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Zinc in PDB 5yiq: Crystal Structure of Ankg Lir/LC3B Complex

Protein crystallography data

The structure of Crystal Structure of Ankg Lir/LC3B Complex, PDB code: 5yiq was solved by J.Li, R.Zhu, K.Chen, H.Zheng, C.Yuan, H.Zhang, C.Wang, M.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.60
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 64.553, 64.553, 155.461, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 25.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ankg Lir/LC3B Complex (pdb code 5yiq). 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 Ankg Lir/LC3B Complex, PDB code: 5yiq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5yiq

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Zinc binding site 1 out of 4 in the Crystal Structure of Ankg Lir/LC3B Complex


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 Ankg Lir/LC3B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:39.4
occ:1.00
NE2 A:HIS86 1.9 38.4 1.0
OE2 A:GLU102 2.1 35.9 1.0
OE1 A:GLU102 2.8 37.6 1.0
CD A:GLU102 2.8 39.0 1.0
CE1 A:HIS86 2.8 39.2 1.0
CD2 A:HIS86 2.9 38.4 1.0
ND1 A:HIS86 3.9 40.1 1.0
CG A:HIS86 4.0 39.7 1.0
CB A:SER87 4.2 46.3 1.0
CG A:GLU102 4.3 39.2 1.0
OG A:SER87 4.5 50.0 1.0
ND2 A:ASN84 5.0 40.3 1.0

Zinc binding site 2 out of 4 in 5yiq

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Zinc binding site 2 out of 4 in the Crystal Structure of Ankg Lir/LC3B Complex


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 Ankg Lir/LC3B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:80.2
occ:1.00
O A:HOH301 2.0 50.9 1.0
OE1 A:GLN26 2.9 82.1 1.0
CD A:GLN26 3.6 73.8 1.0
NE2 A:GLN26 3.7 83.1 1.0
O A:GLU25 4.3 65.1 1.0
CA A:GLN26 4.7 59.7 1.0
C A:GLU25 4.8 59.8 1.0
CG A:GLN26 4.8 66.8 1.0

Zinc binding site 3 out of 4 in 5yiq

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Zinc binding site 3 out of 4 in the Crystal Structure of Ankg Lir/LC3B Complex


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 Ankg Lir/LC3B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:67.8
occ:1.00
OE2 A:GLU100 1.8 62.0 1.0
OE2 A:GLU97 2.3 59.5 1.0
OE1 A:GLU97 2.4 54.1 1.0
CD A:GLU97 2.7 55.9 1.0
CD A:GLU100 2.7 61.8 1.0
OE1 A:GLU100 2.9 65.0 1.0
CG A:GLU100 4.1 57.3 1.0
CG A:GLU97 4.2 53.1 1.0
CB A:GLU100 4.5 52.3 1.0
CA A:GLU97 4.8 47.7 1.0
CB A:GLU97 4.9 49.4 1.0

Zinc binding site 4 out of 4 in 5yiq

Go back to Zinc Binding Sites List in 5yiq
Zinc binding site 4 out of 4 in the Crystal Structure of Ankg Lir/LC3B Complex


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 Ankg Lir/LC3B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:0.9
occ:1.00
OE1 D:GLU130 2.5 92.3 1.0
OE1 D:GLU134 2.9 0.1 1.0
OE2 D:GLU134 3.2 98.2 1.0
CD D:GLU134 3.4 97.2 1.0
CD D:GLU130 3.4 90.6 1.0
CG D:GLU130 3.9 83.0 1.0
OE2 D:GLU130 4.4 92.8 1.0
CG D:GLU134 4.9 93.2 1.0

Reference:

J.Li, R.Zhu, K.Chen, H.Zheng, H.Zhao, C.Yuan, H.Zhang, C.Wang, M.Zhang. Potent and Specific ATG8-Targeting Autophagy Inhibitory Peptides From Giant Ankyrins. Nat. Chem. Biol. V. 14 778 2018.
ISSN: ESSN 1552-4469
PubMed: 29867141
DOI: 10.1038/S41589-018-0082-8
Page generated: Wed Dec 16 11:23:03 2020

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