Zinc in PDB 3lcn: NAB2:GFD1 Complex

The structure of NAB2:GFD1 Complex, PDB code: 3lcn was solved by M.Stewart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.07 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.833, 121.762, 37.376, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.6

The binding sites of Zinc atom in the NAB2:GFD1 Complex (pdb code 3lcn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the NAB2:GFD1 Complex, PDB code: 3lcn:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the NAB2:GFD1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of NAB2:GFD1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn106 b:37.2 occ:1.00 OE2 B:GLU76 2.0 38.2 1.0 OE2 A:GLU76 2.1 45.3 1.0 OE1 A:GLU76 2.5 39.2 1.0 CD A:GLU76 2.6 41.2 1.0 CD B:GLU76 2.9 38.4 1.0 OE1 B:GLU76 3.0 42.6 1.0 HE22 B:GLN80 3.1 69.7 1.0 HE22 A:GLN80 3.7 66.2 1.0 NE2 B:GLN80 3.9 58.1 1.0 NE2 A:GLN80 4.1 55.2 1.0 CG A:GLU76 4.1 37.3 1.0 HG2 A:GLN80 4.1 54.0 1.0 HG3 B:GLN80 4.2 47.4 1.0 HG2 B:GLN80 4.2 47.4 1.0 CG B:GLU76 4.3 34.6 1.0 HE21 B:GLN80 4.3 69.7 1.0 HE21 A:GLN80 4.4 66.2 1.0 HG2 A:GLU76 4.5 44.7 1.0 OE1 A:GLN79 4.5 59.9 1.0 HG3 A:GLU76 4.5 44.7 1.0 O A:HOH121 4.5 49.5 1.0 HG3 B:GLU76 4.6 41.5 1.0 HG2 B:GLU76 4.6 41.5 1.0 CG B:GLN80 4.6 39.5 1.0 CD A:GLN80 4.7 52.2 1.0 CD B:GLN80 4.8 49.1 1.0 HB2 A:GLN79 4.8 46.7 1.0 HA A:GLU76 4.8 37.1 1.0 CG A:GLN80 4.8 45.0 1.0 HB2 A:GLU76 5.0 40.2 1.0

Zinc binding site 2 out of 3 in the NAB2:GFD1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of NAB2:GFD1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn107 b:42.9 occ:1.00 OE2 A:GLU46 2.0 51.4 1.0 OD1 B:ASP62 2.1 45.3 1.0 OD2 A:ASP50 2.2 50.9 1.0 OD1 A:ASP50 2.7 40.9 1.0 HH22 A:ARG61 2.7 81.8 1.0 CG A:ASP50 2.7 45.2 1.0 HG3 A:GLU46 2.9 54.3 1.0 CD A:GLU46 3.0 49.9 1.0 CG B:ASP62 3.1 49.7 1.0 NH2 A:ARG61 3.3 68.2 1.0 CG A:GLU46 3.3 45.2 1.0 HG2 A:GLU46 3.4 54.3 1.0 HH21 A:ARG61 3.5 81.8 1.0 OD2 B:ASP62 3.5 54.5 1.0 HD3 B:ARG61 4.0 71.0 1.0 HG2 B:ARG61 4.0 54.9 1.0 HA B:ASP62 4.0 45.4 1.0 OE1 A:GLU46 4.2 50.4 1.0 HH12 A:ARG61 4.2 91.3 1.0 CB A:ASP50 4.2 40.2 1.0 CZ A:ARG61 4.3 76.2 1.0 O A:HOH144 4.3 65.3 1.0 CB B:ASP62 4.4 42.2 1.0 O A:GLU46 4.5 32.4 1.0 HB3 A:ASP50 4.6 48.2 1.0 HB2 A:ASP50 4.6 48.2 1.0 CA B:ASP62 4.6 37.8 1.0 NH1 A:ARG61 4.6 76.1 1.0 HE B:ARG61 4.7 86.6 1.0 CD B:ARG61 4.7 59.1 1.0 HB3 B:ARG61 4.7 46.0 1.0 CG B:ARG61 4.8 45.8 1.0 CB A:GLU46 4.8 39.7 1.0 N B:ASP62 4.8 35.7 1.0 H B:ASP62 4.9 42.8 1.0 HB2 B:ASP62 4.9 50.6 1.0 HB3 B:ASP62 5.0 50.6 1.0

Zinc binding site 3 out of 3 in the NAB2:GFD1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of NAB2:GFD1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn106 b:53.1 occ:1.00 OD1 A:ASP62 2.1 54.1 1.0 OD2 B:ASP50 2.3 52.7 1.0 OE2 B:GLU46 2.3 57.0 1.0 O B:HOH135 2.4 48.9 1.0 OD1 B:ASP50 2.6 44.9 1.0 CG B:ASP50 2.8 48.4 1.0 HH22 B:ARG61 2.8 73.5 1.0 HG3 B:GLU46 3.1 64.6 1.0 CG A:ASP62 3.1 56.9 1.0 CD B:GLU46 3.2 55.5 1.0 NH2 B:ARG61 3.4 61.3 1.0 OD2 A:ASP62 3.5 67.8 1.0 HH21 B:ARG61 3.5 73.5 1.0 CG B:GLU46 3.5 53.9 1.0 HG2 B:GLU46 3.6 64.6 1.0 HD3 A:ARG61 3.8 88.1 1.0 HG2 A:ARG61 3.9 74.2 1.0 HA A:ASP62 4.1 52.0 1.0 CB B:ASP50 4.3 41.1 1.0 O B:HOH133 4.3 56.0 1.0 OE1 B:GLU46 4.4 57.1 1.0 CZ B:ARG61 4.4 71.6 1.0 HH12 B:ARG61 4.4 90.6 1.0 CB A:ASP62 4.5 46.9 1.0 HB3 A:ARG61 4.5 68.2 1.0 HB3 B:ASP50 4.6 49.3 1.0 HB2 B:ASP50 4.6 49.3 1.0 CG A:ARG61 4.6 61.9 1.0 CD A:ARG61 4.6 73.5 1.0 O B:GLU46 4.6 37.0 1.0 CA A:ASP62 4.7 43.4 1.0 N A:ASP62 4.7 44.6 1.0 HE A:ARG61 4.8 90.3 1.0 H A:ASP62 4.8 53.5 1.0 NH1 B:ARG61 4.8 75.5 1.0 CB B:GLU46 4.9 48.4 1.0 HB3 A:ASP62 5.0 56.2 1.0

C.Zheng, M.B.Fasken, N.J.Marshall, C.Brockmann, M.E.Rubinson, S.R.Wente, A.H.Corbett, M.Stewart. Structural Basis For the Function of the Saccharomyces Cerevisiae GFD1 Protein in Mrna Nuclear Export. J.Biol.Chem. V. 285 20704 2010.
ISSN: ISSN 0021-9258
PubMed: 20463024
DOI: 10.1074/JBC.M110.107276