Magnesium in PDB 5v3j: MOUSEZFP568-ZNF1-10 in Complex with Dna

The structure of MOUSEZFP568-ZNF1-10 in Complex with Dna, PDB code: 5v3j was solved by A.Patel, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.50 / 2.06
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	55.787, 65.706, 73.022, 100.52, 104.25, 97.25
R / Rfree (%)	19.2 / 23.7

The structure of MOUSEZFP568-ZNF1-10 in Complex with Dna also contains other interesting chemical elements:

Zinc

(Zn)

20 atoms

The binding sites of Magnesium atom in the MOUSEZFP568-ZNF1-10 in Complex with Dna (pdb code 5v3j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the MOUSEZFP568-ZNF1-10 in Complex with Dna, PDB code: 5v3j:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the MOUSEZFP568-ZNF1-10 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of MOUSEZFP568-ZNF1-10 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1012 b:60.2 occ:1.00 O E:CYS480 2.0 59.7 1.0 O E:HOH1109 2.2 84.3 1.0 O2 E:TRS1011 2.2 92.9 1.0 O E:CYS477 2.4 48.3 1.0 C1 E:TRS1011 2.8 1.0 1.0 C2 E:TRS1011 2.9 96.2 1.0 C E:CYS480 3.2 59.9 1.0 C E:TRS1011 3.4 0.1 1.0 C E:CYS477 3.5 48.5 1.0 CA E:ASP481 3.9 58.0 1.0 N E:CYS477 4.0 49.8 1.0 O1 E:TRS1011 4.0 1.0 1.0 N E:ASP481 4.0 55.5 1.0 C3 E:TRS1011 4.1 98.0 1.0 N E:CYS480 4.1 56.4 1.0 CA E:CYS477 4.2 47.9 1.0 O E:LYS482 4.3 50.0 1.0 CA E:CYS480 4.3 51.1 1.0 CB E:CYS477 4.4 49.6 1.0 OD1 E:ASP481 4.4 83.0 1.0 CB E:GLU476 4.5 59.0 1.0 C E:ASP481 4.5 47.9 1.0 C E:LYS478 4.6 45.7 1.0 C E:GLU476 4.6 47.3 1.0 N E:LYS478 4.6 45.9 1.0 O E:LYS478 4.6 55.5 1.0 N E:TRS1011 4.6 0.4 1.0 OE2 E:GLU476 4.7 68.5 1.0 CA E:LYS478 4.8 45.7 1.0 N E:LYS482 4.9 43.6 1.0 N E:ASP479 4.9 45.8 1.0 CA E:GLU476 5.0 54.8 1.0

Magnesium binding site 2 out of 2 in the MOUSEZFP568-ZNF1-10 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of MOUSEZFP568-ZNF1-10 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1012 b:56.0 occ:1.00 O F:CYS477 2.1 41.9 1.0 C3 F:TRS1011 2.2 69.5 1.0 O F:CYS480 2.3 37.4 1.0 C F:TRS1011 2.3 85.8 1.0 N F:TRS1011 2.3 75.7 1.0 O F:HOH1141 2.3 73.5 1.0 C2 F:TRS1011 2.4 86.8 1.0 O2 F:TRS1011 3.1 82.0 1.0 C F:CYS477 3.3 40.3 1.0 O3 F:TRS1011 3.4 80.0 1.0 C F:CYS480 3.5 45.6 1.0 N F:CYS477 3.8 35.3 1.0 C1 F:TRS1011 3.9 84.2 1.0 CA F:ASP481 3.9 39.9 1.0 CA F:CYS477 4.0 40.2 1.0 N F:ASP481 4.2 41.2 1.0 O F:LYS482 4.2 37.3 1.0 C F:ASP481 4.3 35.3 1.0 CB F:GLU476 4.3 40.4 1.0 N F:LYS478 4.4 40.7 1.0 CB F:CYS477 4.4 44.3 1.0 N F:CYS480 4.4 45.5 1.0 C F:GLU476 4.4 41.9 1.0 C F:LYS478 4.5 42.8 1.0 CA F:LYS478 4.5 37.6 1.0 O F:LYS478 4.6 40.5 1.0 O1 F:TRS1011 4.6 84.2 1.0 CA F:CYS480 4.6 39.8 1.0 OE1 F:GLU476 4.6 72.8 1.0 O F:HOH1187 4.7 50.5 1.0 N F:LYS482 4.7 30.9 1.0 O F:ASP481 4.7 41.3 1.0 OD2 F:ASP481 4.7 49.6 1.0 CA F:GLU476 4.8 36.2 1.0 N F:ASP479 4.8 41.8 1.0

A.Patel, P.Yang, M.Tinkham, M.Pradhan, M.A.Sun, Y.Wang, D.Hoang, G.Wolf, J.R.Horton, X.Zhang, T.Macfarlan, X.Cheng. Dna Conformation Induces Adaptable Binding By Tandem Zinc Finger Proteins. Cell V. 173 221 2018.
ISSN: ISSN 1097-4172
PubMed: 29551271
DOI: 10.1016/J.CELL.2018.02.058