Zinc in PDB 8t33: Crystal Structure of K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor

The structure of Crystal Structure of K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor, PDB code: 8t33 was solved by M.G.H.Ali, H.M.Wahba, N.Cyr, J.G.Omichinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.87 / 1.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	53.488, 89.178, 63.967, 90, 90, 90
R / Rfree (%)	18.5 / 21.2

The binding sites of Zinc atom in the Crystal Structure of K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor (pdb code 8t33). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor, PDB code: 8t33:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Crystal Structure of K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor


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 K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:13.9 occ:0.80 ZN A:ZN206 1.9 14.7 0.5 OXT A:ACT210 2.0 26.6 1.0 OE1 A:GLU97 2.0 18.6 1.0 ZN A:ZN207 2.2 15.6 0.4 C A:ACT210 2.7 26.6 1.0 O A:ACT210 2.9 26.6 1.0 CD A:GLU97 2.9 19.8 1.0 OE2 A:GLU97 3.2 21.0 1.0 NE2 A:HIS98 3.7 15.3 1.0 CD2 A:HIS98 4.1 14.1 1.0 CH3 A:ACT210 4.2 26.6 1.0 CD1 A:LEU94 4.3 13.1 1.0 CG A:GLU97 4.3 19.8 1.0 CB A:GLU97 4.6 18.6 1.0 CD A:PRO86 4.7 15.0 1.0 NE2 A:GLN93 4.9 20.8 1.0 CE1 A:HIS98 4.9 15.8 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor


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 K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:19.7 occ:0.51 O A:HOH412 2.1 43.0 1.0 O A:HOH305 2.1 28.8 1.0 OE2 A:GLU101 2.3 26.0 1.0 CD A:GLU101 3.1 26.1 1.0 OE1 A:GLU101 3.3 27.4 1.0 OXT A:ACT212 4.6 26.6 1.0 CG A:GLU101 4.6 24.9 1.0 C A:ACT212 4.7 26.6 1.0 O A:HOH313 4.7 42.7 1.0 O A:ACT212 5.0 26.6 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor


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 K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:20.8 occ:1.00 NE2 A:HIS99 2.0 15.4 1.0 CE1 A:HIS99 2.8 15.2 1.0 CD2 A:HIS99 3.1 14.5 1.0 O A:HOH458 3.6 43.7 1.0 O A:HOH344 3.9 29.8 1.0 ND1 A:HIS99 4.0 14.3 1.0 CG A:HIS99 4.2 13.8 1.0 CE1 A:PHE103 4.7 15.3 1.0 CD1 A:PHE103 4.7 14.2 1.0 CE1 A:TYR95 5.0 11.8 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor


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 K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:46.9 occ:0.93 O A:HOH413 2.0 46.7 1.0 NE2 A:HIS9 2.1 27.8 1.0 CE1 A:HIS9 2.9 27.5 1.0 CD2 A:HIS9 3.2 27.7 1.0 O A:HOH448 3.7 49.5 1.0 ND1 A:HIS9 4.1 27.2 1.0 CG A:HIS9 4.2 27.4 1.0 OE1 A:GLU8 4.7 33.3 1.0 O A:HOH425 4.8 43.4 1.0 O A:HOH484 4.9 46.5 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:58.2 occ:1.00 OD1 A:ASP54 2.0 21.1 1.0 O A:HOH372 2.2 58.9 1.0 O A:HOH437 2.2 44.5 1.0 CG A:ASP54 2.9 20.4 1.0 OD2 A:ASP54 3.0 20.5 1.0 O A:HOH411 4.2 20.7 1.0 O A:HOH309 4.3 39.1 1.0 CB A:ASP54 4.3 19.6 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:14.7 occ:0.51 OE1 A:GLU97 1.8 18.6 1.0 ZN A:ZN201 1.9 13.9 0.8 NE2 A:HIS98 2.3 15.3 1.0 CD A:GLU97 2.5 19.8 1.0 OXT A:ACT210 2.6 26.6 1.0 OE2 A:GLU97 3.1 21.0 1.0 CD2 A:HIS98 3.1 14.1 1.0 CE1 A:HIS98 3.3 15.8 1.0 C A:ACT210 3.5 26.6 1.0 CG A:GLU97 3.5 19.8 1.0 CB A:GLU97 3.6 18.6 1.0 O A:ACT210 4.0 26.6 1.0 ZN A:ZN207 4.0 15.6 0.4 CG A:HIS98 4.3 13.9 1.0 ND1 A:HIS98 4.4 15.0 1.0 CH3 A:ACT210 4.6 26.6 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn207 b:15.6 occ:0.39 ZN A:ZN201 2.2 13.9 0.8 NE2 A:GLN93 3.3 20.8 1.0 OE1 A:GLU97 3.4 18.6 1.0 CD A:PRO86 3.5 15.0 1.0 OXT A:ACT210 3.6 26.6 1.0 OE2 A:GLU97 3.7 21.0 1.0 CB A:ALA89 3.8 13.3 1.0 O A:ACT210 3.8 26.6 1.0 CG A:PRO86 3.8 15.6 1.0 CD A:GLU97 3.9 19.8 1.0 ZN A:ZN206 4.0 14.7 0.5 C A:ACT210 4.0 26.6 1.0 CD A:GLN93 4.3 20.6 1.0 CG A:GLN93 4.4 19.3 1.0 CD1 A:LEU94 4.8 13.1 1.0 N A:PRO86 4.9 14.2 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn208 b:34.0 occ:0.86 OE2 A:GLU8 1.8 34.8 1.0 O A:HOH390 2.3 44.5 1.0 CD A:GLU8 2.7 34.0 1.0 OE1 A:GLU8 2.9 33.3 1.0 O A:HOH301 3.1 36.3 1.0 CG A:GLU8 4.1 34.1 1.0 CG1 A:VAL4 4.1 25.9 1.0 O A:HOH318 4.2 22.9 1.0 O A:HOH413 4.8 46.7 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of K46 Acetylated Gabarap in Complex with the Lir of TP53INP2/Dor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn209 b:47.4 occ:0.37 O A:HOH426 1.9 37.7 1.0 ND1 A:HIS69 2.1 24.2 1.0 O A:HOH382 2.2 39.6 1.0 CG A:HIS69 2.9 23.8 1.0 CE1 A:HIS69 3.1 24.4 1.0 CB A:HIS69 3.2 23.6 1.0 CA A:HIS69 3.6 22.2 1.0 O A:LYS66 4.0 23.1 1.0 CD2 A:HIS69 4.1 23.7 1.0 NE2 A:HIS69 4.2 24.1 1.0 N A:HIS69 4.5 21.1 1.0 O A:HOH365 4.5 25.6 1.0 C A:HIS69 4.7 22.1 1.0

M.G.Ali, H.M.Wahba, S.Igelmann, N.Cyr, G.Ferbeyre, J.G.Omichinski. Structural and Functional Characterization of the Role of Acetylation on the Interactions of the Human ATG8-Family Proteins with the Autophagy Receptor TP53INP2/Dor. Autophagy 2024.
ISSN: ESSN 1554-8635
PubMed: 38726830
DOI: 10.1080/15548627.2024.2353443