Zinc in PDB 6hue: PARKINS65N

All present enzymatic activity of PARKINS65N:
2.3.2.31;

The structure of PARKINS65N, PDB code: 6hue was solved by T.G.Mcwilliams, E.Barini, R.Pohjolan-Pirhonen, S.P.Brooks, F.Singh, S.Burel, K.Balk, A.Kumar, L.Montava-Garriga, A.R.Prescott, S.M.Hassoun, F.Mouton-Liger, G.Ball, R.Hills, A.Knebel, A.Ulusoy, D.A.Di Monte, J.Tamjar, O.Antico, K.Fears, L.Smith, R.Brambilla, E.Palin, M.Valori, J.Eerola-Rautio, P.Tienari, O.Corti, S.B.Dunnett, I.G.Ganley, A.Suomalainen, M.M.K.Muqit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.98 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.431, 66.870, 206.690, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 25.5

The structure of PARKINS65N also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

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

Binding sites:

The binding sites of Zinc atom in the PARKINS65N (pdb code 6hue). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the PARKINS65N, PDB code: 6hue:
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 PARKINS65N


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PARKINS65N within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:42.7 occ:1.00 NE2 A:HIS215 1.9 45.6 1.0 SG A:CYS154 2.3 44.5 1.0 SG A:CYS150 2.3 40.4 1.0 SG A:CYS212 2.3 48.6 1.0 CE1 A:HIS215 2.9 47.0 1.0 CD2 A:HIS215 2.9 46.2 1.0 CB A:CYS150 3.2 44.4 1.0 CB A:CYS212 3.2 46.0 1.0 CB A:CYS154 3.4 49.2 1.0 ND1 A:HIS215 4.0 47.6 1.0 CG A:HIS215 4.0 47.9 1.0 N A:CYS154 4.0 51.6 1.0 O A:HOH632 4.1 48.1 1.0 CD A:PRO153 4.2 64.5 1.0 CA A:CYS154 4.3 50.4 1.0 O A:GLY152 4.6 64.8 1.0 CA A:CYS150 4.6 48.2 1.0 CG A:PRO153 4.7 63.5 1.0 CG A:GLN158 4.7 44.9 1.0 CA A:CYS212 4.7 42.9 1.0 CB A:ALA214 4.8 48.2 1.0 N A:PRO153 4.8 62.8 1.0 C A:GLY152 4.9 60.0 1.0 NE2 A:GLN158 5.0 40.1 1.0

Zinc binding site 2 out of 16 in the PARKINS65N


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of PARKINS65N within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:52.8 occ:1.00 SG A:CYS196 2.3 46.1 1.0 SG A:CYS169 2.3 51.4 1.0 SG A:CYS166 2.3 53.5 1.0 SG A:CYS201 2.4 53.0 1.0 CB A:CYS166 3.1 54.0 1.0 CB A:CYS196 3.2 46.6 1.0 CB A:CYS201 3.4 55.3 1.0 CB A:CYS169 3.4 51.3 1.0 N A:CYS169 3.9 49.8 1.0 CA A:GLY203 4.1 59.7 1.0 CA A:CYS169 4.3 51.0 1.0 CB A:SER198 4.3 59.7 1.0 OG1 A:THR173 4.5 53.8 1.0 N A:GLY203 4.5 61.8 1.0 CA A:CYS196 4.5 47.9 1.0 CA A:CYS166 4.6 48.8 1.0 CB A:THR168 4.7 54.1 1.0 CA A:CYS201 4.8 54.6 1.0 N A:ARG170 5.0 58.9 1.0

Zinc binding site 3 out of 16 in the PARKINS65N


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of PARKINS65N within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:40.8 occ:1.00 SG A:CYS241 2.3 41.5 1.0 SG A:CYS260 2.3 43.0 1.0 SG A:CYS263 2.3 39.6 1.0 SG A:CYS238 2.3 44.8 1.0 CB A:CYS238 3.2 45.1 1.0 CB A:CYS241 3.3 43.5 1.0 CB A:CYS263 3.3 41.7 1.0 CB A:CYS260 3.3 43.2 1.0 N A:CYS241 3.8 44.1 1.0 OG1 A:THR240 3.9 42.4 0.5 N A:CYS260 4.0 41.3 1.0 CA A:CYS241 4.1 45.6 1.0 CA A:CYS260 4.2 41.0 1.0 N A:CYS263 4.2 41.6 1.0 CA A:CYS263 4.3 42.0 1.0 CA A:CYS238 4.7 43.8 1.0 C A:CYS241 4.8 47.7 1.0 C A:CYS260 4.8 39.9 1.0 N A:THR242 4.9 48.2 1.0 C A:THR240 4.9 43.5 0.5 CB A:THR240 4.9 50.9 0.5 C A:THR240 4.9 45.8 0.5 CB A:THR240 4.9 43.8 0.5 O A:CYS260 4.9 35.8 1.0

Zinc binding site 4 out of 16 in the PARKINS65N


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of PARKINS65N within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:61.0 occ:1.00 ND1 A:HIS257 1.9 54.9 1.0 SG A:CYS289 2.3 60.1 1.0 SG A:CYS293 2.3 54.6 1.0 SG A:CYS253 2.4 61.8 1.0 CG A:HIS257 2.9 52.2 1.0 CE1 A:HIS257 2.9 53.8 1.0 CB A:HIS257 3.2 50.1 1.0 CB A:CYS253 3.3 63.8 1.0 CB A:CYS289 3.3 60.1 1.0 CB A:CYS293 3.4 58.6 1.0 CD2 A:HIS257 4.0 51.3 1.0 NE2 A:HIS257 4.0 53.0 1.0 N A:HIS257 4.1 50.9 1.0 CA A:HIS257 4.3 49.4 1.0 CB A:ALA291 4.6 59.3 1.0 CA A:CYS293 4.7 61.1 1.0 O A:HOH614 4.7 46.4 1.0 CA A:CYS289 4.8 56.8 1.0 CA A:CYS253 4.8 63.0 1.0 CB A:PHE251 4.8 52.2 1.0 N A:CYS293 4.8 59.0 1.0 CB A:SER255 4.9 56.3 1.0

Zinc binding site 5 out of 16 in the PARKINS65N


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of PARKINS65N within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:87.9 occ:1.00 SG A:CYS332 2.4 88.6 1.0 SG A:CYS352 2.4 85.3 1.0 SG A:CYS337 2.6 73.9 1.0 N A:GLY361 2.6 84.1 1.0 CB A:CYS337 3.1 77.5 1.0 CB A:CYS352 3.6 83.5 1.0 CB A:CYS332 3.6 81.0 1.0 CA A:GLY361 4.0 83.7 1.0 N A:PHE362 4.3 0.5 1.0 C A:GLY361 4.5 94.8 1.0 CA A:CYS337 4.6 80.2 1.0 O A:CYS337 4.7 91.9 1.0 CB A:ARG334 4.7 0.1 1.0 C A:CYS337 5.0 80.8 1.0 CA A:CYS352 5.0 88.3 1.0

Zinc binding site 6 out of 16 in the PARKINS65N


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of PARKINS65N within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:79.1 occ:1.00 NE2 A:HIS373 2.0 82.9 1.0 SG A:CYS365 2.3 88.5 1.0 SG A:CYS377 2.4 68.6 1.0 SG A:CYS368 2.4 78.3 1.0 CE1 A:HIS373 2.9 80.3 1.0 CD2 A:HIS373 3.0 80.7 1.0 CB A:CYS365 3.3 88.6 1.0 CB A:CYS368 3.3 75.7 1.0 CB A:CYS377 3.5 72.7 1.0 NH1 A:ARG348 3.5 92.4 1.0 N A:CYS368 3.7 78.7 1.0 CA A:CYS377 3.9 78.3 1.0 ND1 A:HIS373 4.0 79.2 1.0 CG A:HIS373 4.0 76.4 1.0 CA A:CYS368 4.1 73.3 1.0 O A:HOH658 4.3 32.6 1.0 CB A:GLU367 4.6 92.9 1.0 N A:CYS377 4.6 81.9 1.0 CA A:CYS365 4.7 87.0 1.0 CZ A:ARG348 4.8 86.9 1.0 C A:CYS368 4.9 73.0 1.0 C A:GLU367 4.9 89.3 1.0 N A:LYS369 5.0 81.2 1.0

Zinc binding site 7 out of 16 in the PARKINS65N


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of PARKINS65N within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:73.9 occ:1.00 SG A:CYS436 2.3 70.0 1.0 SG A:CYS421 2.3 75.5 1.0 SG A:CYS418 2.3 76.8 1.0 SG A:CYS441 2.3 86.2 1.0 CB A:CYS436 3.1 72.0 1.0 CB A:CYS421 3.3 78.5 1.0 CB A:CYS441 3.3 88.6 1.0 CB A:CYS418 3.3 85.4 1.0 N A:CYS421 3.8 73.5 1.0 N A:ARG442 4.0 76.7 1.0 CA A:CYS421 4.1 79.1 1.0 N A:LEU443 4.2 64.7 1.0 CA A:CYS441 4.5 95.1 1.0 CA A:CYS436 4.5 74.7 1.0 C A:CYS441 4.5 88.2 1.0 CB A:LEU443 4.7 59.3 1.0 CA A:ARG442 4.8 74.8 1.0 O A:HOH637 4.8 0.6 1.0 CB A:GLN438 4.8 89.6 1.0 CA A:CYS418 4.8 79.4 1.0 O A:GLN438 4.9 0.4 1.0 CB A:ARG420 5.0 84.4 1.0 C A:ARG420 5.0 77.2 1.0

Zinc binding site 8 out of 16 in the PARKINS65N


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of PARKINS65N within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:53.5 occ:1.00 NE2 A:HIS461 1.9 58.1 1.0 SG A:CYS446 2.3 52.7 1.0 SG A:CYS457 2.3 49.4 1.0 SG A:CYS449 2.3 67.9 1.0 CE1 A:HIS461 2.8 58.8 1.0 CD2 A:HIS461 3.0 55.7 1.0 CB A:CYS457 3.2 51.8 1.0 CB A:CYS446 3.3 55.6 1.0 CB A:CYS449 3.4 65.9 1.0 ND1 A:HIS461 4.0 56.1 1.0 N A:CYS449 4.0 60.1 1.0 CG A:HIS461 4.1 56.4 1.0 CB A:ASN448 4.1 60.2 0.5 CA A:CYS457 4.1 53.9 1.0 CA A:CYS449 4.4 64.4 1.0 CB A:ASN448 4.5 63.0 0.5 ND2 A:ASN448 4.6 56.5 0.5 CA A:CYS446 4.6 56.8 1.0 CG A:ASN448 4.8 58.0 0.5 SG A:CYS451 4.8 66.0 1.0 C A:ASN448 4.9 58.7 0.5 CA A:ASN448 4.9 60.0 0.5 C A:ASN448 4.9 59.5 0.5

Zinc binding site 9 out of 16 in the PARKINS65N


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of PARKINS65N within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:44.6 occ:1.00 NE2 B:HIS215 1.9 45.4 1.0 SG B:CYS150 2.3 51.6 1.0 SG B:CYS154 2.3 55.1 1.0 SG B:CYS212 2.3 52.0 1.0 CD2 B:HIS215 2.8 45.8 1.0 CE1 B:HIS215 2.9 46.6 1.0 CB B:CYS212 3.1 50.1 1.0 CB B:CYS150 3.2 50.7 1.0 CB B:CYS154 3.4 59.0 1.0 ND1 B:HIS215 3.9 47.8 1.0 CG B:HIS215 4.0 46.6 1.0 N B:CYS154 4.2 58.1 1.0 CA B:CYS154 4.4 60.6 1.0 CD B:PRO153 4.5 69.6 1.0 CB B:ALA214 4.5 44.1 1.0 CA B:CYS212 4.6 45.9 1.0 CA B:CYS150 4.7 51.1 1.0 CG B:GLN158 4.7 48.5 1.0 O B:GLY152 4.7 79.6 1.0 NE2 B:GLN158 4.9 47.6 1.0 N B:PRO153 5.0 69.4 1.0

Zinc binding site 10 out of 16 in the PARKINS65N


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of PARKINS65N within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:48.1 occ:1.00 SG B:CYS196 2.3 47.4 1.0 SG B:CYS166 2.3 50.7 1.0 SG B:CYS201 2.3 59.7 1.0 SG B:CYS169 2.3 47.2 1.0 CB B:CYS166 3.2 48.1 1.0 CB B:CYS196 3.4 47.1 1.0 CB B:CYS169 3.4 48.0 1.0 CB B:CYS201 3.4 58.9 1.0 N B:CYS169 3.8 47.4 1.0 OG1 B:THR173 4.1 48.8 1.0 CA B:CYS169 4.2 49.0 1.0 CB B:SER198 4.3 62.2 1.0 CA B:GLY203 4.5 60.7 1.0 CA B:CYS166 4.6 46.0 1.0 CB B:THR168 4.7 53.9 1.0 N B:GLY203 4.7 60.6 1.0 CA B:CYS196 4.7 48.6 1.0 CA B:CYS201 4.8 57.5 1.0 N B:ARG170 4.8 57.6 1.0 C B:CYS169 4.9 54.7 1.0 C B:THR168 5.0 47.2 1.0

T.G.Mcwilliams, E.Barini, R.Pohjolan-Pirhonen, S.P.Brooks, F.Singh, S.Burel, K.Balk, A.Kumar, L.Montava-Garriga, A.R.Prescott, S.M.Hassoun, F.Mouton-Liger, G.Ball, R.Hills, A.Knebel, A.Ulusoy, D.A.Di Monte, J.Tamjar, O.Antico, K.Fears, L.Smith, R.Brambilla, E.Palin, M.Valori, J.Eerola-Rautio, P.Tienari, O.Corti, S.B.Dunnett, I.G.Ganley, A.Suomalainen, M.M.K.Muqit. Phosphorylation of Parkin at Serine 65 Is Essential For Its Activationin Vivo. Open Biol V. 8 2018.
ISSN: ESSN 2046-2441
PubMed: 30404819
DOI: 10.1098/RSOB.180108