Zinc in PDB 8wms: Crystal Structure of Human DPPA3 in Complex with Human UHRF1 Phd Domain

All present enzymatic activity of Crystal Structure of Human DPPA3 in Complex with Human UHRF1 Phd Domain:
2.3.2.27;

The structure of Crystal Structure of Human DPPA3 in Complex with Human UHRF1 Phd Domain, PDB code: 8wms was solved by N.Shiraishi, K.Arita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.33 / 2.40
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	77.802, 77.802, 140.674, 90, 90, 90
R / Rfree (%)	23.3 / 26.6

The binding sites of Zinc atom in the Crystal Structure of Human DPPA3 in Complex with Human UHRF1 Phd Domain (pdb code 8wms). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human DPPA3 in Complex with Human UHRF1 Phd Domain, PDB code: 8wms:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Human DPPA3 in Complex with Human UHRF1 Phd Domain


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 Human DPPA3 in Complex with Human UHRF1 Phd Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:77.7 occ:1.00 SG A:CYS302 2.3 81.0 1.0 SG A:CYS313 2.3 63.8 1.0 SG A:CYS305 2.3 82.9 1.0 SG A:CYS316 2.3 72.7 1.0 CB A:CYS302 3.1 70.2 1.0 CB A:CYS305 3.2 69.1 1.0 CB A:CYS313 3.2 85.4 1.0 CB A:CYS316 3.6 65.2 1.0 N A:CYS305 3.8 80.0 1.0 N A:CYS316 3.9 75.0 1.0 CA A:CYS305 4.1 92.4 1.0 CA A:CYS316 4.3 71.4 1.0 CA A:CYS302 4.5 92.6 1.0 CB A:VAL315 4.6 75.3 1.0 CA A:CYS313 4.6 74.5 1.0 C A:CYS305 4.8 96.4 1.0 O A:CYS302 4.8 83.1 1.0 C A:HIS304 4.8 84.4 1.0 NH2 A:ARG324 4.8 74.2 1.0 CB A:HIS304 4.9 78.4 1.0 C A:CYS302 4.9 91.0 1.0 C A:VAL315 4.9 75.5 1.0 NH1 A:ARG324 5.0 59.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Human DPPA3 in Complex with Human UHRF1 Phd Domain


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 Human DPPA3 in Complex with Human UHRF1 Phd Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:66.4 occ:1.00 ND1 A:HIS341 2.1 63.9 1.0 SG A:CYS321 2.3 65.8 1.0 SG A:CYS344 2.3 66.2 1.0 SG A:CYS318 2.3 62.5 1.0 CG A:HIS341 3.0 62.3 1.0 CB A:CYS318 3.0 58.0 1.0 CE1 A:HIS341 3.2 68.5 1.0 CB A:HIS341 3.2 56.2 1.0 CB A:CYS321 3.4 57.8 1.0 CB A:CYS344 3.4 74.6 1.0 N A:CYS321 3.9 65.7 1.0 CD2 A:HIS341 4.2 63.5 1.0 N A:HIS341 4.2 69.4 1.0 NE2 A:HIS341 4.2 60.0 1.0 CA A:CYS321 4.2 50.8 1.0 CA A:HIS341 4.3 67.2 1.0 CA A:CYS318 4.5 58.8 1.0 CB A:LEU320 4.7 65.2 1.0 N A:GLY322 4.7 62.3 1.0 CA A:CYS344 4.8 79.5 1.0 C A:CYS321 4.8 62.5 1.0 N A:GLY323 4.9 63.1 1.0 C A:LEU320 4.9 69.2 1.0 CE1 A:TYR343 5.0 56.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Human DPPA3 in Complex with Human UHRF1 Phd Domain


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 Human DPPA3 in Complex with Human UHRF1 Phd Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:68.8 occ:1.00 SG A:CYS363 2.3 67.3 1.0 SG A:CYS360 2.3 73.3 1.0 SG A:CYS333 2.3 76.2 1.0 SG A:CYS336 2.3 71.7 1.0 CB A:CYS333 3.2 74.1 1.0 CB A:CYS336 3.3 68.1 1.0 CB A:CYS363 3.5 69.9 1.0 CB A:CYS360 3.5 63.0 1.0 N A:CYS336 3.7 77.0 1.0 N A:CYS360 4.0 76.0 1.0 CA A:CYS336 4.1 82.6 1.0 N A:CYS363 4.2 85.1 1.0 CA A:CYS360 4.3 76.8 1.0 CA A:CYS363 4.5 81.8 1.0 CB A:GLU335 4.5 88.0 1.0 CA A:CYS333 4.6 72.8 1.0 C A:GLU335 4.8 71.2 1.0 C A:CYS336 4.8 73.5 1.0 CE1 A:PHE340 4.9 63.6 1.0 C A:CYS360 4.9 76.0 1.0 O A:CYS360 4.9 82.8 1.0 CB A:GLU362 4.9 69.9 1.0 CG A:GLU335 5.0 92.1 1.0 C A:GLU362 5.0 92.3 1.0 N A:ASP337 5.0 75.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Human DPPA3 in Complex with Human UHRF1 Phd Domain


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 Human DPPA3 in Complex with Human UHRF1 Phd Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:57.6 occ:0.48 OE2 A:GLU362 1.9 63.9 1.0 OE1 A:GLU362 2.3 64.4 1.0 NE2 A:HIS319 2.3 77.9 1.0 CD A:GLU362 2.3 68.7 1.0 CD2 A:HIS319 2.9 57.7 1.0 CE1 A:HIS319 3.5 65.7 1.0 CG A:GLU362 3.7 70.1 1.0 CG A:HIS319 4.2 76.6 1.0 ND1 A:HIS319 4.4 66.7 1.0 CB A:GLU362 4.7 69.9 1.0

N.Shiraishi, K.Arita. Crystal Structure of Human DPPA3 in Complex with Human UHRF1 Phd Domain To Be Published.