Calcium 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
Chlorine	(Cl)	2 atoms
Sodium	(Na)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Calcium 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 Calcium atom.
In total 17 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 17 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 Calcium with other atoms in the Ca 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:Ca1706 b:67.2 occ:1.00 O A:HOH1870 2.3 55.5 1.0 ND1 A:HIS1162 2.4 46.0 1.0 O A:HOH1851 2.4 53.2 1.0 OD2 A:ASP11 2.6 53.7 1.0 OE2 A:GLU903 2.9 36.4 0.4 OD1 A:ASP11 2.9 51.3 1.0 OE1 A:GLU903 3.0 48.2 0.4 CG A:ASP11 3.1 51.0 1.0 OE2 A:GLU903 3.2 48.2 0.3 OE2 A:GLU903 3.2 48.2 0.3 CE1 A:HIS1162 3.3 42.8 1.0 CD A:GLU903 3.3 44.2 0.4 CG A:HIS1162 3.5 45.4 1.0 O A:HOH1960 3.6 53.4 1.0 CB A:HIS1162 3.8 42.8 1.0 CA A:HIS1162 4.1 40.3 1.0 O A:HOH2199 4.3 57.2 1.0 CD A:GLU903 4.3 47.8 0.3 CD A:GLU903 4.3 47.8 0.3 OD2 A:ASP1165 4.4 49.0 1.0 NE2 A:HIS1162 4.4 47.1 1.0 NE2 A:GLN1157 4.5 58.7 1.0 OE1 A:GLN1157 4.5 65.5 1.0 O A:ASN16 4.5 43.5 1.0 CD2 A:HIS1162 4.6 45.6 1.0 CB A:ASP11 4.7 42.7 1.0 OE1 A:GLU903 4.8 46.6 0.3 OE1 A:GLU903 4.8 46.6 0.3 O A:ASP11 4.8 39.1 1.0 CG A:GLU903 4.8 44.5 0.4 CD A:GLN1157 4.9 63.7 1.0 N A:HIS1162 5.0 44.7 1.0

Calcium binding site 2 out of 17 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 Calcium with other atoms in the Ca 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:Ca1707 b:36.4 occ:1.00 OP2 B:A60 2.4 31.4 1.0 OD2 A:ASP66 2.4 29.9 1.0 O B:HOH318 2.4 27.4 1.0 O B:HOH458 2.5 43.0 1.0 O B:HOH493 2.5 40.1 1.0 O A:HOH1931 2.5 32.9 1.0 O B:HOH479 2.6 42.3 1.0 O B:HOH328 3.5 28.0 1.0 CG A:ASP66 3.6 28.8 1.0 P B:A60 3.7 29.2 1.0 OD1 A:ASP66 4.0 24.3 1.0 O B:HOH415 4.0 31.1 1.0 O B:HOH288 4.2 59.5 1.0 O6 B:G62 4.2 22.9 1.0 O5' B:A60 4.2 30.2 1.0 OP1 B:A60 4.2 25.2 1.0 CA A:CA1709 4.3 49.1 1.0 N7 B:A61 4.7 24.1 1.0 O2 B:EDO112 4.7 26.2 1.0 CB A:ASP66 4.7 19.4 1.0 O B:HOH273 4.8 46.0 1.0 OP2 B:A61 4.8 20.3 1.0 O B:HOH266 4.9 23.2 1.0 O3' B:A59 4.9 28.0 1.0 N7 B:A60 5.0 34.1 1.0

Calcium binding site 3 out of 17 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 Calcium with other atoms in the Ca 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 A:Ca1708 b:47.0 occ:1.00 O A:HOH2342 2.3 50.9 1.0 O A:HOH2088 2.3 31.3 1.0 O C:HOH157 2.4 52.5 1.0 O A:HOH1804 2.4 39.6 1.0 O A:HOH2335 2.5 59.1 1.0 O C:HOH117 2.6 38.4 1.0 O C:HOH111 2.7 33.0 1.0 O C:HOH138 3.7 42.3 1.0 OP1 C:DC18 4.3 33.7 1.0 OD2 A:ASP451 4.3 29.7 1.0 OD1 A:ASP451 4.5 27.5 1.0 CG A:LYS808 4.6 41.0 1.0 OP1 C:DG17 4.7 28.9 1.0 OP2 C:DC18 4.8 28.0 1.0 O A:HOH1927 4.8 58.0 1.0 OE1 A:GLN663 4.9 34.5 0.6 P C:DC18 4.9 29.7 1.0 CG A:ASP451 4.9 30.8 1.0

Calcium binding site 4 out of 17 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 Calcium with other atoms in the Ca 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 A:Ca1709 b:49.1 occ:1.00 O B:HOH267 2.3 29.0 1.0 OD1 A:ASP66 2.3 24.3 1.0 O A:HOH1808 2.3 22.9 1.0 O B:HOH458 2.4 43.0 1.0 O B:HOH288 2.4 59.5 1.0 O B:HOH520 2.7 48.1 1.0 O B:HOH398 2.8 27.1 1.0 O B:HOH368 2.8 24.4 1.0 CG A:ASP66 3.4 28.8 1.0 OD2 A:ASP66 3.7 29.9 1.0 O B:HOH493 3.9 40.1 1.0 O B:HOH273 4.0 46.0 1.0 O B:HOH345 4.2 27.5 1.0 OE1 A:GLN69 4.3 24.8 1.0 CA A:CA1707 4.3 36.4 1.0 OP1 B:U52 4.3 22.3 1.0 O A:HOH1931 4.4 32.9 1.0 OP1 B:C53 4.4 22.5 1.0 O6 B:G62 4.6 22.9 1.0 O A:HOH2211 4.7 33.1 1.0 CB A:ASP66 4.7 19.4 1.0 OP2 B:U52 4.7 19.9 1.0 CG2 A:ILE65 4.9 19.3 1.0 O A:ARG62 4.9 18.3 1.0

Calcium binding site 5 out of 17 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 Calcium with other atoms in the Ca binding site number 5 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:Ca1710 b:47.4 occ:1.00 OP1 B:U83 2.1 48.8 1.0 O A:VAL402 2.3 34.5 1.0 O B:HOH503 2.5 47.3 1.0 O B:HOH335 2.5 56.8 1.0 O A:HOH2299 2.5 33.5 1.0 O A:HOH2283 2.9 47.7 1.0 C A:VAL402 3.5 33.8 1.0 P B:U83 3.5 42.4 1.0 O3' B:U82 4.0 32.9 1.0 N A:VAL402 4.2 27.1 1.0 O5' B:U83 4.2 49.7 1.0 CA A:VAL402 4.3 29.8 1.0 N A:GLY403 4.4 32.8 1.0 C6 B:U83 4.4 77.9 1.0 CA A:GLY403 4.5 36.9 1.0 OP2 B:U83 4.6 46.2 1.0 O A:HOH2030 4.6 29.6 1.0 C5 B:U83 4.6 79.9 1.0 O B:HOH454 4.8 49.7 1.0 CB A:VAL402 4.8 34.7 1.0 O A:HOH2170 4.9 32.0 1.0

Calcium binding site 6 out of 17 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 Calcium with other atoms in the Ca binding site number 6 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:Ca1711 b:75.7 occ:1.00 O A:HOH2387 2.3 49.0 1.0 O B:HOH490 2.5 59.9 1.0 O B:HOH218 2.6 59.6 1.0 O A:HOH1906 2.7 60.9 1.0 O A:HOH1901 2.8 43.7 1.0 O B:HOH257 3.0 47.5 1.0 OP1 B:G41 4.3 35.9 1.0 OD2 A:ASP1297 4.4 34.3 1.0 OP2 B:G28 4.5 29.2 1.0 OD1 A:ASP1297 4.7 36.3 1.0 O A:HOH2072 4.9 40.6 1.0 O B:HOH259 5.0 43.8 1.0 CG A:ASP1297 5.0 36.1 1.0

Calcium binding site 7 out of 17 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 Calcium with other atoms in the Ca binding site number 7 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:Ca1712 b:72.5 occ:1.00 O B:HOH440 2.3 52.3 1.0 O A:SER507 2.5 36.2 1.0 O A:HOH2327 2.5 52.6 1.0 O B:HOH336 2.5 59.2 1.0 O A:HOH2286 2.7 73.4 1.0 C A:SER507 3.7 36.0 1.0 O4 B:U84 4.2 87.8 1.0 CA A:SER507 4.5 27.3 1.0 O A:HOH1938 4.5 28.6 1.0 O A:HOH2163 4.6 47.6 1.0 O B:HOH439 4.6 47.8 1.0 O4 B:U82 4.6 35.0 1.0 N A:LYS508 4.6 31.9 1.0 CB A:SER507 4.7 31.9 1.0 CA A:LYS508 4.7 35.7 1.0 O B:HOH325 4.8 28.4 1.0 C4 B:U84 4.9 85.2 1.0 O6 B:G85 5.0 50.0 1.0

Calcium binding site 8 out of 17 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 Calcium with other atoms in the Ca binding site number 8 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:Ca1713 b:82.2 occ:1.00 O A:HOH2332 2.6 74.0 1.0 OD1 A:ASP1417 2.7 38.8 1.0 O A:LYS1415 2.7 46.7 1.0 O A:HOH1902 2.9 47.4 1.0 O A:HOH2336 3.0 51.8 1.0 CG A:ASP1417 3.7 37.1 1.0 C A:LYS1415 3.8 44.2 1.0 O A:HOH2139 4.0 35.8 1.0 OD2 A:ASP1417 4.2 39.9 1.0 O A:HOH2056 4.4 42.7 1.0 CA A:LYS1415 4.4 47.0 1.0 N A:ASP1417 4.6 35.9 1.0 NE1 A:TRP1409 4.7 32.1 1.0 O A:ILE1414 4.8 47.9 1.0 CA A:ASP1417 4.9 37.5 1.0 CB A:ASP1417 4.9 34.8 1.0 N A:ASP1416 4.9 40.7 1.0 C A:ASP1416 4.9 39.3 1.0

Calcium binding site 9 out of 17 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 Calcium with other atoms in the Ca binding site number 9 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:Ca1714 b:69.9 occ:1.00 O A:HOH2059 2.4 54.2 1.0 O A:HOH1948 2.5 44.8 1.0 O B:HOH506 2.5 53.2 1.0 O B:HOH282 2.6 51.5 1.0 O C:HOH103 2.6 44.7 1.0 O C:HOH152 2.7 54.6 1.0 O A:HOH2242 2.8 45.0 1.0 NZ A:LYS664 4.2 52.8 1.0 O C:HOH102 4.3 47.6 1.0 OP2 B:A6 4.3 41.7 1.0 OP2 C:DC20 4.3 39.9 1.0 O A:ASN810 4.3 29.1 1.0 OD1 A:ASN812 4.4 40.8 1.0 O C:HOH109 4.5 41.0 1.0 CG A:ASN812 4.7 36.8 1.0 CB A:ASN812 4.7 26.8 1.0 O C:HOH136 4.8 45.8 1.0 CE A:LYS664 4.9 48.1 1.0

Calcium binding site 10 out of 17 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 Calcium with other atoms in the Ca binding site number 10 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:Ca1715 b:54.0 occ:1.00 OE2 A:GLU1231 2.6 52.8 1.0 OG A:SER1499 2.9 37.2 1.0 N A:SER1499 3.1 28.9 1.0 OD1 A:ASN1234 3.2 35.5 1.0 CD A:GLU1231 3.4 54.9 1.0 O A:HOH2117 3.4 34.5 1.0 CB A:SER1499 3.4 33.3 1.0 N A:ASP1498 3.5 34.0 1.0 CB A:ILE1497 3.7 33.7 1.0 OE1 A:GLU1231 3.8 53.6 1.0 CA A:SER1499 3.8 33.2 1.0 CD1 A:ILE1497 3.9 29.4 1.0 CG1 A:ILE1497 3.9 31.7 1.0 CB A:ASP1498 3.9 30.8 1.0 C A:ASP1498 4.0 35.3 1.0 CA A:ASP1498 4.0 37.6 1.0 CG A:ASN1234 4.0 29.9 1.0 ND2 A:ASN1234 4.1 28.6 1.0 C A:ILE1497 4.2 30.3 1.0 CG A:GLU1231 4.5 54.5 1.0 CA A:ILE1497 4.5 33.9 1.0 CA A:GLU1231 4.6 38.2 1.0 N A:GLY1232 4.8 39.5 1.0 CG2 A:ILE1497 4.8 36.5 1.0 CB A:GLU1231 4.9 46.5 1.0 O A:ILE1497 4.9 27.9 1.0 CG A:ASP1498 4.9 39.1 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