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Zinc in PDB 5yt6: Crystal Structure of TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin

Protein crystallography data

The structure of Crystal Structure of TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin, PDB code: 5yt6 was solved by L.Pan, S.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.89 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.709, 72.938, 119.879, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 22.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin (pdb code 5yt6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin, PDB code: 5yt6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5yt6

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Zinc binding site 1 out of 4 in the Crystal Structure of TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin


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 TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:10.3
occ:1.00
NE2 F:HIS60 2.1 9.6 1.0
NE2 F:HIS56 2.1 12.2 1.0
SG F:CYS37 2.3 9.6 1.0
SG F:CYS40 2.3 11.1 1.0
CD2 F:HIS60 3.0 9.6 1.0
CD2 F:HIS56 3.0 9.5 1.0
CE1 F:HIS56 3.1 13.2 1.0
CE1 F:HIS60 3.1 9.7 1.0
CB F:CYS37 3.1 9.4 1.0
CB F:CYS40 3.3 10.7 1.0
N F:CYS40 3.7 11.9 1.0
O F:HOH226 3.8 13.9 1.0
CA F:CYS40 4.1 10.9 1.0
ND1 F:HIS56 4.1 12.7 1.0
CG F:HIS56 4.1 8.1 1.0
CG F:HIS60 4.1 10.5 1.0
ND1 F:HIS60 4.2 10.2 1.0
CA F:CYS37 4.6 8.8 1.0
C F:MET39 4.7 12.8 1.0
CB F:MET39 4.7 12.5 1.0
C F:CYS40 4.7 10.9 1.0
N F:SER41 4.9 10.4 1.0
O F:HIS56 5.0 11.5 1.0
N F:MET39 5.0 9.9 1.0
CB F:GLU42 5.0 11.6 1.0

Zinc binding site 2 out of 4 in 5yt6

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Zinc binding site 2 out of 4 in the Crystal Structure of TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin


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 TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:11.2
occ:1.00
NE2 B:HIS60 2.1 10.5 1.0
NE2 B:HIS56 2.1 11.8 1.0
SG B:CYS37 2.3 10.8 1.0
SG B:CYS40 2.3 12.2 1.0
CD2 B:HIS60 3.0 9.6 1.0
CD2 B:HIS56 3.0 10.7 1.0
CE1 B:HIS56 3.0 14.9 1.0
CE1 B:HIS60 3.1 9.9 1.0
CB B:CYS37 3.2 10.6 1.0
CB B:CYS40 3.3 12.9 1.0
N B:CYS40 3.7 10.3 1.0
CA B:CYS40 4.0 12.9 1.0
ND1 B:HIS56 4.1 16.2 1.0
CG B:HIS60 4.1 9.8 1.0
ND1 B:HIS60 4.2 9.9 1.0
CG B:HIS56 4.2 13.6 1.0
C B:MET39 4.5 13.8 1.0
CA B:CYS37 4.6 11.3 1.0
CB B:MET39 4.6 12.4 1.0
C B:CYS40 4.7 13.1 1.0
N B:MET39 4.8 10.7 1.0
ND2 B:ASN67 4.8 32.2 1.0
CB B:GLU42 4.9 15.1 1.0
CA B:MET39 4.9 11.5 1.0
N B:SER41 4.9 13.7 1.0

Zinc binding site 3 out of 4 in 5yt6

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Zinc binding site 3 out of 4 in the Crystal Structure of TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn101

b:11.1
occ:1.00
NE2 D:HIS56 2.0 9.1 1.0
NE2 D:HIS60 2.1 11.8 1.0
SG D:CYS40 2.3 12.2 1.0
SG D:CYS37 2.3 9.0 1.0
CD2 D:HIS56 3.0 9.4 1.0
CE1 D:HIS56 3.0 12.1 1.0
CE1 D:HIS60 3.0 17.1 1.0
CD2 D:HIS60 3.0 9.9 1.0
CB D:CYS37 3.1 9.8 1.0
CB D:CYS40 3.4 12.9 1.0
N D:CYS40 3.7 11.6 1.0
ND1 D:HIS56 4.1 12.7 1.0
CA D:CYS40 4.1 12.4 1.0
CG D:HIS56 4.1 9.7 1.0
ND1 D:HIS60 4.1 14.6 1.0
CG D:HIS60 4.2 10.3 1.0
O D:HOH229 4.4 31.2 1.0
CA D:CYS37 4.6 9.0 1.0
CB D:MET39 4.7 13.0 1.0
C D:MET39 4.8 11.7 1.0
O D:HIS56 4.8 10.7 1.0
C D:CYS40 4.8 13.8 1.0
N D:SER41 5.0 12.5 1.0
CA D:VAL57 5.0 7.7 1.0
N D:MET39 5.0 11.1 1.0

Zinc binding site 4 out of 4 in 5yt6

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Zinc binding site 4 out of 4 in the Crystal Structure of TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of TAX1BP1 UBZ2 in Complex with Mono-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn101

b:11.2
occ:1.00
NE2 H:HIS60 2.1 12.7 1.0
NE2 H:HIS56 2.1 12.8 1.0
SG H:CYS40 2.3 12.2 1.0
SG H:CYS37 2.3 9.9 1.0
CE1 H:HIS56 3.0 13.7 1.0
CE1 H:HIS60 3.0 19.0 1.0
CD2 H:HIS56 3.1 11.6 1.0
CD2 H:HIS60 3.1 8.6 1.0
CB H:CYS37 3.1 9.2 1.0
CB H:CYS40 3.3 13.1 1.0
N H:CYS40 3.8 12.5 1.0
CA H:CYS40 4.1 12.7 1.0
ND1 H:HIS56 4.1 16.2 1.0
ND1 H:HIS60 4.1 18.5 1.0
CG H:HIS56 4.1 10.8 1.0
CG H:HIS60 4.2 10.6 1.0
CA H:CYS37 4.6 9.5 1.0
C H:CYS40 4.7 14.4 1.0
O H:HIS56 4.8 10.3 1.0
CB H:MET39 4.8 12.5 1.0
C H:MET39 4.8 16.9 1.0
CB H:GLU42 4.9 15.3 1.0
CA H:VAL57 4.9 8.1 1.0
N H:SER41 5.0 14.0 1.0

Reference:

S.Hu, Y.Wang, Y.Gong, J.Liu, Y.Li, L.Pan. Mechanistic Insights Into Recognitions of Ubiquitin and Myosin VI By Autophagy Receptor TAX1BP1. J. Mol. Biol. V. 430 3283 2018.
ISSN: ESSN 1089-8638
PubMed: 29940186
DOI: 10.1016/J.JMB.2018.06.030
Page generated: Wed Dec 16 11:24:27 2020

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