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Zinc in PDB 4i1h: Structure of Parkin E3 Ligase

Protein crystallography data

The structure of Structure of Parkin E3 Ligase, PDB code: 4i1h was solved by J.C.Lougheed, E.Brecht, N.H.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.97 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 87.110, 133.930, 66.210, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Parkin E3 Ligase (pdb code 4i1h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Parkin E3 Ligase, PDB code: 4i1h:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4i1h

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Zinc binding site 1 out of 8 in the Structure of Parkin E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Parkin E3 Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:6.5
occ:0.70
NE2 A:HIS215 2.2 13.1 1.0
SG A:CYS150 2.2 15.4 1.0
SG A:CYS154 2.3 17.1 1.0
SG A:CYS212 2.3 14.5 1.0
CD2 A:HIS215 2.8 13.2 1.0
CB A:CYS150 3.0 15.6 1.0
CB A:CYS212 3.2 12.8 1.0
CB A:CYS154 3.3 20.2 1.0
CE1 A:HIS215 3.3 14.5 1.0
N A:CYS154 4.0 22.1 1.0
O A:HOH673 4.0 18.0 1.0
CG A:HIS215 4.1 14.6 1.0
CA A:CYS154 4.3 20.7 1.0
CG A:GLN158 4.3 16.5 1.0
ND1 A:HIS215 4.3 14.1 1.0
CD A:PRO153 4.4 25.7 1.0
CB A:ALA214 4.5 14.7 1.0
CA A:CYS150 4.5 17.0 1.0
CA A:CYS212 4.6 14.8 1.0
N A:PRO153 4.6 27.4 1.0
CG A:PRO153 4.7 28.2 1.0
O A:GLY152 4.7 34.8 1.0
NE2 A:GLN158 4.9 19.1 1.0
C A:GLY152 4.9 27.9 1.0
N A:ALA214 4.9 15.5 1.0
CB A:GLN158 5.0 14.8 1.0

Zinc binding site 2 out of 8 in 4i1h

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Zinc binding site 2 out of 8 in the Structure of Parkin E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Parkin E3 Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:28.7
occ:1.00
SG A:CYS196 2.0 25.3 1.0
SG A:CYS169 2.4 31.0 1.0
SG A:CYS166 2.4 24.3 1.0
SG A:CYS201 2.5 33.6 1.0
CB A:CYS166 3.1 21.1 1.0
CB A:CYS196 3.1 26.3 1.0
CB A:CYS201 3.2 38.6 1.0
CB A:CYS169 3.4 31.4 1.0
N A:CYS169 3.8 32.2 1.0
OG1 A:THR173 4.2 24.9 1.0
CA A:CYS169 4.2 33.5 1.0
CA A:CYS196 4.5 26.7 1.0
CA A:CYS166 4.5 20.8 1.0
CA A:GLY203 4.5 27.3 1.0
CB A:SER198 4.6 42.8 1.0
N A:GLY203 4.6 29.8 1.0
CB A:THR168 4.6 28.8 1.0
CA A:CYS201 4.7 39.4 1.0
OG A:SER198 4.8 47.3 1.0
C A:THR168 4.9 31.9 1.0

Zinc binding site 3 out of 8 in 4i1h

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Zinc binding site 3 out of 8 in the Structure of Parkin E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Parkin E3 Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:12.2
occ:1.00
SG A:CYS241 2.3 14.4 1.0
SG A:CYS260 2.4 11.9 1.0
SG A:CYS263 2.4 14.4 1.0
SG A:CYS238 2.4 10.1 1.0
CB A:CYS263 3.2 12.7 1.0
CB A:CYS238 3.3 10.5 1.0
CB A:CYS241 3.3 12.8 1.0
CB A:CYS260 3.6 10.8 1.0
N A:CYS241 3.7 13.3 1.0
OG1 A:THR240 4.0 12.7 1.0
N A:CYS260 4.0 11.4 1.0
CA A:CYS241 4.1 13.2 1.0
N A:CYS263 4.2 13.2 1.0
CA A:CYS260 4.3 11.1 1.0
CA A:CYS263 4.3 13.1 1.0
O A:HOH632 4.4 11.9 1.0
CA A:CYS238 4.7 10.7 1.0
C A:THR240 4.8 14.2 1.0
O A:CYS260 4.9 9.8 1.0
C A:CYS260 4.9 10.6 1.0
C A:CYS241 4.9 13.2 1.0

Zinc binding site 4 out of 8 in 4i1h

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Zinc binding site 4 out of 8 in the Structure of Parkin E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Parkin E3 Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:11.6
occ:1.00
ND1 A:HIS257 2.0 9.0 1.0
SG A:CYS289 2.3 11.2 1.0
SG A:CYS253 2.3 11.9 1.0
SG A:CYS293 2.3 12.7 1.0
CE1 A:HIS257 3.0 9.3 1.0
CG A:HIS257 3.1 9.8 1.0
CB A:CYS289 3.2 11.7 1.0
CB A:CYS293 3.2 12.3 1.0
CB A:CYS253 3.3 12.2 1.0
CB A:HIS257 3.4 9.2 1.0
O A:HOH615 4.1 11.9 1.0
NE2 A:HIS257 4.2 9.6 1.0
CB A:ALA291 4.2 13.0 1.0
CD2 A:HIS257 4.2 9.9 1.0
N A:HIS257 4.4 9.5 1.0
CB A:SER255 4.5 10.7 1.0
CA A:CYS293 4.5 14.3 1.0
N A:CYS293 4.5 15.3 1.0
CA A:HIS257 4.5 9.8 1.0
CA A:CYS289 4.7 11.9 1.0
CA A:CYS253 4.8 12.7 1.0
CB A:PHE251 4.9 9.4 1.0
N A:ALA291 4.9 13.5 1.0

Zinc binding site 5 out of 8 in 4i1h

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Zinc binding site 5 out of 8 in the Structure of Parkin E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Parkin E3 Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:21.1
occ:1.00
SG A:CYS332 2.2 21.3 1.0
SG A:CYS352 2.3 22.7 1.0
SG A:CYS360 2.4 26.2 1.0
SG A:CYS337 2.4 23.0 1.0
CB A:CYS332 3.1 22.3 1.0
CB A:CYS352 3.1 25.8 1.0
CB A:CYS337 3.3 23.5 1.0
CB A:CYS360 3.4 30.2 1.0
N A:CYS360 3.7 34.4 1.0
CA A:CYS360 4.1 33.4 1.0
CB A:ARG334 4.5 26.8 1.0
CA A:CYS332 4.5 21.5 1.0
CA A:CYS352 4.6 28.8 1.0
CA A:CYS337 4.6 26.8 1.0
N A:GLY338 4.7 27.2 1.0
N A:ALA339 4.7 21.2 1.0
CB A:ALA339 4.8 20.2 1.0
C A:GLY359 4.8 39.4 1.0
CB A:PHE362 4.8 25.5 1.0
C A:CYS360 4.8 32.4 1.0
CA A:GLY359 4.9 42.9 1.0
N A:GLY361 4.9 32.5 1.0
N A:PHE362 5.0 29.1 1.0

Zinc binding site 6 out of 8 in 4i1h

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Zinc binding site 6 out of 8 in the Structure of Parkin E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Parkin E3 Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:33.3
occ:1.00
NE2 A:HIS373 2.2 33.2 1.0
SG A:CYS377 2.3 34.3 1.0
SG A:CYS368 2.4 35.5 1.0
SG A:CYS365 2.5 30.0 1.0
CE1 A:HIS373 3.1 32.0 1.0
CB A:CYS365 3.1 26.0 1.0
CD2 A:HIS373 3.2 34.7 1.0
CB A:CYS368 3.2 29.2 1.0
CB A:CYS377 3.4 44.0 1.0
N A:CYS368 3.7 33.2 1.0
CA A:CYS377 3.9 49.3 1.0
CA A:CYS368 4.1 32.0 1.0
NH1 A:ARG348 4.1 34.0 1.0
ND1 A:HIS373 4.3 31.6 1.0
CG A:HIS373 4.4 32.7 1.0
N A:CYS377 4.5 47.3 1.0
CA A:CYS365 4.6 27.0 1.0
CB A:GLU367 4.8 30.0 1.0
C A:GLU367 4.8 31.6 1.0
C A:CYS368 4.9 32.3 1.0
O A:CYS365 4.9 27.3 1.0
C A:CYS365 5.0 28.6 1.0

Zinc binding site 7 out of 8 in 4i1h

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Zinc binding site 7 out of 8 in the Structure of Parkin E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Parkin E3 Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:17.5
occ:1.00
SG A:CYS441 2.3 18.5 1.0
SG A:CYS436 2.4 16.0 1.0
SG A:CYS418 2.4 15.9 1.0
SG A:CYS421 2.4 17.4 1.0
CB A:CYS441 3.0 18.9 1.0
CB A:CYS418 3.1 14.2 1.0
CB A:CYS436 3.2 13.8 1.0
CB A:CYS421 3.3 17.7 1.0
N A:CYS421 3.6 19.9 1.0
CA A:CYS421 4.0 18.2 1.0
CA A:CYS441 4.5 19.1 1.0
CA A:CYS418 4.6 14.6 1.0
CB A:GLN438 4.6 24.7 1.0
CA A:CYS436 4.6 16.1 1.0
CG A:GLN438 4.6 28.2 1.0
CB A:ARG420 4.7 22.8 1.0
C A:ARG420 4.7 21.3 1.0
N A:ARG442 4.7 19.8 1.0
CB A:LEU443 4.8 14.4 1.0
N A:LEU443 4.8 16.3 1.0
C A:CYS421 4.8 19.3 1.0
C A:CYS441 4.9 20.7 1.0
N A:ARG420 5.0 19.3 1.0

Zinc binding site 8 out of 8 in 4i1h

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Zinc binding site 8 out of 8 in the Structure of Parkin E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Parkin E3 Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn508

b:10.9
occ:1.00
NE2 A:HIS461 2.0 11.2 1.0
SG A:CYS446 2.2 10.2 1.0
SG A:CYS457 2.3 10.5 1.0
SG A:CYS449 2.4 12.8 1.0
CE1 A:HIS461 2.9 11.5 1.0
CD2 A:HIS461 3.1 11.2 1.0
CB A:CYS446 3.2 10.0 1.0
CB A:CYS449 3.2 12.6 1.0
CB A:CYS457 3.2 9.4 1.0
O A:HOH617 3.6 13.3 1.0
N A:CYS449 3.8 12.5 1.0
CA A:CYS457 4.0 9.6 1.0
ND1 A:HIS461 4.1 10.9 1.0
CA A:CYS449 4.2 13.2 1.0
CG A:HIS461 4.2 11.2 1.0
CB A:ASN448 4.4 9.9 1.0
CA A:CYS446 4.6 10.0 1.0
ND2 A:ASN448 4.7 10.3 1.0
C A:ASN448 4.9 12.0 1.0
N A:CYS457 4.9 9.3 1.0

Reference:

B.E.Riley, J.C.Lougheed, K.Callaway, M.Velasquez, E.Brecht, L.Nguyen, T.Shaler, D.Walker, Y.Yang, K.Regnstrom, L.Diep, Z.Zhang, S.Chiou, M.Bova, D.R.Artis, N.Yao, J.Baker, T.Yednock, J.A.Johnston. Structure and Function of Parkin E3 Ubiquitin Ligase Reveals Aspects of Ring and Hect Ligases. Nat Commun V. 4 1982 2013.
ISSN: ESSN 2041-1723
PubMed: 23770887
DOI: 10.1038/NCOMMS2982
Page generated: Wed Dec 16 05:23:13 2020

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