Zinc in PDB 5vnm: Crystal Structure of SEC23A/SEC24A/SEC22 Complexed with 4- Phenylbutyric Acid (15MM Soaking)

The structure of Crystal Structure of SEC23A/SEC24A/SEC22 Complexed with 4- Phenylbutyric Acid (15MM Soaking), PDB code: 5vnm was solved by W.Ma, J.Goldberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	130.61 / 2.77
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	149.183, 96.800, 130.609, 90.00, 90.22, 90.00
R / Rfree (%)	26.8 / 29.7

The binding sites of Zinc atom in the Crystal Structure of SEC23A/SEC24A/SEC22 Complexed with 4- Phenylbutyric Acid (15MM Soaking) (pdb code 5vnm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of SEC23A/SEC24A/SEC22 Complexed with 4- Phenylbutyric Acid (15MM Soaking), PDB code: 5vnm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of SEC23A/SEC24A/SEC22 Complexed with 4- Phenylbutyric Acid (15MM Soaking)


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 SEC23A/SEC24A/SEC22 Complexed with 4- Phenylbutyric Acid (15MM Soaking) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:0.7 occ:1.00 SG A:CYS88 2.3 0.2 1.0 SG A:CYS66 2.4 0.5 1.0 SG A:CYS85 2.4 98.8 1.0 SG A:CYS61 2.4 0.8 1.0 CB A:CYS61 3.0 0.6 1.0 CB A:CYS85 3.1 0.1 1.0 CB A:CYS66 3.1 0.2 1.0 CB A:CYS88 3.8 0.1 1.0 N A:CYS88 4.2 0.4 1.0 N A:ARG67 4.3 0.7 1.0 CB A:GLN90 4.4 0.3 1.0 CA A:CYS66 4.5 0.5 1.0 CA A:CYS61 4.5 0.4 1.0 CA A:CYS88 4.5 0.7 1.0 N A:ALA68 4.5 90.4 1.0 CA A:CYS85 4.6 0.3 1.0 C A:CYS66 4.6 1.0 1.0 CB A:ARG63 4.7 0.2 1.0 CB A:ALA68 4.8 88.9 1.0 CB A:PHE87 4.8 0.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of SEC23A/SEC24A/SEC22 Complexed with 4- Phenylbutyric Acid (15MM Soaking)


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 SEC23A/SEC24A/SEC22 Complexed with 4- Phenylbutyric Acid (15MM Soaking) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1101 b:100.0 occ:1.00 SG B:CYS455 2.3 0.7 1.0 SG B:CYS431 2.3 95.0 1.0 SG B:CYS434 2.3 0.2 1.0 SG B:CYS452 2.3 90.0 1.0 CB B:CYS431 3.2 76.1 1.0 CB B:CYS452 3.2 94.2 1.0 CB B:CYS455 3.2 0.4 1.0 CB B:CYS434 3.7 0.4 1.0 N B:CYS434 3.7 0.6 1.0 N B:CYS455 3.8 89.0 1.0 CA B:CYS455 4.0 92.8 1.0 CA B:CYS434 4.2 0.3 1.0 CB B:SER433 4.3 98.1 1.0 OG1 B:THR436 4.3 71.0 1.0 CB B:THR436 4.5 72.5 1.0 C B:CYS455 4.5 90.5 1.0 CA B:CYS431 4.6 78.8 1.0 CA B:CYS452 4.7 93.7 1.0 C B:SER433 4.7 96.2 1.0 C B:CYS434 4.7 93.6 1.0 C B:LEU454 4.8 82.8 1.0 N B:SER433 4.8 91.5 1.0 N B:TYR456 4.8 90.1 1.0 N B:ARG435 4.8 80.2 1.0 N B:THR436 4.8 71.5 1.0 CA B:SER433 4.9 93.5 1.0 CB B:ARG457 5.0 95.3 1.0 C B:CYS431 5.0 83.2 1.0

W.Ma, E.Goldberg, J.Goldberg. Er Retention Is Imposed By Copii Protein Sorting and Attenuated By 4-Phenylbutyrate. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28594326
DOI: 10.7554/ELIFE.26624