Zinc in PDB 5zfr: Crystal Structure of Pilb, An Extension Atpase Motor of Type IV Pilus, From Geobacter Sulfurreducens

The structure of Crystal Structure of Pilb, An Extension Atpase Motor of Type IV Pilus, From Geobacter Sulfurreducens, PDB code: 5zfr was solved by K.G.Thakur, V.Solanki, S.Kapoor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.34 / 3.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	176.301, 176.301, 138.561, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 24.7

The binding sites of Zinc atom in the Crystal Structure of Pilb, An Extension Atpase Motor of Type IV Pilus, From Geobacter Sulfurreducens (pdb code 5zfr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Pilb, An Extension Atpase Motor of Type IV Pilus, From Geobacter Sulfurreducens, PDB code: 5zfr:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Pilb, An Extension Atpase Motor of Type IV Pilus, From Geobacter Sulfurreducens


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 Pilb, An Extension Atpase Motor of Type IV Pilus, From Geobacter Sulfurreducens within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:0.2 occ:1.00 SG A:CYS461 2.3 99.1 1.0 SG A:CYS496 2.4 0.2 1.0 SG A:CYS493 2.4 0.2 1.0 SG A:CYS458 2.4 99.2 1.0 CB A:CYS496 2.7 1.0 1.0 CB A:CYS458 2.9 0.4 1.0 CB A:CYS493 3.4 0.8 1.0 CB A:CYS461 3.5 1.0 1.0 N A:CYS493 3.5 0.8 1.0 N A:CYS496 3.6 0.6 1.0 CA A:CYS496 3.7 0.9 1.0 N A:CYS461 3.8 0.2 1.0 CA A:CYS493 4.0 0.9 1.0 CA A:CYS461 4.3 0.2 1.0 C A:GLY492 4.4 0.7 1.0 CA A:CYS458 4.4 0.3 1.0 C A:CYS493 4.5 0.7 1.0 CA A:GLY492 4.6 0.2 1.0 C A:LYS495 4.7 0.6 1.0 O A:CYS493 4.7 0.4 1.0 CA A:GLY500 4.7 94.8 1.0 N A:GLY492 4.7 0.4 1.0 C A:CYS496 4.8 0.1 1.0 CB A:GLU460 4.9 0.6 1.0 C A:CYS458 4.9 0.3 1.0 C A:GLU460 4.9 0.7 1.0 C A:GLY500 4.9 91.8 1.0 N A:GLY500 5.0 94.6 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Pilb, An Extension Atpase Motor of Type IV Pilus, From Geobacter Sulfurreducens


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 Pilb, An Extension Atpase Motor of Type IV Pilus, From Geobacter Sulfurreducens within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:0.7 occ:1.00 SG B:CYS461 2.3 0.0 1.0 SG B:CYS493 2.4 0.7 1.0 SG B:CYS458 2.4 0.2 1.0 SG B:CYS496 2.6 0.7 1.0 CB B:CYS458 2.8 0.1 1.0 CB B:CYS496 2.9 0.8 1.0 CB B:CYS461 3.5 0.5 1.0 CB B:CYS493 3.6 0.1 1.0 N B:CYS496 3.6 0.4 1.0 N B:CYS461 3.7 0.1 1.0 N B:CYS493 3.7 0.8 1.0 CA B:CYS496 3.9 0.2 1.0 CA B:CYS493 4.1 0.4 1.0 CA B:CYS461 4.2 0.0 1.0 CA B:CYS458 4.3 0.3 1.0 C B:CYS493 4.5 0.9 1.0 C B:LYS495 4.6 0.4 1.0 CB B:GLU460 4.6 0.9 1.0 C B:GLY492 4.6 0.5 1.0 CB B:LYS495 4.7 0.4 1.0 C B:GLU460 4.7 0.8 1.0 O B:CYS493 4.7 0.1 1.0 C B:CYS458 4.8 0.7 1.0 CA B:GLY500 4.8 0.3 1.0 N B:GLU460 4.8 0.5 1.0 N B:LYS495 4.8 0.7 1.0 CA B:GLY492 4.9 0.8 1.0 CA B:LYS495 4.9 0.1 1.0 CA B:GLU460 5.0 0.8 1.0 O B:CYS458 5.0 0.4 1.0 C B:CYS461 5.0 0.3 1.0 C B:GLY500 5.0 0.7 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Pilb, An Extension Atpase Motor of Type IV Pilus, From Geobacter Sulfurreducens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Pilb, An Extension Atpase Motor of Type IV Pilus, From Geobacter Sulfurreducens within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:0.1 occ:1.00 SG C:CYS461 2.2 0.1 1.0 SG C:CYS493 2.3 0.4 1.0 SG C:CYS496 2.4 0.9 1.0 SG C:CYS458 2.4 1.0 1.0 CB C:CYS496 2.7 0.1 1.0 CB C:CYS458 2.9 1.0 1.0 CB C:CYS493 3.3 0.1 1.0 CB C:CYS461 3.4 0.2 1.0 N C:CYS493 3.5 0.8 1.0 N C:CYS496 3.6 0.1 1.0 CA C:CYS496 3.7 0.7 1.0 N C:CYS461 3.8 0.9 1.0 CA C:CYS493 3.9 0.0 1.0 CA C:CYS461 4.2 0.9 1.0 CA C:CYS458 4.4 0.4 1.0 C C:GLY492 4.4 0.2 1.0 C C:CYS493 4.4 0.9 1.0 CA C:GLY500 4.6 0.5 1.0 O C:CYS493 4.6 0.8 1.0 C C:LYS495 4.6 0.1 1.0 CA C:GLY492 4.6 0.6 1.0 N C:GLY492 4.8 0.9 1.0 C C:GLY500 4.8 0.8 1.0 CB C:GLU460 4.8 0.4 1.0 N C:GLY500 4.8 0.5 1.0 C C:CYS496 4.8 0.0 1.0 N C:LYS495 4.9 1.0 1.0 C C:GLU460 4.9 0.4 1.0 C C:CYS458 4.9 0.6 1.0 CB C:LYS495 4.9 0.0 1.0 C C:CYS461 5.0 0.3 1.0

V.Solanki, S.Kapoor, K.G.Thakur. Structural Insights Into the Mechanism of Type Iva Pilus Extension and Retraction Atpase Motors Febs J. V. 285 3402 2018.
ISSN: ISSN 1742-4658
PubMed: 30066435
DOI: 10.1111/FEBS.14619