Zinc in PDB 5wzz: The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation

The structure of The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation, PDB code: 5wzz was solved by L.Ji, B.Jiang, X.Jiang, O.Charlat, A.Chen, C.Mickanin, A.Bauer, W.Xu, X.-X.Yan, F.Cong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.73 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.502, 86.450, 117.454, 90.00, 98.43, 90.00
R / Rfree (%)	18.5 / 20.8

The binding sites of Zinc atom in the The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation (pdb code 5wzz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation, PDB code: 5wzz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:45.0 occ:1.00 NE2 A:HIS117 2.0 48.6 1.0 SG A:CYS105 2.3 45.0 1.0 SG A:CYS121 2.4 51.8 1.0 SG A:CYS98 2.4 42.7 1.0 CE1 A:HIS117 3.0 53.5 1.0 CD2 A:HIS117 3.0 50.9 1.0 CB A:CYS98 3.1 37.9 1.0 CB A:CYS121 3.2 55.1 1.0 CB A:CYS105 3.3 42.4 1.0 ND1 A:HIS117 4.1 51.8 1.0 CG A:HIS117 4.1 54.6 1.0 CA A:CYS121 4.4 50.7 1.0 CB A:ILE107 4.5 58.2 1.0 CA A:CYS98 4.6 39.5 1.0 CB A:TYR100 4.6 53.3 1.0 CA A:CYS105 4.6 59.6 1.0 CD2 A:TYR100 4.6 48.3 1.0 CG1 A:ILE107 4.8 67.8 1.0

Zinc binding site 2 out of 8 in the The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:45.5 occ:1.00 NE2 A:HIS152 2.0 45.5 1.0 NE2 A:HIS147 2.1 41.0 1.0 SG A:CYS135 2.3 47.1 1.0 SG A:CYS128 2.4 45.7 1.0 CE1 A:HIS147 2.9 50.7 1.0 CE1 A:HIS152 3.0 48.5 1.0 CD2 A:HIS152 3.0 45.3 1.0 CB A:CYS135 3.1 51.0 1.0 CB A:CYS128 3.2 44.2 1.0 CD2 A:HIS147 3.2 41.3 1.0 ND1 A:HIS152 4.1 45.8 1.0 CG A:HIS152 4.1 41.6 1.0 ND1 A:HIS147 4.1 42.5 1.0 CB A:TRP137 4.2 52.2 1.0 CG A:HIS147 4.3 46.0 1.0 CA A:CYS128 4.5 53.5 1.0 CA A:CYS135 4.6 47.3 1.0 CB A:GLN151 4.8 47.8 1.0 SG A:CYS130 4.9 54.2 1.0 CB A:CYS130 4.9 49.4 1.0

Zinc binding site 3 out of 8 in the The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:45.0 occ:1.00 NE2 B:HIS117 2.1 54.0 1.0 SG B:CYS105 2.3 42.5 1.0 SG B:CYS121 2.3 46.7 1.0 SG B:CYS98 2.3 42.4 1.0 CD2 B:HIS117 3.0 52.0 1.0 CB B:CYS98 3.1 39.4 1.0 CE1 B:HIS117 3.1 56.4 1.0 CB B:CYS105 3.2 47.9 1.0 CB B:CYS121 3.2 47.8 1.0 CG B:HIS117 4.2 49.6 1.0 ND1 B:HIS117 4.2 45.0 1.0 CA B:CYS121 4.4 52.8 1.0 CD2 B:TYR100 4.6 46.9 1.0 CA B:CYS105 4.6 49.5 1.0 CA B:CYS98 4.6 42.2 1.0 CB B:TYR100 4.7 44.5 1.0 CB B:ILE107 4.8 67.3 1.0 CG1 B:ILE107 4.9 65.5 1.0

Zinc binding site 4 out of 8 in the The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:44.1 occ:1.00 NE2 B:HIS152 2.0 45.9 1.0 NE2 B:HIS147 2.1 32.9 1.0 SG B:CYS135 2.3 47.7 1.0 SG B:CYS128 2.4 44.7 1.0 CE1 B:HIS152 2.9 53.0 1.0 CE1 B:HIS147 3.0 35.4 1.0 CD2 B:HIS152 3.1 51.5 1.0 CB B:CYS128 3.1 55.3 1.0 CD2 B:HIS147 3.1 51.0 1.0 CB B:CYS135 3.3 59.6 1.0 ND1 B:HIS152 4.0 50.2 1.0 CG B:HIS152 4.1 53.7 1.0 ND1 B:HIS147 4.1 41.9 1.0 CG B:HIS147 4.2 48.9 1.0 CB B:TRP137 4.5 63.5 1.0 CA B:CYS128 4.5 52.4 1.0 CA B:CYS135 4.7 75.6 1.0 O B:HOH405 4.9 58.7 1.0 SG B:CYS130 5.0 51.4 1.0

Zinc binding site 5 out of 8 in the The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:54.8 occ:1.00 O C:HOH440 2.0 58.0 1.0 NE2 C:HIS117 2.1 44.4 1.0 SG C:CYS105 2.3 61.3 1.0 SG C:CYS98 2.4 58.2 1.0 SG C:CYS121 2.5 59.5 1.0 CD2 C:HIS117 3.0 60.1 1.0 CB C:CYS105 3.0 69.6 1.0 CE1 C:HIS117 3.0 57.4 1.0 CB C:CYS98 3.2 45.8 1.0 CB C:CYS121 3.2 54.5 1.0 ND1 C:HIS117 4.1 58.8 1.0 CG C:HIS117 4.1 55.6 1.0 CA C:CYS105 4.5 60.1 1.0 CA C:CYS121 4.5 57.6 1.0 CA C:CYS98 4.6 70.1 1.0 CD1 C:PHE123 4.8 60.4 1.0 CD2 C:TYR100 4.8 53.6 1.0 CB C:TYR100 4.9 52.4 1.0

Zinc binding site 6 out of 8 in the The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:63.3 occ:1.00 NE2 C:HIS152 2.1 55.1 1.0 NE2 C:HIS147 2.1 69.6 1.0 SG C:CYS135 2.3 74.0 1.0 SG C:CYS128 2.4 61.2 1.0 CE1 C:HIS152 3.0 70.7 1.0 CE1 C:HIS147 3.0 70.2 1.0 CD2 C:HIS152 3.1 61.5 1.0 CD2 C:HIS147 3.1 71.3 1.0 CB C:CYS128 3.2 74.9 1.0 CB C:CYS135 3.4 68.7 1.0 ND1 C:HIS152 4.1 64.3 1.0 ND1 C:HIS147 4.2 71.4 1.0 CG C:HIS152 4.2 69.7 1.0 CB C:TRP137 4.2 59.9 1.0 CG C:HIS147 4.2 75.8 1.0 CA C:CYS128 4.4 60.7 1.0 CA C:CYS135 4.8 81.0 1.0 CB C:CYS130 4.9 75.5 1.0 CG C:TRP137 4.9 75.1 1.0 CB C:GLN151 5.0 86.2 1.0

Zinc binding site 7 out of 8 in the The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:52.4 occ:1.00 NE2 D:HIS117 2.0 46.4 1.0 SG D:CYS105 2.3 51.9 1.0 SG D:CYS98 2.4 51.7 1.0 SG D:CYS121 2.4 48.2 1.0 CE1 D:HIS117 3.0 63.4 1.0 CD2 D:HIS117 3.0 60.3 1.0 CB D:CYS98 3.2 53.0 1.0 CB D:CYS121 3.2 45.9 1.0 CB D:CYS105 3.3 71.4 1.0 ND1 D:HIS117 4.1 51.1 1.0 CG D:HIS117 4.1 57.5 1.0 CA D:CYS121 4.4 52.5 1.0 CB D:TYR100 4.6 47.2 1.0 CD2 D:TYR100 4.6 46.7 1.0 CA D:CYS98 4.6 47.3 1.0 CA D:CYS105 4.7 75.8 1.0 CB D:ILE107 4.8 60.9 1.0 CD1 D:PHE123 4.9 75.2 1.0 N D:TYR100 5.0 67.4 1.0

Zinc binding site 8 out of 8 in the The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:48.6 occ:1.00 NE2 D:HIS152 2.0 50.3 1.0 NE2 D:HIS147 2.0 48.6 1.0 SG D:CYS135 2.2 54.3 1.0 SG D:CYS128 2.2 44.5 1.0 CE1 D:HIS147 2.9 45.5 1.0 CD2 D:HIS152 2.9 42.5 1.0 CE1 D:HIS152 3.0 48.6 1.0 CD2 D:HIS147 3.1 47.9 1.0 CB D:CYS128 3.1 55.1 1.0 CB D:CYS135 3.2 61.2 1.0 CG D:HIS152 4.0 46.5 1.0 ND1 D:HIS147 4.1 41.2 1.0 ND1 D:HIS152 4.1 49.4 1.0 CG D:HIS147 4.2 44.4 1.0 CB D:TRP137 4.3 56.6 1.0 CA D:CYS128 4.5 49.7 1.0 CA D:CYS135 4.6 74.8 1.0 CB D:CYS130 5.0 48.9 1.0

L.Ji, B.Jiang, X.Jiang, O.Charlat, A.Chen, C.Mickanin, A.Bauer, W.Xu, X.-X.Yan, F.Cong. The Siah E3 Ubiquitin Ligases Promote Wnt/ Beta-Catenin Signaling Through Mediating Wnt-Induced Axin Degradation Genes Dev. V. 31 904 2017.
ISSN: ISSN 1549-5477
PubMed: 28546513
DOI: 10.1101/GAD.300053.117