Zinc in PDB 9edl: Crystal Structure of Francisella Tularensis DSBA1

The structure of Crystal Structure of Francisella Tularensis DSBA1, PDB code: 9edl was solved by S.Penning, B.Heras, J.J.Paxman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.20 / 1.96
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.744, 57.275, 168.809, 90, 90, 90
R / Rfree (%)	18.4 / 22.6

The binding sites of Zinc atom in the Crystal Structure of Francisella Tularensis DSBA1 (pdb code 9edl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Francisella Tularensis DSBA1, PDB code: 9edl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Francisella Tularensis DSBA1


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 Francisella Tularensis DSBA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:81.3 occ:1.00 SG A:CYS60 2.3 35.1 1.0 ND1 A:HIS175 2.3 40.0 1.0 SG A:CYS57 2.3 45.5 1.0 CE1 A:HIS175 2.5 40.9 1.0 N A:CYS60 2.8 38.0 1.0 CB A:CYS60 3.1 29.1 1.0 CB A:CYS57 3.2 39.3 1.0 CA A:CYS60 3.3 35.5 1.0 CG A:HIS175 3.6 36.6 1.0 C A:LYS59 3.8 36.0 1.0 NE2 A:HIS175 3.8 36.4 1.0 CB A:LYS59 3.8 36.8 1.0 CG A:PRO174 4.0 29.2 1.0 CA A:LYS59 4.2 36.8 1.0 CB A:PRO174 4.2 24.5 1.0 N A:LYS59 4.3 37.3 1.0 CD2 A:HIS175 4.4 40.5 1.0 CA A:CYS57 4.5 35.1 1.0 CB A:HIS175 4.5 34.4 1.0 O A:CYS57 4.5 36.6 1.0 N A:HIS175 4.5 31.1 1.0 CG A:LYS59 4.6 39.3 1.0 C A:CYS57 4.6 38.0 1.0 O A:LYS59 4.7 30.8 1.0 C A:CYS60 4.8 32.6 1.0 CB A:ASP54 4.8 28.1 1.0 O A:HOH471 4.8 27.4 1.0 CD A:LYS59 4.8 40.8 1.0 C A:PRO174 4.9 29.1 1.0 O A:ASP54 4.9 24.6 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Francisella Tularensis DSBA1


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 Francisella Tularensis DSBA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:108.0 occ:1.00 OE1 A:GLN206 4.5 55.6 1.0 CE1 A:HIS12 4.9 77.8 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Francisella Tularensis DSBA1


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 Francisella Tularensis DSBA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:48.6 occ:1.00 NE2 A:HIS12 2.3 82.2 1.0 CE1 A:HIS12 2.8 77.8 1.0 CD2 A:HIS12 3.5 86.8 1.0 ND1 A:HIS12 3.9 83.6 1.0 CG A:HIS12 4.3 89.1 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Francisella Tularensis DSBA1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Francisella Tularensis DSBA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:34.3 occ:1.00 OE1 A:GLU111 2.0 31.6 1.0 OE2 B:GLU125 2.1 48.6 1.0 OE1 B:GLU62 2.1 32.5 1.0 NZ B:LYS65 2.4 38.3 1.0 CD B:GLU125 2.6 36.1 1.0 CD B:GLU62 2.8 31.9 1.0 CD A:GLU111 2.9 38.3 1.0 OE2 B:GLU62 2.9 40.9 1.0 OE2 A:GLU111 3.1 41.6 1.0 OE1 B:GLU125 3.3 39.4 1.0 CG B:GLU125 3.4 38.9 1.0 CE B:LYS65 3.7 40.4 1.0 O B:HOH460 3.9 34.5 1.0 O A:HOH404 4.0 26.9 1.0 CG B:GLU62 4.3 35.0 1.0 CG A:GLU111 4.3 29.9 1.0 CD B:LYS65 4.4 35.4 1.0 O B:HOH481 4.5 31.7 1.0 O A:HOH453 4.6 58.5 1.0 CB B:GLU125 4.8 27.0 1.0 CB A:GLU111 4.9 21.3 1.0 CB B:GLU62 4.9 22.9 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Francisella Tularensis DSBA1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Francisella Tularensis DSBA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:41.7 occ:1.00 SG B:CYS57 2.3 27.6 1.0 N B:CYS60 2.3 22.3 1.0 SG B:CYS60 2.3 23.1 1.0 CB B:CYS60 2.9 17.2 1.0 CA B:CYS60 3.0 18.5 1.0 ND1 B:HIS175 3.1 27.8 1.0 CB B:CYS57 3.2 25.4 1.0 C B:LYS59 3.2 22.8 1.0 CB B:LYS59 3.4 24.7 1.0 CE1 B:HIS175 3.5 24.4 1.0 CA B:LYS59 3.6 22.1 1.0 N B:LYS59 3.8 24.2 1.0 O B:LYS59 4.2 17.3 1.0 O B:CYS57 4.2 21.8 1.0 C B:CYS57 4.3 25.1 1.0 CA B:CYS57 4.4 25.5 1.0 CG B:HIS175 4.4 22.9 1.0 C B:CYS60 4.4 19.9 1.0 CG B:LYS59 4.4 27.5 1.0 CG B:PRO174 4.7 22.8 1.0 C B:GLY58 4.8 24.2 1.0 NE2 B:HIS175 4.8 25.8 1.0 N B:ALA61 4.8 20.2 1.0 O B:ASP54 4.8 22.6 1.0 N B:GLY58 4.9 25.0 1.0 O B:HOH503 4.9 25.3 1.0 CD B:LYS59 4.9 33.3 1.0 CD1 B:ILE63 4.9 23.5 1.0 CB B:ASP54 4.9 19.9 1.0 CB B:PRO174 5.0 23.6 1.0 CB B:HIS175 5.0 25.0 1.0 O B:HOH532 5.0 44.7 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Francisella Tularensis DSBA1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Francisella Tularensis DSBA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:43.2 occ:1.00 NE2 B:HIS12 2.3 41.5 1.0 CD2 B:HIS12 3.2 39.6 1.0 CE1 B:HIS12 3.3 49.5 1.0 CG B:HIS12 4.4 41.5 1.0 ND1 B:HIS12 4.4 43.5 1.0 CB B:SER9 4.7 49.5 1.0

S.Penning, Y.Hong, T.Cunliffe, L.Hor, M.Totsika, J.J.Paxman, B.Heras. Unveiling the Versatility of the Thioredoxin Framework: Insights From the Structural Examination of Francisella Tularensis DSBA1 Comput Struct Biotechnol J V. 23 2024.
ISSN: ESSN 2001-0370
DOI: 10.1016/J.CSBJ.2024.11.034