Zinc in PDB 3dh1: Crystal Structure of Human Trna-Specific Adenosine-34 Deaminase Subunit ADAT2

The structure of Crystal Structure of Human Trna-Specific Adenosine-34 Deaminase Subunit ADAT2, PDB code: 3dh1 was solved by M.Welin, L.Tresaugues, J.Andersson, C.H.Arrowsmith, H.Berglund, R.Collins, L.G.Dahlgren, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, A.Johansson, I.Johansson, T.Karlberg, T.Kotenyova, L.Lehtio, M.Moche, M.E.Nilsson, T.Nyman, K.Olesen, C.Persson, J.Sagemark, H.Schueler, A.G.Thorsell, S.Van Der Berg, M.Wisniewska, M.Wikstrom, P.Nordlund, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.530, 103.120, 77.590, 90.00, 97.60, 90.00
R / Rfree (%)	20.2 / 25.6

The binding sites of Zinc atom in the Crystal Structure of Human Trna-Specific Adenosine-34 Deaminase Subunit ADAT2 (pdb code 3dh1). 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 Trna-Specific Adenosine-34 Deaminase Subunit ADAT2, PDB code: 3dh1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Human Trna-Specific Adenosine-34 Deaminase Subunit ADAT2


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 Trna-Specific Adenosine-34 Deaminase Subunit ADAT2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:45.6 occ:1.00 ND1 A:HIS71 2.0 27.2 1.0 O A:HOH202 2.0 31.2 1.0 SG A:CYS107 2.3 26.8 1.0 SG A:CYS110 2.6 29.9 1.0 CE1 A:HIS71 2.8 25.4 1.0 CG A:HIS71 3.2 26.9 1.0 CB A:CYS107 3.2 27.2 1.0 CB A:CYS110 3.5 28.2 1.0 OE2 A:GLU73 3.6 30.2 1.0 N A:CYS107 3.6 27.5 1.0 CB A:HIS71 3.7 27.6 1.0 NE2 A:HIS71 4.0 25.6 1.0 CA A:CYS107 4.0 27.2 1.0 CD A:GLU73 4.1 29.0 1.0 OE1 A:GLU73 4.1 27.0 1.0 CD2 A:HIS71 4.2 26.7 1.0 N A:CYS110 4.2 27.3 1.0 CA A:CYS110 4.5 28.0 1.0 C A:CYS107 4.7 27.6 1.0 C A:PRO106 4.7 27.3 1.0 O A:CYS107 4.9 27.2 1.0 CA A:PRO106 4.9 27.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Human Trna-Specific Adenosine-34 Deaminase Subunit ADAT2


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 Trna-Specific Adenosine-34 Deaminase Subunit ADAT2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:48.9 occ:1.00 ND1 B:HIS71 2.3 28.4 1.0 SG B:CYS110 2.5 27.5 1.0 SG B:CYS107 2.5 27.5 1.0 O B:HOH202 2.7 13.4 1.0 CE1 B:HIS71 3.2 27.4 1.0 CG B:HIS71 3.3 27.9 1.0 OE2 B:GLU73 3.3 27.7 1.0 CB B:CYS107 3.4 27.9 1.0 CB B:CYS110 3.4 28.5 1.0 N B:CYS107 3.6 27.7 1.0 CB B:HIS71 3.6 28.3 1.0 CD B:GLU73 3.9 28.2 1.0 CA B:CYS107 4.0 27.9 1.0 OE1 B:GLU73 4.1 30.0 1.0 N B:CYS110 4.4 28.2 1.0 NE2 B:HIS71 4.4 26.6 1.0 CD2 B:HIS71 4.4 26.8 1.0 CA B:CYS110 4.5 28.0 1.0 C B:PRO106 4.7 27.9 1.0 C B:CYS107 4.7 27.9 1.0 O B:CYS107 4.8 28.4 1.0 CA B:PRO106 4.9 27.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Human Trna-Specific Adenosine-34 Deaminase Subunit ADAT2


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 Trna-Specific Adenosine-34 Deaminase Subunit ADAT2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:51.6 occ:1.00 ND1 C:HIS71 2.1 28.1 1.0 SG C:CYS107 2.4 27.2 1.0 SG C:CYS110 2.4 29.8 1.0 O C:HOH202 2.7 22.2 1.0 CE1 C:HIS71 3.0 27.4 1.0 CG C:HIS71 3.2 27.2 1.0 CB C:CYS110 3.3 27.4 1.0 OE2 C:GLU73 3.3 31.4 1.0 CB C:CYS107 3.5 27.5 1.0 CB C:HIS71 3.6 27.9 1.0 N C:CYS107 3.7 27.4 1.0 CD C:GLU73 3.8 29.1 1.0 OE1 C:GLU73 3.9 27.9 1.0 CA C:CYS107 4.2 27.6 1.0 NE2 C:HIS71 4.2 26.9 1.0 N C:CYS110 4.3 27.0 1.0 CD2 C:HIS71 4.3 26.0 1.0 CA C:CYS110 4.4 27.4 1.0 C C:PRO106 4.7 27.4 1.0 CA C:PRO106 4.9 27.7 1.0 C C:CYS107 4.9 27.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Human Trna-Specific Adenosine-34 Deaminase Subunit ADAT2


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 Trna-Specific Adenosine-34 Deaminase Subunit ADAT2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:45.5 occ:1.00 ND1 D:HIS71 2.2 27.3 1.0 SG D:CYS110 2.6 30.1 1.0 SG D:CYS107 2.6 27.9 1.0 O D:HOH202 2.8 15.9 1.0 CE1 D:HIS71 3.2 26.6 1.0 CG D:HIS71 3.2 27.3 1.0 OE2 D:GLU73 3.3 31.2 1.0 CB D:CYS107 3.4 27.5 1.0 CB D:CYS110 3.5 28.7 1.0 CB D:HIS71 3.5 28.2 1.0 N D:CYS107 3.6 27.2 1.0 CD D:GLU73 4.0 29.8 1.0 CA D:CYS107 4.1 27.5 1.0 OE1 D:GLU73 4.1 29.0 1.0 N D:CYS110 4.3 28.4 1.0 NE2 D:HIS71 4.3 26.6 1.0 CD2 D:HIS71 4.4 26.3 1.0 CA D:CYS110 4.5 28.4 1.0 C D:CYS107 4.7 27.8 1.0 C D:PRO106 4.7 27.0 1.0 O D:CYS107 4.8 27.9 1.0 CA D:PRO106 4.9 27.4 1.0

M.Welin, L.Tresaugues, J.Andersson, C.H.Arrowsmith, H.Berglund, R.Collins, L.G.Dahlgren, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, A.Johansson, I.Johansson, T.Karlberg, T.Kotenyova, L.Lehtio, M.Moche, M.E.Nilsson, T.Nyman, K.Olesen, C.Persson, J.Sagemark, H.Schueler, A.G.Thorsell, S.Van Der Berg, M.Wisniewska, M.Wikstrom, P.Nordlund. Crystal Structure of Human Trna-Specific Adenosine-34 Deaminase Subunit ADAT2. To Be Published.