Magnesium in PDB 5b2t: Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam)

The structure of Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam), PDB code: 5b2t was solved by S.Hirano, 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)	49.01 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	176.967, 69.448, 188.199, 90.00, 109.67, 90.00
R / Rfree (%)	20.4 / 22.3

The structure of Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam) also contains other interesting chemical elements:

Potassium

(K)

10 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam) (pdb code 5b2t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam), PDB code: 5b2t:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam)


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 the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:61.1 occ:1.00 O A:HOH234 2.0 59.5 1.0 O A:HOH235 2.0 40.9 1.0 O A:HOH255 2.1 41.1 1.0 O A:HOH351 2.1 49.9 1.0 O A:HOH260 2.5 54.7 1.0 OP1 A:U50 2.7 32.2 1.0 O B:HOH1769 2.9 40.5 1.0 O6 A:G62 3.9 37.8 1.0 P A:U50 4.0 30.1 1.0 OP1 A:A51 4.3 31.2 1.0 O6 A:G53 4.5 31.0 1.0 OP2 A:U50 4.5 31.5 1.0 N1 A:G62 4.5 35.2 1.0 OP2 A:A52 4.5 32.8 1.0 O5' A:U50 4.6 30.6 1.0 C6 A:G62 4.7 35.1 1.0 OG1 B:THR73 4.7 30.3 1.0 O A:HOH371 4.8 45.5 1.0 N7 A:G53 4.9 28.4 1.0 O A:HOH209 4.9 44.7 1.0 OP1 A:A52 4.9 31.3 1.0 C5' A:U50 4.9 30.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam)


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 the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:57.8 occ:1.00 O A:HOH245 2.0 48.9 1.0 O A:HOH370 2.1 36.2 1.0 O B:HOH1879 2.1 29.3 1.0 O A:HOH332 2.6 28.2 1.0 OP2 A:G21 3.5 28.0 1.0 O A:HOH243 3.9 32.9 1.0 O A:HOH375 4.1 57.5 1.0 NH1 B:ARG403 4.1 27.8 1.0 O4 A:U22 4.2 32.3 1.0 O A:HOH229 4.3 25.7 1.0 K A:K103 4.3 39.6 1.0 CZ B:ARG403 4.4 30.0 1.0 N7 A:G21 4.5 31.3 1.0 NH2 B:ARG403 4.7 29.4 1.0 O A:HOH361 4.8 29.2 1.0 O A:HOH358 4.8 44.1 1.0 O A:HOH261 4.9 38.2 1.0 O A:HOH283 4.9 30.1 1.0 O A:HOH285 4.9 33.9 1.0 C5' A:C20 5.0 30.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam)


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 the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:50.0 occ:1.00 O A:HOH373 2.2 35.5 1.0 O B:HOH1873 2.2 47.0 1.0 O A:HOH327 2.2 35.9 1.0 O A:HOH217 2.3 39.5 1.0 NH2 B:ARG71 3.2 50.2 1.0 N7 A:G19 3.4 31.8 1.0 N7 A:G18 3.5 34.0 1.0 C5 A:G18 4.1 35.2 1.0 CZ B:ARG71 4.1 48.5 1.0 C8 A:G18 4.2 33.8 1.0 O6 A:G19 4.3 32.5 1.0 O6 A:G18 4.3 37.6 1.0 O A:HOH330 4.3 38.1 1.0 C8 A:G19 4.3 33.5 1.0 NE B:ARG71 4.4 43.6 1.0 C6 A:G18 4.4 36.4 1.0 C5 A:G19 4.4 33.0 1.0 O B:HOH1663 4.5 40.9 1.0 OP2 A:G18 4.5 30.7 1.0 O B:HOH1635 4.6 30.1 1.0 C6 A:G19 4.7 32.9 1.0 C4 A:G18 5.0 34.2 1.0 OP2 A:G19 5.0 28.9 1.0

S.Hirano, H.Nishimasu, R.Ishitani, O.Nureki. Structural Basis For the Altered Pam Specificities of Engineered Crispr-CAS9 Mol.Cell V. 61 886 2016.
ISSN: ISSN 1097-2765
PubMed: 26990991
DOI: 10.1016/J.MOLCEL.2016.02.018