Atomistry » Zinc » PDB 3wym-3zqr » 3zlz
Atomistry »
  Zinc »
    PDB 3wym-3zqr »
      3zlz »

Zinc in PDB 3zlz: LYS6-Linked Tri-Ubiquitin

Protein crystallography data

The structure of LYS6-Linked Tri-Ubiquitin, PDB code: 3zlz was solved by M.K.Hospenthal, S.M.V.Freund, D.Komander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.18 / 2.90
Space group P 43 3 2
Cell size a, b, c (Å), α, β, γ (°) 104.930, 104.930, 104.930, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 28.8

Zinc Binding Sites:

The binding sites of Zinc atom in the LYS6-Linked Tri-Ubiquitin (pdb code 3zlz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the LYS6-Linked Tri-Ubiquitin, PDB code: 3zlz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 3zlz

Go back to Zinc Binding Sites List in 3zlz
Zinc binding site 1 out of 5 in the LYS6-Linked Tri-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of LYS6-Linked Tri-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1074

b:0.1
occ:1.00
OD2 A:ASP32 2.5 0.7 1.0
CG A:ASP32 3.4 0.2 1.0
OD1 A:ASP32 3.9 0.5 1.0
CB A:ASP32 4.4 0.9 1.0

Zinc binding site 2 out of 5 in 3zlz

Go back to Zinc Binding Sites List in 3zlz
Zinc binding site 2 out of 5 in the LYS6-Linked Tri-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of LYS6-Linked Tri-Ubiquitin within 5.0Å range:

Zinc binding site 3 out of 5 in 3zlz

Go back to Zinc Binding Sites List in 3zlz
Zinc binding site 3 out of 5 in the LYS6-Linked Tri-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of LYS6-Linked Tri-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1074

b:78.6
occ:1.00
OD1 B:ASP21 2.1 65.4 1.0
OD2 B:ASP21 2.6 57.8 1.0
CG B:ASP21 2.6 60.3 1.0
NZ B:LYS29 3.6 73.2 1.0
CE B:LYS29 3.8 70.4 1.0
CB B:ASP21 4.1 57.1 1.0
ND2 B:ASN25 4.5 58.5 1.0
CB B:GLU18 4.6 61.7 1.0
CB B:ASN25 4.7 56.2 1.0
CG B:ASN25 4.8 58.1 1.0
CA B:ASP21 4.8 59.3 1.0
N B:GLU18 4.8 60.9 1.0

Zinc binding site 4 out of 5 in 3zlz

Go back to Zinc Binding Sites List in 3zlz
Zinc binding site 4 out of 5 in the LYS6-Linked Tri-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of LYS6-Linked Tri-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1075

b:0.3
occ:1.00
NE2 B:HIS68 2.3 78.5 1.0
CD2 B:HIS68 2.8 76.9 1.0
CE1 B:HIS68 3.5 79.8 1.0
O B:THR66 3.7 67.6 1.0
CG B:HIS68 4.1 77.1 1.0
ND1 B:HIS68 4.4 78.7 1.0
CB B:THR66 4.4 69.4 1.0
CG2 B:THR66 4.6 68.7 1.0
C B:THR66 4.6 64.9 1.0

Zinc binding site 5 out of 5 in 3zlz

Go back to Zinc Binding Sites List in 3zlz
Zinc binding site 5 out of 5 in the LYS6-Linked Tri-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of LYS6-Linked Tri-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1076

b:0.1
occ:1.00
OE2 B:GLU16 2.1 72.0 1.0
N B:MET1 2.1 67.6 1.0
OE1 B:GLU16 2.6 74.0 1.0
CD B:GLU16 2.7 73.0 1.0
CA B:MET1 3.2 65.6 1.0
O B:MET1 3.4 67.6 1.0
C B:MET1 3.6 67.5 1.0
CB B:MET1 3.7 60.7 1.0
O B:VAL17 3.7 62.4 1.0
CG B:GLU16 4.2 72.1 1.0
N B:GLN2 4.8 67.7 1.0
N B:VAL17 4.8 56.7 1.0
C B:VAL17 4.8 60.0 1.0

Reference:

M.K.Hospenthal, S.M.V.Freund, D.Komander. Assembly, Analysis and Architecture of Atypical Ubiquitin Chains Nat.Struct.Mol.Biol. V. 20 555 2013.
ISSN: ISSN 1545-9993
PubMed: 23563141
DOI: 10.1038/NSMB.2547
Page generated: Wed Dec 16 04:59:22 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy