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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

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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

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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

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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

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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

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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

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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

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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

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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

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