Zinc in PDB 3dwd: Crystal Structure of the Arfgap Domain of Human ARFGAP1

The structure of Crystal Structure of the Arfgap Domain of Human ARFGAP1, PDB code: 3dwd was solved by L.Nedyalkova, Y.Tong, W.Tempel, R.Landry, C.H.Arrowsmith, A.M.Edwards, C.Bountra, M.Wilkstrom, A.Bochkarev, H.Park, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.40
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	82.422, 82.422, 81.008, 90.00, 90.00, 120.00
R / Rfree (%)	23.4 / 27.3

The binding sites of Zinc atom in the Crystal Structure of the Arfgap Domain of Human ARFGAP1 (pdb code 3dwd). 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 the Arfgap Domain of Human ARFGAP1, PDB code: 3dwd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Arfgap Domain of Human ARFGAP1


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 the Arfgap Domain of Human ARFGAP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:28.7 occ:1.00 SG A:CYS22 2.3 26.5 1.0 SG A:CYS42 2.3 29.9 1.0 SG A:CYS45 2.4 32.1 1.0 SG A:CYS25 2.4 24.2 1.0 CB A:CYS22 3.3 26.8 1.0 CB A:CYS45 3.4 28.9 1.0 CB A:CYS25 3.6 26.0 1.0 CB A:CYS42 3.6 27.3 1.0 N A:CYS25 3.9 25.1 1.0 N A:CYS42 4.0 24.2 1.0 CA A:CYS25 4.3 25.5 1.0 CA A:CYS42 4.3 25.4 1.0 N A:CYS45 4.4 25.3 1.0 CB A:GLU24 4.5 25.6 1.0 CA A:CYS45 4.5 25.6 1.0 CA A:CYS22 4.7 23.9 1.0 CB A:ALA27 4.8 15.4 1.0 N A:GLY26 4.8 25.4 1.0 C A:CYS25 4.9 25.6 1.0 N A:ALA27 5.0 20.7 1.0 C A:CYS42 5.0 25.5 1.0 C A:GLU24 5.0 25.7 1.0 O A:CYS42 5.0 26.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Arfgap Domain of Human ARFGAP1


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 the Arfgap Domain of Human ARFGAP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:26.0 occ:1.00 SG B:CYS25 2.3 24.5 1.0 SG B:CYS45 2.3 29.5 1.0 SG B:CYS22 2.3 29.5 1.0 SG B:CYS42 2.3 23.3 1.0 CB B:CYS25 3.2 25.0 1.0 CB B:CYS22 3.3 25.8 1.0 CB B:CYS45 3.4 27.9 1.0 CB B:CYS42 3.6 23.4 1.0 N B:CYS25 3.8 23.7 1.0 CA B:CYS25 4.1 23.4 1.0 N B:CYS42 4.1 24.8 1.0 N B:CYS45 4.4 27.5 1.0 CA B:CYS42 4.4 23.7 1.0 CA B:CYS45 4.5 26.8 1.0 C B:CYS25 4.6 21.5 1.0 CB B:GLU24 4.6 23.4 1.0 CB B:ALA27 4.6 16.7 1.0 CA B:CYS22 4.7 24.3 1.0 N B:GLY26 4.7 21.8 1.0 C B:GLU24 4.9 23.2 1.0 N B:ALA27 4.9 19.6 1.0

L.Nedyalkova, Y.Tong, W.Tempel, R.Landry, C.H.Arrowsmith, A.M.Edwards, C.Bountra, M.Wilkstrom, A.Bochkarev, H.Park. Crystal Structure of the Arfgap Domain of Human ARFGAP1 To Be Published.