Zinc in PDB 2dcu: Crystal Structure of Translation Initiation Factor AIF2BETAGAMMA Heterodimer with Gdp

The structure of Crystal Structure of Translation Initiation Factor AIF2BETAGAMMA Heterodimer with Gdp, PDB code: 2dcu was solved by M.Sokabe, M.Yao, N.Sakai, S.Toya, I.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.198, 76.561, 97.857, 90.00, 90.00, 90.00
R / Rfree (%)	24.9 / 29.8

The structure of Crystal Structure of Translation Initiation Factor AIF2BETAGAMMA Heterodimer with Gdp also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Translation Initiation Factor AIF2BETAGAMMA Heterodimer with Gdp (pdb code 2dcu). 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 Translation Initiation Factor AIF2BETAGAMMA Heterodimer with Gdp, PDB code: 2dcu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Translation Initiation Factor AIF2BETAGAMMA Heterodimer with Gdp


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 Translation Initiation Factor AIF2BETAGAMMA Heterodimer with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3001 b:27.0 occ:1.00 SG A:CYS64 2.1 35.2 1.0 SG A:CYS76 2.1 41.8 1.0 SG A:CYS61 2.1 25.8 1.0 SG A:CYS73 2.1 31.2 1.0 CB A:CYS64 3.0 36.8 1.0 CB A:CYS61 3.2 31.1 1.0 CB A:CYS73 3.3 32.9 1.0 CB A:CYS76 3.4 48.4 1.0 N A:CYS64 3.6 38.0 1.0 N A:CYS76 3.8 50.0 1.0 CA A:CYS64 3.9 36.4 1.0 CA A:CYS76 4.2 49.9 1.0 CD1 A:TYR75 4.6 54.3 1.0 CA A:CYS61 4.6 32.5 1.0 CA A:CYS73 4.7 33.1 1.0 C A:CYS64 4.7 35.8 1.0 N A:GLY65 4.7 36.1 1.0 C A:ASN63 4.7 38.4 1.0 N A:GLY77 4.8 52.3 1.0 CB A:ASN63 4.8 40.2 1.0 CB A:TYR75 4.8 50.3 1.0 C A:TYR75 5.0 49.5 1.0 C A:CYS76 5.0 51.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Translation Initiation Factor AIF2BETAGAMMA Heterodimer with Gdp


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 Translation Initiation Factor AIF2BETAGAMMA Heterodimer with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3002 b:62.0 occ:1.00 SG B:CYS128 2.1 65.8 1.0 SG B:CYS107 2.1 55.9 1.0 SG B:CYS110 2.1 63.3 1.0 SG B:CYS131 2.1 72.2 1.0 CB B:CYS107 2.9 53.4 1.0 O B:CYS110 3.0 69.9 1.0 CB B:CYS128 3.2 68.3 1.0 CB B:CYS131 3.2 75.1 1.0 CB B:CYS110 3.6 66.4 1.0 C B:CYS110 3.8 68.4 1.0 N B:CYS110 3.9 64.9 1.0 CA B:CYS110 4.0 66.8 1.0 N B:CYS131 4.1 76.5 1.0 CG2 B:VAL109 4.2 60.6 1.0 CA B:CYS131 4.2 75.9 1.0 OG B:SER112 4.3 67.8 1.0 CA B:CYS107 4.4 52.8 1.0 CA B:CYS128 4.5 70.3 1.0 CB B:SER112 4.6 68.4 1.0 CB B:ALA133 4.7 75.2 1.0 N B:GLY132 4.8 76.1 1.0 N B:ALA133 4.9 75.3 1.0 C B:CYS107 4.9 55.2 1.0 C B:CYS131 5.0 76.2 1.0

M.Sokabe, M.Yao, N.Sakai, S.Toya, I.Tanaka. Structure of Archaeal Translational Initiation Factor 2 Betagamma-Gdp Reveals Significant Conformational Change of the Beta-Subunit and Switch 1 Region. Proc.Natl.Acad.Sci.Usa V. 103 13016 2006.
ISSN: ISSN 0027-8424
PubMed: 16924118
DOI: 10.1073/PNAS.0604165103