Zinc in PDB 5w9q: Zinc Finger Region of MBD1 in Complex with Cpg Dna

The structure of Zinc Finger Region of MBD1 in Complex with Cpg Dna, PDB code: 5w9q was solved by K.Liu, C.Xu, W.Tempel, J.R.Walker, C.H.Arrowsmith, C.Bountra, A.M.Edwards, J.Min, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.69 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	139.339, 27.800, 64.914, 90.00, 106.52, 90.00
R / Rfree (%)	22.6 / 25.3

The binding sites of Zinc atom in the Zinc Finger Region of MBD1 in Complex with Cpg Dna (pdb code 5w9q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Zinc Finger Region of MBD1 in Complex with Cpg Dna, PDB code: 5w9q:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Zinc Finger Region of MBD1 in Complex with Cpg Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zinc Finger Region of MBD1 in Complex with Cpg Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:34.6 occ:1.00 SG A:CYS353 2.3 34.2 1.0 SG A:CYS372 2.3 33.5 1.0 SG A:CYS350 2.3 41.8 1.0 SG A:CYS356 2.3 33.6 1.0 CB A:CYS356 3.2 34.6 1.0 CB A:CYS350 3.3 46.7 1.0 CB A:CYS372 3.3 31.8 1.0 CB A:CYS353 3.3 37.0 1.0 CA A:CYS372 3.6 29.1 1.0 N A:CYS350 3.6 45.0 1.0 N A:GLY351 3.7 47.2 1.0 N A:CYS353 3.8 42.4 1.0 CA A:CYS350 3.9 48.6 1.0 N A:ARG373 4.0 29.4 1.0 C A:CYS350 4.2 50.3 1.0 CA A:CYS353 4.2 39.5 1.0 C A:CYS372 4.2 29.4 1.0 N A:CYS356 4.2 30.9 1.0 CA A:CYS356 4.3 32.6 1.0 N A:ARG352 4.4 48.3 1.0 CD1 A:TRP374 4.4 42.1 1.0 CA A:GLY351 4.7 48.8 1.0 C A:ASP349 4.7 47.0 1.0 N A:TRP374 4.8 34.9 1.0 C A:CYS353 4.9 37.5 1.0 N A:CYS372 4.9 28.8 1.0 C A:ARG352 5.0 46.5 1.0 O A:CYS353 5.0 38.1 1.0

Zinc binding site 2 out of 4 in the Zinc Finger Region of MBD1 in Complex with Cpg Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zinc Finger Region of MBD1 in Complex with Cpg Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:54.6 occ:1.00 SG A:CYS338 2.3 64.9 1.0 SG A:CYS377 2.3 49.3 1.0 SG A:CYS341 2.3 54.2 1.0 SG A:CYS344 2.4 51.9 1.0 CB A:CYS338 3.3 64.8 1.0 N A:CYS338 3.4 58.0 1.0 CB A:CYS377 3.4 43.6 1.0 CB A:CYS341 3.4 62.6 1.0 CB A:CYS344 3.4 56.6 1.0 N A:GLY339 3.7 63.4 1.0 CA A:CYS377 3.8 42.3 1.0 CA A:CYS338 3.8 63.5 1.0 N A:CYS341 4.0 69.3 1.0 N A:LEU378 4.0 48.0 1.0 C A:CYS338 4.2 66.6 1.0 N A:CYS344 4.3 53.7 1.0 CA A:CYS341 4.3 67.5 1.0 C A:CYS377 4.3 44.1 1.0 N A:ALA340 4.4 72.2 1.0 CA A:CYS344 4.4 54.3 1.0 C A:LYS337 4.5 57.5 1.0 N A:GLN379 4.7 55.3 1.0 CA A:GLY339 4.7 66.6 1.0 CA A:LYS337 4.8 53.4 1.0 C A:CYS341 4.9 65.4 1.0 O A:CYS341 4.9 64.5 1.0 C A:GLY339 5.0 71.7 1.0 C A:ALA340 5.0 76.4 1.0

Zinc binding site 3 out of 4 in the Zinc Finger Region of MBD1 in Complex with Cpg Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zinc Finger Region of MBD1 in Complex with Cpg Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:39.6 occ:1.00 SG B:CYS372 2.3 39.2 1.0 SG B:CYS353 2.3 39.2 1.0 SG B:CYS350 2.3 44.8 1.0 SG B:CYS356 2.4 37.8 1.0 CB B:CYS356 3.3 38.5 1.0 CB B:CYS350 3.3 49.3 1.0 CB B:CYS372 3.3 36.0 1.0 CB B:CYS353 3.4 42.5 1.0 N B:CYS350 3.6 48.0 1.0 CA B:CYS372 3.6 32.9 1.0 N B:GLY351 3.8 49.0 1.0 N B:CYS353 3.8 47.0 1.0 CA B:CYS350 3.8 51.1 1.0 N B:ARG373 3.9 33.5 1.0 CA B:CYS353 4.1 44.3 1.0 C B:CYS350 4.2 52.2 1.0 C B:CYS372 4.2 33.3 1.0 N B:CYS356 4.2 34.1 1.0 CA B:CYS356 4.3 36.4 1.0 N B:ARG352 4.4 51.6 1.0 CD1 B:TRP374 4.5 45.6 1.0 N B:TRP374 4.6 40.2 1.0 C B:ASP349 4.7 50.0 1.0 C B:CYS353 4.8 42.6 1.0 O B:CYS353 4.8 44.0 1.0 CA B:GLY351 4.8 50.8 1.0 N B:CYS372 4.9 31.4 1.0 CA B:ARG373 4.9 34.7 1.0 C B:ARG352 4.9 50.9 1.0 CB B:ARG373 5.0 35.4 1.0

Zinc binding site 4 out of 4 in the Zinc Finger Region of MBD1 in Complex with Cpg Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zinc Finger Region of MBD1 in Complex with Cpg Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:78.7 occ:1.00 SG B:CYS341 2.3 76.7 1.0 SG B:CYS377 2.3 73.6 1.0 SG B:CYS338 2.3 93.5 1.0 SG B:CYS344 2.4 74.8 1.0 CB B:CYS377 3.3 63.8 1.0 CB B:CYS341 3.3 87.2 1.0 CB B:CYS338 3.3 95.1 1.0 N B:CYS338 3.4 86.7 1.0 CB B:CYS344 3.5 78.6 1.0 CA B:CYS377 3.7 60.6 1.0 N B:GLY339 3.8 96.5 1.0 CA B:CYS338 3.8 95.1 1.0 N B:LEU378 3.9 68.8 1.0 N B:CYS341 4.1 98.7 1.0 C B:CYS377 4.1 62.6 1.0 C B:CYS338 4.3 0.7 1.0 CA B:CYS341 4.3 94.3 1.0 N B:GLN379 4.3 79.2 1.0 N B:CYS344 4.3 71.3 1.0 CA B:CYS344 4.5 73.2 1.0 C B:LYS337 4.5 85.6 1.0 CB B:GLN379 4.7 91.3 1.0 CA B:LYS337 4.7 78.0 1.0 CA B:GLY339 4.9 0.8 1.0 CA B:LEU378 4.9 72.5 1.0 C B:CYS341 4.9 90.9 1.0 N B:CYS377 5.0 53.4 1.0

C.Xu, K.Liu, M.Lei, A.Yang, Y.Li, T.R.Hughes, J.Min. Dna Sequence Recognition of Human Cxxc Domains and Their Structural Determinants. Structure V. 26 85 2018.
ISSN: ISSN 1878-4186
PubMed: 29276034
DOI: 10.1016/J.STR.2017.11.022