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Zinc in PDB 5h7r: Structural Basis of the Flanking Zinc-Finger Motifs Crucial For the E3 Ligase Activity of the LNX1 Ring Domain

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: 5h7r 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) 79.88 / 1.70
Space group P 62 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.375, 92.375, 84.410, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 21.5

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 5h7r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 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: 5h7r:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5h7r

Go back to Zinc Binding Sites List in 5h7r
Zinc binding site 1 out of 4 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:27.0
occ:1.00
NE2 D:HIS11 2.0 23.9 1.0
SG D:CYS4 2.3 29.8 1.0
CD2 D:HIS17 2.3 30.1 1.0
SG D:CYS7 2.3 23.5 1.0
NE2 D:HIS17 2.7 30.3 1.0
CE1 D:HIS11 2.9 33.3 1.0
CD2 D:HIS11 3.0 25.3 1.0
CB D:CYS4 3.0 44.1 1.0
CG D:HIS17 3.2 29.6 1.0
CB D:CYS7 3.4 23.3 1.0
CA D:HIS17 3.7 25.4 1.0
CE1 D:HIS17 3.7 27.0 1.0
N D:CYS7 3.7 19.3 1.0
CB D:HIS17 3.9 26.2 1.0
ND1 D:HIS17 3.9 33.0 1.0
ND1 D:HIS11 4.1 28.5 1.0
CA D:CYS7 4.1 23.5 1.0
CG D:HIS11 4.2 30.6 1.0
N D:HIS17 4.4 20.1 1.0
CB D:VAL6 4.5 27.4 1.0
CA D:CYS4 4.5 34.4 1.0
N D:PHE18 4.7 22.2 1.0
C D:VAL6 4.7 21.5 1.0
C D:HIS17 4.8 23.9 1.0
C D:CYS7 4.8 23.4 1.0
CA D:VAL6 5.0 26.1 1.0
N D:VAL6 5.0 29.9 1.0
C D:CYS4 5.0 28.4 1.0
N D:GLY8 5.0 22.4 1.0

Zinc binding site 2 out of 4 in 5h7r

Go back to Zinc Binding Sites List in 5h7r
Zinc binding site 2 out of 4 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:22.7
occ:1.00
SG D:CYS31 2.3 21.8 1.0
SG D:CYS54 2.3 23.4 1.0
SG D:CYS34 2.3 23.2 1.0
SG D:CYS51 2.3 21.4 1.0
CB D:CYS31 3.0 22.1 1.0
CB D:CYS51 3.2 20.5 1.0
CB D:CYS34 3.3 26.9 1.0
CB D:CYS54 3.3 21.3 1.0
N D:CYS34 3.8 28.9 1.0
N D:CYS51 4.0 20.2 1.0
ND2 D:ASN16 4.1 28.4 1.0
O D:HOH361 4.2 31.6 1.0
CA D:CYS34 4.2 25.3 1.0
CA D:CYS51 4.2 18.8 1.0
CA D:CYS31 4.5 23.4 1.0
CA D:CYS54 4.7 20.7 1.0
CB D:ILE33 4.7 28.0 1.0
C D:ILE33 4.9 30.4 1.0
O D:GLN36 4.9 21.8 1.0
C D:CYS31 4.9 24.5 1.0
C D:CYS34 5.0 27.3 1.0

Zinc binding site 3 out of 4 in 5h7r

Go back to Zinc Binding Sites List in 5h7r
Zinc binding site 3 out of 4 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:31.5
occ:1.00
NE2 D:HIS113 2.1 18.5 1.0
SG D:CYS95 2.3 24.0 1.0
SG D:CYS101 2.4 26.8 1.0
SG D:CYS118 2.4 36.5 1.0
CE1 D:HIS113 3.1 26.7 1.0
CD2 D:HIS113 3.1 20.0 1.0
CB D:CYS101 3.1 27.1 1.0
CB D:CYS118 3.3 27.1 1.0
CB D:CYS95 3.3 23.2 1.0
CA D:CYS118 4.1 37.7 1.0
ND1 D:HIS113 4.2 25.5 1.0
CG D:HIS113 4.2 23.7 1.0
O D:HOH355 4.4 36.4 1.0
CB D:GLN103 4.4 28.6 1.0
CA D:CYS101 4.6 25.2 1.0
CA D:CYS95 4.7 20.9 1.0
CE1 D:PHE114 4.8 24.3 1.0
CD2 D:PHE97 4.8 25.1 1.0
CD1 D:PHE114 4.8 21.0 1.0
CB D:PHE97 4.9 24.9 1.0
C D:CYS118 4.9 35.6 1.0
N D:LYS119 5.0 39.4 1.0

Zinc binding site 4 out of 4 in 5h7r

Go back to Zinc Binding Sites List in 5h7r
Zinc binding site 4 out of 4 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:27.3
occ:1.00
OD2 D:ASP68 2.0 25.4 1.0
SG D:CYS65 2.2 28.5 1.0
CD2 D:HIS48 2.3 24.5 1.0
SG D:CYS46 2.4 28.7 1.0
CG D:ASP68 2.8 32.5 1.0
OD1 D:ASP68 3.0 31.0 1.0
CB D:CYS65 3.2 28.5 1.0
CG D:HIS48 3.2 24.3 1.0
NE2 D:HIS48 3.3 28.7 1.0
CB D:CYS46 3.3 26.9 1.0
CB D:HIS48 3.7 21.9 1.0
OG1 D:THR44 4.0 25.5 1.0
CB D:ASP68 4.1 27.9 1.0
CE1 D:HIS48 4.3 25.7 1.0
ND1 D:HIS48 4.3 30.8 1.0
O D:CYS46 4.3 30.6 1.0
N D:ASP68 4.4 32.6 1.0
C D:CYS46 4.5 28.7 1.0
CA D:CYS46 4.5 28.5 1.0
CB D:MET67 4.6 29.5 1.0
CA D:CYS65 4.6 29.6 1.0
OH D:TYR50 4.6 31.1 1.0
N D:HIS48 4.7 19.9 1.0
CA D:HIS48 4.9 20.8 1.0
CA D:ASP68 4.9 31.2 1.0
CB D:THR44 5.0 22.5 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: Wed Dec 16 06:20:04 2020

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