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Zinc in PDB 2znr: Crystal Structure of the Dub Domain of Human Amsh-Lp

Enzymatic activity of Crystal Structure of the Dub Domain of Human Amsh-Lp

All present enzymatic activity of Crystal Structure of the Dub Domain of Human Amsh-Lp:
3.1.2.15;

Protein crystallography data

The structure of Crystal Structure of the Dub Domain of Human Amsh-Lp, PDB code: 2znr 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) 31.09 / 1.20
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 81.865, 81.865, 64.693, 90.00, 90.00, 120.00
R / Rfree (%) 14.9 / 16.5

Other elements in 2znr:

The structure of Crystal Structure of the Dub Domain of Human Amsh-Lp also contains other interesting chemical elements:

Praseodymium (Pr) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Dub Domain of Human Amsh-Lp (pdb code 2znr). 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 the Dub Domain of Human Amsh-Lp, PDB code: 2znr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2znr

Go back to Zinc Binding Sites List in 2znr
Zinc binding site 1 out of 2 in the Crystal Structure of the Dub Domain of Human Amsh-Lp


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 the Dub Domain of Human Amsh-Lp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:9.5
occ:1.00
NE2 A:HIS408 2.0 8.6 1.0
NE2 A:HIS362 2.0 8.8 1.0
NE2 A:HIS410 2.1 10.5 1.0
SG A:CYS402 2.3 9.8 1.0
CE1 A:HIS410 2.9 11.6 1.0
CE1 A:HIS362 3.0 9.8 1.0
CD2 A:HIS408 3.0 8.5 1.0
CE1 A:HIS408 3.0 9.6 1.0
CD2 A:HIS362 3.1 8.0 1.0
CD2 A:HIS410 3.1 12.1 1.0
CB A:CYS402 3.2 10.5 1.0
ND1 A:HIS410 4.1 12.4 1.0
ND1 A:HIS408 4.1 9.5 1.0
ND1 A:HIS362 4.1 9.2 1.0
CG A:HIS408 4.1 8.9 1.0
CG A:HIS410 4.2 10.9 1.0
CG A:HIS362 4.2 8.3 1.0
O A:HOH525 4.4 16.1 1.0
O A:LYS404 4.5 13.4 1.0
CA A:CYS402 4.5 11.3 1.0
CB A:LYS404 4.6 12.8 1.0
C A:CYS402 4.8 12.0 1.0
O A:CYS402 4.8 13.1 1.0
N A:LYS404 4.9 13.5 1.0
O A:VAL399 5.0 9.9 1.0

Zinc binding site 2 out of 2 in 2znr

Go back to Zinc Binding Sites List in 2znr
Zinc binding site 2 out of 2 in the Crystal Structure of the Dub Domain of Human Amsh-Lp


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 the Dub Domain of Human Amsh-Lp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:10.1
occ:1.00
O A:HOH517 1.9 11.8 1.0
OD2 A:ASP360 1.9 8.4 1.0
NE2 A:HIS349 2.0 10.5 1.0
NE2 A:HIS347 2.0 8.6 1.0
CG A:ASP360 2.7 7.1 1.0
CD2 A:HIS349 2.9 10.3 1.0
OD1 A:ASP360 2.9 8.1 1.0
CE1 A:HIS347 3.0 8.7 1.0
CD2 A:HIS347 3.1 8.7 1.0
CE1 A:HIS349 3.1 11.3 1.0
O A:HOH542 3.9 16.0 1.0
OE2 A:GLU292 4.0 11.9 1.0
O A:HOH537 4.0 17.6 1.0
ND1 A:HIS347 4.1 8.2 1.0
CG A:HIS349 4.1 10.3 1.0
CB A:ASP360 4.2 7.0 1.0
ND1 A:HIS349 4.2 11.1 1.0
CG A:HIS347 4.2 7.4 1.0
O A:PHE355 4.2 12.4 1.0
OG A:SER357 4.3 10.0 1.0
N A:SER357 4.5 10.6 1.0
CB A:SER357 4.7 10.7 1.0
O A:HOH658 4.7 31.4 1.0
CD A:GLU292 4.7 10.2 1.0
OE1 A:GLU292 4.7 11.4 1.0
CG1 A:VAL378 5.0 12.9 1.0

Reference:

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
Page generated: Wed Dec 16 04:05:30 2020

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