Zinc in PDB 5caw: Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin

The structure of Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin, PDB code: 5caw was solved by T.Wauer, D.Komander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.06 / 2.62
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.170, 44.120, 204.531, 90.00, 92.55, 90.00
R / Rfree (%)	22.8 / 26

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin (pdb code 5caw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin, PDB code: 5caw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:62.7 occ:1.00 ND1 A:HIS216 2.1 68.6 1.0 SG A:CYS151 2.4 54.2 1.0 SG A:CYS213 2.4 45.9 1.0 SG A:CYS155 2.4 66.7 1.0 CE1 A:HIS216 2.9 67.2 1.0 CB A:CYS213 3.1 59.0 1.0 CB A:CYS155 3.2 68.6 1.0 CG A:HIS216 3.3 69.3 1.0 CB A:CYS151 3.3 58.5 1.0 CB A:HIS216 3.7 72.2 1.0 NE2 A:HIS216 4.1 67.1 1.0 N A:CYS155 4.1 74.8 1.0 ND2 A:ASN159 4.2 64.0 1.0 N A:HIS216 4.3 73.4 1.0 CD2 A:HIS216 4.3 69.1 1.0 CD A:PRO154 4.3 88.4 1.0 CA A:CYS155 4.3 70.8 1.0 CA A:CYS213 4.6 58.7 1.0 C A:SER215 4.6 73.2 1.0 CA A:HIS216 4.6 75.2 1.0 O A:ASN153 4.7 95.5 1.0 N A:PRO154 4.7 89.0 1.0 CA A:CYS151 4.8 58.0 1.0 CB A:SER215 4.8 71.2 1.0 C A:ASN153 4.9 93.8 1.0 N A:SER215 4.9 66.2 1.0 C A:CYS213 5.0 61.2 1.0

Zinc binding site 2 out of 16 in the Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:65.0 occ:1.00 SG A:CYS167 2.3 58.4 1.0 SG A:CYS202 2.3 66.0 1.0 SG A:CYS197 2.3 66.2 1.0 SG A:CYS170 2.3 84.7 1.0 CB A:CYS167 3.0 73.1 1.0 CB A:CYS197 3.3 73.5 1.0 CB A:CYS202 3.3 73.4 1.0 CB A:CYS170 3.3 83.2 1.0 N A:CYS170 3.7 84.4 1.0 CA A:CYS170 4.1 83.4 1.0 CB A:ASN199 4.5 81.2 1.0 CA A:CYS167 4.5 71.7 1.0 CB A:GLU169 4.5 95.3 1.0 CA A:CYS197 4.7 73.0 1.0 N A:GLY204 4.7 74.1 1.0 CA A:CYS202 4.7 78.3 1.0 CA A:GLY204 4.8 71.7 1.0 C A:GLU169 4.8 87.3 1.0 C A:CYS170 4.8 83.9 1.0 N A:LYS171 5.0 85.3 1.0

Zinc binding site 3 out of 16 in the Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:79.2 occ:1.00 SG A:CYS265 2.4 63.7 1.0 SG A:CYS243 2.4 86.9 1.0 SG A:CYS240 2.4 90.0 1.0 SG A:CYS262 2.4 74.0 1.0 CB A:CYS240 2.9 65.2 1.0 CB A:CYS265 3.3 65.6 1.0 CB A:CYS262 3.6 63.3 1.0 CB A:CYS243 3.6 93.7 1.0 N A:CYS243 3.7 89.0 1.0 N A:CYS262 4.0 60.1 1.0 CA A:CYS243 4.2 94.0 1.0 CA A:CYS262 4.3 61.0 1.0 CA A:CYS240 4.4 66.0 1.0 CB A:ALA242 4.5 82.6 1.0 CA A:CYS265 4.5 64.4 1.0 N A:CYS265 4.5 66.9 1.0 OG1 A:THR261 4.7 59.7 1.0 C A:CYS243 4.8 95.3 1.0 C A:ALA242 4.8 90.1 1.0 N A:ALA242 4.8 85.0 1.0 O A:CYS262 4.8 60.1 1.0 N A:THR244 4.9 93.5 1.0 C A:CYS240 4.9 82.4 1.0 C A:CYS262 4.9 61.0 1.0 CA A:ALA242 4.9 86.1 1.0 CB A:ASP245 4.9 94.3 1.0 N A:ASP245 5.0 94.3 1.0

Zinc binding site 4 out of 16 in the Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:65.6 occ:1.00 ND1 A:HIS259 2.1 68.8 1.0 SG A:CYS295 2.4 64.4 1.0 SG A:CYS291 2.4 67.2 1.0 SG A:CYS255 2.6 81.3 1.0 CE1 A:HIS259 2.8 71.0 1.0 CG A:HIS259 3.1 69.8 1.0 CB A:CYS291 3.2 64.1 1.0 CB A:CYS295 3.4 72.1 1.0 CB A:CYS255 3.5 70.0 1.0 CB A:HIS259 3.7 67.8 1.0 NE2 A:HIS259 3.9 73.3 1.0 CD2 A:HIS259 4.1 72.3 1.0 CB A:ALA293 4.1 65.0 1.0 N A:HIS259 4.2 78.8 1.0 N A:CYS295 4.6 70.7 1.0 CA A:HIS259 4.6 71.5 1.0 CA A:CYS295 4.6 71.5 1.0 CA A:CYS291 4.7 61.6 1.0 CB A:ASN257 4.7 0.3 1.0 N A:ARG258 4.9 0.0 1.0 CB A:PHE253 5.0 58.7 1.0

Zinc binding site 5 out of 16 in the Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:59.5 occ:1.00 SG A:CYS334 2.3 46.8 1.0 SG A:CYS354 2.4 75.6 1.0 SG A:CYS356 2.4 60.5 1.0 SG A:CYS339 2.5 68.4 1.0 CB A:CYS334 3.0 61.5 1.0 CB A:CYS354 3.1 57.5 1.0 CB A:CYS356 3.3 52.0 1.0 CB A:CYS339 3.5 82.1 1.0 O A:CYS339 3.8 83.7 1.0 N A:CYS356 4.1 53.6 1.0 CA A:CYS356 4.3 57.0 1.0 C A:CYS339 4.3 79.8 1.0 CG A:GLN336 4.4 82.5 1.0 CB A:GLN336 4.5 80.8 1.0 CB A:GLN341 4.5 50.8 1.0 CA A:CYS334 4.5 62.3 1.0 CA A:CYS339 4.5 80.4 1.0 CA A:CYS354 4.5 57.9 1.0 N A:GLN341 4.8 59.6 1.0 N A:SER355 4.8 58.2 1.0 CB A:TYR358 4.9 55.7 1.0 C A:CYS354 4.9 59.7 1.0

Zinc binding site 6 out of 16 in the Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1006 b:67.3 occ:1.00 NE2 A:HIS369 2.1 60.5 1.0 SG A:CYS364 2.3 68.0 1.0 SG A:CYS373 2.4 81.8 1.0 SG A:CYS361 2.4 63.9 1.0 CE1 A:HIS369 2.9 62.7 1.0 CB A:CYS364 3.1 73.2 1.0 CD2 A:HIS369 3.2 60.8 1.0 CB A:CYS373 3.2 71.5 1.0 CB A:CYS361 3.3 62.9 1.0 N A:CYS364 3.7 71.4 1.0 CA A:CYS364 4.0 72.4 1.0 CA A:CYS373 4.0 73.6 1.0 ND1 A:HIS369 4.0 64.6 1.0 CG A:HIS369 4.2 63.0 1.0 CB A:LYS363 4.6 73.7 1.0 N A:CYS373 4.6 73.5 1.0 C A:LYS363 4.7 70.8 1.0 CA A:CYS361 4.7 62.4 1.0 C A:CYS364 4.8 72.3 1.0

Zinc binding site 7 out of 16 in the Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1007 b:97.0 occ:1.00 SG A:CYS418 2.4 82.7 1.0 SG A:CYS415 2.4 75.5 1.0 SG A:CYS438 2.4 0.4 1.0 SG A:CYS433 2.4 86.0 1.0 CB A:CYS433 3.1 87.9 1.0 CB A:CYS438 3.3 0.3 1.0 CB A:CYS418 3.4 0.5 1.0 CB A:CYS415 3.5 0.6 1.0 N A:CYS418 3.8 97.4 1.0 CB A:LYS417 4.1 91.0 1.0 C A:LYS417 4.2 94.8 1.0 CA A:CYS418 4.2 0.8 1.0 O A:CYS438 4.3 0.9 1.0 CA A:LYS417 4.5 92.9 1.0 CA A:CYS438 4.5 0.6 1.0 N A:LYS417 4.5 93.0 1.0 CA A:CYS433 4.6 85.7 1.0 C A:CYS438 4.6 0.9 1.0 CB A:ARG435 4.7 0.9 1.0 CG2 A:THR420 4.7 0.5 1.0 CB A:PHE440 4.8 77.6 1.0 O A:LYS417 4.8 94.6 1.0 CA A:CYS415 4.9 0.1 1.0

Zinc binding site 8 out of 16 in the Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1008 b:55.2 occ:1.00 NE2 A:HIS458 2.2 54.9 1.0 SG A:CYS446 2.4 61.6 1.0 SG A:CYS454 2.4 49.8 1.0 SG A:CYS443 2.4 54.4 1.0 CD2 A:HIS458 3.2 53.9 1.0 CB A:CYS443 3.2 68.7 1.0 CE1 A:HIS458 3.3 55.8 1.0 CB A:CYS454 3.4 54.9 1.0 CB A:CYS446 3.4 68.8 1.0 N A:CYS446 3.9 66.1 1.0 CA A:CYS454 4.0 53.5 1.0 CA A:CYS446 4.3 70.3 1.0 CG A:HIS458 4.3 53.7 1.0 ND1 A:HIS458 4.4 55.8 1.0 CB A:VAL445 4.4 62.3 1.0 CA A:CYS443 4.7 69.4 1.0 C A:VAL445 4.9 65.0 1.0 N A:CYS454 4.9 52.5 1.0 CG1 A:VAL445 5.0 60.6 1.0

Zinc binding site 9 out of 16 in the Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:65.7 occ:1.00 ND1 C:HIS216 2.1 76.4 1.0 SG C:CYS155 2.4 60.2 1.0 SG C:CYS151 2.4 62.4 1.0 SG C:CYS213 2.4 58.4 1.0 CB C:CYS213 2.9 53.5 1.0 CE1 C:HIS216 2.9 74.3 1.0 CG C:HIS216 3.1 77.0 1.0 CB C:CYS151 3.2 65.5 1.0 CB C:CYS155 3.4 74.1 1.0 CB C:HIS216 3.6 79.1 1.0 N C:HIS216 3.8 79.7 1.0 NE2 C:HIS216 4.1 74.7 1.0 CD2 C:HIS216 4.2 76.3 1.0 N C:CYS155 4.2 77.3 1.0 CA C:HIS216 4.3 82.2 1.0 CA C:CYS213 4.4 55.9 1.0 ND2 C:ASN159 4.4 68.7 1.0 CA C:CYS155 4.4 75.2 1.0 CD C:PRO154 4.4 91.4 1.0 CB C:SER215 4.5 77.1 1.0 CA C:CYS151 4.7 64.8 1.0 O C:ASN153 4.7 94.3 1.0 N C:SER215 4.8 71.3 1.0 C C:SER215 4.8 79.8 1.0 N C:PRO154 4.8 89.5 1.0 C C:CYS213 4.9 60.1 1.0 C C:ASN153 5.0 93.2 1.0 CA C:SER215 5.0 76.7 1.0

Zinc binding site 10 out of 16 in the Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Pediculus Humanus Parkin Bound to Phospho-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1002 b:60.0 occ:1.00 SG C:CYS170 2.3 65.3 1.0 SG C:CYS167 2.3 64.6 1.0 SG C:CYS202 2.3 56.9 1.0 SG C:CYS197 2.5 74.1 1.0 CB C:CYS167 3.0 61.3 1.0 CB C:CYS170 3.2 76.5 1.0 CB C:CYS202 3.3 60.6 1.0 CB C:CYS197 3.3 64.8 1.0 N C:CYS170 3.9 72.6 1.0 CA C:CYS170 4.1 74.8 1.0 CA C:GLY204 4.4 69.1 1.0 N C:GLY204 4.4 70.0 1.0 CA C:CYS167 4.5 59.1 1.0 CB C:ASN199 4.6 75.9 1.0 CA C:CYS202 4.7 63.9 1.0 C C:CYS170 4.8 77.2 1.0 CA C:CYS197 4.8 66.2 1.0 N C:LYS171 4.9 79.6 1.0 C C:GLU169 4.9 70.5 1.0 CB C:GLU169 5.0 66.7 1.0 C C:CYS167 5.0 60.2 1.0 ND2 C:ASN199 5.0 81.7 1.0 C C:CYS202 5.0 68.0 1.0

T.Wauer, M.Simicek, A.Schubert, D.Komander. Mechanism of Phospho-Ubiquitin-Induced Parkin Activation. Nature V. 524 370 2015.
ISSN: ESSN 1476-4687
PubMed: 26161729
DOI: 10.1038/NATURE14879