:HOH521 3.1 46.3 1.0 C4 B:U45 3.6 22.9 1.0 NA B:NA101 3.6 28.1 1.0 O B:HOH401 3.8 28.6 1.0 O6 B:G28 3.9 23.0 1.0 C5 B:U45 4.1 21.2 1.0 O1 B:EDO118 4.1 58.1 1.0 O2 B:EDO118 4.2 45.3 1.0 O B:HOH407 4.2 41.4 1.0 N4 B:C44 4.3 20.5 1.0 O B:HOH528 4.5 46.9 1.0 O B:HOH402 4.6 28.4 1.0 O B:HOH452 4.6 25.7 1.0 N4 B:C46 4.6 22.8 1.0 O B:HOH525 4.6 37.8 1.0 C5 B:C44 4.8 24.4 1.0 N3 B:U45 4.8 21.1 1.0 O B:HOH334 4.8 29.9 1.0 O B:HOH359 4.9 30.4 1.0 O B:HOH291 4.9 46.1 1.0 C4 B:C44 5.0 21.6 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