Sodium in PDB 5czz: Crystal Structure of Staphylococcus Aureus CAS9 in Complex with Sgrna and Target Dna (Ttgaat Pam)

The structure of Crystal Structure of Staphylococcus Aureus CAS9 in Complex with Sgrna and Target Dna (Ttgaat Pam), PDB code: 5czz was solved by 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)	49.04 / 2.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.585, 345.584, 98.089, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.1

The binding sites of Sodium atom in the Crystal Structure of Staphylococcus Aureus CAS9 in Complex with Sgrna and Target Dna (Ttgaat Pam) (pdb code 5czz). 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 Staphylococcus Aureus CAS9 in Complex with Sgrna and Target Dna (Ttgaat Pam), PDB code: 5czz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of Staphylococcus Aureus CAS9 in Complex with Sgrna and Target Dna (Ttgaat 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 Staphylococcus Aureus CAS9 in Complex with Sgrna and Target Dna (Ttgaat Pam) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1101 b:65.4 occ:1.00 O A:TYR389 2.5 71.0 1.0 OG1 A:THR390 2.6 75.3 1.0 O A:HOH1254 2.6 76.2 1.0 O A:HOH1205 2.6 68.8 1.0 O C:HOH201 2.6 63.2 1.0 O A:HOH1223 2.8 46.2 1.0 C A:TYR389 3.4 71.4 1.0 CB A:THR390 3.6 70.3 1.0 CA A:THR390 3.8 69.4 1.0 OE1 A:GLN359 3.9 71.5 1.0 N A:THR390 4.0 71.4 1.0 O A:THR356 4.2 67.9 1.0 CG2 A:THR390 4.2 69.5 1.0 O A:LEU355 4.3 70.4 1.0 OP1 C:DG16 4.3 68.4 1.0 CA A:TYR389 4.4 69.8 1.0 N A:TYR389 4.6 68.3 1.0 CA A:THR356 4.7 69.1 1.0 CD A:GLN359 4.8 73.2 1.0 CB A:TYR389 4.8 69.9 1.0 C A:THR356 4.9 68.8 1.0 NE2 A:GLN359 5.0 72.0 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of Staphylococcus Aureus CAS9 in Complex with Sgrna and Target Dna (Ttgaat 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 Staphylococcus Aureus CAS9 in Complex with Sgrna and Target Dna (Ttgaat Pam) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:89.0 occ:1.00 O A:ILE599 2.8 94.4 1.0 O A:SER594 2.9 0.9 1.0 O A:LEU592 3.0 96.2 1.0 CB A:SER597 3.3 0.2 1.0 C A:ILE599 3.8 93.7 1.0 C A:LEU592 3.9 95.5 1.0 O A:SER597 4.1 0.9 1.0 OG A:SER597 4.1 99.4 1.0 C A:SER597 4.1 0.4 1.0 CA A:SER597 4.1 0.2 1.0 C A:SER594 4.2 0.8 1.0 CA A:SER600 4.4 91.0 1.0 N A:SER597 4.4 0.7 1.0 N A:SER600 4.4 91.3 1.0 CA A:LEU592 4.5 93.3 1.0 N A:ILE599 4.5 96.1 1.0 N A:LYS598 4.7 0.7 1.0 CA A:ILE599 4.7 94.9 1.0 C A:SER593 4.7 98.9 1.0 N A:SER594 4.8 99.3 1.0 CA A:SER595 4.9 0.8 1.0 N A:SER593 4.9 95.5 1.0 O A:SER593 4.9 0.2 1.0 N A:SER595 5.0 0.4 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of Staphylococcus Aureus CAS9 in Complex with Sgrna and Target Dna (Ttgaat 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 Staphylococcus Aureus CAS9 in Complex with Sgrna and Target Dna (Ttgaat Pam) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1103 b:86.0 occ:1.00 O A:MET234 2.6 63.6 1.0 O A:GLU231 2.7 76.7 1.0 O A:MET232 2.9 71.7 1.0 C A:MET232 3.3 70.9 1.0 CA A:MET232 3.6 75.3 1.0 NE2 A:HIS236 3.7 78.0 1.0 C A:GLU231 3.8 76.7 1.0 C A:MET234 3.8 65.7 1.0 CD2 A:HIS236 4.2 76.8 1.0 N A:MET232 4.2 76.4 1.0 N A:LEU233 4.2 67.4 1.0 CD2 A:LEU244 4.2 65.3 1.0 N A:MET234 4.3 65.5 1.0 C A:LEU233 4.4 65.6 1.0 CE1 A:HIS236 4.6 78.7 1.0 O A:LEU233 4.6 65.2 1.0 CA A:MET234 4.6 65.2 1.0 CG A:MET234 4.7 64.2 1.0 CA A:LEU233 4.8 65.9 1.0 N A:GLY235 4.8 67.2 1.0 CA A:GLY235 4.9 69.0 1.0 CB A:MET232 5.0 78.3 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of Staphylococcus Aureus CAS9 in Complex with Sgrna and Target Dna (Ttgaat 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 Staphylococcus Aureus CAS9 in Complex with Sgrna and Target Dna (Ttgaat Pam) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:88.6 occ:1.00 O6 B:G12 2.5 54.5 1.0 O B:HOH216 2.6 90.1 1.0 O B:HOH217 2.6 76.4 1.0 O B:HOH215 2.6 92.7 1.0 O4 B:U11 2.7 61.5 1.0 O C:HOH203 2.9 61.2 1.0 C4 B:U11 3.4 59.8 1.0 C6 B:G12 3.5 53.7 1.0 N7 B:G12 3.8 52.6 1.0 C5 B:G12 4.0 53.4 1.0 C5 B:U11 4.0 58.5 1.0 N4 C:DC17 4.1 51.5 1.0 N3 B:U11 4.3 61.0 1.0 O6 C:DG16 4.4 57.9 1.0 N6 C:DA18 4.5 58.2 1.0 N4 B:C13 4.7 48.9 1.0 N1 B:G12 4.8 54.3 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of Staphylococcus Aureus CAS9 in Complex with Sgrna and Target Dna (Ttgaat 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 Staphylococcus Aureus CAS9 in Complex with Sgrna and Target Dna (Ttgaat Pam) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:63.0 occ:1.00 O C:HOH202 2.4 51.8 1.0 O2 C:DT5 2.4 60.5 1.0 O A:HOH1222 2.5 60.5 1.0 O C:HOH204 2.6 56.9 1.0 O D:HOH206 2.6 56.5 1.0 O4' C:DC6 2.6 51.9 1.0 C4' C:DC6 3.4 53.9 1.0 C2 C:DT5 3.5 58.6 1.0 C1' C:DC6 3.7 51.0 1.0 C5' C:DC6 3.7 56.4 1.0 C1' C:DT5 3.7 64.4 1.0 OD1 A:ASN885 4.0 59.5 1.0 N1 C:DC6 4.0 49.7 1.0 N1 C:DT5 4.1 59.3 1.0 C2' C:DT5 4.4 66.4 1.0 C2 C:DC6 4.4 49.0 1.0 N3 D:DA5 4.5 46.6 1.0 C6 C:DC6 4.5 49.2 1.0 O2 C:DC6 4.5 49.8 1.0 C2 D:DA5 4.6 46.1 1.0 N3 C:DT5 4.7 57.2 1.0 O4' C:DT5 4.7 67.8 1.0 O5' C:DC6 4.7 59.8 1.0 C3' C:DC6 4.8 53.2 1.0 CG A:ASN885 4.8 56.5 1.0 ND2 A:ASN885 4.8 57.5 1.0 C2' C:DC6 4.9 51.3 1.0

H.Nishimasu, L.Cong, W.X.Yan, F.A.Ran, B.Zetsche, Y.Li, A.Kurabayashi, R.Ishitani, F.Zhang, O.Nureki. Crystal Structure of Staphylococcus Aureus CAS9 Cell(Cambridge,Mass.) V. 162 1 2015.
ISSN: ISSN 0092-8674
DOI: 10.1016/J.CELL.2015.08.007