Zinc in PDB 5tsg: Pilb From Geobacter Metallireducens Bound to Adp

The structure of Pilb From Geobacter Metallireducens Bound to Adp, PDB code: 5tsg was solved by M.Mccallum, S.Tammam, A.Khan, L.Burrows, P.L.Howell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.55 / 3.40
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.120, 112.120, 299.180, 90.00, 90.00, 120.00
R / Rfree (%)	27.3 / 29

The structure of Pilb From Geobacter Metallireducens Bound to Adp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Pilb From Geobacter Metallireducens Bound to Adp (pdb code 5tsg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Pilb From Geobacter Metallireducens Bound to Adp, PDB code: 5tsg:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Pilb From Geobacter Metallireducens Bound to Adp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pilb From Geobacter Metallireducens Bound to Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:16.8 occ:1.00 SG B:CYS461 2.3 89.0 1.0 SG B:CYS493 2.4 89.2 1.0 SG B:CYS458 2.7 85.0 1.0 SG B:CYS496 2.7 83.4 1.0 CB B:CYS458 3.1 84.5 1.0 N B:CYS493 3.2 85.1 1.0 CB B:CYS461 3.2 91.2 1.0 CB B:CYS496 3.4 81.7 1.0 CB B:CYS493 3.4 89.5 1.0 C B:GLY492 3.5 84.8 1.0 CA B:GLY492 3.8 83.8 1.0 CA B:CYS493 3.8 86.2 1.0 N B:CYS496 4.1 85.8 1.0 N B:CYS461 4.1 92.6 1.0 O B:GLY492 4.2 86.2 1.0 N B:GLY492 4.2 85.2 1.0 CA B:CYS461 4.3 92.3 1.0 CA B:CYS496 4.4 84.1 1.0 C B:CYS493 4.5 84.8 1.0 O B:CYS493 4.5 83.1 1.0 CA B:CYS458 4.6 88.3 1.0 CA B:GLY500 4.7 85.3 1.0 N B:GLY500 4.9 83.8 1.0 CB B:LYS495 5.0 81.9 1.0

Zinc binding site 2 out of 3 in the Pilb From Geobacter Metallireducens Bound to Adp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pilb From Geobacter Metallireducens Bound to Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:16.8 occ:1.00 SG C:CYS493 2.3 69.0 1.0 SG C:CYS461 2.3 77.5 1.0 SG C:CYS496 2.4 68.5 1.0 CB C:CYS461 2.9 80.0 1.0 SG C:CYS458 3.0 70.9 1.0 N C:CYS493 3.2 73.0 1.0 CB C:CYS493 3.2 72.0 1.0 C C:GLY492 3.5 74.1 1.0 CB C:CYS458 3.6 70.4 1.0 CB C:CYS496 3.7 68.6 1.0 N C:CYS461 3.7 78.8 1.0 CA C:CYS493 3.8 74.8 1.0 CA C:GLY492 3.9 72.2 1.0 CA C:CYS461 3.9 79.8 1.0 O C:GLY492 4.1 76.4 1.0 N C:CYS496 4.2 72.1 1.0 N C:GLY492 4.3 73.2 1.0 C C:CYS493 4.5 74.2 1.0 CA C:CYS496 4.5 71.0 1.0 CB C:GLU460 4.6 87.8 1.0 O C:CYS493 4.7 72.6 1.0 C C:GLU460 4.7 84.5 1.0 CB C:LYS495 4.8 71.1 1.0

Zinc binding site 3 out of 3 in the Pilb From Geobacter Metallireducens Bound to Adp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pilb From Geobacter Metallireducens Bound to Adp within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:16.8 occ:1.00 SG D:CYS496 2.5 0.5 1.0 SG D:CYS461 2.5 0.6 1.0 SG D:CYS458 2.5 0.1 1.0 SG D:CYS493 2.5 0.3 1.0 CB D:CYS461 3.1 0.3 1.0 CB D:CYS496 3.3 1.0 1.0 CB D:CYS458 3.4 0.2 1.0 CB D:CYS493 3.6 0.1 1.0 N D:CYS493 3.6 0.9 1.0 C D:GLY492 3.7 0.0 1.0 CA D:GLY492 3.9 0.3 1.0 CA D:CYS493 4.1 0.5 1.0 O D:GLY492 4.3 1.0 1.0 N D:CYS496 4.3 0.3 1.0 CA D:CYS461 4.4 0.9 1.0 N D:GLY492 4.4 0.3 1.0 CA D:CYS496 4.5 0.7 1.0 N D:CYS461 4.5 0.7 1.0 CG D:GLU460 4.7 0.4 1.0 C D:CYS493 4.9 0.6 1.0 CA D:CYS458 4.9 0.9 1.0 OE2 D:GLU460 4.9 0.2 1.0 O D:TYR501 5.0 98.4 1.0

M.Mccallum, S.Tammam, A.Khan, L.L.Burrows, P.L.Howell. The Molecular Mechanism of the Type Iva Pilus Motors. Nat Commun V. 8 15091 2017.
ISSN: ESSN 2041-1723
PubMed: 28474682
DOI: 10.1038/NCOMMS15091