Zinc in PDB 8qjd: T6SS-Linked Rhs Repeat Protein - Salmonella Bongori Rhs-Core Domain

The structure of T6SS-Linked Rhs Repeat Protein - Salmonella Bongori Rhs-Core Domain, PDB code: 8qjd was solved by C.S.Kielkopf, M.M.Shneider, P.G.Leiman, N.M.I.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.17 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	99.071, 118.26, 131.757, 90, 105.52, 90
R / Rfree (%)	18.2 / 21.1

The binding sites of Zinc atom in the T6SS-Linked Rhs Repeat Protein - Salmonella Bongori Rhs-Core Domain (pdb code 8qjd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the T6SS-Linked Rhs Repeat Protein - Salmonella Bongori Rhs-Core Domain, PDB code: 8qjd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the T6SS-Linked Rhs Repeat Protein - Salmonella Bongori Rhs-Core Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of T6SS-Linked Rhs Repeat Protein - Salmonella Bongori Rhs-Core Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1501 b:102.8 occ:1.00 NE2 A:HIS420 2.1 89.7 1.0 ND1 A:HIS415 2.3 99.6 1.0 O A:HOH2012 2.5 74.5 1.0 CE1 A:HIS420 2.8 89.7 1.0 OD2 A:ASP418 2.8 87.1 1.0 OD1 A:ASP418 2.9 86.8 1.0 CG A:HIS415 2.9 95.4 1.0 CG A:ASP418 3.2 85.5 1.0 CE1 A:HIS415 3.2 98.8 1.0 CB A:HIS415 3.2 83.6 1.0 CD2 A:HIS420 3.2 83.8 1.0 O A:HIS415 3.7 87.4 1.0 ND1 A:HIS420 3.9 85.1 1.0 CD2 A:HIS415 4.0 99.2 1.0 NE2 A:HIS415 4.1 97.9 1.0 CG A:HIS420 4.1 78.1 1.0 CA A:HIS415 4.4 78.6 1.0 C A:HIS415 4.5 87.1 1.0 CD1 A:TYR430 4.5 84.3 1.0 CE1 A:TYR430 4.6 90.1 1.0 CB A:ASP418 4.7 76.1 1.0 O A:ASP418 5.0 73.4 1.0

Zinc binding site 2 out of 2 in the T6SS-Linked Rhs Repeat Protein - Salmonella Bongori Rhs-Core Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of T6SS-Linked Rhs Repeat Protein - Salmonella Bongori Rhs-Core Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1501 b:87.0 occ:1.00 NE2 B:HIS420 2.1 74.0 1.0 OD1 B:ASP418 2.3 79.6 1.0 ND1 B:HIS415 2.4 86.1 1.0 OD2 B:ASP418 2.6 80.0 1.0 O B:HOH2119 2.7 71.0 1.0 CG B:ASP418 2.7 76.0 1.0 CE1 B:HIS420 3.0 81.4 1.0 CE1 B:HIS415 3.1 82.0 1.0 CD2 B:HIS420 3.2 69.2 1.0 CG B:HIS415 3.2 81.1 1.0 CB B:HIS415 3.6 70.7 1.0 CD1 B:TYR430 4.0 72.2 1.0 NE2 B:HIS415 4.1 89.1 1.0 O B:HIS415 4.1 73.8 1.0 CD2 B:HIS415 4.1 85.1 1.0 CB B:ASP418 4.1 67.1 1.0 ND1 B:HIS420 4.1 77.7 1.0 CG B:HIS420 4.3 67.1 1.0 CE1 B:TYR430 4.3 75.5 1.0 CA B:HIS415 4.8 69.5 1.0 C B:HIS415 4.9 70.2 1.0

C.S.Kielkopf, P.G.Leiman, N.M.I.Taylor. T6SS-Associated Rhs Proteins Form Toxin Containers: Structural and Functional Insights Into Bacterial Weaponry and Self-Protection To Be Published.