Magnesium in PDB 5dqz: Crystal Structure of Cas-Dna-Pam Complex

The structure of Crystal Structure of Cas-Dna-Pam Complex, PDB code: 5dqz was solved by J.Wang, J.Li, H.Zhao, G.Sheng, M.Wang, M.Yin, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.53 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.771, 193.380, 193.230, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 22.4

The binding sites of Magnesium atom in the Crystal Structure of Cas-Dna-Pam Complex (pdb code 5dqz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Cas-Dna-Pam Complex, PDB code: 5dqz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Cas-Dna-Pam Complex


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 Cas-Dna-Pam Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:70.5 occ:1.00 O C:HOH504 2.2 57.4 1.0 O C:HOH503 2.3 79.8 1.0 NE2 C:HIS208 2.6 80.3 1.0 CE1 C:HIS208 2.6 80.3 1.0 OE2 C:GLU141 2.6 94.4 1.0 OD2 C:ASP221 2.7 89.6 1.0 CD C:GLU141 3.4 92.5 1.0 OE1 C:GLU141 3.6 94.7 1.0 ND1 C:HIS208 3.8 80.0 1.0 CD2 C:HIS208 3.9 80.2 1.0 CG C:ASP221 3.9 86.5 1.0 O C:HOH528 4.3 91.0 1.0 NH1 C:ARG123 4.4 86.5 1.0 CG C:HIS208 4.5 78.3 1.0 O C:HOH536 4.5 93.8 1.0 CG1 C:VAL207 4.6 70.5 1.0 CB C:ASP221 4.6 79.4 1.0 CG C:GLU141 4.8 87.1 1.0 OD1 C:ASP221 4.8 88.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Cas-Dna-Pam Complex


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 Cas-Dna-Pam Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:68.6 occ:1.00 O B:HOH518 2.1 77.9 1.0 OD2 B:ASP221 2.4 90.8 1.0 NE2 B:HIS208 2.4 74.4 1.0 O B:HOH531 2.4 0.1 1.0 O B:HOH532 2.5 0.5 1.0 CE1 B:HIS208 2.6 75.2 1.0 O B:HOH507 3.0 97.9 1.0 OE2 B:GLU141 3.2 97.3 1.0 O B:HOH534 3.4 98.4 1.0 CG B:ASP221 3.6 86.6 1.0 CD2 B:HIS208 3.8 74.5 1.0 ND1 B:HIS208 3.9 75.1 1.0 CD B:GLU141 4.2 96.7 1.0 OD1 B:ASP221 4.4 88.2 1.0 OE1 B:GLU141 4.5 0.1 1.0 CG B:HIS208 4.5 73.3 1.0 CB B:ASP221 4.6 77.9 1.0 O B:HOH538 4.8 68.5 1.0 NH1 B:ARG123 4.8 81.7 1.0 O B:HOH524 5.0 70.7 1.0

J.Wang, J.Li, H.Zhao, G.Sheng, M.Wang, M.Yin, Y.Wang. Structural and Mechanistic Basis of Pam-Dependent Spacer Acquisition in Crispr-Cas Systems. Cell V. 163 840 2015.
ISSN: ISSN 1097-4172
PubMed: 26478180
DOI: 10.1016/J.CELL.2015.10.008