Atomistry » Zinc » PDB 5d88-5dro » 5din
Atomistry »
  Zinc »
    PDB 5d88-5dro »
      5din »

Zinc in PDB 5din: Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination

Enzymatic activity of Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination

All present enzymatic activity of Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination:
6.3.2.19;

Protein crystallography data

The structure of Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination, PDB code: 5din was solved by J.Sivaraman, D.Nayak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.24 / 1.86
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.969, 69.399, 52.249, 90.00, 115.41, 90.00
R / Rfree (%) 19 / 23.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination (pdb code 5din). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination, PDB code: 5din:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5din

Go back to Zinc Binding Sites List in 5din
Zinc binding site 1 out of 8 in the Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:14.5
occ:1.00
 SG A:CYS54 2.3 15.0 1.0
SG A:CYS51 2.3 12.6 1.0
SG A:CYS34 2.4 14.9 1.0
SG A:CYS31 2.4 14.3 1.0
CB A:CYS31 3.0 12.3 1.0
CB A:CYS51 3.1 14.6 1.0
CB A:CYS54 3.3 13.4 1.0
CB A:CYS34 3.3 17.1 1.0
ND2 A:ASN16 3.8 15.8 1.0
N A:CYS34 3.8 14.8 1.0
N A:CYS51 4.0 12.0 1.0
CA A:CYS34 4.2 17.3 1.0
CA A:CYS51 4.2 12.6 1.0
CA A:CYS31 4.5 11.7 1.0
O A:HOH375 4.5 21.0 1.0
CA A:CYS54 4.7 15.7 1.0
CB A:ILE33 4.8 17.4 1.0
O A:GLN36 4.9 12.4 1.0
C A:ILE33 4.9 17.0 1.0
O A:HOH404 4.9 23.9 1.0
N A:CYS54 5.0 14.6 1.0
C A:CYS31 5.0 15.2 1.0

Zinc binding site 2 out of 8 in 5din

Go back to Zinc Binding Sites List in 5din
Zinc binding site 2 out of 8 in the Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:22.3
occ:1.00
 CD2 A:HIS48 2.0 20.1 1.0
OD2 A:ASP68 2.1 25.7 1.0
OD1 A:ASP68 2.1 28.5 1.0
SG A:CYS46 2.2 24.6 1.0
SG A:CYS65 2.3 26.0 1.0
CG A:ASP68 2.4 26.4 1.0
NE2 A:HIS48 2.9 25.4 1.0
CG A:HIS48 3.1 21.0 1.0
CB A:CYS65 3.2 28.5 1.0
CB A:CYS46 3.3 24.2 1.0
CB A:HIS48 3.8 20.2 1.0
CB A:ASP68 3.9 30.0 1.0
CE1 A:HIS48 4.0 21.1 1.0
O A:HOH303 4.1 26.2 1.0
ND1 A:HIS48 4.2 23.3 1.0
N A:ASP68 4.3 31.5 1.0
OG1 A:THR44 4.3 21.8 1.0
O A:CYS46 4.5 23.9 1.0
CA A:CYS46 4.5 21.6 1.0
C A:CYS46 4.5 21.5 1.0
CB A:LEU67 4.5 27.5 1.0
N A:HIS48 4.6 18.4 1.0
CA A:CYS65 4.6 29.1 1.0
CA A:ASP68 4.7 32.4 1.0
CA A:HIS48 4.9 16.8 1.0
C A:LEU67 5.0 32.7 1.0

Zinc binding site 3 out of 8 in 5din

Go back to Zinc Binding Sites List in 5din
Zinc binding site 3 out of 8 in the Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:21.0
occ:1.00
 ND1 A:HIS17 2.0 19.9 1.0
NE2 A:HIS11 2.0 22.1 1.0
SG A:CYS7 2.3 22.6 1.0
SG A:CYS4 2.3 22.6 1.0
CB A:CYS4 2.8 22.1 1.0
CE1 A:HIS17 2.9 22.4 1.0
CD2 A:HIS11 3.0 19.5 1.0
CE1 A:HIS11 3.1 21.4 1.0
CG A:HIS17 3.1 19.9 1.0
CB A:CYS7 3.3 23.4 1.0
CB A:HIS17 3.5 19.4 1.0
CA A:HIS17 3.6 20.2 1.0
N A:CYS7 3.9 25.1 1.0
NE2 A:HIS17 4.1 23.9 1.0
CG A:HIS11 4.1 19.8 1.0
ND1 A:HIS11 4.1 18.4 1.0
CD2 A:HIS17 4.2 19.4 1.0
CA A:CYS7 4.2 23.2 1.0
CA A:CYS4 4.3 26.6 1.0
N A:HIS17 4.4 16.6 1.0
O A:GLN9 4.6 28.7 1.0
N A:LEU18 4.7 17.6 1.0
CB A:GLU6 4.7 29.2 1.0
C A:HIS17 4.7 19.3 1.0
C A:GLU6 4.7 26.9 1.0
N A:GLU6 4.9 28.9 1.0
C A:CYS4 4.9 28.3 1.0
C A:CYS7 5.0 22.7 1.0

Zinc binding site 4 out of 8 in 5din

Go back to Zinc Binding Sites List in 5din
Zinc binding site 4 out of 8 in the Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:24.5
occ:1.00
 NE2 A:HIS113 2.1 25.6 1.0
SG A:CYS118 2.3 25.1 1.0
SG A:CYS101 2.3 28.3 1.0
SG A:CYS95 2.4 23.6 1.0
CB A:CYS101 2.9 26.1 1.0
CE1 A:HIS113 3.0 26.0 1.0
CD2 A:HIS113 3.1 22.3 1.0
CB A:CYS118 3.2 22.1 1.0
CB A:CYS95 3.2 24.9 1.0
ND1 A:HIS113 4.1 25.3 1.0
CA A:CYS118 4.2 21.0 1.0
CG A:HIS113 4.2 24.7 1.0
CA A:CYS101 4.4 29.0 1.0
CA A:CYS95 4.7 24.2 1.0
CB A:ASP103 4.7 28.9 1.0
CD2 A:LEU114 4.7 25.0 1.0
C A:CYS101 5.0 29.3 1.0

Zinc binding site 5 out of 8 in 5din

Go back to Zinc Binding Sites List in 5din
Zinc binding site 5 out of 8 in the Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:16.8
occ:1.00
 NE2 B:HIS113 2.0 16.6 1.0
SG B:CYS118 2.3 16.6 1.0
SG B:CYS95 2.3 14.5 1.0
SG B:CYS101 2.4 17.1 1.0
CD2 B:HIS113 3.0 15.3 1.0
CE1 B:HIS113 3.0 18.3 1.0
CB B:CYS118 3.2 16.5 1.0
CB B:CYS101 3.2 17.7 1.0
CB B:CYS95 3.2 16.1 1.0
CA B:CYS118 4.0 15.6 1.0
ND1 B:HIS113 4.1 15.8 1.0
CG B:HIS113 4.2 16.5 1.0
CD B:PRO119 4.5 17.7 1.0
CA B:CYS101 4.6 20.4 1.0
CA B:CYS95 4.7 16.6 1.0
CD2 B:LEU114 4.7 18.2 1.0
CD2 B:PHE97 4.9 19.4 1.0
CB B:PHE97 4.9 18.1 1.0
N B:CYS118 4.9 17.0 1.0
C B:CYS118 5.0 17.7 1.0

Zinc binding site 6 out of 8 in 5din

Go back to Zinc Binding Sites List in 5din
Zinc binding site 6 out of 8 in the Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:14.8
occ:1.00
 ND1 B:HIS17 2.1 18.7 1.0
NE2 B:HIS11 2.1 16.6 1.0
SG B:CYS7 2.2 14.4 1.0
SG B:CYS4 2.3 17.8 1.0
CE1 B:HIS17 3.0 19.1 1.0
CB B:CYS4 3.0 18.1 1.0
CD2 B:HIS11 3.0 15.8 1.0
CE1 B:HIS11 3.1 16.4 1.0
CG B:HIS17 3.1 16.2 1.0
CB B:CYS7 3.2 13.7 1.0
CB B:HIS17 3.5 14.4 1.0
CA B:HIS17 3.6 13.1 1.0
N B:CYS7 3.8 16.6 1.0
CA B:CYS7 4.0 15.7 1.0
NE2 B:HIS17 4.1 22.7 1.0
ND1 B:HIS11 4.2 16.7 1.0
CG B:HIS11 4.2 14.0 1.0
CD2 B:HIS17 4.2 21.1 1.0
CA B:CYS4 4.5 17.9 1.0
N B:LEU18 4.5 13.4 1.0
N B:HIS17 4.5 14.2 1.0
C B:HIS17 4.6 14.9 1.0
C B:GLU6 4.7 19.6 1.0
C B:CYS7 4.8 15.8 1.0
O B:GLN9 4.8 14.9 1.0
CB B:GLU6 4.8 21.4 1.0
N B:GLU6 5.0 21.3 1.0
C B:CYS4 5.0 19.8 1.0

Zinc binding site 7 out of 8 in 5din

Go back to Zinc Binding Sites List in 5din
Zinc binding site 7 out of 8 in the Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn203

b:14.8
occ:1.00
 SG B:CYS34 2.2 17.2 1.0
SG B:CYS54 2.3 15.2 1.0
SG B:CYS51 2.3 13.9 1.0
SG B:CYS31 2.4 15.7 1.0
CB B:CYS31 3.0 14.8 1.0
CB B:CYS51 3.0 12.5 1.0
CB B:CYS34 3.2 17.6 1.0
CB B:CYS54 3.3 15.9 1.0
N B:CYS34 3.7 16.6 1.0
ND2 B:ASN16 3.9 16.0 1.0
N B:CYS51 4.0 11.8 1.0
CA B:CYS34 4.0 17.8 1.0
CA B:CYS51 4.1 12.6 1.0
CA B:CYS31 4.5 17.0 1.0
O B:HOH356 4.5 16.8 1.0
CA B:CYS54 4.6 16.9 1.0
CB B:ILE33 4.7 18.0 1.0
C B:ILE33 4.8 19.3 1.0
C B:CYS34 4.9 19.1 1.0
N B:CYS54 4.9 15.7 1.0

Zinc binding site 8 out of 8 in 5din

Go back to Zinc Binding Sites List in 5din
Zinc binding site 8 out of 8 in the Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn204

b:18.0
occ:1.00
 ND1 B:HIS48 2.1 20.1 1.0
OD2 B:ASP68 2.2 20.7 1.0
SG B:CYS65 2.2 19.0 1.0
SG B:CYS46 2.2 20.1 1.0
CG B:ASP68 2.8 23.0 1.0
CE1 B:HIS48 2.9 23.1 1.0
OD1 B:ASP68 3.0 22.0 1.0
CB B:CYS65 3.2 19.4 1.0
CG B:HIS48 3.2 20.2 1.0
CB B:CYS46 3.3 20.0 1.0
CB B:HIS48 3.7 16.9 1.0
NE2 B:HIS48 4.1 25.3 1.0
OG1 B:THR44 4.1 17.2 1.0
CB B:ASP68 4.2 22.9 1.0
O B:HOH324 4.2 28.6 1.0
CD2 B:HIS48 4.2 20.6 1.0
N B:ASP68 4.4 20.5 1.0
CB B:LEU67 4.5 20.4 1.0
CA B:CYS46 4.5 22.8 1.0
CA B:CYS65 4.6 17.4 1.0
O B:CYS46 4.6 25.8 1.0
C B:CYS46 4.7 24.9 1.0
N B:HIS48 4.8 16.1 1.0
CA B:HIS48 4.9 17.0 1.0
CA B:ASP68 4.9 22.4 1.0

Reference:

D.Nayak, J.Sivaraman. Structural Basis For the Indispensable Role of A Unique Zinc Finger Motif in LNX2 Ubiquitination. Oncotarget V. 6 34342 2015.
ISSN: ESSN 1949-2553
PubMed: 26451611
DOI: 10.18632/ONCOTARGET.5326
Page generated: Sun Oct 27 14:46:23 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy