Zinc in PDB 6wcw: Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7

The structure of Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7, PDB code: 6wcw was solved by H.K.Bhargava, J.M.Byck, D.P.Farrell, I.Anishchenko, F.Dimaio, Y.J.Im, J.H.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.22 / 2.80
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	60.040, 45.330, 186.277, 90.00, 98.51, 90.00
R / Rfree (%)	20 / 25.8

The structure of Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7 (pdb code 6wcw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7, PDB code: 6wcw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:0.9 occ:1.00 SG A:CYS721 2.0 28.7 1.0 SG A:CYS747 2.0 29.9 1.0 SG A:CYS724 2.0 33.5 1.0 SG A:CYS750 2.2 30.4 1.0 CB A:CYS721 3.1 33.0 1.0 CB A:CYS747 3.2 20.7 1.0 CB A:CYS750 3.4 28.6 1.0 CB A:CYS724 3.4 28.9 1.0 N A:CYS724 3.8 23.9 1.0 N A:CYS747 3.8 20.8 1.0 CA A:CYS747 4.1 20.5 1.0 N A:CYS750 4.2 26.4 1.0 CA A:CYS724 4.2 24.3 1.0 CG2 A:ILE726 4.3 21.8 1.0 CA A:CYS750 4.4 26.8 1.0 CA A:CYS721 4.5 30.8 1.0 O A:CYS747 4.6 21.1 1.0 N A:GLY723 4.6 39.7 1.0 C A:GLY723 4.6 43.0 1.0 C A:CYS747 4.6 23.6 1.0 CA A:GLY723 4.8 38.8 1.0 C A:CYS721 4.8 35.6 1.0 C A:CYS724 4.9 26.9 1.0 C A:PHE746 5.0 26.0 1.0

Zinc binding site 2 out of 4 in the Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:1.0 occ:1.00 NE2 A:HIS877 1.8 59.1 1.0 SG A:CYS826 2.1 75.2 1.0 SG A:CYS884 2.1 59.4 1.0 SG A:CYS881 2.3 57.4 1.0 CE1 A:HIS877 2.8 58.8 1.0 CD2 A:HIS877 2.9 60.4 1.0 CB A:CYS826 3.3 70.8 1.0 CB A:CYS881 3.5 60.8 1.0 CB A:CYS884 3.6 59.2 1.0 CB A:ALA829 3.8 71.2 1.0 ND1 A:HIS877 3.9 59.6 1.0 CG A:HIS877 4.0 60.3 1.0 N A:CYS884 4.1 64.9 1.0 N A:ALA829 4.4 78.3 1.0 CA A:CYS884 4.4 58.9 1.0 O A:CYS881 4.5 77.0 1.0 CB A:LEU883 4.7 47.0 1.0 CA A:ALA829 4.7 76.9 1.0 CA A:CYS826 4.7 63.8 1.0 CB A:LEU828 4.7 65.1 1.0 CA A:CYS881 4.8 63.8 1.0 C A:CYS881 4.8 70.8 1.0 C A:LEU883 4.9 56.3 1.0 C A:LEU828 4.9 68.7 1.0 CD1 A:PHE823 4.9 68.4 1.0 CE1 A:PHE823 4.9 68.2 1.0 O A:HIS877 5.0 56.1 1.0

Zinc binding site 3 out of 4 in the Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:0.1 occ:1.00 ND1 A:HIS920 1.9 53.3 1.0 SG A:CYS923 2.0 67.5 1.0 SG A:CYS891 2.1 52.5 1.0 SG A:CYS894 2.2 63.8 1.0 CB A:CYS891 2.8 53.7 1.0 CE1 A:HIS920 2.8 49.8 1.0 CG A:HIS920 2.9 56.5 1.0 CB A:HIS920 3.3 56.8 1.0 CB A:CYS923 3.4 75.1 1.0 CB A:CYS894 3.5 59.4 1.0 NE2 A:HIS920 3.9 50.6 1.0 N A:HIS920 4.0 59.8 1.0 CD2 A:HIS920 4.0 52.3 1.0 N A:CYS894 4.1 57.4 1.0 CA A:HIS920 4.3 61.4 1.0 CA A:CYS891 4.3 46.3 1.0 CA A:CYS894 4.4 59.1 1.0 CB A:PHE893 4.7 62.6 1.0 CA A:CYS923 4.8 72.7 1.0 C A:CYS891 4.8 43.2 1.0 O A:CYS891 4.9 52.2 1.0

Zinc binding site 4 out of 4 in the Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human Rubicon Rh Domain in Complex with Gtp-Bound RAB7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:0.2 occ:1.00 SG A:CYS912 2.3 62.4 1.0 SG A:CYS915 2.3 83.0 1.0 CB A:CYS929 2.4 96.9 1.0 SG A:CYS929 2.4 94.2 1.0 SG A:CYS932 3.1 0.6 1.0 CB A:CYS912 3.5 59.5 1.0 CB A:CYS915 3.6 75.5 1.0 CA A:CYS929 3.9 95.0 1.0 N A:CYS915 4.0 86.6 1.0 OE1 A:GLU914 4.3 0.4 1.0 CB A:CYS932 4.4 0.9 1.0 CB A:GLU914 4.4 0.3 1.0 N A:CYS929 4.5 98.1 1.0 CA A:CYS915 4.5 74.3 1.0 C A:CYS929 4.5 92.5 1.0 O A:CYS929 4.6 92.7 1.0 N A:CYS932 4.8 0.8 1.0 CA A:CYS912 4.9 63.1 1.0 CZ A:PHE924 4.9 65.3 1.0 C A:GLU914 4.9 0.0 1.0

H.K.Bhargava, K.Tabata, J.M.Byck, M.Hamasaki, D.P.Farrell, I.Anishchenko, F.Dimaio, Y.J.Im, T.Yoshimori, J.H.Hurley. Structural Basis For Autophagy Inhibition By the Human Rubicon-RAB7 Complex. Proc.Natl.Acad.Sci.Usa V. 117 17003 2020.
ISSN: ESSN 1091-6490
PubMed: 32632011
DOI: 10.1073/PNAS.2008030117