Manganese in PDB 5n6x: Crystal Structure of the Legionella Effector Wipa

The structure of Crystal Structure of the Legionella Effector Wipa, PDB code: 5n6x was solved by N.Pinotsis, G.Waksman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.53 / 1.75
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	80.650, 80.650, 321.980, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 21.5

The structure of Crystal Structure of the Legionella Effector Wipa also contains other interesting chemical elements:

Bromine

(Br)

6 atoms

The binding sites of Manganese atom in the Crystal Structure of the Legionella Effector Wipa (pdb code 5n6x). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the Legionella Effector Wipa, PDB code: 5n6x:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of the Legionella Effector Wipa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Legionella Effector Wipa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:26.9 occ:1.00 OD1 A:ASN212 2.2 24.4 1.0 OD2 A:ASP180 2.2 23.7 1.0 O1 A:PO4503 2.2 34.6 1.0 O A:HOH865 2.2 28.4 1.0 NE2 A:HIS290 2.2 27.9 1.0 O A:HOH729 2.2 26.7 1.0 OD1 A:ASP180 3.0 30.3 1.0 CG A:ASP180 3.0 28.1 1.0 CE1 A:HIS290 3.1 27.9 1.0 CG A:ASN212 3.2 26.8 1.0 CD2 A:HIS290 3.3 26.0 1.0 P A:PO4503 3.5 59.1 1.0 ND2 A:ASN212 3.5 26.9 1.0 O3 A:PO4503 3.9 75.8 1.0 O A:HOH601 3.9 61.2 1.0 O A:VAL366 4.1 27.9 1.0 CD2 A:HIS213 4.2 28.5 1.0 ND1 A:HIS290 4.2 25.7 1.0 O2 A:PO4503 4.3 78.9 1.0 O A:HOH769 4.4 43.2 1.0 O A:HOH777 4.4 31.7 1.0 CG A:HIS290 4.4 25.7 1.0 CB A:ASP180 4.5 28.5 1.0 CB A:ASN212 4.5 25.2 1.0 N A:ASN212 4.5 27.6 1.0 O4 A:PO4503 4.6 65.7 1.0 O A:HOH776 4.7 40.2 1.0 NE2 A:HIS395 4.8 86.3 1.0 CE1 A:HIS395 4.8 86.0 1.0 NE2 A:HIS213 4.9 28.3 1.0 N A:HIS213 5.0 24.7 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the Legionella Effector Wipa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Legionella Effector Wipa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:33.2 occ:0.52 O A:HOH843 2.2 51.5 1.0 O A:HOH724 2.2 43.2 1.0 OD1 A:ASP409 2.3 46.5 1.0 CG A:ASP409 3.3 53.9 1.0 OD2 A:ASP409 3.7 49.7 1.0 O A:ASN407 3.8 36.0 1.0 O A:HOH929 4.4 42.4 1.0 O A:HOH813 4.5 36.6 1.0 N A:ASP409 4.5 37.8 1.0 CB A:ASP409 4.7 48.8 1.0 OE1 A:GLN399 4.7 52.7 1.0 CG2 A:THR410 4.9 46.2 1.0 C A:ASP409 5.0 48.5 1.0 CA A:ASP409 5.0 40.6 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the Legionella Effector Wipa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Legionella Effector Wipa within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:26.3 occ:1.00 O1 B:PO4503 2.2 28.9 1.0 OD2 B:ASP180 2.2 23.8 1.0 NE2 B:HIS290 2.2 25.3 1.0 OD1 B:ASN212 2.2 26.4 1.0 O B:HOH787 2.3 26.3 1.0 O B:HOH666 2.3 27.0 1.0 OD1 B:ASP180 3.0 28.1 1.0 CG B:ASP180 3.0 26.1 1.0 CE1 B:HIS290 3.1 29.7 1.0 CG B:ASN212 3.2 23.9 1.0 CD2 B:HIS290 3.3 25.8 1.0 P B:PO4503 3.4 41.2 1.0 ND2 B:ASN212 3.6 24.7 1.0 O3 B:PO4503 3.7 44.9 1.0 O B:VAL366 4.2 26.2 1.0 O2 B:PO4503 4.2 56.6 1.0 CD2 B:HIS213 4.2 29.2 1.0 ND1 B:HIS290 4.2 25.7 1.0 O B:HOH764 4.3 45.0 1.0 CG B:HIS290 4.4 24.5 1.0 O B:HOH693 4.4 27.6 1.0 CB B:ASP180 4.5 26.6 1.0 O B:HOH631 4.5 53.7 1.0 O B:HOH645 4.5 33.7 1.0 CB B:ASN212 4.5 24.7 1.0 N B:ASN212 4.5 22.4 1.0 O4 B:PO4503 4.6 40.5 1.0 O B:HOH751 4.6 39.0 1.0 NE2 B:HIS213 4.9 30.8 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of the Legionella Effector Wipa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Legionella Effector Wipa within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:39.1 occ:0.34 NE2 B:HIS32 2.1 62.5 1.0 O B:HOH801 2.2 82.2 1.0 CE1 B:HIS32 2.2 62.8 1.0 O B:HOH796 2.3 72.3 1.0 OD2 B:ASP30 2.3 96.2 1.0 ND1 B:HIS395 2.4 52.4 1.0 CE1 B:HIS395 3.3 67.4 1.0 CG B:HIS395 3.4 51.8 1.0 CD2 B:HIS32 3.5 49.8 1.0 CG B:ASP30 3.5 83.4 1.0 ND1 B:HIS32 3.5 54.7 1.0 CB B:HIS395 3.8 33.4 1.0 O B:HOH764 4.1 45.0 1.0 CG B:HIS32 4.1 39.2 1.0 OD1 B:ASP30 4.2 89.5 1.0 NE2 B:HIS395 4.5 57.9 1.0 CB B:ASP30 4.5 54.7 1.0 CD2 B:HIS395 4.5 61.9 1.0 O B:HIS395 4.7 29.0 1.0 CA B:ASP30 4.7 31.9 1.0 O B:GLY29 4.8 32.6 1.0 CA B:HIS395 4.9 27.7 1.0 O B:HOH795 4.9 48.8 1.0 C B:HIS395 5.0 32.3 1.0

N.Pinotsis, G.Waksman. Structure of the Wipa Protein Reveals A Novel Tyrosine Protein Phosphatase Effector From Legionella Pneumophila. J. Biol. Chem. V. 292 9240 2017.
ISSN: ESSN 1083-351X
PubMed: 28389563
DOI: 10.1074/JBC.M117.781948