Zinc in PDB 7wg1: Dvaa-KLATE1

All present enzymatic activity of Dvaa-KLATE1:
2.3.2.8;

The structure of Dvaa-KLATE1, PDB code: 7wg1 was solved by M.K.Kim, B.H.Kim, S.-J.Oh, H.K.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.16 / 2.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.088, 107.736, 161.53, 90, 90, 90
R / Rfree (%)	17.8 / 23.4

The binding sites of Zinc atom in the Dvaa-KLATE1 (pdb code 7wg1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Dvaa-KLATE1, PDB code: 7wg1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Dvaa-KLATE1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dvaa-KLATE1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:32.3 occ:1.00 SG A:CYS95 2.3 28.1 1.0 SG A:CYS23 2.3 30.3 1.0 SG A:CYS96 2.3 27.4 1.0 SG A:CYS26 2.4 34.7 1.0 HB2 A:CYS95 2.9 32.6 1.0 HB3 A:CYS26 3.0 47.6 1.0 CB A:CYS23 3.2 33.7 1.0 HB3 A:CYS23 3.2 40.5 1.0 CB A:CYS95 3.2 27.1 1.0 HB2 A:CYS23 3.2 40.5 1.0 CB A:CYS26 3.3 39.7 1.0 H A:CYS26 3.3 47.5 1.0 HB2 A:CYS96 3.3 31.0 1.0 H A:CYS96 3.4 30.1 1.0 CB A:CYS96 3.4 25.8 1.0 N A:CYS96 3.6 25.1 1.0 HE3 A:LYS30 3.8 47.0 1.0 HB2 A:TYR25 3.8 41.9 1.0 N A:CYS26 3.9 39.6 1.0 HB3 A:CYS95 3.9 32.6 1.0 C A:CYS95 4.0 23.5 1.0 HB2 A:CYS26 4.1 47.6 1.0 HB3 A:ALA19 4.1 42.2 1.0 CA A:CYS96 4.1 27.6 1.0 CA A:CYS26 4.2 36.8 1.0 CA A:CYS95 4.2 30.3 1.0 H A:GLY28 4.2 53.7 1.0 HE2 A:LYS30 4.2 47.0 1.0 HB3 A:CYS96 4.3 31.0 1.0 HD2 A:TYR25 4.3 35.2 1.0 H A:TYR25 4.4 39.8 1.0 CE A:LYS30 4.4 39.2 1.0 HA A:CYS96 4.5 33.1 1.0 H A:CYS95 4.6 35.8 1.0 HD22 A:ASN94 4.6 29.8 1.0 CA A:CYS23 4.7 39.0 1.0 H A:ASN27 4.7 49.4 1.0 CB A:TYR25 4.7 34.9 1.0 O A:CYS95 4.8 28.5 1.0 C A:TYR25 4.8 35.6 1.0 C A:CYS26 4.8 37.6 1.0 N A:CYS95 4.8 29.8 1.0 HB2 A:SER56 4.9 45.9 1.0 HZ3 A:LYS30 4.9 42.3 1.0 N A:ASN27 4.9 41.2 1.0 HB2 A:ALA19 4.9 42.2 1.0 CB A:ALA19 4.9 35.2 1.0 HA A:CYS23 4.9 46.8 1.0 HA A:CYS95 5.0 36.4 1.0 HA A:CYS26 5.0 44.2 1.0

Zinc binding site 2 out of 2 in the Dvaa-KLATE1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dvaa-KLATE1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:47.0 occ:1.00 SG B:CYS23 2.1 53.0 1.0 SG B:CYS96 2.3 47.0 1.0 SG B:CYS95 2.5 49.0 1.0 SG B:CYS26 2.5 56.1 1.0 HB2 B:CYS95 3.0 44.9 1.0 H B:CYS26 3.0 63.4 1.0 HB3 B:CYS23 3.1 60.4 1.0 CB B:CYS23 3.1 50.3 1.0 HB2 B:CYS23 3.2 60.4 1.0 CB B:CYS95 3.3 37.4 1.0 HB3 B:CYS26 3.4 70.8 1.0 H B:CYS96 3.4 60.0 1.0 HB2 B:TYR25 3.4 54.1 1.0 CB B:CYS26 3.5 59.0 1.0 CB B:CYS96 3.6 43.2 1.0 HB2 B:CYS96 3.7 51.9 1.0 N B:CYS26 3.8 52.9 1.0 N B:CYS96 3.8 50.0 1.0 HE2 B:LYS30 3.9 66.2 1.0 H B:ASN27 4.0 86.9 1.0 HB3 B:CYS95 4.0 44.9 1.0 HB3 B:ALA19 4.1 74.2 1.0 HD2 B:TYR25 4.2 47.0 1.0 CA B:CYS26 4.2 58.7 1.0 H B:TYR25 4.2 57.8 1.0 H B:GLY28 4.2 76.3 1.0 C B:CYS95 4.3 47.5 1.0 CA B:CYS96 4.3 45.0 1.0 HB2 B:CYS26 4.3 70.8 1.0 CB B:TYR25 4.4 45.1 1.0 CA B:CYS95 4.4 46.6 1.0 HB3 B:CYS96 4.4 51.9 1.0 HB2 B:SER56 4.5 61.2 1.0 CA B:CYS23 4.5 54.0 1.0 N B:ASN27 4.6 72.4 1.0 HD21 B:ASN94 4.7 32.8 1.0 HA B:CYS96 4.7 54.0 1.0 H B:CYS95 4.7 56.5 1.0 C B:TYR25 4.7 49.4 1.0 CE B:LYS30 4.8 55.1 1.0 HA B:CYS23 4.8 64.8 1.0 HB3 B:TYR25 4.8 54.1 1.0 C B:CYS26 4.8 71.7 1.0 N B:TYR25 4.9 48.2 1.0 CA B:TYR25 4.9 48.8 1.0 HB1 B:ALA19 4.9 74.2 1.0 HZ2 B:LYS30 4.9 66.1 1.0 CB B:ALA19 5.0 61.8 1.0 CD2 B:TYR25 5.0 39.2 1.0 N B:CYS95 5.0 47.1 1.0 C B:CYS23 5.0 52.9 1.0

B.H.Kim, M.K.Kim, S.J.Oh, K.T.Nguyen, J.H.Kim, A.Varshavsky, C.S.Hwang, H.K.Song. Crystal Structure of the ATE1 Arginyl-Trna-Protein Transferase and Arginylation of N-Degron Substrates. Proc.Natl.Acad.Sci.Usa V. 119 97119 2022.
ISSN: ESSN 1091-6490
PubMed: 35878037
DOI: 10.1073/PNAS.2209597119