Zinc in PDB 6djx: Crystal Structure of Pparkin-Pub-UBCH7 Complex

All present enzymatic activity of Crystal Structure of Pparkin-Pub-UBCH7 Complex:
2.3.2.23; 2.3.2.31;

The structure of Crystal Structure of Pparkin-Pub-UBCH7 Complex, PDB code: 6djx was solved by V.Sauve, G.Sung, J.F.Trempe, K.Gehring, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.86 / 4.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.669, 135.669, 87.993, 90.00, 90.00, 120.00
R / Rfree (%)	25.7 / 29

The binding sites of Zinc atom in the Crystal Structure of Pparkin-Pub-UBCH7 Complex (pdb code 6djx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Pparkin-Pub-UBCH7 Complex, PDB code: 6djx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Pparkin-Pub-UBCH7 Complex


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 Pparkin-Pub-UBCH7 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:0.8 occ:1.00 SG A:CYS195 2.3 0.6 1.0 SG A:CYS229 2.3 0.2 1.0 SG A:CYS222 2.3 0.6 1.0 SG A:CYS192 2.4 0.7 1.0 CB A:CYS192 2.9 0.3 1.0 CB A:CYS222 3.0 0.3 1.0 CB A:CYS195 3.7 0.3 1.0 CB A:CYS229 3.8 0.5 1.0 N A:CYS195 4.3 0.3 1.0 CA A:CYS192 4.4 0.1 1.0 CA A:CYS222 4.5 0.1 1.0 CA A:CYS195 4.6 0.0 1.0 O A:GLY197 5.0 0.7 1.0 C A:CYS192 5.0 0.1 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Pparkin-Pub-UBCH7 Complex


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 Pparkin-Pub-UBCH7 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:0.5 occ:1.00 NE2 A:HIS249 2.0 0.4 1.0 SG A:CYS246 2.3 0.2 1.0 SG A:CYS177 2.3 0.5 1.0 SG A:CYS180 2.3 0.9 1.0 CD2 A:HIS249 2.4 0.0 1.0 CB A:CYS177 2.9 0.5 1.0 CB A:CYS246 3.0 0.5 1.0 CE1 A:HIS249 3.2 0.6 1.0 CB A:CYS180 3.3 1.0 1.0 CG A:HIS249 3.6 0.7 1.0 N A:CYS180 3.9 0.2 1.0 ND1 A:HIS249 4.0 0.8 1.0 CA A:CYS180 4.2 0.9 1.0 CA A:CYS177 4.4 0.7 1.0 SG A:CYS184 4.4 0.3 1.0 CA A:CYS246 4.5 0.3 1.0 CB A:GLN179 4.5 0.3 1.0 C A:GLN179 4.8 0.0 1.0 CB A:HIS249 4.9 0.9 1.0 C A:CYS246 4.9 0.8 1.0 N A:GLN179 5.0 0.9 1.0 CA A:GLN179 5.0 0.1 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Pparkin-Pub-UBCH7 Complex


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 Pparkin-Pub-UBCH7 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:0.1 occ:1.00 SG A:CYS298 2.3 0.5 1.0 SG A:CYS295 2.3 0.1 1.0 SG A:CYS273 2.3 0.2 1.0 SG A:CYS276 2.3 0.6 1.0 CB A:CYS273 3.2 1.0 1.0 CB A:CYS298 3.3 0.7 1.0 CB A:CYS276 3.5 0.3 1.0 CB A:CYS295 3.7 0.0 1.0 N A:CYS276 3.8 0.0 1.0 N A:CYS295 3.8 0.1 1.0 CB A:ALA275 4.1 0.4 1.0 CA A:CYS276 4.3 0.8 1.0 CA A:CYS295 4.3 0.4 1.0 C A:ALA275 4.4 0.1 1.0 N A:CYS298 4.4 0.9 1.0 CB C:ALA2 4.4 0.4 1.0 CA A:CYS298 4.5 0.3 1.0 N A:ALA275 4.5 0.7 1.0 CA A:ALA275 4.6 0.9 1.0 CA A:CYS273 4.6 0.7 1.0 C A:CYS295 4.8 0.9 1.0 O A:CYS295 4.8 0.1 1.0 C A:CYS273 4.9 0.3 1.0 C A:THR294 4.9 0.4 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Pparkin-Pub-UBCH7 Complex


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 Pparkin-Pub-UBCH7 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:1.0 occ:1.00 ND1 A:HIS292 2.0 0.4 1.0 SG A:CYS324 2.3 0.2 1.0 SG A:CYS328 2.3 0.4 1.0 SG A:CYS288 2.3 0.9 1.0 CE1 A:HIS292 2.6 0.5 1.0 CB A:CYS328 3.0 0.6 1.0 CB A:CYS288 3.2 0.1 1.0 CG A:HIS292 3.2 0.9 1.0 CB A:CYS324 3.4 0.6 1.0 NE2 A:HIS292 3.8 0.6 1.0 CB A:HIS292 3.9 0.4 1.0 CD2 A:HIS292 4.1 0.1 1.0 CA A:CYS328 4.2 0.2 1.0 N A:CYS328 4.3 0.1 1.0 CB A:ALA326 4.4 0.1 1.0 CA A:CYS288 4.6 0.2 1.0 N A:HIS292 4.8 0.9 1.0 CB A:SER290 4.8 0.7 1.0 CA A:CYS324 4.9 0.1 1.0 OG A:SER331 4.9 0.2 1.0 CA A:HIS292 5.0 0.9 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Pparkin-Pub-UBCH7 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Pparkin-Pub-UBCH7 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:0.1 occ:1.00 NE2 A:HIS404 2.0 0.6 1.0 SG A:CYS396 2.2 0.9 1.0 SG A:CYS399 2.3 0.3 1.0 SG A:CYS408 2.3 0.9 1.0 CB A:CYS396 2.5 0.2 1.0 CE1 A:HIS404 2.6 0.9 1.0 CB A:CYS399 2.8 0.2 1.0 CB A:CYS408 3.2 0.3 1.0 CD2 A:HIS404 3.2 0.7 1.0 N A:CYS399 3.6 0.7 1.0 CA A:CYS399 3.8 0.9 1.0 ND1 A:HIS404 3.8 0.7 1.0 C A:ASN398 3.9 0.2 1.0 CA A:CYS396 3.9 0.4 1.0 CG A:HIS404 4.1 0.0 1.0 O A:ASN398 4.3 1.0 1.0 CB A:ASN398 4.3 0.8 1.0 N A:ASN398 4.4 0.7 1.0 N A:CYS408 4.4 0.7 1.0 CA A:CYS408 4.4 0.8 1.0 CA A:ASN398 4.4 0.3 1.0 C A:CYS396 4.4 0.1 1.0 N A:CYS396 4.7 0.2 1.0 O A:CYS396 4.8 0.5 1.0 C A:CYS399 4.8 0.5 1.0 N A:ARG397 4.9 0.8 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Pparkin-Pub-UBCH7 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Pparkin-Pub-UBCH7 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1006 b:0.5 occ:1.00 SG A:CYS391 2.2 0.1 1.0 SG A:CYS367 2.3 0.8 1.0 SG A:CYS372 2.3 1.0 1.0 SG A:CYS387 2.3 0.1 1.0 CB A:CYS367 3.4 0.3 1.0 CB A:CYS387 3.4 0.1 1.0 CB A:CYS391 3.5 0.2 1.0 CB A:CYS372 3.5 0.2 1.0 N A:CYS391 3.5 0.3 1.0 CA A:CYS391 4.0 0.9 1.0 CB A:MET374 4.4 0.5 1.0 C A:GLY390 4.6 0.3 1.0 C A:CYS391 4.7 0.4 1.0 CA A:GLY390 4.7 1.0 1.0 CA A:CYS387 4.8 0.3 1.0 CA A:CYS367 4.8 0.3 1.0 N A:GLY392 4.8 0.1 1.0 CB A:GLN369 4.9 0.2 1.0 CA A:CYS372 4.9 0.7 1.0

V.Sauve, G.Sung, N.Soya, G.Kozlov, N.Blaimschein, L.S.Miotto, J.F.Trempe, G.L.Lukacs, K.Gehring. Mechanism of Parkin Activation By Phosphorylation. Nat. Struct. Mol. Biol. V. 25 623 2018.
ISSN: ESSN 1545-9985
PubMed: 29967542
DOI: 10.1038/S41594-018-0088-7