Zinc in PDB 5vnl: Crystal Structure of SEC23A/SEC24A/SEC22 Complexed with 4- Phenylbutyric Acid (1MM Soaking)

The structure of Crystal Structure of SEC23A/SEC24A/SEC22 Complexed with 4- Phenylbutyric Acid (1MM Soaking), PDB code: 5vnl 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)	48.78 / 2.39
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	147.756, 96.770, 129.590, 90.00, 90.15, 90.00
R / Rfree (%)	20.8 / 24.6

The binding sites of Zinc atom in the Crystal Structure of SEC23A/SEC24A/SEC22 Complexed with 4- Phenylbutyric Acid (1MM Soaking) (pdb code 5vnl). 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 (1MM Soaking), PDB code: 5vnl:
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 (1MM 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 (1MM Soaking) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:0.9 occ:1.00 SG A:CYS88 2.1 0.4 1.0 SG A:CYS85 2.3 83.7 1.0 SG A:CYS61 2.4 88.8 1.0 SG A:CYS66 2.4 87.8 1.0 CB A:CYS85 3.0 85.8 1.0 CB A:CYS66 3.2 91.0 1.0 CB A:CYS61 3.2 84.9 1.0 CB A:CYS88 3.6 0.6 1.0 N A:CYS88 4.0 97.8 1.0 CA A:CYS88 4.3 0.6 1.0 N A:ARG67 4.3 88.5 1.0 CB A:GLN90 4.4 99.3 1.0 CA A:CYS85 4.5 85.5 1.0 N A:ALA68 4.5 81.9 1.0 CA A:CYS66 4.5 91.9 1.0 CB A:ARG63 4.6 98.8 1.0 C A:CYS66 4.7 87.5 1.0 CA A:CYS61 4.7 82.6 1.0 CB A:PHE87 4.7 67.8 1.0 CB A:ALA68 4.8 76.5 1.0 C A:CYS88 4.9 0.5 1.0 C A:PHE87 5.0 80.2 1.0 CD A:ARG63 5.0 0.3 1.0 N A:GLN90 5.0 0.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of SEC23A/SEC24A/SEC22 Complexed with 4- Phenylbutyric Acid (1MM 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 (1MM Soaking) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1101 b:67.8 occ:1.00 SG B:CYS455 2.2 85.6 1.0 SG B:CYS431 2.2 78.3 1.0 SG B:CYS452 2.3 71.3 1.0 SG B:CYS434 2.4 79.1 1.0 CB B:CYS431 3.1 70.9 1.0 CB B:CYS452 3.2 71.5 1.0 CB B:CYS455 3.4 77.2 1.0 CB B:CYS434 3.6 78.1 1.0 N B:CYS434 3.7 83.2 1.0 N B:CYS455 3.8 75.2 1.0 CA B:CYS455 4.1 76.7 1.0 CA B:CYS434 4.2 79.5 1.0 CB B:SER433 4.4 83.2 1.0 CA B:CYS431 4.5 71.7 1.0 OG1 B:THR436 4.6 73.5 1.0 C B:CYS455 4.6 79.6 1.0 CA B:CYS452 4.6 71.3 1.0 CB B:THR436 4.7 68.5 1.0 C B:SER433 4.8 82.7 1.0 C B:LEU454 4.8 71.5 1.0 C B:CYS434 4.8 77.1 1.0 N B:SER433 4.8 81.3 1.0 C B:CYS431 4.9 76.0 1.0 N B:TYR456 4.9 72.5 1.0 CA B:SER433 4.9 80.9 1.0 CB B:ARG457 4.9 80.2 1.0 N B:ARG435 4.9 71.9 1.0 N B:THR436 5.0 67.2 1.0 N B:ARG457 5.0 78.2 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