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Zinc in PDB 6mj7: Crystal Structure of P62 Zz Domain in Complex with Free Arginine

Protein crystallography data

The structure of Crystal Structure of P62 Zz Domain in Complex with Free Arginine, PDB code: 6mj7 was solved by J.Ahn, Y.Zhang, T.G.Kutateladze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.58 / 1.41
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 44.971, 32.269, 34.941, 90.00, 122.16, 90.00
R / Rfree (%) 13.6 / 16.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of P62 Zz Domain in Complex with Free Arginine (pdb code 6mj7). 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 P62 Zz Domain in Complex with Free Arginine, PDB code: 6mj7:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6mj7

Go back to Zinc Binding Sites List in 6mj7
Zinc binding site 1 out of 2 in the Crystal Structure of P62 Zz Domain in Complex with Free Arginine


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 P62 Zz Domain in Complex with Free Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:7.6
occ:0.75
SG A:CYS128 2.3 6.2 1.0
SG A:CYS154 2.3 7.4 1.0
SG A:CYS151 2.4 6.8 1.0
SG A:CYS131 2.4 8.5 1.0
CB A:CYS128 3.3 6.6 1.0
CB A:CYS154 3.3 6.3 1.0
CB A:CYS131 3.3 10.5 1.0
CB A:CYS151 3.4 6.7 1.0
N A:CYS131 3.6 6.5 1.0
N A:CYS151 3.9 6.9 1.0
CA A:CYS131 4.0 7.0 1.0
N A:CYS154 4.1 7.7 1.0
CA A:CYS151 4.2 7.0 1.0
O A:HOH334 4.3 13.6 1.0
CA A:CYS154 4.3 7.1 1.0
C A:GLY130 4.4 8.6 1.0
CA A:GLY130 4.6 6.8 1.0
CA A:CYS128 4.7 6.5 1.0
C A:CYS151 4.7 5.8 1.0
N A:GLY130 4.7 7.7 1.0
O A:CYS151 4.8 7.7 1.0
C A:CYS131 4.9 7.5 1.0
O A:HOH370 5.0 19.5 1.0

Zinc binding site 2 out of 2 in 6mj7

Go back to Zinc Binding Sites List in 6mj7
Zinc binding site 2 out of 2 in the Crystal Structure of P62 Zz Domain in Complex with Free Arginine


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 P62 Zz Domain in Complex with Free Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:10.0
occ:0.76
NE2 A:HIS160 2.1 8.7 1.0
ND1 A:HIS163 2.1 9.5 1.0
SG A:CYS145 2.3 9.9 1.0
SG A:CYS142 2.3 8.4 1.0
CE1 A:HIS160 3.0 8.8 1.0
CD2 A:HIS160 3.1 8.2 1.0
CE1 A:HIS163 3.1 10.7 1.0
CG A:HIS163 3.1 7.7 1.0
CB A:CYS145 3.3 12.1 1.0
CB A:CYS142 3.4 7.6 1.0
CB A:HIS163 3.4 9.0 1.0
N A:CYS145 3.6 10.1 1.0
CA A:CYS145 4.1 10.7 1.0
ND1 A:HIS160 4.1 11.3 1.0
CG A:HIS160 4.2 9.6 1.0
NE2 A:HIS163 4.2 12.0 1.0
CD2 A:HIS163 4.3 10.4 1.0
CB A:VAL144 4.3 11.1 1.0
C A:VAL144 4.6 12.2 1.0
CB A:TYR148 4.7 7.7 1.0
O A:HOH388 4.8 22.2 1.0
CA A:CYS142 4.8 6.4 1.0
CG A:TYR148 4.8 8.9 1.0
O A:HOH397 4.9 23.6 1.0
CA A:VAL144 4.9 11.1 1.0
N A:VAL144 4.9 8.6 1.0
CG1 A:VAL144 5.0 15.2 1.0
CA A:HIS163 5.0 8.5 1.0
CD2 A:TYR148 5.0 8.4 1.0

Reference:

Y.Zhang, S.R.Mun, J.F.Linares, J.Ahn, C.G.Towers, C.H.Ji, B.E.Fitzwalter, M.R.Holden, W.Mi, X.Shi, J.Moscat, A.Thorburn, M.T.Diaz-Meco, Y.T.Kwon, T.G.Kutateladze. Zz-Dependent Regulation of P62/SQSTM1 in Autophagy. Nat Commun V. 9 4373 2018.
ISSN: ESSN 2041-1723
PubMed: 30349045
DOI: 10.1038/S41467-018-06878-8
Page generated: Wed Dec 16 12:19:51 2020

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