Zinc in PDB 3kfu: Crystal Structure of the Transamidosome

The structure of Crystal Structure of the Transamidosome, PDB code: 3kfu was solved by M.Blaise, M.Bailly, M.Frechin, S.Thirup, H.D.Becker, D.Kern, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.19 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	115.920, 214.000, 127.840, 90.00, 93.36, 90.00
R / Rfree (%)	19.9 / 25.2

The structure of Crystal Structure of the Transamidosome also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Transamidosome (pdb code 3kfu). 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 Transamidosome, PDB code: 3kfu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Transamidosome


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 Transamidosome within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn673 b:0.4 occ:1.00 SG F:CYS41 2.0 80.2 1.0 SG F:CYS24 2.1 0.0 1.0 SG F:CYS38 2.2 46.1 1.0 SG F:CYS22 2.2 68.5 1.0 CB F:CYS24 3.1 29.2 1.0 CB F:CYS22 3.2 20.7 1.0 CB F:CYS38 3.3 62.5 1.0 N F:CYS38 3.6 66.5 1.0 N F:CYS24 3.8 56.1 1.0 CB F:CYS41 3.8 21.3 1.0 CA F:CYS38 4.0 57.1 1.0 CA F:CYS24 4.0 43.1 1.0 N F:CYS41 4.1 50.4 1.0 C F:THR37 4.3 59.9 1.0 CD F:LYS19 4.4 51.0 1.0 N F:GLY23 4.5 16.0 1.0 CA F:CYS22 4.5 30.0 1.0 CA F:CYS41 4.6 50.3 1.0 CA F:THR37 4.6 25.5 1.0 C F:CYS22 4.6 39.3 1.0 C F:CYS38 4.7 56.0 1.0 NZ F:LYS19 4.7 23.4 1.0 O F:CYS38 4.7 67.5 1.0 CB F:VAL40 4.7 32.7 1.0 CE F:LYS19 4.8 58.8 1.0 C F:GLY23 5.0 29.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Transamidosome


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 Transamidosome within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn467 b:0.1 occ:1.00 SG I:CYS41 2.0 51.2 1.0 SG I:CYS24 2.1 53.2 1.0 SG I:CYS22 2.1 51.8 1.0 SG I:CYS38 2.2 26.9 1.0 CB I:CYS24 3.1 12.6 1.0 CB I:CYS22 3.2 36.3 1.0 CB I:CYS38 3.4 72.8 1.0 N I:CYS38 3.7 48.7 1.0 N I:CYS24 3.8 44.6 1.0 CB I:CYS41 3.8 10.0 1.0 CA I:CYS24 4.0 27.2 1.0 CA I:CYS38 4.1 28.9 1.0 N I:CYS41 4.1 56.4 1.0 C I:THR37 4.3 54.8 1.0 CD I:LYS19 4.4 42.9 1.0 N I:GLY23 4.5 16.3 1.0 CA I:CYS22 4.5 31.6 1.0 CA I:CYS41 4.6 68.4 1.0 C I:CYS22 4.6 44.4 1.0 CA I:THR37 4.6 26.1 1.0 NZ I:LYS19 4.6 20.4 1.0 C I:CYS38 4.7 37.8 1.0 CE I:LYS19 4.7 41.0 1.0 O I:CYS38 4.8 47.6 1.0 CB I:VAL40 4.8 29.9 1.0 C I:GLY23 4.9 16.1 1.0

M.Blaise, M.Bailly, M.Frechin, M.A.Behrens, F.Fischer, C.L.Oliveira, H.D.Becker, J.S.Pedersen, S.Thirup, D.Kern. Crystal Structure of A Transfer-Ribonucleoprotein Particle That Promotes Asparagine Formation. Embo J. V. 29 3118 2010.
ISSN: ISSN 0261-4189
PubMed: 20717102
DOI: 10.1038/EMBOJ.2010.192