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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

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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

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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

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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

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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

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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

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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

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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

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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

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