Zinc in PDB 4gy5: Crystal Structure of the Tandem Tudor Domain and Plant Homeodomain of UHRF1 with Histone H3K9ME3

The structure of Crystal Structure of the Tandem Tudor Domain and Plant Homeodomain of UHRF1 with Histone H3K9ME3, PDB code: 4gy5 was solved by J.Cheng, Y.Yang, J.Fang, J.Xiao, T.Zhu, F.Chen, P.Wang, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.38 / 2.96
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	145.940, 145.940, 125.903, 90.00, 90.00, 90.00
R / Rfree (%)	25.5 / 28.8

The binding sites of Zinc atom in the Crystal Structure of the Tandem Tudor Domain and Plant Homeodomain of UHRF1 with Histone H3K9ME3 (pdb code 4gy5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of the Tandem Tudor Domain and Plant Homeodomain of UHRF1 with Histone H3K9ME3, PDB code: 4gy5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Crystal Structure of the Tandem Tudor Domain and Plant Homeodomain of UHRF1 with Histone H3K9ME3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Tandem Tudor Domain and Plant Homeodomain of UHRF1 with Histone H3K9ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:0.3 occ:1.00 SG A:CYS316 2.5 0.9 1.0 SG A:CYS302 2.5 0.6 1.0 SG A:CYS313 2.6 0.4 1.0 SG A:CYS305 2.6 0.5 1.0 CB A:CYS305 2.9 0.1 1.0 CB A:CYS302 3.2 91.5 1.0 CB A:CYS316 3.2 0.2 1.0 CB A:CYS313 3.2 0.9 1.0 N A:CYS305 3.6 0.4 1.0 CA A:CYS305 3.8 0.6 1.0 N A:CYS316 4.0 0.3 1.0 CA A:CYS316 4.2 0.3 1.0 NH2 A:ARG324 4.3 0.9 1.0 C A:HIS304 4.3 0.3 1.0 C A:CYS305 4.6 0.3 1.0 CA A:CYS302 4.6 0.9 1.0 CB A:HIS304 4.7 0.2 1.0 N A:LYS306 4.7 0.8 1.0 CA A:CYS313 4.7 0.9 1.0 N A:HIS304 4.8 0.0 1.0 CA A:HIS304 4.8 0.7 1.0 C A:CYS302 4.8 0.0 1.0 O A:CYS302 4.9 0.8 1.0 NH1 A:ARG324 4.9 0.7 1.0 N A:ASP307 4.9 0.2 1.0 CZ A:ARG324 5.0 0.5 1.0

Zinc binding site 2 out of 7 in the Crystal Structure of the Tandem Tudor Domain and Plant Homeodomain of UHRF1 with Histone H3K9ME3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Tandem Tudor Domain and Plant Homeodomain of UHRF1 with Histone H3K9ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:0.1 occ:1.00 SG A:CYS321 2.6 0.6 1.0 SG A:CYS318 2.6 0.1 1.0 SG A:CYS344 2.7 0.5 1.0 ND1 A:HIS341 2.7 76.3 1.0 CB A:CYS318 3.3 96.0 1.0 CG A:HIS341 3.5 0.4 1.0 CB A:HIS341 3.5 0.4 1.0 CB A:CYS321 3.6 0.5 1.0 CE1 A:HIS341 3.7 97.3 1.0 CB A:CYS344 3.9 1.0 1.0 N A:CYS321 3.9 0.7 1.0 CA A:CYS321 4.3 1.0 1.0 N A:GLY322 4.6 0.9 1.0 N A:HIS341 4.6 0.8 1.0 CB A:LEU320 4.6 0.3 1.0 CA A:HIS341 4.7 0.2 1.0 CD2 A:HIS341 4.7 0.5 1.0 CE1 A:TYR343 4.8 0.3 1.0 N A:GLY323 4.8 0.7 1.0 NE2 A:HIS341 4.8 0.9 1.0 CA A:CYS318 4.8 96.3 1.0

Zinc binding site 3 out of 7 in the Crystal Structure of the Tandem Tudor Domain and Plant Homeodomain of UHRF1 with Histone H3K9ME3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Tandem Tudor Domain and Plant Homeodomain of UHRF1 with Histone H3K9ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:0.4 occ:1.00 SG A:CYS363 2.5 0.9 1.0 SG A:CYS360 2.5 1.0 1.0 SG A:CYS336 2.5 0.1 1.0 SG A:CYS333 2.7 0.6 1.0 CB A:CYS333 3.3 90.4 1.0 CB A:CYS360 3.6 0.1 1.0 CB A:CYS336 3.6 0.7 1.0 N A:CYS336 3.7 0.2 1.0 CB A:CYS363 3.7 0.5 1.0 CB A:GLU335 4.0 0.3 1.0 N A:CYS360 4.2 0.3 1.0 CA A:CYS336 4.2 1.0 1.0 N A:CYS363 4.4 0.6 1.0 CA A:CYS360 4.4 0.4 1.0 CE2 A:PHE340 4.5 0.1 1.0 CG A:GLU335 4.5 0.2 1.0 CZ A:PHE340 4.6 0.9 1.0 C A:GLU335 4.7 0.4 1.0 CA A:CYS363 4.7 0.1 1.0 CA A:GLU335 4.7 0.2 1.0 CA A:CYS333 4.8 86.5 1.0 N A:GLU335 4.9 0.7 1.0 CB A:GLU362 4.9 0.6 1.0 C A:CYS360 4.9 0.5 1.0 C A:CYS336 4.9 0.3 1.0 O A:CYS360 5.0 0.5 1.0

Zinc binding site 4 out of 7 in the Crystal Structure of the Tandem Tudor Domain and Plant Homeodomain of UHRF1 with Histone H3K9ME3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Tandem Tudor Domain and Plant Homeodomain of UHRF1 with Histone H3K9ME3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:0.3 occ:1.00 SG B:CYS363 2.4 1.0 1.0 SG B:CYS336 2.6 0.9 1.0 SG B:CYS360 2.6 0.0 1.0 SG B:CYS333 2.7 0.4 1.0 CB B:CYS333 3.3 0.4 1.0 CB B:CYS360 3.6 0.1 1.0 CB B:CYS336 3.6 0.9 1.0 N B:CYS336 3.7 0.2 1.0 CB B:CYS363 3.7 0.3 1.0 CB B:GLU335 4.0 0.0 1.0 N B:CYS360 4.2 0.1 1.0 CA B:CYS336 4.2 0.3 1.0 N B:CYS363 4.4 0.5 1.0 CA B:CYS360 4.4 0.7 1.0 CE2 B:PHE340 4.5 0.8 1.0 CG B:GLU335 4.5 0.4 1.0 CZ B:PHE340 4.6 0.5 1.0 C B:GLU335 4.6 0.5 1.0 CA B:CYS363 4.7 0.6 1.0 CA B:GLU335 4.7 0.5 1.0 CA B:CYS333 4.8 0.6 1.0 N B:GLU335 4.9 0.8 1.0 CB B:GLU362 4.9 0.6 1.0 C B:CYS360 4.9 0.3 1.0 C B:CYS336 4.9 0.3 1.0 O B:CYS360 5.0 0.5 1.0

Zinc binding site 5 out of 7 in the Crystal Structure of the Tandem Tudor Domain and Plant Homeodomain of UHRF1 with Histone H3K9ME3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Tandem Tudor Domain and Plant Homeodomain of UHRF1 with Histone H3K9ME3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:0.1 occ:1.00 SG B:CYS316 2.6 0.9 1.0 SG B:CYS305 2.6 0.9 1.0 SG B:CYS313 2.7 0.7 1.0 SG B:CYS302 2.7 0.3 1.0 CB B:CYS305 3.0 0.8 1.0 CB B:CYS302 3.1 0.6 1.0 CB B:CYS316 3.3 0.8 1.0 CB B:CYS313 3.4 0.6 1.0 N B:CYS305 3.4 0.2 1.0 CA B:CYS305 3.7 0.9 1.0 N B:CYS316 4.1 0.2 1.0 C B:HIS304 4.2 0.9 1.0 CA B:CYS316 4.3 0.4 1.0 CA B:CYS302 4.4 0.2 1.0 CB B:HIS304 4.5 0.3 1.0 C B:CYS305 4.5 1.0 1.0 N B:HIS304 4.5 0.7 1.0 CA B:HIS304 4.6 0.2 1.0 N B:LYS306 4.6 1.0 1.0 C B:CYS302 4.6 0.8 1.0 O B:CYS302 4.7 0.3 1.0 CA B:CYS313 4.9 0.5 1.0 N B:ASP307 4.9 0.5 1.0 O B:HIS304 5.0 0.1 1.0 CB B:VAL315 5.0 0.5 1.0

Zinc binding site 6 out of 7 in the Crystal Structure of the Tandem Tudor Domain and Plant Homeodomain of UHRF1 with Histone H3K9ME3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Tandem Tudor Domain and Plant Homeodomain of UHRF1 with Histone H3K9ME3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:0.2 occ:1.00 ND1 B:HIS341 2.4 0.3 1.0 SG B:CYS321 2.6 0.6 1.0 SG B:CYS318 2.6 0.9 1.0 SG B:CYS344 2.7 0.5 1.0 CG B:HIS341 3.2 0.5 1.0 CB B:CYS318 3.3 0.4 1.0 CB B:HIS341 3.3 0.4 1.0 CE1 B:HIS341 3.5 0.5 1.0 CB B:CYS321 3.8 0.8 1.0 CB B:CYS344 4.0 0.6 1.0 N B:CYS321 4.2 0.9 1.0 CD2 B:HIS341 4.4 0.7 1.0 N B:HIS341 4.5 0.5 1.0 CA B:HIS341 4.5 0.1 1.0 NE2 B:HIS341 4.5 0.8 1.0 CA B:CYS321 4.6 0.9 1.0 CE1 B:TYR343 4.6 0.7 1.0 N B:GLY322 4.7 0.8 1.0 N B:GLY323 4.8 0.5 1.0 CA B:CYS318 4.8 0.0 1.0 CB B:LEU320 4.8 0.3 1.0

Zinc binding site 7 out of 7 in the Crystal Structure of the Tandem Tudor Domain and Plant Homeodomain of UHRF1 with Histone H3K9ME3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Tandem Tudor Domain and Plant Homeodomain of UHRF1 with Histone H3K9ME3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:0.0 occ:1.00 SG C:CYS302 2.9 90.3 1.0 CB C:CYS302 3.3 0.4 1.0 CA C:CYS302 4.7 0.8 1.0

J.Cheng, Y.Yang, J.Fang, J.Xiao, T.Zhu, F.Chen, P.Wang, Z.Li, H.Yang, Y.Xu. Structural Insight Into Coordinated Recognition of Trimethylated Histone H3 Lysine 9 (H3K9ME3) By the Plant Homeodomain (Phd) and Tandem Tudor Domain (Ttd) of UHRF1 (Ubiquitin-Like, Containing Phd and Ring Finger Domains, 1) Protein J.Biol.Chem. V. 288 1329 2013.
ISSN: ISSN 0021-9258
PubMed: 23161542
DOI: 10.1074/JBC.M112.415398