Zinc in PDB 3ask: Structure of UHRF1 in Complex with Histone Tail

The structure of Structure of UHRF1 in Complex with Histone Tail, PDB code: 3ask was solved by K.Arita, K.Sugita, M.Unoki, R.Hamamoto, N.Sekiyama, H.Tochio, M.Ariyoshi, M.Shirakawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.27 / 2.90
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	145.178, 145.178, 125.413, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 28.6

The binding sites of Zinc atom in the Structure of UHRF1 in Complex with Histone Tail (pdb code 3ask). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Structure of UHRF1 in Complex with Histone Tail, PDB code: 3ask:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Structure of UHRF1 in Complex with Histone Tail


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of UHRF1 in Complex with Histone Tail within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:0.1 occ:1.00 SG A:CYS316 2.3 0.2 1.0 SG A:CYS313 2.3 0.2 1.0 SG A:CYS305 2.3 0.1 1.0 SG A:CYS302 2.3 78.8 1.0 CB A:CYS302 2.8 0.9 1.0 CB A:CYS305 3.0 99.0 1.0 CB A:CYS316 3.1 0.6 1.0 CB A:CYS313 3.4 0.2 1.0 NH2 A:ARG324 3.6 42.9 1.0 N A:CYS316 4.0 0.8 1.0 CA A:CYS305 4.1 72.7 1.0 CA A:CYS316 4.1 0.5 1.0 N A:CYS305 4.2 84.2 1.0 CA A:CYS302 4.4 0.1 1.0 C A:CYS305 4.7 93.7 1.0 CZ A:ARG324 4.8 82.9 1.0 CA A:CYS313 4.8 0.2 1.0 N A:ASP307 4.8 0.6 1.0 C A:CYS316 4.9 92.4 1.0 O A:CYS302 5.0 92.5 1.0

Zinc binding site 2 out of 7 in the Structure of UHRF1 in Complex with Histone Tail


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of UHRF1 in Complex with Histone Tail within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:0.7 occ:1.00 ND1 A:HIS341 2.2 90.6 1.0 SG A:CYS318 2.3 85.2 1.0 SG A:CYS321 2.3 0.7 1.0 SG A:CYS344 2.4 0.9 1.0 CE1 A:HIS341 2.5 89.5 1.0 CB A:CYS318 3.2 0.6 1.0 CG A:HIS341 3.3 75.7 1.0 NE2 A:HIS341 3.7 71.4 1.0 CB A:CYS321 3.7 0.4 1.0 N A:CYS321 3.7 0.6 1.0 CB A:CYS344 3.9 54.0 1.0 CD2 A:HIS341 4.1 41.8 1.0 CB A:HIS341 4.1 0.9 1.0 CB A:LEU320 4.2 0.7 1.0 CA A:CYS321 4.3 99.3 1.0 CE1 A:TYR343 4.4 66.3 1.0 OE1 A:GLN325 4.4 66.5 1.0 CA A:CYS318 4.7 0.1 1.0 C A:LEU320 4.7 0.9 1.0 CD1 A:TYR343 4.8 77.0 1.0 N A:GLY322 4.8 84.7 1.0 CA A:LEU320 4.8 0.8 1.0 N A:LEU320 4.9 99.8 1.0

Zinc binding site 3 out of 7 in the Structure of UHRF1 in Complex with Histone Tail


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of UHRF1 in Complex with Histone Tail within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:0.8 occ:1.00 SG A:CYS363 2.3 75.8 1.0 SG A:CYS360 2.3 64.3 1.0 SG A:CYS336 2.4 86.5 1.0 SG A:CYS333 2.4 84.5 1.0 O A:CYS360 2.9 85.0 1.0 CB A:CYS333 3.1 93.9 1.0 CB A:CYS363 3.3 0.7 1.0 CB A:CYS336 3.3 82.8 1.0 N A:CYS363 3.8 0.8 1.0 C A:CYS360 3.8 0.8 1.0 CB A:CYS360 3.8 97.4 1.0 N A:CYS336 4.0 0.2 1.0 CA A:CYS363 4.2 0.2 1.0 CA A:CYS360 4.2 0.6 1.0 N A:CYS360 4.2 0.0 1.0 CA A:CYS336 4.3 0.3 1.0 CA A:CYS333 4.5 81.9 1.0 C A:GLU362 4.6 0.6 1.0 N A:GLU362 4.6 0.4 1.0 CB A:GLU362 4.8 99.3 1.0 CA A:GLU362 4.8 0.3 1.0 CE2 A:PHE340 4.9 0.3 1.0

Zinc binding site 4 out of 7 in the Structure of UHRF1 in Complex with Histone Tail


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of UHRF1 in Complex with Histone Tail within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:0.7 occ:1.00 SG B:CYS316 2.3 0.9 1.0 SG B:CYS305 2.3 0.8 1.0 SG B:CYS313 2.3 90.1 1.0 SG B:CYS302 2.3 99.1 1.0 CB B:CYS302 2.8 86.5 1.0 CB B:CYS305 2.8 99.4 1.0 CB B:CYS313 3.0 0.5 1.0 CB B:CYS316 3.3 86.5 1.0 N B:CYS305 3.5 0.1 1.0 CA B:CYS305 3.7 0.6 1.0 CA B:CYS302 4.3 90.6 1.0 C B:CYS305 4.4 0.6 1.0 N B:CYS316 4.4 0.2 1.0 CA B:CYS316 4.5 0.7 1.0 CA B:CYS313 4.5 0.8 1.0 N B:LYS306 4.5 99.8 1.0 C B:HIS304 4.6 0.4 1.0 C B:CYS302 4.8 0.5 1.0 CB B:HIS304 4.9 99.1 1.0 N B:ASP307 4.9 0.9 1.0 O B:CYS302 5.0 98.5 1.0 N B:HIS304 5.0 0.7 1.0

Zinc binding site 5 out of 7 in the Structure of UHRF1 in Complex with Histone Tail


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of UHRF1 in Complex with Histone Tail within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn505 b:1.0 occ:1.00 ND1 B:HIS341 2.2 0.3 1.0 SG B:CYS318 2.3 0.5 1.0 SG B:CYS321 2.4 0.1 1.0 SG B:CYS344 2.4 0.5 1.0 CG B:HIS341 3.0 1.0 1.0 CB B:HIS341 3.1 0.8 1.0 CB B:CYS318 3.1 0.1 1.0 CE1 B:HIS341 3.3 0.9 1.0 CB B:CYS321 3.7 0.3 1.0 CB B:CYS344 3.9 0.4 1.0 N B:HIS341 4.0 0.4 1.0 N B:CYS321 4.1 0.9 1.0 CA B:HIS341 4.2 0.4 1.0 CD2 B:HIS341 4.2 0.1 1.0 NE2 B:HIS341 4.3 0.4 1.0 CA B:CYS321 4.5 0.3 1.0 CA B:CYS318 4.6 0.6 1.0 CB B:LEU320 4.8 0.4 1.0 CE1 B:TYR343 4.9 0.1 1.0 C B:LEU320 4.9 0.3 1.0 N B:GLY322 4.9 0.8 1.0

Zinc binding site 6 out of 7 in the Structure of UHRF1 in Complex with Histone Tail


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of UHRF1 in Complex with Histone Tail within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn506 b:0.5 occ:1.00 SG B:CYS333 2.3 0.9 1.0 SG B:CYS360 2.3 0.2 1.0 SG B:CYS336 2.3 0.5 1.0 SG B:CYS363 2.3 0.6 1.0 CB B:CYS333 3.3 0.8 1.0 CB B:CYS336 3.5 1.0 1.0 N B:CYS336 3.8 0.4 1.0 CB B:CYS360 3.9 0.6 1.0 CB B:CYS363 3.9 0.3 1.0 N B:CYS360 4.0 0.9 1.0 CA B:CYS336 4.2 0.4 1.0 CB B:GLU335 4.4 0.3 1.0 CA B:CYS360 4.5 0.1 1.0 N B:CYS363 4.5 0.9 1.0 CA B:CYS333 4.7 0.9 1.0 CE2 B:PHE340 4.8 0.6 1.0 CB B:GLU362 4.8 0.8 1.0 CZ B:PHE340 4.8 1.0 1.0 C B:GLU335 4.9 0.1 1.0 CA B:CYS363 4.9 0.1 1.0 C B:CYS360 4.9 0.5 1.0 O B:CYS360 5.0 1.0 1.0

Zinc binding site 7 out of 7 in the Structure of UHRF1 in Complex with Histone Tail


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of UHRF1 in Complex with Histone Tail within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:0.9 occ:1.00 CB C:CYS302 2.9 0.8 1.0 SG C:CYS302 3.4 0.5 1.0 CA C:CYS302 4.4 0.1 1.0 O C:SER301 4.5 73.7 1.0 N C:CYS302 4.8 0.4 1.0 C C:SER301 4.9 0.5 1.0

K.Arita, S.Isogai, T.Oda, M.Unoki, K.Sugita, N.Sekiyama, K.Kuwata, R.Hamamoto, H.Tochio, M.Sato, M.Ariyoshi, M.Shirakawa. Recognition of Modification Status on A Histone H3 Tail By Linked Histone Reader Modules of the Epigenetic Regulator UHRF1 Proc.Natl.Acad.Sci.Usa V. 109 12950 2012.
ISSN: ISSN 0027-8424
PubMed: 22837395
DOI: 10.1073/PNAS.1203701109