Zinc in PDB 8c61: Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa

The structure of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa, PDB code: 8c61 was solved by K.Wendrich, M.Gersch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.28 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	122.743, 126.559, 144.167, 90, 90, 90
R / Rfree (%)	20 / 24.3

The structure of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa also contains other interesting chemical elements:

Sodium	(Na)	2 atoms
Chlorine	(Cl)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa (pdb code 8c61). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa, PDB code: 8c61:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:80.3 occ:1.00 NE2 A:HIS67 2.1 85.8 1.0 SG A:CYS74 2.3 84.3 1.0 SG A:CYS77 2.3 74.9 1.0 SG A:CYS69 2.3 80.4 1.0 CE1 A:HIS67 3.0 85.0 1.0 CB A:CYS69 3.1 85.3 1.0 CD2 A:HIS67 3.1 80.1 1.0 CB A:CYS74 3.4 78.7 1.0 CB A:CYS77 3.4 67.3 1.0 CA A:CYS69 3.4 86.3 1.0 N A:CYS77 3.8 65.6 1.0 CA A:CYS77 4.1 70.1 1.0 N A:MET70 4.1 81.0 1.0 ND1 A:HIS67 4.1 84.1 1.0 CG A:HIS67 4.2 77.8 1.0 C A:CYS69 4.3 91.7 1.0 N A:CYS69 4.5 80.0 1.0 CB A:PHE76 4.6 73.1 1.0 CA A:CYS74 4.8 77.4 1.0 O A:GLY71 4.8 102.0 1.0 C A:PHE76 4.8 70.4 1.0 O A:LYS68 5.0 79.9 1.0

Zinc binding site 2 out of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:65.9 occ:1.00 ND1 A:HIS153 2.0 60.3 1.0 ND1 A:HIS133 2.0 62.1 1.0 SG A:CYS150 2.3 63.9 1.0 SG A:CYS145 2.3 72.5 1.0 CE1 A:HIS153 2.9 64.6 1.0 CE1 A:HIS133 3.0 63.1 1.0 CG A:HIS133 3.0 65.8 1.0 CG A:HIS153 3.1 63.5 1.0 CB A:CYS145 3.2 73.1 1.0 CB A:HIS133 3.3 60.1 1.0 CB A:CYS150 3.3 70.5 1.0 CB A:HIS153 3.5 50.7 1.0 NE2 A:HIS133 4.1 60.1 1.0 CA A:HIS133 4.1 67.1 1.0 NE2 A:HIS153 4.1 71.0 1.0 CD2 A:HIS133 4.1 54.9 1.0 CD2 A:HIS153 4.2 58.4 1.0 CB A:ALA137 4.2 67.4 1.0 N A:HIS153 4.3 64.1 1.0 CA A:HIS153 4.5 68.4 1.0 CA A:CYS145 4.6 82.4 1.0 O A:HIS133 4.7 71.0 1.0 CA A:CYS150 4.8 76.8 1.0 C A:HIS133 4.8 71.3 1.0

Zinc binding site 3 out of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:81.4 occ:1.00 SG A:CYS229 2.3 89.8 1.0 SG A:CYS169 2.3 72.9 1.0 SG A:CYS166 2.3 78.5 1.0 SG A:CYS225 2.4 69.3 1.0 CB A:CYS229 3.1 68.7 1.0 CB A:CYS169 3.1 71.6 1.0 CB A:CYS166 3.1 67.4 1.0 CB A:CYS225 3.3 68.7 1.0 N A:CYS169 3.8 76.3 1.0 CA A:CYS169 4.0 77.0 1.0 OG A:SER168 4.1 105.6 1.0 N A:CYS229 4.1 75.8 1.0 CA A:CYS229 4.2 83.3 1.0 CA A:CYS166 4.6 77.1 1.0 CA A:CYS225 4.6 71.0 1.0 CB A:ALA171 4.6 69.0 1.0 C A:CYS169 4.7 80.2 1.0 N A:GLY170 4.9 76.4 1.0 N A:ALA171 4.9 74.3 1.0 C A:SER168 5.0 89.0 1.0

Zinc binding site 4 out of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn801 b:122.1 occ:1.00 NE2 D:HIS67 2.0 123.6 1.0 SG D:CYS77 2.3 135.9 1.0 SG D:CYS69 2.3 140.3 1.0 SG D:CYS74 2.3 129.9 1.0 CB D:CYS69 3.0 128.8 1.0 CD2 D:HIS67 3.0 122.3 1.0 CE1 D:HIS67 3.0 116.9 1.0 CA D:CYS69 3.2 127.2 1.0 CB D:CYS77 3.3 116.3 1.0 CB D:CYS74 3.3 134.5 1.0 N D:CYS77 3.8 112.1 1.0 N D:MET70 4.1 136.2 1.0 CA D:CYS77 4.1 115.5 1.0 ND1 D:HIS67 4.1 121.8 1.0 CG D:HIS67 4.1 118.0 1.0 C D:CYS69 4.2 134.0 1.0 N D:CYS69 4.3 128.6 1.0 CB D:PHE76 4.5 113.9 1.0 CA D:CYS74 4.8 133.6 1.0 N D:GLY71 4.8 146.7 1.0 C D:PHE76 4.8 119.2 1.0

Zinc binding site 5 out of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn802 b:90.4 occ:1.00 ND1 D:HIS133 2.1 88.1 1.0 ND1 D:HIS153 2.1 95.7 1.0 SG D:CYS150 2.3 95.6 1.0 SG D:CYS145 2.3 109.4 1.0 CE1 D:HIS133 2.9 91.3 1.0 CE1 D:HIS153 3.0 93.3 1.0 CG D:HIS153 3.1 89.7 1.0 CG D:HIS133 3.1 94.1 1.0 CB D:CYS145 3.3 104.6 1.0 CB D:HIS153 3.4 89.6 1.0 CB D:CYS150 3.5 104.7 1.0 CB D:HIS133 3.5 97.7 1.0 NE2 D:HIS133 4.1 94.6 1.0 NE2 D:HIS153 4.1 87.0 1.0 CD2 D:HIS133 4.2 96.5 1.0 CD2 D:HIS153 4.2 90.5 1.0 CA D:HIS133 4.3 103.6 1.0 N D:HIS153 4.3 98.2 1.0 CA D:HIS153 4.5 90.1 1.0 CA D:CYS145 4.7 111.6 1.0 CA D:CYS150 4.9 108.2 1.0 O D:HIS133 5.0 120.4 1.0

Zinc binding site 6 out of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn803 b:84.3 occ:1.00 SG D:CYS166 2.3 89.4 1.0 SG D:CYS229 2.3 94.1 1.0 SG D:CYS225 2.3 89.1 1.0 SG D:CYS169 2.4 88.7 1.0 CB D:CYS166 3.2 85.5 1.0 CB D:CYS225 3.2 90.6 1.0 CB D:CYS229 3.2 91.0 1.0 CB D:CYS169 3.4 90.6 1.0 N D:CYS169 4.1 89.6 1.0 CA D:CYS169 4.3 94.8 1.0 N D:CYS229 4.3 89.0 1.0 CA D:CYS229 4.4 85.0 1.0 CB D:ALA171 4.5 90.5 1.0 CB D:GLU231 4.5 95.2 1.0 CA D:CYS225 4.6 92.2 1.0 CA D:CYS166 4.6 88.7 1.0 C D:CYS169 4.9 90.2 1.0 CG D:GLU231 4.9 96.8 1.0

Zinc binding site 7 out of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn801 b:77.2 occ:1.00 NE2 G:HIS67 2.1 75.0 1.0 SG G:CYS69 2.3 81.8 1.0 SG G:CYS77 2.3 77.5 1.0 SG G:CYS74 2.3 85.4 1.0 CB G:CYS69 2.9 73.3 1.0 CE1 G:HIS67 3.0 79.3 1.0 CD2 G:HIS67 3.2 79.8 1.0 CB G:CYS74 3.2 89.2 1.0 CB G:CYS77 3.3 77.4 1.0 CA G:CYS69 3.4 85.0 1.0 N G:CYS77 3.8 71.4 1.0 CA G:CYS77 4.0 73.7 1.0 ND1 G:HIS67 4.2 78.5 1.0 N G:MET70 4.2 87.5 1.0 C G:CYS69 4.3 89.6 1.0 CG G:HIS67 4.3 77.8 1.0 N G:CYS69 4.4 81.9 1.0 CB G:PHE76 4.5 64.2 1.0 CA G:CYS74 4.7 92.0 1.0 C G:PHE76 4.7 73.8 1.0 O G:GLY71 4.8 107.9 1.0 CD1 G:PHE76 4.8 69.2 1.0

Zinc binding site 8 out of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn802 b:65.5 occ:1.00 ND1 G:HIS153 2.0 61.7 1.0 ND1 G:HIS133 2.1 50.4 1.0 SG G:CYS150 2.3 64.5 1.0 SG G:CYS145 2.3 71.5 1.0 CE1 G:HIS133 2.9 63.7 1.0 CE1 G:HIS153 3.0 57.7 1.0 CG G:HIS153 3.0 63.5 1.0 CG G:HIS133 3.1 65.0 1.0 CB G:CYS145 3.2 56.2 1.0 CB G:CYS150 3.3 72.6 1.0 CB G:HIS153 3.4 52.5 1.0 CB G:HIS133 3.5 60.3 1.0 NE2 G:HIS133 4.1 69.1 1.0 NE2 G:HIS153 4.1 68.8 1.0 CD2 G:HIS153 4.1 63.6 1.0 CD2 G:HIS133 4.2 60.5 1.0 CA G:HIS133 4.2 73.0 1.0 N G:HIS153 4.3 59.1 1.0 CB G:ALA137 4.3 81.1 1.0 CA G:HIS153 4.5 63.9 1.0 CA G:CYS145 4.6 66.6 1.0 CA G:CYS150 4.7 72.4 1.0 O G:HIS133 4.8 72.7 1.0 C G:HIS133 4.9 72.9 1.0

Zinc binding site 9 out of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn803 b:74.4 occ:1.00 SG G:CYS166 2.3 77.0 1.0 SG G:CYS169 2.3 74.8 1.0 SG G:CYS225 2.3 74.1 1.0 SG G:CYS229 2.3 84.2 1.0 CB G:CYS229 3.2 64.7 1.0 CB G:CYS166 3.2 63.9 1.0 CB G:CYS225 3.3 78.6 1.0 CB G:CYS169 3.5 80.1 1.0 N G:CYS169 3.9 77.9 1.0 CB G:ALA171 4.2 73.5 1.0 CA G:CYS169 4.3 78.9 1.0 N G:CYS229 4.3 85.7 1.0 CA G:CYS229 4.3 89.0 1.0 CA G:CYS166 4.7 75.0 1.0 CA G:CYS225 4.7 72.8 1.0 CB G:SER168 4.7 88.1 1.0 N G:ALA171 4.8 81.8 1.0 CB G:GLU231 4.8 85.0 1.0 C G:CYS169 4.9 81.3 1.0 C G:SER168 4.9 89.6 1.0

Zinc binding site 10 out of 12 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn801 b:113.3 occ:1.00 NE2 J:HIS67 2.1 112.5 1.0 SG J:CYS77 2.3 122.9 1.0 SG J:CYS74 2.3 118.8 1.0 SG J:CYS69 2.3 125.8 1.0 CE1 J:HIS67 3.0 114.8 1.0 CB J:CYS69 3.1 119.8 1.0 CD2 J:HIS67 3.1 117.4 1.0 CB J:CYS74 3.2 124.2 1.0 CB J:CYS77 3.4 110.7 1.0 CA J:CYS69 3.4 119.2 1.0 N J:CYS77 3.9 105.2 1.0 ND1 J:HIS67 4.1 119.3 1.0 CA J:CYS77 4.1 108.0 1.0 CG J:HIS67 4.2 114.6 1.0 N J:MET70 4.4 123.3 1.0 C J:CYS69 4.4 125.2 1.0 N J:CYS69 4.5 127.3 1.0 CA J:CYS74 4.6 130.5 1.0 O J:GLY71 4.6 143.7 1.0 CB J:PHE76 4.8 108.6 1.0 C J:PHE76 5.0 110.6 1.0 O J:CYS74 5.0 111.0 1.0 C J:CYS74 5.0 116.3 1.0

K.Wendrich, M.Gersch. Structure of USP54 in Complex with LYS63 Linked Diubiquitin-Pa To Be Published.