Nickel 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:

Zinc

(Zn)

4 atoms

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of the Human Tatd-Domain Protein 3 (TATDN3), PDB code: 2y1h:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of the Human Tatd-Domain Protein 3 (TATDN3)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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:Ni1276 b:54.4 occ:1.00 OE1 B:GLU225 2.0 64.1 1.0 OE2 A:GLU231 2.1 59.7 1.0 O A:HOH2022 2.3 35.6 1.0 CD B:GLU225 2.8 70.7 1.0 OE2 B:GLU225 2.9 69.8 1.0 CD A:GLU231 3.0 69.8 1.0 OE1 A:GLU231 3.2 59.4 1.0 O A:ARG229 3.6 55.9 1.0 O A:HOH2007 3.7 68.9 1.0 NE A:ARG229 4.0 60.4 1.0 CB A:ARG229 4.0 51.9 1.0 O B:HOH2018 4.1 45.3 1.0 CG1 B:VAL228 4.1 57.5 1.0 NH2 A:ARG229 4.2 50.1 1.0 CG B:GLU225 4.2 57.2 1.0 CG A:GLU231 4.3 62.1 1.0 C A:ARG229 4.4 55.6 1.0 O A:HOH2023 4.4 52.8 1.0 CZ A:ARG229 4.5 72.3 1.0 O A:HOH2002 4.6 53.2 1.0 CA A:ARG229 4.6 51.0 1.0 CG2 B:VAL228 4.7 61.5 1.0 CB B:GLU225 4.7 56.4 1.0 CG A:ARG229 4.8 57.9 1.0 CB B:VAL228 4.9 59.5 1.0 N A:ARG229 4.9 52.1 1.0 CD A:ARG229 4.9 63.7 1.0

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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 B:Ni1276 b:58.2 occ:1.00 OE2 B:GLU231 2.0 50.1 1.0 OE1 A:GLU225 2.0 83.0 1.0 O B:HOH2021 2.1 54.7 1.0 O B:HOH2007 2.3 35.5 1.0 CD A:GLU225 2.7 80.4 1.0 OE2 A:GLU225 2.8 74.1 1.0 CD B:GLU231 2.9 59.8 1.0 OE1 B:GLU231 3.2 46.0 1.0 O B:ARG229 3.7 52.4 1.0 NE B:ARG229 3.8 58.0 1.0 NH2 B:ARG229 4.0 57.9 1.0 CB B:ARG229 4.0 50.2 1.0 CG A:GLU225 4.1 62.7 1.0 O A:HOH2020 4.2 58.2 1.0 CG B:GLU231 4.2 55.3 1.0 CG1 A:VAL228 4.3 55.5 1.0 CZ B:ARG229 4.3 73.8 1.0 C B:ARG229 4.4 53.8 1.0 O B:HOH2022 4.5 42.9 1.0 O A:HOH2007 4.5 68.9 1.0 CA B:ARG229 4.7 51.8 1.0 CB A:GLU225 4.7 55.6 1.0 CG2 A:VAL228 4.7 60.5 1.0 CG B:ARG229 4.7 52.8 1.0 CD B:ARG229 4.8 52.9 1.0 CB A:VAL228 5.0 57.9 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.