Zinc in PDB 7wfx: Evaa-KLATE1

All present enzymatic activity of Evaa-KLATE1:
2.3.2.8;

The structure of Evaa-KLATE1, PDB code: 7wfx 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)	46.51 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.72, 114.505, 159.469, 90, 90, 90
R / Rfree (%)	16.4 / 20.2

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

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Evaa-KLATE1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:22.0 occ:1.00 SG A:CYS96 2.3 21.5 1.0 SG A:CYS26 2.3 23.4 1.0 SG A:CYS23 2.3 21.4 1.0 SG A:CYS95 2.4 19.0 1.0 HB2 A:CYS95 3.0 21.6 1.0 HB3 A:CYS26 3.0 28.9 1.0 H A:CYS26 3.2 32.0 1.0 HB3 A:CYS23 3.2 26.8 1.0 CB A:CYS26 3.3 24.0 1.0 CB A:CYS23 3.3 22.3 1.0 CB A:CYS95 3.3 18.0 1.0 HB2 A:CYS23 3.4 26.8 1.0 HB2 A:CYS96 3.4 26.9 1.0 CB A:CYS96 3.4 22.4 1.0 H A:CYS96 3.5 18.5 1.0 HB2 A:TYR25 3.7 30.8 1.0 N A:CYS96 3.7 15.3 1.0 HE2 A:LYS30 3.7 36.9 1.0 N A:CYS26 3.7 26.6 1.0 HB3 A:CYS95 3.9 21.6 1.0 HB2 A:CYS26 4.1 28.9 1.0 CA A:CYS26 4.1 24.8 1.0 C A:CYS95 4.1 19.8 1.0 H A:GLY28 4.1 34.4 1.0 HB1 A:ALA19 4.1 32.2 1.0 CA A:CYS96 4.1 15.1 1.0 O A:HOH980 4.2 23.5 1.0 HD2 A:TYR25 4.2 27.8 1.0 HB3 A:CYS96 4.2 26.9 1.0 CA A:CYS95 4.3 19.8 1.0 H A:TYR25 4.5 29.5 1.0 HA A:CYS96 4.5 18.2 1.0 HZ2 A:LYS30 4.5 37.5 1.0 H A:ASN27 4.6 30.9 1.0 CB A:TYR25 4.6 25.6 1.0 CE A:LYS30 4.6 30.7 1.0 HD21 A:ASN94 4.7 19.8 1.0 CA A:CYS23 4.7 28.5 1.0 C A:TYR25 4.7 29.3 1.0 C A:CYS26 4.8 26.9 1.0 H A:CYS95 4.8 19.4 1.0 HE3 A:LYS30 4.8 36.9 1.0 O A:CYS95 4.8 20.9 1.0 HA A:CYS26 4.9 29.8 1.0 N A:ASN27 4.9 25.7 1.0 N A:CYS95 4.9 16.1 1.0 N A:GLY28 4.9 28.6 1.0 NZ A:LYS30 5.0 31.2 1.0 CB A:ALA19 5.0 26.8 1.0 HA2 A:GLY28 5.0 32.5 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Evaa-KLATE1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:34.4 occ:1.00 SG B:CYS23 2.3 32.7 1.0 SG B:CYS96 2.3 32.6 1.0 SG B:CYS95 2.4 32.6 1.0 SG B:CYS26 2.4 35.2 1.0 HB2 B:CYS95 2.9 41.2 1.0 H B:CYS26 3.2 42.2 1.0 HB3 B:CYS26 3.2 50.3 1.0 HB3 B:CYS23 3.2 42.2 1.0 CB B:CYS23 3.2 35.1 1.0 CB B:CYS95 3.2 34.3 1.0 HB2 B:CYS23 3.3 42.2 1.0 H B:CYS96 3.4 37.0 1.0 HB2 B:CYS96 3.4 41.5 1.0 CB B:CYS26 3.4 41.9 1.0 CB B:CYS96 3.5 34.6 1.0 HB2 B:TYR25 3.6 39.2 1.0 N B:CYS96 3.6 30.8 1.0 N B:CYS26 3.8 35.1 1.0 HB3 B:CYS95 3.9 41.2 1.0 HD2 B:LYS30 4.0 60.6 1.0 HB1 B:ALA19 4.0 47.4 1.0 C B:CYS95 4.1 29.9 1.0 CA B:CYS96 4.1 30.4 1.0 CA B:CYS26 4.1 42.8 1.0 HD2 B:TYR25 4.1 42.9 1.0 HB2 B:CYS26 4.2 50.3 1.0 CA B:CYS95 4.2 32.2 1.0 HZ3 B:LYS30 4.3 54.0 1.0 HB3 B:CYS96 4.3 41.5 1.0 O B:HOH907 4.3 35.0 1.0 H B:GLY28 4.3 55.9 1.0 H B:TYR25 4.4 43.8 1.0 CB B:TYR25 4.5 32.6 1.0 HZ2 B:LYS30 4.5 54.0 1.0 HA B:CYS96 4.5 36.5 1.0 H B:ASN27 4.6 50.7 1.0 H B:CYS95 4.6 35.7 1.0 HD21 B:ASN94 4.6 33.0 1.0 CA B:CYS23 4.7 38.9 1.0 C B:TYR25 4.7 38.8 1.0 C B:CYS26 4.8 41.0 1.0 HB2 B:ALA19 4.8 47.4 1.0 NZ B:LYS30 4.8 45.0 1.0 N B:CYS95 4.8 29.7 1.0 CB B:ALA19 4.9 39.4 1.0 N B:ASN27 4.9 42.2 1.0 O B:CYS95 4.9 35.8 1.0 CD B:LYS30 4.9 50.5 1.0 HA B:CYS23 5.0 46.7 1.0 HA B:CYS26 5.0 51.4 1.0 CD2 B:TYR25 5.0 35.7 1.0 HB3 B:TYR25 5.0 39.2 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