Sodium in PDB 5xh6: Crystal Structure of the Acidaminococcus Sp. BV3L6 CPF1 Rvr Variant in Complex with Crrna and Target Dna (Tata Pam)

The structure of Crystal Structure of the Acidaminococcus Sp. BV3L6 CPF1 Rvr Variant in Complex with Crrna and Target Dna (Tata Pam), PDB code: 5xh6 was solved by H.Nishimasu, T.Yamano, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.99 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.162, 133.676, 199.633, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 21

The structure of Crystal Structure of the Acidaminococcus Sp. BV3L6 CPF1 Rvr Variant in Complex with Crrna and Target Dna (Tata Pam) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Acidaminococcus Sp. BV3L6 CPF1 Rvr Variant in Complex with Crrna and Target Dna (Tata Pam) (pdb code 5xh6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of the Acidaminococcus Sp. BV3L6 CPF1 Rvr Variant in Complex with Crrna and Target Dna (Tata Pam), PDB code: 5xh6:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of the Acidaminococcus Sp. BV3L6 CPF1 Rvr Variant in Complex with Crrna and Target Dna (Tata 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 the Acidaminococcus Sp. BV3L6 CPF1 Rvr Variant in Complex with Crrna and Target Dna (Tata Pam) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1401 b:26.3 occ:1.00 OP2 B:A-4 2.2 36.6 1.0 O B:HOH256 2.3 40.2 1.0 O A:LYS757 2.3 41.7 1.0 O A:HOH1822 2.4 62.5 1.0 O A:HOH1575 2.4 33.0 1.0 O B:HOH246 2.4 36.5 1.0 C A:LYS757 3.5 32.8 1.0 P B:A-4 3.7 37.1 1.0 O B:HOH240 3.9 42.1 1.0 OD1 A:ASP749 4.1 33.6 1.0 N A:LYS757 4.1 35.0 1.0 O5' B:A-4 4.2 35.1 1.0 OP2 B:U-5 4.3 35.2 1.0 CA A:LYS757 4.3 34.6 1.0 O A:HOH1713 4.4 31.1 1.0 N A:PRO758 4.5 32.1 1.0 CA A:PRO758 4.5 35.4 1.0 C A:PRO758 4.6 32.7 1.0 C A:GLY756 4.6 40.9 1.0 OP1 B:A-4 4.6 37.3 1.0 O3' B:U-5 4.7 38.3 1.0 C3' B:U-5 4.7 33.9 1.0 O5' B:U-5 4.7 37.6 1.0 CB A:LYS757 4.8 38.9 1.0 N7 B:A-4 4.8 34.0 1.0 N A:ASN759 4.8 33.5 1.0 O A:PRO758 4.8 33.2 1.0 P B:U-5 4.9 36.5 1.0 C8 B:A-4 4.9 32.9 1.0 CA A:GLY756 4.9 43.9 1.0 OP2 B:G-3 4.9 35.7 1.0 OD1 A:ASN759 4.9 32.7 1.0 CE1 A:HIS754 5.0 45.6 1.0 OP1 B:U-5 5.0 36.8 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of the Acidaminococcus Sp. BV3L6 CPF1 Rvr Variant in Complex with Crrna and Target Dna (Tata 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 the Acidaminococcus Sp. BV3L6 CPF1 Rvr Variant in Complex with Crrna and Target Dna (Tata Pam) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:52.3 occ:1.00 O C:HOH218 2.3 49.0 1.0 O6 B:G11 2.5 38.0 1.0 O B:HOH245 2.6 46.2 1.0 O4 B:U10 2.6 39.3 1.0 O B:HOH284 2.7 54.7 1.0 O B:HOH294 2.8 68.8 1.0 C4 B:U10 3.4 39.8 1.0 O C:HOH261 3.5 56.7 1.0 C6 B:G11 3.5 42.9 1.0 N4 C:DC-11 3.8 36.0 1.0 C5 B:U10 3.9 40.1 1.0 N7 B:G11 3.9 39.0 1.0 C5 B:G11 4.1 38.3 1.0 N6 C:DA-10 4.3 37.0 1.0 O6 C:DG-12 4.4 39.1 1.0 N4 B:C12 4.5 38.2 1.0 N3 B:U10 4.5 38.8 1.0 O C:HOH221 4.7 50.1 1.0 N1 B:G11 4.7 41.1 1.0 O B:HOH248 4.8 59.7 1.0 O B:HOH277 4.9 56.0 1.0 O C:HOH239 5.0 51.5 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of the Acidaminococcus Sp. BV3L6 CPF1 Rvr Variant in Complex with Crrna and Target Dna (Tata 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 the Acidaminococcus Sp. BV3L6 CPF1 Rvr Variant in Complex with Crrna and Target Dna (Tata Pam) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:58.2 occ:1.00 O B:HOH219 2.2 49.1 1.0 O B:HOH291 2.3 54.6 1.0 O B:HOH268 2.4 44.3 1.0 N7 B:A2 2.5 31.1 1.0 C8 B:A2 3.4 32.8 1.0 C5 B:A2 3.6 30.5 1.0 O B:HOH209 3.7 52.0 1.0 N6 B:A2 3.7 32.7 1.0 C6 B:A2 4.1 36.0 1.0 N6 B:A3 4.1 33.1 1.0 C8 B:G1 4.3 31.1 1.0 N7 B:G1 4.3 30.2 1.0 O C:HOH212 4.4 48.5 1.0 N7 B:A3 4.5 34.1 1.0 OP2 B:A2 4.6 39.3 1.0 N9 B:A2 4.7 37.5 1.0 O C:HOH229 4.7 39.9 1.0 C4 B:A2 4.7 30.2 1.0 C6 B:A3 4.8 34.9 1.0 N9 B:G1 4.9 35.3 1.0 C5 B:G1 4.9 32.1 1.0 C5 B:A3 5.0 34.3 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of the Acidaminococcus Sp. BV3L6 CPF1 Rvr Variant in Complex with Crrna and Target Dna (Tata 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 the Acidaminococcus Sp. BV3L6 CPF1 Rvr Variant in Complex with Crrna and Target Dna (Tata Pam) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na103 b:56.3 occ:1.00 O B:HOH295 2.3 56.9 1.0 O4 B:U16 2.3 47.0 1.0 O B:HOH202 2.5 42.5 1.0 O B:HOH285 2.5 55.5 1.0 O6 B:G17 2.6 41.3 1.0 O B:HOH276 2.6 49.7 1.0 C4 B:U16 3.3 43.7 1.0 O B:HOH203 3.3 53.7 1.0 C6 B:G17 3.5 45.7 1.0 N7 B:G17 3.7 45.8 1.0 C5 B:U16 3.9 48.4 1.0 C5 B:G17 3.9 49.5 1.0 N6 C:DA-16 3.9 47.8 1.0 N4 C:DC-17 4.2 53.0 1.0 O4 B:U15 4.3 47.0 1.0 N3 B:U16 4.4 37.9 1.0 C4 B:U15 4.6 48.3 1.0 N1 B:G17 4.7 40.1 1.0 O B:HOH261 4.7 52.7 1.0 C5 B:U15 4.8 48.6 1.0 C8 B:G17 4.9 44.6 1.0 C6 C:DA-16 5.0 47.0 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of the Acidaminococcus Sp. BV3L6 CPF1 Rvr Variant in Complex with Crrna and Target Dna (Tata Pam)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Acidaminococcus Sp. BV3L6 CPF1 Rvr Variant in Complex with Crrna and Target Dna (Tata Pam) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:56.9 occ:1.00 O C:HOH252 2.4 63.0 1.0 O6 C:DG-14 2.4 35.6 1.0 O C:HOH246 2.4 60.4 1.0 O B:HOH224 2.6 47.9 1.0 O B:HOH292 2.6 76.2 1.0 C6 C:DG-14 3.5 42.5 1.0 O C:HOH241 3.7 59.4 1.0 O C:HOH235 3.8 64.4 1.0 N7 C:DG-14 3.9 39.2 1.0 N6 C:DA-15 3.9 43.6 1.0 O C:HOH261 4.0 56.7 1.0 C5 C:DG-14 4.1 39.2 1.0 N4 B:C14 4.1 43.9 1.0 O C:HOH253 4.1 56.2 1.0 N4 C:DC-13 4.2 39.9 1.0 O6 B:G13 4.5 40.6 1.0 N1 C:DG-14 4.7 42.1 1.0 O B:HOH277 5.0 56.0 1.0 C6 C:DA-15 5.0 42.3 1.0

H.Nishimasu, T.Yamano, L.Gao, F.Zhang, R.Ishitani, O.Nureki. Structural Basis For the Altered Pam Recognition By Engineered Crispr-CPF1 Mol. Cell V. 67 139 2017.
ISSN: ISSN 1097-4164
PubMed: 28595896
DOI: 10.1016/J.MOLCEL.2017.04.019