Zinc in PDB 6djw: Crystal Structure of Pparkin (Rep and RING2 Deleted)-Pub-UBCH7 Complex

Enzymatic activity of Crystal Structure of Pparkin (Rep and RING2 Deleted)-Pub-UBCH7 Complex

All present enzymatic activity of Crystal Structure of Pparkin (Rep and RING2 Deleted)-Pub-UBCH7 Complex:
2.3.2.23; 2.3.2.31;

Protein crystallography data

The structure of Crystal Structure of Pparkin (Rep and RING2 Deleted)-Pub-UBCH7 Complex, PDB code: 6djw 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) 48.28 / 3.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.606, 134.606, 86.193, 90.00, 90.00, 120.00
R / Rfree (%) 26.3 / 29.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Pparkin (Rep and RING2 Deleted)-Pub-UBCH7 Complex (pdb code 6djw). 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 (Rep and RING2 Deleted)-Pub-UBCH7 Complex, PDB code: 6djw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6djw

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Zinc binding site 1 out of 6 in the Crystal Structure of Pparkin (Rep and RING2 Deleted)-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 (Rep and RING2 Deleted)-Pub-UBCH7 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:0.7
occ:1.00
 SG A:CYS195 2.3 0.1 1.0
SG A:CYS222 2.3 0.3 1.0
SG A:CYS229 2.3 0.1 1.0
SG A:CYS192 2.4 0.1 1.0
CB A:CYS192 2.9 0.8 1.0
CB A:CYS222 3.0 0.3 1.0
CB A:CYS195 3.7 0.0 1.0
CB A:CYS229 3.8 0.9 1.0
N A:CYS195 4.4 0.5 1.0
CA A:CYS192 4.4 0.4 1.0
CA A:CYS222 4.5 1.0 1.0
CA A:CYS195 4.6 0.5 1.0
O A:GLY197 4.9 0.8 1.0

Zinc binding site 2 out of 6 in 6djw

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Zinc binding site 2 out of 6 in the Crystal Structure of Pparkin (Rep and RING2 Deleted)-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 (Rep and RING2 Deleted)-Pub-UBCH7 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:0.0
occ:1.00
 NE2 A:HIS249 2.0 0.9 1.0
SG A:CYS246 2.3 0.7 1.0
SG A:CYS177 2.3 0.6 1.0
CD2 A:HIS249 2.3 0.3 1.0
SG A:CYS180 2.4 0.7 1.0
CB A:CYS177 2.9 0.7 1.0
CB A:CYS246 2.9 0.8 1.0
CE1 A:HIS249 3.2 0.2 1.0
CB A:CYS180 3.4 0.6 1.0
CG A:HIS249 3.6 0.2 1.0
N A:CYS180 3.9 0.1 1.0
ND1 A:HIS249 4.0 0.9 1.0
CA A:CYS180 4.3 0.2 1.0
CA A:CYS177 4.4 0.2 1.0
CA A:CYS246 4.4 0.2 1.0
SG A:CYS184 4.5 0.3 1.0
CB A:GLN179 4.5 0.5 1.0
C A:GLN179 4.8 0.5 1.0
CB A:HIS249 4.8 0.7 1.0
C A:CYS246 4.9 0.2 1.0
N A:GLN179 5.0 0.4 1.0

Zinc binding site 3 out of 6 in 6djw

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Zinc binding site 3 out of 6 in the Crystal Structure of Pparkin (Rep and RING2 Deleted)-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 (Rep and RING2 Deleted)-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 2.2 0.1 1.0
SG A:CYS276 2.3 0.0 1.0
SG A:CYS273 2.3 0.2 1.0
SG A:CYS295 2.3 0.2 1.0
CB A:CYS273 3.2 0.8 1.0
CB A:CYS298 3.4 0.5 1.0
CB A:CYS276 3.5 0.3 1.0
N A:CYS276 3.7 0.6 1.0
CB A:CYS295 3.8 0.8 1.0
N A:CYS295 3.9 0.7 1.0
CB A:ALA275 4.0 0.7 1.0
CA A:CYS276 4.2 0.6 1.0
C A:ALA275 4.4 0.9 1.0
CA A:CYS295 4.4 0.8 1.0
N A:CYS298 4.5 0.9 1.0
CA A:ALA275 4.5 0.4 1.0
CA A:CYS298 4.5 0.8 1.0
N A:ALA275 4.6 0.1 1.0
CA A:CYS273 4.6 0.2 1.0
CB C:ALA2 4.7 0.5 1.0
C A:CYS295 4.9 0.6 1.0
C A:CYS273 4.9 0.2 1.0
O A:CYS295 4.9 0.8 1.0

Zinc binding site 4 out of 6 in 6djw

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Zinc binding site 4 out of 6 in the Crystal Structure of Pparkin (Rep and RING2 Deleted)-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 (Rep and RING2 Deleted)-Pub-UBCH7 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1004

b:0.9
occ:1.00
 ND1 A:HIS292 2.0 0.6 1.0
SG A:CYS324 2.3 0.7 1.0
SG A:CYS288 2.3 0.7 1.0
SG A:CYS328 2.4 0.0 1.0
CE1 A:HIS292 2.7 0.7 1.0
CB A:CYS328 3.0 0.1 1.0
CB A:CYS288 3.2 0.3 1.0
CG A:HIS292 3.2 0.3 1.0
CB A:CYS324 3.4 0.9 1.0
CB A:HIS292 3.8 1.0 1.0
NE2 A:HIS292 3.9 0.3 1.0
CD2 A:HIS292 4.1 0.2 1.0
CA A:CYS328 4.2 0.2 1.0
N A:CYS328 4.3 0.7 1.0
CB A:ALA326 4.4 0.6 1.0
CA A:CYS288 4.7 0.7 1.0
N A:HIS292 4.8 0.2 1.0
CB A:SER290 4.8 0.2 1.0
CA A:CYS324 4.9 0.9 1.0
OG A:SER331 5.0 0.8 1.0
CA A:HIS292 5.0 0.9 1.0

Zinc binding site 5 out of 6 in 6djw

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Zinc binding site 5 out of 6 in the Crystal Structure of Pparkin (Rep and RING2 Deleted)-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 (Rep and RING2 Deleted)-Pub-UBCH7 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1005

b:0.2
occ:1.00
 NE2 A:HIS404 2.0 0.6 1.0
SG A:CYS399 2.3 0.3 1.0
SG A:CYS408 2.4 0.5 1.0
SG A:CYS396 2.4 0.4 1.0
CB A:CYS396 2.6 0.8 1.0
CE1 A:HIS404 2.7 0.9 1.0
CB A:CYS399 2.8 0.1 1.0
CD2 A:HIS404 3.2 0.5 1.0
CB A:CYS408 3.3 0.6 1.0
N A:CYS399 3.6 0.4 1.0
CA A:CYS399 3.8 0.6 1.0
ND1 A:HIS404 3.9 0.2 1.0
CA A:CYS396 4.0 0.4 1.0
CG A:HIS404 4.2 0.2 1.0
C A:CYS396 4.4 0.2 1.0
N A:CYS408 4.4 0.7 1.0
CA A:CYS408 4.5 0.6 1.0
O A:CYS396 4.5 0.2 1.0
C A:ASN398 4.7 0.8 1.0
N A:CYS396 4.7 0.5 1.0
N A:ASN398 4.8 0.3 1.0
CB A:ASN398 4.8 1.0 1.0
C A:CYS399 4.9 0.3 1.0
CA A:ASN398 5.0 0.6 1.0

Zinc binding site 6 out of 6 in 6djw

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Zinc binding site 6 out of 6 in the Crystal Structure of Pparkin (Rep and RING2 Deleted)-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 (Rep and RING2 Deleted)-Pub-UBCH7 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1006

b:0.5
occ:1.00
 SG A:CYS367 2.3 0.6 1.0
SG A:CYS372 2.3 0.5 1.0
SG A:CYS391 2.3 0.9 1.0
SG A:CYS387 2.3 0.4 1.0
CB A:CYS367 3.2 0.8 1.0
CB A:CYS372 3.4 0.3 1.0
CB A:CYS387 3.5 0.8 1.0
N A:CYS391 3.6 0.2 1.0
CB A:CYS391 3.6 0.1 1.0
CA A:CYS391 4.2 0.8 1.0
C A:GLY390 4.6 0.6 1.0
CA A:CYS367 4.6 0.8 1.0
CA A:GLY390 4.7 0.8 1.0
C A:CYS391 4.8 0.6 1.0
N A:GLY392 4.8 0.5 1.0
CA A:CYS387 4.8 0.7 1.0
CA A:CYS372 4.8 0.8 1.0
CB A:GLN369 4.8 0.9 1.0

Reference:

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
Page generated: Wed Dec 16 11:40:17 2020

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