Zinc in PDB 2znv: Crystal Structure of Human Amsh-Lp Dub Domain in Complex with LYS63-Linked Ubiquitin Dimer

All present enzymatic activity of Crystal Structure of Human Amsh-Lp Dub Domain in Complex with LYS63-Linked Ubiquitin Dimer:
3.1.2.15;

The structure of Crystal Structure of Human Amsh-Lp Dub Domain in Complex with LYS63-Linked Ubiquitin Dimer, PDB code: 2znv was solved by Y.Sato, Y.Azusa, A.Yamagata, H.Mimura, X.Wang, M.Yamashita, K.Ookata, O.Nureki, K.Iwai, M.Komada, S.Fukai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.47 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.089, 97.363, 87.894, 90.00, 97.49, 90.00
R / Rfree (%)	18.3 / 21.5

The binding sites of Zinc atom in the Crystal Structure of Human Amsh-Lp Dub Domain in Complex with LYS63-Linked Ubiquitin Dimer (pdb code 2znv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human Amsh-Lp Dub Domain in Complex with LYS63-Linked Ubiquitin Dimer, PDB code: 2znv:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human Amsh-Lp Dub Domain in Complex with LYS63-Linked Ubiquitin Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Amsh-Lp Dub Domain in Complex with LYS63-Linked Ubiquitin Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:11.3 occ:1.00 NE2 A:HIS410 2.1 17.1 1.0 NE2 A:HIS408 2.1 11.8 1.0 NE2 A:HIS362 2.1 8.2 1.0 SG A:CYS402 2.3 10.7 1.0 CE1 A:HIS410 2.8 17.4 1.0 CE1 A:HIS362 3.0 9.4 1.0 CD2 A:HIS408 3.0 14.7 1.0 CE1 A:HIS408 3.1 13.2 1.0 CD2 A:HIS362 3.1 9.4 1.0 CD2 A:HIS410 3.2 17.8 1.0 CB A:CYS402 3.2 13.0 1.0 ND1 A:HIS410 4.0 18.9 1.0 ND1 A:HIS362 4.1 9.5 1.0 ND1 A:HIS408 4.2 15.1 1.0 CG A:HIS408 4.2 14.1 1.0 CG A:HIS410 4.2 18.8 1.0 CG A:HIS362 4.2 6.8 1.0 CB A:LYS404 4.5 17.6 1.0 O A:LYS404 4.5 17.0 1.0 CA A:CYS402 4.6 13.3 1.0 C A:CYS402 4.7 14.4 1.0 O A:CYS402 4.8 14.6 1.0 N A:LYS404 4.8 17.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human Amsh-Lp Dub Domain in Complex with LYS63-Linked Ubiquitin Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Amsh-Lp Dub Domain in Complex with LYS63-Linked Ubiquitin Dimer within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2 b:13.2 occ:1.00 NE2 D:HIS410 2.0 8.9 1.0 NE2 D:HIS362 2.0 12.1 1.0 NE2 D:HIS408 2.0 12.1 1.0 SG D:CYS402 2.3 14.7 1.0 CD2 D:HIS410 2.7 14.5 1.0 CE1 D:HIS408 2.9 12.3 1.0 CE1 D:HIS362 3.0 13.6 1.0 CD2 D:HIS408 3.1 12.3 1.0 CD2 D:HIS362 3.1 13.6 1.0 CB D:CYS402 3.2 17.0 1.0 CE1 D:HIS410 3.2 14.3 1.0 O D:HOH577 3.6 18.8 1.0 CG D:HIS410 4.0 14.2 1.0 ND1 D:HIS408 4.1 13.7 1.0 ND1 D:HIS362 4.1 13.3 1.0 CG D:HIS408 4.2 12.7 1.0 ND1 D:HIS410 4.2 13.3 1.0 CG D:HIS362 4.2 11.3 1.0 OG D:SER358 4.2 12.8 0.5 O D:HOH587 4.6 28.4 1.0 CB D:LYS404 4.6 19.6 1.0 CA D:CYS402 4.6 16.9 1.0 O D:LYS404 4.7 19.1 1.0 C D:CYS402 4.9 18.4 1.0

Y.Sato, A.Yoshikawa, A.Yamagata, H.Mimura, M.Yamashita, K.Ookata, O.Nureki, K.Iwai, M.Komada, S.Fukai. Structural Basis For Specific Cleavage of Lys 63-Linked Polyubiquitin Chains Nature V. 455 358 2008.
ISSN: ISSN 0028-0836
PubMed: 18758443
DOI: 10.1038/NATURE07254