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Sodium in PDB 5xh7: Crystal Structure of the Acidaminococcus Sp. BV3L6 CPF1 Rr Variant in Complex with Crrna and Target Dna (Tcca Pam)

Protein crystallography data

The structure of Crystal Structure of the Acidaminococcus Sp. BV3L6 CPF1 Rr Variant in Complex with Crrna and Target Dna (Tcca Pam), PDB code: 5xh7 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) 40.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.656, 133.298, 200.020, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 21.4

Other elements in 5xh7:

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

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Acidaminococcus Sp. BV3L6 CPF1 Rr Variant in Complex with Crrna and Target Dna (Tcca Pam) (pdb code 5xh7). 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 Rr Variant in Complex with Crrna and Target Dna (Tcca Pam), PDB code: 5xh7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5xh7

Go back to Sodium Binding Sites List in 5xh7
Sodium binding site 1 out of 5 in the Crystal Structure of the Acidaminococcus Sp. BV3L6 CPF1 Rr Variant in Complex with Crrna and Target Dna (Tcca 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 Rr Variant in Complex with Crrna and Target Dna (Tcca Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1401

b:23.8
occ:1.00
 OP2 B:A-4 2.3 36.6 1.0
O A:HOH1752 2.3 55.9 1.0
O A:LYS757 2.3 37.7 1.0
O A:HOH1575 2.3 32.2 1.0
O B:HOH263 2.3 31.8 1.0
O B:HOH265 2.4 37.8 1.0
C A:LYS757 3.5 33.0 1.0
P B:A-4 3.7 33.5 1.0
O B:HOH245 3.9 41.3 1.0
N A:LYS757 4.1 32.5 1.0
OD1 A:ASP749 4.1 34.0 1.0
O5' B:A-4 4.2 32.0 1.0
CA A:LYS757 4.3 36.9 1.0
O B:HOH249 4.3 29.4 1.0
OP2 B:U-5 4.4 32.8 1.0
N A:PRO758 4.4 31.7 1.0
CA A:PRO758 4.5 29.4 1.0
C A:PRO758 4.5 26.5 1.0
C A:GLY756 4.6 37.5 1.0
OP1 B:A-4 4.6 34.6 1.0
O3' B:U-5 4.7 36.8 1.0
C3' B:U-5 4.7 30.3 1.0
CB A:LYS757 4.7 36.4 1.0
O5' B:U-5 4.8 34.6 1.0
N A:ASN759 4.8 28.1 1.0
CE1 A:HIS754 4.8 40.7 1.0
N7 B:A-4 4.8 31.9 1.0
OD1 A:ASN759 4.9 32.8 1.0
C8 B:A-4 4.9 30.7 1.0
OP2 B:G-3 4.9 31.6 1.0
O A:PRO758 4.9 31.8 1.0
P B:U-5 4.9 32.4 1.0
CA A:GLY756 4.9 40.7 1.0
OP1 B:U-5 5.0 34.9 1.0

Sodium binding site 2 out of 5 in 5xh7

Go back to Sodium Binding Sites List in 5xh7
Sodium binding site 2 out of 5 in the Crystal Structure of the Acidaminococcus Sp. BV3L6 CPF1 Rr Variant in Complex with Crrna and Target Dna (Tcca 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 Rr Variant in Complex with Crrna and Target Dna (Tcca Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na101

b:47.5
occ:1.00
 O B:HOH251 2.4 40.5 1.0
O C:HOH214 2.4 45.2 1.0
O6 B:G11 2.5 38.4 1.0
O4 B:U10 2.6 38.9 1.0
O B:HOH294 2.8 62.8 1.0
O B:HOH309 2.9 64.6 1.0
C4 B:U10 3.4 37.6 1.0
C6 B:G11 3.5 37.1 1.0
O C:HOH257 3.5 50.5 1.0
N4 C:DC-11 3.8 30.8 1.0
N7 B:G11 3.8 39.8 1.0
C5 B:U10 3.9 39.3 1.0
C5 B:G11 4.0 35.7 1.0
N6 C:DA-10 4.3 34.4 1.0
N4 B:C12 4.4 36.2 1.0
O6 C:DG-12 4.4 41.0 1.0
N3 B:U10 4.5 37.7 1.0
O C:HOH227 4.7 45.3 1.0
N1 B:G11 4.7 34.0 1.0

Sodium binding site 3 out of 5 in 5xh7

Go back to Sodium Binding Sites List in 5xh7
Sodium binding site 3 out of 5 in the Crystal Structure of the Acidaminococcus Sp. BV3L6 CPF1 Rr Variant in Complex with Crrna and Target Dna (Tcca 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 Rr Variant in Complex with Crrna and Target Dna (Tcca Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na102

b:50.4
occ:1.00
 O B:HOH303 2.3 57.5 1.0
O B:HOH293 2.3 37.6 1.0
O B:HOH202 2.4 46.0 1.0
N7 B:A2 2.5 31.2 1.0
O B:HOH212 2.8 43.4 1.0
C8 B:A2 3.4 28.0 1.0
C5 B:A2 3.6 30.5 1.0
O B:HOH266 3.8 54.7 1.0
N6 B:A2 3.9 32.7 1.0
C6 B:A2 4.2 34.1 1.0
N6 B:A3 4.2 29.9 1.0
C8 B:G1 4.3 31.3 1.0
N7 B:G1 4.3 29.2 1.0
OP2 B:A2 4.5 35.0 1.0
O C:HOH204 4.5 42.3 1.0
N7 B:A3 4.5 33.3 1.0
O B:HOH267 4.5 52.3 1.0
N9 B:A2 4.6 29.3 1.0
C4 B:A2 4.7 28.7 1.0
N9 B:G1 4.9 32.0 1.0
C5 B:G1 4.9 29.4 1.0
O C:HOH221 4.9 36.2 1.0
C6 B:A3 5.0 31.8 1.0

Sodium binding site 4 out of 5 in 5xh7

Go back to Sodium Binding Sites List in 5xh7
Sodium binding site 4 out of 5 in the Crystal Structure of the Acidaminococcus Sp. BV3L6 CPF1 Rr Variant in Complex with Crrna and Target Dna (Tcca 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 Rr Variant in Complex with Crrna and Target Dna (Tcca Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na103

b:48.7
occ:1.00
 O B:HOH308 2.4 51.9 1.0
O4 B:U16 2.4 38.6 1.0
O B:HOH215 2.4 45.8 1.0
O B:HOH297 2.5 59.9 1.0
O6 B:G17 2.6 40.2 1.0
O B:HOH260 2.8 47.6 1.0
O B:HOH203 3.2 52.9 1.0
C4 B:U16 3.3 41.9 1.0
C6 B:G17 3.4 41.2 1.0
N7 B:G17 3.6 44.2 1.0
C5 B:G17 3.8 46.9 1.0
C5 B:U16 3.9 43.4 1.0
N6 C:DA-16 3.9 46.7 1.0
N4 C:DC-17 4.2 50.6 1.0
O4 B:U15 4.4 43.0 1.0
N3 B:U16 4.4 39.6 1.0
O B:HOH273 4.5 48.0 1.0
N1 B:G17 4.7 38.9 1.0
C4 B:U15 4.7 43.8 1.0
C8 B:G17 4.8 44.5 1.0
C5 B:U15 4.9 43.0 1.0
C6 C:DA-16 4.9 48.8 1.0
O B:HOH257 4.9 53.4 1.0

Sodium binding site 5 out of 5 in 5xh7

Go back to Sodium Binding Sites List in 5xh7
Sodium binding site 5 out of 5 in the Crystal Structure of the Acidaminococcus Sp. BV3L6 CPF1 Rr Variant in Complex with Crrna and Target Dna (Tcca 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 Rr Variant in Complex with Crrna and Target Dna (Tcca Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na101

b:51.0
occ:1.00
 O C:HOH242 2.4 52.1 1.0
O6 C:DG-14 2.4 35.7 1.0
O B:HOH264 2.5 42.4 1.0
O C:HOH247 2.6 64.8 1.0
O B:HOH307 2.8 67.7 1.0
O C:HOH261 2.8 61.0 1.0
O C:HOH244 3.3 63.0 1.0
C6 C:DG-14 3.5 40.3 1.0
N7 C:DG-14 3.9 38.8 1.0
O C:HOH233 3.9 56.4 1.0
N6 C:DA-15 3.9 42.2 1.0
O C:HOH257 4.0 50.5 1.0
N4 B:C14 4.0 39.3 1.0
C5 C:DG-14 4.0 39.3 1.0
N4 C:DC-13 4.3 37.2 1.0
O6 B:G13 4.5 40.3 1.0
N1 C:DG-14 4.7 38.0 1.0
O B:HOH306 4.8 63.6 1.0
C6 C:DA-15 5.0 42.1 1.0

Reference:

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
Page generated: Tue Oct 8 01:14:14 2024

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