Zinc in PDB 2y1h: Crystal Structure of the Human Tatd-Domain Protein 3 (TATDN3)

The structure of Crystal Structure of the Human Tatd-Domain Protein 3 (TATDN3), PDB code: 2y1h was solved by J.R.C.Muniz, S.Puranik, T.Krojer, W.W.Yue, E.Ugochukwu, P.Filippakopoulos, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, J.Weigelt, C.Bountra, K.L.Kavanagh, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.89 / 2.50
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	44.910, 44.910, 233.112, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 21.8

The structure of Crystal Structure of the Human Tatd-Domain Protein 3 (TATDN3) also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Human Tatd-Domain Protein 3 (TATDN3) (pdb code 2y1h). 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 the Human Tatd-Domain Protein 3 (TATDN3), PDB code: 2y1h:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Human Tatd-Domain Protein 3 (TATDN3)


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 Human Tatd-Domain Protein 3 (TATDN3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1273 b:55.0 occ:1.00 NE2 A:HIS170 2.0 43.9 1.0 ND1 A:HIS147 2.0 55.2 1.0 OE2 A:GLU107 2.1 43.4 1.0 O3 A:PO41275 2.4 74.3 1.0 O2 A:PO41275 2.8 65.2 1.0 CE1 A:HIS170 2.8 43.5 1.0 CE1 A:HIS147 2.8 55.9 1.0 P A:PO41275 3.1 66.9 1.0 CD2 A:HIS170 3.2 44.4 1.0 CG A:HIS147 3.2 54.3 1.0 CD A:GLU107 3.3 58.8 1.0 ZN A:ZN1274 3.7 52.2 1.0 CB A:HIS147 3.7 49.7 1.0 O1 A:PO41275 3.8 74.3 1.0 OE1 A:GLU107 3.8 55.5 1.0 NE2 A:HIS70 3.8 55.5 1.0 ND1 A:HIS170 4.0 44.7 1.0 NE2 A:HIS147 4.0 58.0 1.0 CG A:HIS170 4.2 44.0 1.0 CD2 A:HIS147 4.2 57.5 1.0 CA A:HIS147 4.3 48.2 1.0 CG A:GLU107 4.5 56.2 1.0 O4 A:PO41275 4.5 72.9 1.0 NE2 A:HIS12 4.5 46.6 1.0 OD2 A:ASP218 4.7 62.1 1.0 CE1 A:HIS70 4.7 56.8 1.0 CD2 A:HIS70 4.7 56.1 1.0 CE1 A:HIS12 4.8 47.0 1.0 OD1 A:ASP218 4.9 58.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Human Tatd-Domain Protein 3 (TATDN3)


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 Human Tatd-Domain Protein 3 (TATDN3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1274 b:52.2 occ:1.00 O2 A:PO41275 1.8 65.2 1.0 NE2 A:HIS12 2.0 46.6 1.0 OE1 A:GLU107 2.1 55.5 1.0 NE2 A:HIS14 2.1 56.8 1.0 OD1 A:ASP218 2.4 58.6 1.0 CD A:GLU107 2.9 58.8 1.0 CD2 A:HIS12 3.0 46.1 1.0 CE1 A:HIS12 3.0 47.0 1.0 CE1 A:HIS14 3.0 57.5 1.0 OE2 A:GLU107 3.2 43.4 1.0 CD2 A:HIS14 3.2 56.2 1.0 P A:PO41275 3.2 66.9 1.0 CG A:ASP218 3.4 57.5 1.0 CE1 A:HIS170 3.6 43.5 1.0 ZN A:ZN1273 3.7 55.0 1.0 NE2 A:HIS170 3.7 43.9 1.0 OD2 A:ASP218 3.8 62.1 1.0 O4 A:PO41275 3.8 72.9 1.0 O3 A:PO41275 4.1 74.3 1.0 CG A:HIS12 4.1 45.8 1.0 ND1 A:HIS12 4.1 47.7 1.0 CG2 A:VAL42 4.2 51.6 1.0 ND1 A:HIS14 4.2 58.7 1.0 O1 A:PO41275 4.2 74.3 1.0 ND1 A:HIS170 4.3 44.7 1.0 CG A:GLU107 4.3 56.2 1.0 CG A:HIS14 4.3 55.5 1.0 CD2 A:HIS170 4.4 44.4 1.0 CB A:ASP218 4.7 49.5 1.0 CG A:HIS170 4.7 44.0 1.0 CB A:GLU107 4.8 57.7 1.0 OE2 A:GLU44 4.9 90.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Human Tatd-Domain Protein 3 (TATDN3)


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 Human Tatd-Domain Protein 3 (TATDN3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1273 b:55.3 occ:1.00 O3 B:PO41275 1.9 66.0 1.0 NE2 B:HIS12 2.0 45.6 1.0 OE1 B:GLU107 2.1 61.1 1.0 NE2 B:HIS14 2.1 52.0 1.0 OD1 B:ASP218 2.4 63.8 1.0 CD B:GLU107 2.9 69.2 1.0 CD2 B:HIS12 3.0 45.8 1.0 CE1 B:HIS14 3.0 51.7 1.0 CE1 B:HIS12 3.0 46.0 1.0 CD2 B:HIS14 3.2 51.9 1.0 OE2 B:GLU107 3.2 62.4 1.0 P B:PO41275 3.3 61.1 1.0 CG B:ASP218 3.5 62.2 1.0 ZN B:ZN1274 3.7 56.4 1.0 CE1 B:HIS170 3.7 62.2 1.0 NE2 B:HIS170 3.8 61.1 1.0 OD2 B:ASP218 3.9 72.0 1.0 O2 B:PO41275 4.0 63.1 1.0 CG B:HIS12 4.1 45.8 1.0 ND1 B:HIS12 4.1 47.2 1.0 O1 B:PO41275 4.1 67.0 1.0 CG2 B:VAL42 4.1 51.4 1.0 O4 B:PO41275 4.1 66.4 1.0 ND1 B:HIS14 4.1 52.4 1.0 CG B:HIS14 4.2 50.6 1.0 CG B:GLU107 4.2 64.9 1.0 ND1 B:HIS170 4.3 61.9 1.0 CD2 B:HIS170 4.5 59.3 1.0 CB B:ASP218 4.7 46.6 1.0 CB B:GLU107 4.8 60.1 1.0 CG B:HIS170 4.8 58.8 1.0 OE2 B:GLU44 4.9 79.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Human Tatd-Domain Protein 3 (TATDN3)


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 Human Tatd-Domain Protein 3 (TATDN3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1274 b:56.4 occ:1.00 NE2 B:HIS170 1.9 61.1 1.0 ND1 B:HIS147 2.1 70.4 1.0 OE2 B:GLU107 2.1 62.4 1.0 O2 B:PO41275 2.3 63.1 1.0 CE1 B:HIS170 2.7 62.2 1.0 CE1 B:HIS147 2.9 72.3 1.0 O3 B:PO41275 3.1 66.0 1.0 CD2 B:HIS170 3.1 59.3 1.0 P B:PO41275 3.1 61.1 1.0 CD B:GLU107 3.2 69.2 1.0 CG B:HIS147 3.2 66.8 1.0 O4 B:PO41275 3.7 66.4 1.0 ZN B:ZN1273 3.7 55.3 1.0 CB B:HIS147 3.7 60.4 1.0 OE1 B:GLU107 3.8 61.1 1.0 NE2 B:HIS70 3.9 65.0 1.0 ND1 B:HIS170 4.0 61.9 1.0 NE2 B:HIS147 4.1 73.1 1.0 CG B:HIS170 4.1 58.8 1.0 CD2 B:HIS147 4.3 70.8 1.0 CA B:HIS147 4.3 58.9 1.0 CG B:GLU107 4.4 64.9 1.0 NE2 B:HIS12 4.4 45.6 1.0 O B:HOH2013 4.5 61.3 1.0 O1 B:PO41275 4.6 67.0 1.0 OD2 B:ASP218 4.7 72.0 1.0 CE1 B:HIS12 4.7 46.0 1.0 CD2 B:HIS70 4.8 64.0 1.0 CE1 B:HIS70 4.8 66.9 1.0 OD1 B:ASP218 4.9 63.8 1.0

J.R.C.Muniz, S.Puranik, T.Krojer, W.W.Yue, E.Ugochukwu, P.Filippakopoulos, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, J.Weigelt, C.Bountra, K.L.Kavanagh, U.Oppermann. Crystal Structure of the Human Tatd-Domain Protein 3 (TATDN3) To Be Published.