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

Protein crystallography data

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

Other elements in 5v3j:

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

Zinc (Zn) 20 atoms

Magnesium Binding Sites:

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 5v3j

Go back to Magnesium Binding Sites List in 5v3j
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 5v3j

Go back to Magnesium Binding Sites List in 5v3j
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

Reference:

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
Page generated: Mon Dec 14 21:17:41 2020

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