Manganese in PDB 6jkv: Pppa, A Key Regulatory Component of T6SS in Pseudomonas Aeruginosa

The structure of Pppa, A Key Regulatory Component of T6SS in Pseudomonas Aeruginosa, PDB code: 6jkv was solved by T.Wang, L.Liu, Y.Wu, D.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.08 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.541, 80.253, 59.084, 90.00, 111.81, 90.00
R / Rfree (%)	23.3 / 28.3

The binding sites of Manganese atom in the Pppa, A Key Regulatory Component of T6SS in Pseudomonas Aeruginosa (pdb code 6jkv). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Pppa, A Key Regulatory Component of T6SS in Pseudomonas Aeruginosa, PDB code: 6jkv:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Pppa, A Key Regulatory Component of T6SS in Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Pppa, A Key Regulatory Component of T6SS in Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:28.8 occ:0.42 O A:HOH497 1.8 23.4 1.0 OD1 A:ASP41 1.9 18.6 1.0 O A:HOH449 2.1 25.6 1.0 O A:HOH466 2.1 26.4 1.0 O A:GLY42 2.2 22.5 1.0 O A:HOH438 2.2 21.3 1.0 CG A:ASP41 3.0 19.3 1.0 C A:GLY42 3.3 22.0 1.0 OD2 A:ASP41 3.5 18.9 1.0 O A:HOH467 3.6 24.3 1.0 O A:HOH532 3.7 26.0 1.0 MN A:MN302 3.7 25.0 0.4 O A:HOH531 3.8 26.4 1.0 N A:GLY42 3.9 19.9 1.0 C A:ASP41 4.0 19.1 1.0 O A:HOH452 4.1 28.3 1.0 CA A:GLY42 4.2 21.1 1.0 N A:MET43 4.2 23.0 1.0 CB A:ASP41 4.2 18.6 1.0 O A:HOH472 4.2 22.2 1.0 OD1 A:ASP26 4.2 20.8 1.0 O A:ASP41 4.3 18.8 1.0 CA A:MET43 4.4 23.6 1.0 CA A:ASP41 4.4 18.5 1.0 CB A:GLU25 4.4 24.3 1.0 OD1 A:ASP232 4.6 23.4 1.0 OD1 A:ASN233 4.8 22.3 1.0 O A:HOH495 4.8 25.8 1.0 CB A:MET43 4.8 23.9 1.0 NH1 A:ARG21 4.8 30.5 1.0 CZ A:ARG21 4.9 29.5 1.0

Manganese binding site 2 out of 4 in the Pppa, A Key Regulatory Component of T6SS in Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Pppa, A Key Regulatory Component of T6SS in Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:25.0 occ:0.40 OD2 A:ASP41 2.0 18.9 1.0 O A:HOH452 2.0 28.3 1.0 OD1 A:ASP194 2.1 20.2 1.0 OD2 A:ASP232 2.2 21.6 1.0 O A:HOH438 2.2 21.3 1.0 O A:HOH472 2.3 22.2 1.0 CG A:ASP41 3.0 19.3 1.0 CG A:ASP194 3.0 20.6 1.0 CG A:ASP232 3.1 21.9 1.0 OD2 A:ASP194 3.3 18.9 1.0 OD1 A:ASP41 3.3 18.6 1.0 OD1 A:ASP232 3.4 23.4 1.0 MN A:MN301 3.7 28.8 0.4 O A:HOH531 3.7 26.4 1.0 O A:HOH495 3.8 25.8 1.0 O A:HOH497 4.0 23.4 1.0 O A:HOH465 4.1 27.0 1.0 CB A:ASP41 4.3 18.6 1.0 CB A:ASP232 4.4 22.6 1.0 N A:GLY195 4.4 20.2 1.0 CB A:ASP194 4.4 20.1 1.0 O A:HOH449 4.5 25.6 1.0 N A:ASP194 4.5 19.4 1.0 OD1 A:ASP26 4.5 20.8 1.0 O A:ASN233 4.6 19.1 1.0 CB A:SER193 4.8 17.4 1.0 CA A:ASP194 4.9 19.6 1.0 C A:ASP194 5.0 19.9 1.0

Manganese binding site 3 out of 4 in the Pppa, A Key Regulatory Component of T6SS in Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Pppa, A Key Regulatory Component of T6SS in Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:27.9 occ:0.45 OD1 B:ASP41 1.8 19.2 1.0 O B:HOH477 2.1 25.2 1.0 O B:HOH461 2.1 22.4 1.0 O B:HOH482 2.1 26.9 1.0 O B:GLY42 2.2 21.1 1.0 O B:HOH524 2.3 27.4 1.0 CG B:ASP41 2.9 18.8 1.0 C B:GLY42 3.3 20.3 1.0 OD2 B:ASP41 3.4 19.0 1.0 O B:HOH541 3.6 34.0 1.0 MN B:MN302 3.8 24.6 0.3 N B:GLY42 3.8 18.3 1.0 O B:HOH472 3.8 27.8 1.0 C B:ASP41 3.9 18.1 1.0 OD1 B:ASP26 4.1 15.6 1.0 O B:HOH435 4.1 24.6 1.0 CB B:ASP41 4.1 17.8 1.0 O B:HOH409 4.2 24.2 1.0 CA B:GLY42 4.2 19.0 1.0 N B:MET43 4.3 21.6 1.0 CA B:ASP41 4.3 17.6 1.0 O B:HOH404 4.3 26.9 1.0 O B:ASP41 4.3 17.8 1.0 CB B:GLU25 4.4 22.3 1.0 CA B:MET43 4.4 22.1 1.0 OD1 B:ASP232 4.5 20.1 1.0 OD1 B:ASN233 4.6 19.9 1.0 CB B:MET43 4.9 22.4 1.0 O B:HOH492 4.9 22.4 1.0 OE2 B:GLU25 4.9 25.9 1.0 OD2 B:ASP232 4.9 19.3 1.0

Manganese binding site 4 out of 4 in the Pppa, A Key Regulatory Component of T6SS in Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Pppa, A Key Regulatory Component of T6SS in Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:24.6 occ:0.32 OD2 B:ASP232 2.0 19.3 1.0 O B:HOH409 2.0 24.2 1.0 OD1 B:ASP194 2.0 18.1 1.0 OD2 B:ASP41 2.1 19.0 1.0 O B:HOH435 2.2 24.6 1.0 O B:HOH461 2.3 22.4 1.0 CG B:ASP232 2.9 18.9 1.0 CG B:ASP194 3.0 18.9 1.0 CG B:ASP41 3.1 18.8 1.0 OD2 B:ASP194 3.3 20.0 1.0 OD1 B:ASP232 3.3 20.1 1.0 OD1 B:ASP41 3.5 19.2 1.0 MN B:MN301 3.8 27.9 0.5 O B:HOH541 3.8 34.0 1.0 O B:HOH487 4.1 21.6 1.0 O B:HOH524 4.1 27.4 1.0 O B:HOH492 4.2 22.4 1.0 CB B:ASP232 4.2 19.8 1.0 NZ B:LYS198 4.3 20.7 1.0 N B:GLY195 4.3 18.8 1.0 O B:ASN233 4.3 16.2 1.0 O B:HOH482 4.4 26.9 1.0 CB B:ASP194 4.4 18.4 1.0 CB B:ASP41 4.5 17.8 1.0 N B:ASP194 4.5 17.8 1.0 OD1 B:ASP26 4.6 15.6 1.0 CA B:ASP194 4.8 18.4 1.0 CB B:SER193 4.8 16.0 1.0 C B:ASP194 4.8 18.6 1.0 CA B:GLY195 5.0 18.8 1.0

Y.Wu, J.Gong, S.Liu, D.Li, Y.Wu, X.Zhang, Y.Ren, S.Xu, J.Sun, T.Wang, Q.Lin, L.Liu. Crystal Structure of Pppa From Pseudomonas Aeruginosa, A Key Regulatory Component of Type VI Secretion Systems. Biochem.Biophys.Res.Commun. V. 516 196 2019.
ISSN: ESSN 1090-2104
PubMed: 31208722
DOI: 10.1016/J.BBRC.2019.06.020