Manganese in PDB 5ksq: Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa

All present enzymatic activity of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa:
3.1.3.5;

The structure of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa, PDB code: 5ksq was solved by A.T.P.Machado, E.M.B.Fonseca, M.A.Dos Reis, A.M.Saraiva, C.A.Dos Santos, M.A.De Toledo, I.Polikarpov, A.P.De Souza, R.Aparicio, J.Iulek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.58 / 2.63
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	91.984, 85.160, 76.603, 90.00, 94.46, 90.00
R / Rfree (%)	21.8 / 27.4

The structure of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa also contains other interesting chemical elements:

Iodine

(I)

3 atoms

The binding sites of Manganese atom in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa (pdb code 5ksq). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa, PDB code: 5ksq:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:46.6 occ:1.00 O2 A:PO4503 2.2 25.8 1.0 OD1 A:ASP9 2.3 34.2 1.0 O A:HOH610 2.4 42.1 1.0 OD1 A:ASN92 2.6 35.9 1.0 OD1 A:ASP8 3.0 50.5 1.0 OD2 A:ASP8 3.2 32.5 1.0 CG A:ASP9 3.3 32.9 1.0 CG A:ASP8 3.4 42.0 1.0 P A:PO4503 3.6 34.1 1.0 CG A:ASN92 3.7 32.8 1.0 OD2 A:ASP9 3.7 29.6 1.0 OG A:SER40 3.8 83.7 1.0 CB A:SER40 4.0 84.3 1.0 O1 A:PO4503 4.0 36.0 1.0 OD1 A:ASN93 4.1 36.9 1.0 ND2 A:ASN92 4.1 34.6 1.0 O A:HOH612 4.2 33.1 1.0 O3 A:PO4503 4.5 30.8 1.0 CB A:ASP9 4.5 34.8 1.0 CA A:ASP9 4.6 32.1 1.0 O4 A:PO4503 4.6 40.1 1.0 N A:ASP9 4.6 31.1 1.0 O A:ASP8 4.6 21.1 1.0 C A:ASP8 4.6 34.6 1.0 OG1 A:THR106 4.7 18.9 1.0 CG A:ASN93 4.8 34.1 1.0 CB A:ASP8 4.9 38.2 1.0 CB A:ASN92 4.9 24.0 1.0 ND2 A:ASN93 4.9 30.2 1.0

Manganese binding site 2 out of 2 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn602 b:54.6 occ:1.00 OD1 B:ASP9 2.3 40.0 1.0 OD1 B:ASN92 2.4 35.7 1.0 O3 B:PO4604 2.4 71.3 1.0 OD1 B:ASP8 3.0 55.0 1.0 CG B:ASP9 3.2 40.5 1.0 OD2 B:ASP8 3.3 29.2 1.0 CG B:ASN92 3.4 33.4 1.0 CG B:ASP8 3.5 42.8 1.0 OG B:SER40 3.5 62.1 1.0 OD2 B:ASP9 3.5 40.6 1.0 P B:PO4604 3.7 72.0 1.0 ND2 B:ASN92 3.7 29.9 1.0 O4 B:PO4604 4.0 69.5 1.0 O B:HOH712 4.2 23.3 1.0 OD1 B:ASN93 4.3 43.8 1.0 O1 B:PO4604 4.3 74.7 1.0 CB B:ASP9 4.5 36.6 1.0 N B:ASP9 4.6 28.1 1.0 C B:ASP8 4.6 28.8 1.0 CA B:ASP9 4.7 32.0 1.0 CB B:SER40 4.7 62.6 1.0 O B:ASP8 4.7 27.6 1.0 CB B:ASN92 4.7 24.8 1.0 OG1 B:THR106 4.8 28.7 1.0 O2 B:PO4604 4.8 74.3 1.0 CB B:ASP8 4.9 36.5 1.0

A.T.P.Machado, E.M.B.Fonseca, M.A.D.Reis, A.M.Saraiva, C.A.D.Santos, M.A.S.De Toledo, I.Polikarpov, A.P.De Souza, R.Aparicio, J.Iulek. Conformational Variability of the Stationary Phase Survival Protein E From Xylella Fastidiosa Revealed By X-Ray Crystallography, Small-Angle X-Ray Scattering Studies, and Normal Mode Analysis. Proteins V. 85 1931 2017.
ISSN: ESSN 1097-0134
PubMed: 28677327
DOI: 10.1002/PROT.25347