Magnesium in PDB 4un3: Crystal Structure of CAS9 Bound to Pam-Containing Dna Target

The structure of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target, PDB code: 4un3 was solved by C.Anders, O.Niewoehner, A.Duerst, M.Jinek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.154 / 2.59
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	177.723, 68.142, 188.230, 90.00, 111.17, 90.00
R / Rfree (%)	21.71 / 25.2

The binding sites of Magnesium atom in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target (pdb code 4un3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target, PDB code: 4un3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1082 b:28.0 occ:1.00 O A:HOH2101 2.0 43.2 1.0 OP1 A:U50 2.1 12.0 1.0 O A:HOH2083 2.1 12.9 1.0 O A:HOH2084 2.1 20.0 1.0 O A:HOH2086 2.2 26.5 1.0 O A:HOH2085 3.0 30.4 1.0 P A:U50 3.4 15.5 1.0 O A:HOH2118 3.7 47.6 1.0 O A:HOH2088 3.8 12.2 1.0 O6 A:G62 3.9 29.2 1.0 OP2 A:U50 4.0 22.6 1.0 O5' A:U50 4.1 22.3 1.0 OP1 A:A51 4.3 15.9 1.0 O6 A:G53 4.3 17.6 1.0 O A:HOH2011 4.3 15.1 1.0 OP1 A:A52 4.5 21.1 1.0 O A:HOH2008 4.5 31.7 1.0 C5' A:U50 4.5 10.0 1.0 O3' A:A49 4.5 22.1 1.0 OP2 A:A52 4.5 15.6 1.0 N7 A:G53 4.6 27.5 1.0 NZ B:LYS1123 4.7 35.6 1.0 N1 A:G62 4.8 32.1 1.0 C6 A:G62 4.8 27.8 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1083 b:11.0 occ:1.00 O A:HOH2137 2.1 30.7 1.0 OG1 B:THR1102 2.3 19.0 1.0 O4 A:U66 2.6 29.2 1.0 OP2 A:A65 2.7 30.4 1.0 O A:HOH2126 3.2 19.4 1.0 O A:HOH2136 3.4 28.0 1.0 CB B:THR1102 3.5 22.9 1.0 C4 A:U66 3.6 29.2 1.0 CG2 B:THR1102 3.6 11.7 1.0 C5 A:U66 3.9 22.1 1.0 P A:A65 4.1 14.5 1.0 O B:HOH2186 4.1 41.5 1.0 OP2 A:U64 4.2 24.9 1.0 O A:HOH2132 4.5 32.5 1.0 N7 A:A65 4.5 22.4 1.0 OP1 A:U64 4.6 16.5 1.0 N4 A:C67 4.6 19.5 1.0 CA B:THR1102 4.7 22.3 1.0 O5' A:A65 4.7 24.6 1.0 OP1 A:A65 4.8 12.1 1.0 P A:U64 4.8 21.1 1.0 N B:THR1102 4.8 14.0 1.0 N3 A:U66 4.8 21.5 1.0 O B:VAL1100 4.8 24.0 1.0 C8 A:A65 4.9 23.3 1.0 O B:HOH2188 4.9 36.0 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1084 b:27.6 occ:1.00 O A:HOH2043 1.9 29.2 1.0 OP2 A:G21 2.5 19.8 1.0 O A:HOH2041 3.0 29.1 1.0 O A:HOH2042 3.3 12.5 1.0 O A:HOH2070 3.3 29.5 1.0 P A:G21 3.6 32.1 1.0 OP1 A:G21 3.8 22.0 1.0 O A:HOH2040 3.9 25.0 1.0 MG A:MG1085 4.0 53.8 1.0 CB B:ARG403 4.3 29.5 1.0 OP2 A:U45 4.4 27.9 1.0 O5' A:G21 4.4 34.8 1.0 O A:HOH2073 4.5 20.4 1.0 O B:ARG403 4.7 27.1 1.0 O3' A:A20 4.8 29.9 1.0 CG B:ARG403 4.9 26.8 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1085 b:53.8 occ:1.00 O A:HOH2045 2.1 47.4 1.0 O A:HOH2043 2.4 29.2 1.0 O A:HOH2071 3.9 23.4 1.0 MG A:MG1084 4.0 27.6 1.0 OP2 A:G21 4.1 19.8 1.0 O4 A:U22 4.1 24.4 1.0 N7 A:G21 4.2 30.0 1.0 NH1 B:ARG403 4.3 39.8 1.0 O A:HOH2076 4.5 26.8 1.0 O A:HOH2038 4.5 22.8 1.0 O A:HOH2042 4.7 12.5 1.0 C8 A:G21 4.8 25.7 1.0 CZ B:ARG403 4.9 43.0 1.0 C4 A:U22 5.0 23.4 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2365 b:53.0 occ:1.00 OD2 B:ASP10 2.1 58.6 1.0 CG B:ASP10 2.8 48.9 1.0 OD1 B:ASP10 2.8 54.1 1.0 OE2 B:GLU762 3.1 37.0 1.0 O B:HOH2244 3.2 28.1 1.0 OD2 B:ASP986 3.3 39.1 1.0 OE1 B:GLU762 3.4 37.7 1.0 CD B:GLU762 3.5 41.2 1.0 CG B:ASP986 4.0 29.0 1.0 O B:HOH2010 4.1 32.9 1.0 CB B:ASP986 4.1 24.1 1.0 CB B:ASP10 4.2 34.1 1.0 CG B:GLU762 4.9 37.7 1.0 NZ B:LYS974 4.9 43.9 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2366 b:25.6 occ:1.00 O B:HOH2139 2.1 39.9 1.0 O B:TYR656 2.1 40.3 1.0 O B:LEU623 2.6 26.1 1.0 O B:THR624 2.7 30.8 1.0 O B:PHE626 3.0 35.6 1.0 C B:THR624 3.3 26.4 1.0 C B:TYR656 3.3 38.7 1.0 CA B:THR624 3.4 22.5 1.0 C B:LEU623 3.6 22.3 1.0 N B:TYR656 3.8 45.8 1.0 C B:PHE626 3.9 29.1 1.0 N B:THR624 4.0 19.4 1.0 CA B:TYR656 4.2 41.8 1.0 N B:THR657 4.2 43.1 1.0 CG2 B:THR657 4.2 33.4 1.0 CB B:GLU627 4.3 47.3 1.0 CA B:THR657 4.4 36.5 1.0 N B:LEU625 4.4 26.2 1.0 N B:PHE626 4.5 31.2 1.0 N B:GLU627 4.5 30.8 1.0 CA B:GLU627 4.6 49.3 1.0 OP1 C:DC16 4.6 43.9 1.0 CB B:THR624 4.7 33.0 1.0 CB B:ARG655 4.7 61.0 1.0 C B:ARG655 4.7 52.3 1.0 CA B:PHE626 4.8 23.6 1.0 CG2 B:THR624 4.8 33.1 1.0 C B:LEU625 4.9 26.5 1.0 CB B:THR657 4.9 28.3 1.0 CA B:ARG655 5.0 58.4 1.0 CG B:ARG655 5.0 67.3 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2367 b:15.8 occ:1.00 O B:GLN1350 2.2 35.4 1.0 O B:HOH2184 2.4 13.9 1.0 O B:HOH2242 2.9 40.4 1.0 O A:HOH2138 3.0 23.2 1.0 O A:HOH2140 3.1 32.1 1.0 O4' A:A68 3.1 34.4 1.0 C B:GLN1350 3.3 30.0 1.0 O B:SER1351 3.6 22.6 1.0 C1' A:A68 3.6 45.4 1.0 C B:SER1351 3.8 26.4 1.0 N9 A:A68 4.0 48.7 1.0 N B:SER1351 4.2 32.7 1.0 CA B:GLN1350 4.2 32.5 1.0 CB B:GLN1350 4.2 31.0 1.0 CA B:SER1351 4.3 28.1 1.0 O5' A:A68 4.4 14.3 1.0 C8 A:A68 4.4 49.4 1.0 C4' A:A68 4.4 33.0 1.0 N B:ILE1352 4.4 22.9 1.0 O A:HOH2139 4.5 36.5 1.0 N B:GLN1350 4.5 33.1 1.0 OP1 A:A68 4.7 26.1 1.0 OG1 B:THR1098 4.8 28.2 1.0 C4 A:A68 4.8 50.2 1.0 CG1 B:VAL1095 4.8 25.1 1.0 CA B:ILE1352 4.8 29.6 1.0 O B:HOH2243 4.8 40.0 1.0 C5' A:A68 4.9 20.7 1.0 CG2 B:THR1098 5.0 17.9 1.0 P A:A68 5.0 25.9 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2368 b:36.8 occ:1.00 O B:GLU584 2.2 65.6 1.0 O B:HOH2128 2.3 39.1 1.0 O B:ARG586 2.7 47.8 1.0 C B:GLU584 3.2 58.5 1.0 ND2 B:ASN588 3.5 41.2 1.0 CB B:GLU584 3.6 80.5 1.0 N B:ARG586 3.7 46.8 1.0 CA B:GLU584 3.7 58.0 1.0 C B:ARG586 3.8 42.1 1.0 O B:HOH2131 3.8 40.0 1.0 N B:GLU584 3.9 48.6 1.0 CG B:ASN588 4.2 40.2 1.0 CG B:GLU584 4.3 0.3 1.0 OD1 B:ASN588 4.3 36.2 1.0 CA B:ARG586 4.3 38.5 1.0 N B:ASP585 4.4 55.8 1.0 CB B:ASP585 4.5 52.2 1.0 C B:ASP585 4.7 51.4 1.0 CA B:ASP585 4.7 52.6 1.0 CG B:ARG586 4.7 48.5 1.0 N B:ASN588 4.8 29.1 1.0 OE1 B:GLU584 4.8 0.7 1.0 CG2 B:VAL583 4.9 36.9 1.0 N B:PHE587 4.9 39.2 1.0 CD B:GLU584 4.9 0.5 1.0

C.Anders, O.Niewoehner, A.Duerst, M.Jinek. Structural Basis of Pam-Dependent Target Dna Recognition By the CAS9 Endonuclease Nature V. 513 569 2014.
ISSN: ISSN 0028-0836
PubMed: 25079318
DOI: 10.1038/NATURE13579