Atomistry » Zinc » PDB 5h6b-5ho1 » 5h7s
Atomistry »
  Zinc »
    PDB 5h6b-5ho1 »
      5h7s »

Zinc in PDB 5h7s: Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain

Enzymatic activity of Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain

All present enzymatic activity of Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain:
2.3.2.23; 2.3.2.27;

Protein crystallography data

The structure of Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain, PDB code: 5h7s was solved by D.Nayak, J.Sivaraman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 105.98 / 3.49
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 122.372, 122.372, 135.199, 90.00, 90.00, 120.00
R / Rfree (%) 24.1 / 28.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain (pdb code 5h7s). 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 of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain, PDB code: 5h7s:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5h7s

Go back to Zinc Binding Sites List in 5h7s
Zinc binding site 1 out of 8 in the Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:93.1
occ:1.00
 ND1 D:HIS17 2.0 89.6 1.0
NE2 D:HIS11 2.0 94.9 1.0
SG D:CYS7 2.3 92.2 1.0
SG D:CYS4 2.3 0.2 1.0
CE1 D:HIS17 2.9 91.7 1.0
CG D:HIS17 3.0 85.8 1.0
CD2 D:HIS11 3.0 96.3 1.0
CE1 D:HIS11 3.0 95.3 1.0
CB D:CYS4 3.3 0.7 1.0
CB D:CYS7 3.3 89.0 1.0
CB D:HIS17 3.5 83.2 1.0
CA D:HIS17 3.8 83.6 1.0
N D:CYS7 3.9 93.8 1.0
NE2 D:HIS17 4.0 89.4 1.0
CD2 D:HIS17 4.1 85.7 1.0
ND1 D:HIS11 4.1 97.0 1.0
CG D:HIS11 4.2 97.7 1.0
CA D:CYS7 4.2 91.5 1.0
CB D:VAL6 4.5 93.9 1.0
N D:PHE18 4.7 83.0 1.0
N D:HIS17 4.7 83.0 1.0
CA D:CYS4 4.7 0.7 1.0
C D:HIS17 4.8 81.6 1.0
N D:VAL6 4.8 0.9 1.0
C D:VAL6 4.9 94.3 1.0
C D:CYS7 4.9 94.2 1.0
C D:CYS4 5.0 0.8 1.0
CA D:VAL6 5.0 96.8 1.0

Zinc binding site 2 out of 8 in 5h7s

Go back to Zinc Binding Sites List in 5h7s
Zinc binding site 2 out of 8 in the Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:71.6
occ:1.00
 SG D:CYS51 2.3 70.0 1.0
SG D:CYS31 2.3 69.4 1.0
SG D:CYS54 2.3 76.1 1.0
SG D:CYS34 2.3 72.5 1.0
CB D:CYS31 3.1 67.1 1.0
CB D:CYS51 3.3 72.2 1.0
CB D:CYS54 3.3 76.7 1.0
CB D:CYS34 3.4 75.2 1.0
N D:CYS34 3.7 74.1 1.0
O D:CYS34 3.8 70.5 1.0
ND2 D:ASN16 3.9 76.7 1.0
CA D:CYS34 4.0 74.6 1.0
N D:CYS51 4.1 69.9 1.0
CA D:CYS51 4.3 71.4 1.0
C D:CYS34 4.4 72.5 1.0
CA D:CYS31 4.5 66.1 1.0
CA D:CYS54 4.7 80.3 1.0
CB D:ILE33 4.8 75.6 1.0
C D:ILE33 4.8 75.0 1.0
C D:CYS31 4.9 67.2 1.0

Zinc binding site 3 out of 8 in 5h7s

Go back to Zinc Binding Sites List in 5h7s
Zinc binding site 3 out of 8 in the Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn203

b:91.9
occ:1.00
 SG D:CYS46 1.4 76.3 1.0
SG D:CYS65 1.9 75.6 1.0
ND1 D:HIS48 2.3 71.7 1.0
OD1 D:ASP68 2.5 79.4 1.0
CB D:CYS65 2.8 79.6 1.0
CB D:CYS46 2.9 78.2 1.0
CE1 D:HIS48 3.0 72.1 1.0
OD2 D:ASP68 3.2 78.0 1.0
CG D:ASP68 3.2 79.2 1.0
CG D:HIS48 3.4 69.7 1.0
CB D:HIS48 3.9 69.2 1.0
CA D:CYS46 4.2 78.4 1.0
NE2 D:HIS48 4.2 70.6 1.0
CA D:CYS65 4.2 81.4 1.0
OG1 D:THR44 4.2 73.6 1.0
CB D:MET67 4.3 73.7 1.0
C D:CYS46 4.4 75.9 1.0
CD2 D:HIS48 4.4 69.0 1.0
N D:ASP68 4.5 79.7 1.0
N D:HIS48 4.6 69.9 1.0
O D:CYS65 4.6 81.9 1.0
OH D:TYR50 4.6 72.2 1.0
CB D:ASP68 4.6 80.9 1.0
C D:CYS65 4.6 81.1 1.0
O D:CYS46 4.7 76.0 1.0
CD D:LYS70 4.8 84.6 1.0
N D:GLY47 4.9 74.1 1.0
CA D:HIS48 4.9 68.4 1.0

Zinc binding site 4 out of 8 in 5h7s

Go back to Zinc Binding Sites List in 5h7s
Zinc binding site 4 out of 8 in the Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn204

b:0.1
occ:1.00
 NE2 D:HIS113 2.0 0.6 1.0
SG D:CYS95 2.3 0.8 1.0
SG D:CYS101 2.3 0.3 1.0
SG D:CYS118 2.3 0.4 1.0
CE1 D:HIS113 3.0 0.7 1.0
CD2 D:HIS113 3.0 0.8 1.0
CB D:CYS101 3.3 0.3 1.0
CB D:CYS95 3.4 0.0 1.0
CB D:CYS118 3.4 0.1 1.0
CA D:CYS118 4.1 0.7 1.0
ND1 D:HIS113 4.1 0.4 1.0
CG D:HIS113 4.1 0.3 1.0
CE1 D:PHE114 4.5 0.9 1.0
CD1 D:PHE114 4.6 0.8 1.0
CA D:CYS95 4.6 97.7 1.0
CB D:GLN103 4.6 0.9 1.0
O D:SER117 4.7 0.2 1.0
CA D:CYS101 4.7 0.8 1.0
C D:CYS101 5.0 0.1 1.0

Zinc binding site 5 out of 8 in 5h7s

Go back to Zinc Binding Sites List in 5h7s
Zinc binding site 5 out of 8 in the Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:90.7
occ:1.00
 NE2 B:HIS11 2.0 91.4 1.0
ND1 B:HIS17 2.0 87.8 1.0
SG B:CYS7 2.3 90.3 1.0
SG B:CYS4 2.3 96.8 1.0
CE1 B:HIS17 2.9 89.7 1.0
CD2 B:HIS11 3.0 92.4 1.0
CE1 B:HIS11 3.0 91.5 1.0
CG B:HIS17 3.1 84.6 1.0
CB B:CYS7 3.3 88.0 1.0
CB B:CYS4 3.3 99.3 1.0
CB B:HIS17 3.5 82.4 1.0
N B:CYS7 3.8 92.5 1.0
CA B:HIS17 3.8 82.4 1.0
NE2 B:HIS17 4.0 87.8 1.0
CD2 B:HIS17 4.1 84.5 1.0
ND1 B:HIS11 4.1 92.6 1.0
CA B:CYS7 4.1 90.5 1.0
CG B:HIS11 4.2 93.2 1.0
CB B:VAL6 4.5 93.0 1.0
N B:PHE18 4.7 82.4 1.0
CA B:CYS4 4.7 0.7 1.0
N B:HIS17 4.8 81.6 1.0
N B:VAL6 4.8 98.8 1.0
C B:VAL6 4.8 93.4 1.0
C B:HIS17 4.9 81.0 1.0
C B:CYS7 4.9 92.8 1.0
C B:CYS4 5.0 0.5 1.0
CA B:VAL6 5.0 95.6 1.0

Zinc binding site 6 out of 8 in 5h7s

Go back to Zinc Binding Sites List in 5h7s
Zinc binding site 6 out of 8 in the Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:71.3
occ:1.00
 SG B:CYS34 2.3 72.6 1.0
SG B:CYS51 2.3 69.9 1.0
SG B:CYS54 2.3 74.7 1.0
SG B:CYS31 2.3 69.4 1.0
CB B:CYS31 3.1 67.7 1.0
CB B:CYS51 3.3 71.5 1.0
CB B:CYS54 3.3 74.8 1.0
CB B:CYS34 3.3 74.9 1.0
N B:CYS34 3.6 74.0 1.0
O B:CYS34 3.8 71.6 1.0
CA B:CYS34 4.0 74.8 1.0
N B:CYS51 4.1 69.4 1.0
ND2 B:ASN16 4.2 74.9 1.0
CA B:CYS51 4.3 70.8 1.0
C B:CYS34 4.4 73.4 1.0
CA B:CYS31 4.5 67.0 1.0
CA B:CYS54 4.7 77.5 1.0
CB B:ILE33 4.7 74.4 1.0
C B:ILE33 4.8 74.8 1.0
C B:CYS31 4.9 68.2 1.0

Zinc binding site 7 out of 8 in 5h7s

Go back to Zinc Binding Sites List in 5h7s
Zinc binding site 7 out of 8 in the Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn203

b:91.9
occ:1.00
 SG B:CYS46 1.4 72.1 1.0
SG B:CYS65 1.9 72.3 1.0
ND1 B:HIS48 2.3 68.9 1.0
OD1 B:ASP68 2.7 75.1 1.0
CB B:CYS46 2.7 73.5 1.0
CB B:CYS65 2.8 75.5 1.0
CE1 B:HIS48 3.1 69.3 1.0
OD2 B:ASP68 3.3 73.6 1.0
CG B:ASP68 3.4 74.8 1.0
CG B:HIS48 3.4 67.5 1.0
CB B:HIS48 3.8 67.1 1.0
OG1 B:THR44 4.0 70.4 1.0
CA B:CYS46 4.0 73.5 1.0
C B:CYS46 4.2 71.4 1.0
NE2 B:HIS48 4.3 68.4 1.0
CA B:CYS65 4.3 77.2 1.0
CD2 B:HIS48 4.4 67.2 1.0
N B:HIS48 4.4 67.2 1.0
CB B:MET67 4.5 71.8 1.0
O B:CYS46 4.6 71.2 1.0
OH B:TYR50 4.6 70.3 1.0
N B:GLY47 4.7 70.1 1.0
N B:ASP68 4.7 76.3 1.0
C B:CYS65 4.7 77.3 1.0
O B:CYS65 4.8 78.0 1.0
CA B:HIS48 4.8 66.3 1.0
CD B:LYS70 4.8 78.2 1.0
CB B:ASP68 4.8 76.6 1.0
CB B:THR44 4.9 72.3 1.0

Zinc binding site 8 out of 8 in 5h7s

Go back to Zinc Binding Sites List in 5h7s
Zinc binding site 8 out of 8 in the Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn204

b:0.7
occ:1.00
 NE2 B:HIS113 2.1 0.7 1.0
SG B:CYS118 2.3 0.7 1.0
SG B:CYS101 2.3 0.8 1.0
SG B:CYS95 2.3 0.2 1.0
CE1 B:HIS113 3.0 0.9 1.0
CD2 B:HIS113 3.1 0.1 1.0
CB B:CYS101 3.3 1.0 1.0
CB B:CYS118 3.4 0.4 1.0
CB B:CYS95 3.4 0.2 1.0
CA B:CYS118 4.0 0.8 1.0
ND1 B:HIS113 4.1 0.9 1.0
CG B:HIS113 4.2 0.9 1.0
CE1 B:PHE114 4.6 0.8 1.0
CD1 B:PHE114 4.6 0.6 1.0
O B:SER117 4.6 0.5 1.0
CA B:CYS95 4.7 98.3 1.0
CB B:GLN103 4.7 0.7 1.0
CA B:CYS101 4.7 0.4 1.0
C B:CYS101 5.0 0.5 1.0

Reference:

D.Nayak, J.Sivaraman. Structure of LNX1:UBC13~Ubiquitin Complex Reveals the Role of Additional Motifs For the E3 Ligase Activity of LNX1. J. Mol. Biol. V. 430 1173 2018.
ISSN: ESSN 1089-8638
PubMed: 29496391
DOI: 10.1016/J.JMB.2018.02.016
Page generated: Sun Oct 27 17:21:42 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