Magnesium in PDB 5xvo: E. Fae CAS1-CAS2/Prespacer/Target Ternary Complex Revealing Dna Sampling and Half-Integration States

The structure of E. Fae CAS1-CAS2/Prespacer/Target Ternary Complex Revealing Dna Sampling and Half-Integration States, PDB code: 5xvo was solved by Y.Xiao, S.Ng, K.H.Nam, A.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.95 / 3.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	131.893, 124.800, 157.905, 90.00, 106.50, 90.00
R / Rfree (%)	19.4 / 23.3

The binding sites of Magnesium atom in the E. Fae CAS1-CAS2/Prespacer/Target Ternary Complex Revealing Dna Sampling and Half-Integration States (pdb code 5xvo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the E. Fae CAS1-CAS2/Prespacer/Target Ternary Complex Revealing Dna Sampling and Half-Integration States, PDB code: 5xvo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the E. Fae CAS1-CAS2/Prespacer/Target Ternary Complex Revealing Dna Sampling and Half-Integration States


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Fae CAS1-CAS2/Prespacer/Target Ternary Complex Revealing Dna Sampling and Half-Integration States within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg201 b:63.6 occ:1.00 OD1 E:ASP13 2.0 73.0 1.0 OG E:SER43 2.0 68.5 1.0 OP1 R:DC-8 2.5 56.3 1.0 O E:PHE12 2.6 67.4 1.0 CB E:SER43 2.9 60.4 1.0 CG E:ASP13 3.3 65.0 1.0 OE1 F:GLN41 3.4 66.3 1.0 C E:PHE12 3.6 64.4 1.0 O F:PHE42 3.6 54.8 1.0 P R:DC-8 4.0 59.3 1.0 OD2 E:ASP13 4.0 61.4 1.0 N E:ASP13 4.2 61.2 1.0 CA E:ASP13 4.2 58.5 1.0 N F:PHE42 4.2 57.4 1.0 CB F:GLN41 4.3 63.0 1.0 CA E:SER43 4.3 60.4 1.0 CB E:ASP13 4.3 62.7 1.0 CB F:PHE42 4.4 63.8 1.0 C F:PHE42 4.5 59.3 1.0 CD F:GLN41 4.5 64.8 1.0 O E:PHE42 4.5 52.9 1.0 O E:SER43 4.6 68.5 1.0 CA F:PHE42 4.6 61.6 1.0 C E:SER43 4.7 62.0 1.0 O3' R:DC-9 4.7 58.2 1.0 C5' R:DC-8 4.7 54.5 1.0 CA E:PHE12 4.7 60.9 1.0 N E:PHE12 4.8 62.6 1.0 CD2 F:PHE42 4.8 71.5 1.0 O5' R:DC-8 4.9 50.6 1.0 OP2 R:DC-8 4.9 56.9 1.0 CG F:GLN41 4.9 65.1 1.0 CG F:PHE42 5.0 66.7 1.0 C F:GLN41 5.0 57.8 1.0

Magnesium binding site 2 out of 4 in the E. Fae CAS1-CAS2/Prespacer/Target Ternary Complex Revealing Dna Sampling and Half-Integration States


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Fae CAS1-CAS2/Prespacer/Target Ternary Complex Revealing Dna Sampling and Half-Integration States within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg201 b:56.9 occ:1.00 OG F:SER43 1.8 75.8 1.0 OD1 F:ASP13 2.0 74.7 1.0 OP1 G:DC15 2.3 52.0 1.0 O F:PHE12 2.4 66.7 1.0 CB F:SER43 2.8 67.3 1.0 CG F:ASP13 3.3 71.7 1.0 OE1 E:GLN41 3.4 76.0 1.0 C F:PHE12 3.5 63.5 1.0 P G:DC15 3.8 60.3 1.0 O E:PHE42 3.8 52.9 1.0 OD2 F:ASP13 4.1 68.7 1.0 N F:ASP13 4.2 65.8 1.0 CA F:ASP13 4.2 68.2 1.0 CA F:SER43 4.2 62.3 1.0 CB F:ASP13 4.3 72.0 1.0 CB E:GLN41 4.4 67.3 1.0 N E:PHE42 4.4 56.0 1.0 CD E:GLN41 4.5 69.4 1.0 O F:SER43 4.5 63.1 1.0 O F:PHE42 4.5 54.8 1.0 C5' G:DC15 4.5 57.2 1.0 O3' G:DC14 4.6 56.6 1.0 CB E:PHE42 4.6 58.3 1.0 OP2 G:DC15 4.6 56.5 1.0 O5' G:DC15 4.6 56.5 1.0 C F:SER43 4.6 59.9 1.0 CA F:PHE12 4.6 61.6 1.0 N F:PHE12 4.7 62.4 1.0 C E:PHE42 4.7 54.4 1.0 CA E:PHE42 4.9 55.7 1.0 CD2 E:PHE42 4.9 65.2 1.0 CG E:GLN41 4.9 68.5 1.0 CG1 E:VAL44 4.9 78.0 1.0

Magnesium binding site 3 out of 4 in the E. Fae CAS1-CAS2/Prespacer/Target Ternary Complex Revealing Dna Sampling and Half-Integration States


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E. Fae CAS1-CAS2/Prespacer/Target Ternary Complex Revealing Dna Sampling and Half-Integration States within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg201 b:63.4 occ:1.00 OG M:SER43 1.8 77.8 1.0 OD1 M:ASP13 2.0 72.0 1.0 OP1 P:DC15 2.2 70.0 1.0 O M:PHE12 2.5 61.5 1.0 CB M:SER43 2.7 65.5 1.0 CG M:ASP13 3.3 68.9 1.0 OE1 N:GLN41 3.5 80.0 1.0 C M:PHE12 3.5 64.4 1.0 P P:DC15 3.7 69.3 1.0 OD2 M:ASP13 4.1 66.0 1.0 CA M:SER43 4.1 61.7 1.0 N M:ASP13 4.2 71.4 1.0 CA M:ASP13 4.2 69.0 1.0 CB M:ASP13 4.3 69.1 1.0 N N:PHE42 4.3 67.1 1.0 O M:PHE42 4.4 62.9 1.0 CB N:GLN41 4.5 64.5 1.0 C5' P:DC15 4.5 70.8 1.0 CB N:PHE42 4.5 72.7 1.0 O M:SER43 4.5 73.4 1.0 O3' P:DC14 4.5 66.9 1.0 O5' P:DC15 4.5 65.9 1.0 C M:SER43 4.5 65.6 1.0 CD N:GLN41 4.6 75.5 1.0 OP2 P:DC15 4.6 62.5 1.0 CA M:PHE12 4.7 62.5 1.0 N M:PHE12 4.7 59.3 1.0 CA N:PHE42 4.8 71.4 1.0 N N:SER43 4.9 78.3 1.0 CD2 N:PHE42 5.0 76.2 1.0

Magnesium binding site 4 out of 4 in the E. Fae CAS1-CAS2/Prespacer/Target Ternary Complex Revealing Dna Sampling and Half-Integration States


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E. Fae CAS1-CAS2/Prespacer/Target Ternary Complex Revealing Dna Sampling and Half-Integration States within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg201 b:60.6 occ:1.00 OD1 N:ASP13 2.1 78.9 1.0 OG N:SER43 2.2 85.1 1.0 CB N:SER43 2.3 86.0 1.0 O N:PHE12 2.6 76.9 1.0 OP1 O:DC15 2.7 65.9 1.0 CG N:ASP13 3.3 81.0 1.0 OE1 M:GLN41 3.4 85.9 1.0 O M:PHE42 3.6 62.9 1.0 C N:PHE12 3.6 74.3 1.0 CA N:SER43 3.7 79.5 1.0 OD2 N:ASP13 4.0 77.9 1.0 P O:DC15 4.2 72.5 1.0 N M:PHE42 4.2 63.4 1.0 N N:SER43 4.2 78.3 1.0 CB M:GLN41 4.3 68.9 1.0 N N:ASP13 4.3 77.1 1.0 CA N:ASP13 4.4 75.8 1.0 O N:SER43 4.4 80.5 1.0 CB M:PHE42 4.4 64.1 1.0 C N:SER43 4.5 77.0 1.0 CB N:ASP13 4.5 80.4 1.0 CD M:GLN41 4.5 78.5 1.0 C M:PHE42 4.5 62.3 1.0 CA M:PHE42 4.6 62.4 1.0 N N:PHE12 4.6 68.0 1.0 CA N:PHE12 4.7 69.8 1.0 C5' O:DC15 4.8 67.0 1.0 CG M:GLN41 4.9 71.5 1.0 CG2 M:VAL44 4.9 78.5 1.0 O5' O:DC15 5.0 68.0 1.0 O3' O:DC14 5.0 80.2 1.0 C M:GLN41 5.0 67.3 1.0

Y.Xiao, S.Ng, K.Hyun Nam, A.Ke. How Type II Crispr-Cas Establish Immunity Through CAS1-CAS2-Mediated Spacer Integration. Nature V. 550 137 2017.
ISSN: ESSN 1476-4687
PubMed: 28869593
DOI: 10.1038/NATURE24020