Sodium in PDB 5xuz: Crystal Structure of Lachnospiraceae Bacterium ND2006 CPF1 in Complex with Crrna and Target Dna (Ccca Pam)

The structure of Crystal Structure of Lachnospiraceae Bacterium ND2006 CPF1 in Complex with Crrna and Target Dna (Ccca Pam), PDB code: 5xuz was solved by T.Yamano, H.Nishimasu, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.85 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.946, 103.540, 342.683, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 22.9

The structure of Crystal Structure of Lachnospiraceae Bacterium ND2006 CPF1 in Complex with Crrna and Target Dna (Ccca Pam) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Lachnospiraceae Bacterium ND2006 CPF1 in Complex with Crrna and Target Dna (Ccca Pam) (pdb code 5xuz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Lachnospiraceae Bacterium ND2006 CPF1 in Complex with Crrna and Target Dna (Ccca Pam), PDB code: 5xuz:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Lachnospiraceae Bacterium ND2006 CPF1 in Complex with Crrna and Target Dna (Ccca 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 Lachnospiraceae Bacterium ND2006 CPF1 in Complex with Crrna and Target Dna (Ccca Pam) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:48.4 occ:1.00 O C:HOH208 2.5 34.6 1.0 O B:HOH223 2.5 34.5 1.0 O4 B:U10 2.5 38.7 1.0 O B:HOH253 2.6 56.0 1.0 O6 B:G11 2.7 37.7 1.0 C4 B:U10 3.3 39.7 1.0 O B:HOH257 3.4 41.6 1.0 C6 B:G11 3.7 34.6 1.0 C5 B:U10 3.7 41.4 1.0 N4 C:DC-11 4.0 31.8 1.0 N7 B:G11 4.1 40.2 1.0 C5 B:G11 4.2 36.9 1.0 O6 C:DG-12 4.3 36.1 1.0 N6 C:DA-10 4.3 32.0 1.0 N3 B:U10 4.5 38.5 1.0 N4 B:C12 4.7 37.0 1.0 N1 B:G11 4.8 38.1 1.0 O6 B:G9 4.9 45.2 1.0 C6 B:U10 5.0 40.6 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Lachnospiraceae Bacterium ND2006 CPF1 in Complex with Crrna and Target Dna (Ccca 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 Lachnospiraceae Bacterium ND2006 CPF1 in Complex with Crrna and Target Dna (Ccca Pam) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:48.6 occ:1.00 O6 C:DG-14 2.4 45.9 1.0 O C:HOH210 2.5 44.7 1.0 O B:HOH255 2.5 49.9 1.0 O C:HOH234 2.6 44.1 1.0 O C:HOH214 2.7 38.2 1.0 C6 C:DG-14 3.4 47.8 1.0 N6 C:DA-15 3.7 38.5 1.0 N7 C:DG-14 3.9 44.1 1.0 C5 C:DG-14 4.0 50.2 1.0 N4 B:C14 4.0 38.1 1.0 N4 C:DC-13 4.0 37.5 1.0 O6 B:G13 4.0 46.5 1.0 O C:HOH228 4.2 36.3 1.0 O B:HOH257 4.2 41.6 1.0 N1 C:DG-14 4.6 46.2 1.0 N7 C:DA-15 4.7 37.9 1.0 C6 C:DA-15 4.7 42.4 1.0 O B:HOH228 4.7 42.1 1.0 O B:HOH251 4.9 54.5 1.0 C5 C:DA-15 5.0 37.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Lachnospiraceae Bacterium ND2006 CPF1 in Complex with Crrna and Target Dna (Ccca 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 Lachnospiraceae Bacterium ND2006 CPF1 in Complex with Crrna and Target Dna (Ccca Pam) within 5.0Å range: probe atom residue distance (Å) B Occ F:Na101 b:54.3 occ:1.00 O F:HOH233 2.3 52.2 1.0 O6 F:G11 2.5 39.2 1.0 O G:HOH103 2.5 42.8 1.0 O F:HOH218 2.6 43.0 1.0 O4 F:U10 2.6 46.5 1.0 O F:HOH232 2.7 46.1 1.0 C4 F:U10 3.4 43.9 1.0 C6 F:G11 3.6 43.4 1.0 C5 F:U10 3.8 41.2 1.0 N4 G:DC-11 3.9 45.6 1.0 N6 G:DA-10 4.1 37.7 1.0 N7 F:G11 4.2 44.7 1.0 C5 F:G11 4.2 48.1 1.0 O6 G:DG-12 4.4 44.3 1.0 N3 F:U10 4.6 51.8 1.0 O G:HOH112 4.6 46.3 1.0 N1 F:G11 4.7 40.4 1.0 N4 F:C12 4.8 38.5 1.0 O6 F:G9 4.9 46.0 1.0

T.Yamano, B.Zetsche, R.Ishitani, F.Zhang, H.Nishimasu, O.Nureki. Structural Basis For the Canonical and Non-Canonical Pam Recognition By Crispr-CPF1. Mol. Cell V. 67 633 2017.
ISSN: ISSN 1097-4164
PubMed: 28781234
DOI: 10.1016/J.MOLCEL.2017.06.035