Zinc in PDB 8j4b: Crystal Structure of 13A

The structure of Crystal Structure of 13A, PDB code: 8j4b was solved by C.Dong, X.Yan, X.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.93 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	90.92, 63.35, 68.56, 90, 90, 90
R / Rfree (%)	17.5 / 21.3

The binding sites of Zinc atom in the Crystal Structure of 13A (pdb code 8j4b). 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 13A, PDB code: 8j4b:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of 13A


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 13A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:41.5 occ:1.00 ND1 B:HIS126 2.1 23.8 1.0 SG B:CYS101 2.3 26.6 1.0 SG B:CYS123 2.4 27.3 1.0 SG B:CYS106 2.4 36.7 1.0 CE1 B:HIS126 3.0 26.2 1.0 CB B:CYS101 3.2 27.5 1.0 CG B:HIS126 3.2 29.9 1.0 CB B:CYS106 3.3 36.3 1.0 CB B:CYS123 3.4 35.0 1.0 CB B:HIS126 3.6 25.9 1.0 N B:CYS123 3.8 28.2 1.0 NE2 B:HIS126 4.2 26.3 1.0 CA B:CYS123 4.2 30.0 1.0 CD2 B:HIS126 4.3 27.8 1.0 CB B:VAL103 4.3 28.3 1.0 CG2 B:VAL103 4.5 28.1 1.0 CB B:SER108 4.5 57.6 1.0 CA B:CYS101 4.6 34.5 1.0 CA B:CYS106 4.6 40.3 1.0 N B:HIS126 4.7 28.0 1.0 CA B:HIS126 4.8 27.4 1.0 C B:CYS123 4.9 29.2 1.0 C B:VAL122 5.0 28.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of 13A


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 13A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:35.4 occ:1.00 NE2 B:HIS149 2.2 23.9 1.0 SG B:CYS142 2.4 19.7 1.0 SG B:CYS161 2.4 25.3 1.0 SG B:CYS145 2.4 23.6 1.0 CD2 B:HIS149 3.0 22.5 1.0 CB B:CYS145 3.2 21.1 1.0 CB B:CYS142 3.2 20.2 1.0 CB B:CYS161 3.3 23.6 1.0 CE1 B:HIS149 3.3 27.9 1.0 N B:CYS161 3.9 24.7 1.0 N B:CYS145 4.0 21.4 1.0 CA B:CYS161 4.2 22.3 1.0 CG B:HIS149 4.2 27.9 1.0 CA B:CYS145 4.2 21.4 1.0 ND1 B:HIS149 4.3 23.2 1.0 O B:HOH301 4.4 39.6 1.0 CA B:CYS142 4.7 18.3 1.0 OE1 B:GLN144 4.7 40.5 1.0 CB B:GLN144 4.8 24.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of 13A


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 13A within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:36.8 occ:1.00 ND1 D:HIS126 2.2 23.1 1.0 SG D:CYS101 2.3 21.9 1.0 SG D:CYS106 2.4 25.6 1.0 SG D:CYS123 2.5 23.9 1.0 CE1 D:HIS126 3.1 25.5 1.0 CB D:CYS106 3.2 27.1 1.0 CG D:HIS126 3.2 23.4 1.0 CB D:CYS101 3.3 23.9 1.0 CB D:CYS123 3.5 23.8 1.0 CB D:HIS126 3.5 24.8 1.0 N D:CYS123 3.9 22.1 1.0 CB D:VAL103 4.3 23.9 1.0 NE2 D:HIS126 4.3 26.5 1.0 CA D:CYS123 4.3 23.7 1.0 CD2 D:HIS126 4.3 25.1 1.0 CG2 D:VAL103 4.5 20.3 1.0 O D:HOH348 4.5 40.5 1.0 N D:HIS126 4.6 23.4 1.0 CB D:SER108 4.6 36.4 1.0 CA D:CYS106 4.6 26.5 1.0 CA D:CYS101 4.7 22.1 1.0 CA D:HIS126 4.7 23.2 1.0 CG1 D:VAL103 5.0 18.3 1.0 C D:CYS123 5.0 22.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of 13A


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 13A within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:40.3 occ:1.00 SG D:CYS145 2.2 26.9 1.0 NE2 D:HIS149 2.3 30.9 1.0 SG D:CYS161 2.3 30.7 1.0 SG D:CYS142 2.5 25.2 1.0 CD2 D:HIS149 3.0 29.5 1.0 CB D:CYS145 3.2 26.3 1.0 CB D:CYS161 3.3 30.5 1.0 CB D:CYS142 3.3 23.3 1.0 CE1 D:HIS149 3.4 34.7 1.0 N D:CYS161 3.9 33.1 1.0 N D:CYS145 4.0 25.8 1.0 CA D:CYS145 4.2 26.0 1.0 CA D:CYS161 4.2 29.7 1.0 CG D:HIS149 4.3 31.0 1.0 ND1 D:HIS149 4.4 27.9 1.0 CA D:CYS142 4.8 23.9 1.0 CB D:GLN144 4.8 29.5 1.0

X.Yan, X.Yuan, J.Lv, B.Zhang, Y.Huang, Q.Li, J.Ma, Y.Li, X.Wang, Y.Li, Y.Yu, Q.Liu, T.Liu, W.Mi, C.Dong. Molecular Basis of SAP05-Mediated Ubiquitin-Independent Proteasomal Degradation of Transcription Factors Nat Commun V. 15 1170 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-45521-7