Atomistry » Zinc » PDB 6dit-6dxq » 6djw
Atomistry »
  Zinc »
    PDB 6dit-6dxq »
      6djw »

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

Go back to Zinc Binding Sites List in 6djw
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

Go back to Zinc Binding Sites List in 6djw
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

Go back to Zinc Binding Sites List in 6djw
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

Go back to Zinc Binding Sites List in 6djw
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

Go back to Zinc Binding Sites List in 6djw
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

Go back to Zinc Binding Sites List in 6djw
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: Mon Oct 28 19:35:35 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy