Iodine 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:

Manganese

(Mn)

2 atoms

The binding sites of Iodine 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 Iodine atom.
In total 3 binding sites of Iodine where determined in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa, PDB code: 5ksq:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I 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:I502 b:57.1 occ:0.54 NE2 A:GLN242 3.3 61.9 1.0 N A:TYR241 3.6 48.8 1.0 NE2 B:HIS235 3.8 32.3 1.0 CE1 B:HIS235 3.9 32.6 1.0 CD A:GLN242 4.2 65.1 1.0 N A:GLN242 4.2 58.6 1.0 O A:HOH670 4.2 42.4 1.0 CB A:TYR241 4.2 36.1 1.0 CD1 A:TYR241 4.2 34.0 1.0 O A:HOH628 4.3 39.1 1.0 O A:THR239 4.3 50.2 1.0 CA A:ARG240 4.3 44.9 1.0 CA A:TYR241 4.3 53.0 1.0 C A:ARG240 4.3 45.3 1.0 CG A:GLN242 4.3 60.8 1.0 O B:HOH758 4.6 51.3 1.0 CB A:GLN242 4.7 56.7 1.0 C A:TYR241 4.7 55.6 1.0 CG A:TYR241 4.7 48.2 1.0 CG A:ARG240 4.8 41.0 1.0 I B:IOD603 4.9 45.3 0.8 NE2 B:GLN242 4.9 70.7 1.0

Iodine binding site 2 out of 3 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I 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:I601 b:32.5 occ:0.84 O B:HOH718 3.8 36.9 1.0 ND2 B:ASN44 3.9 19.0 1.0 N A:ASN44 4.0 30.1 1.0 ND2 A:ASN44 4.1 38.1 1.0 N B:ASN44 4.1 35.6 1.0 CG B:ASN44 4.3 26.9 1.0 CA A:SER43 4.4 30.6 1.0 CG A:ASN44 4.4 37.4 1.0 CD1 B:TYR103 4.4 38.3 1.0 CA B:SER43 4.4 33.0 1.0 CD1 A:TYR103 4.5 45.4 1.0 CB B:ASN44 4.5 25.6 1.0 CB A:ASN44 4.5 31.7 1.0 O B:ALA42 4.6 31.7 1.0 O A:ALA42 4.6 39.1 1.0 C A:SER43 4.7 33.7 1.0 CB B:TYR103 4.7 28.9 1.0 C B:SER43 4.7 35.9 1.0 OG A:SER43 4.7 43.2 1.0 CG B:TYR103 4.7 34.8 1.0 OG B:SER43 4.8 40.4 1.0 CB A:TYR103 4.8 27.7 1.0 CG A:TYR103 4.9 36.9 1.0 CA A:ASN44 4.9 31.5 1.0 OD1 B:ASN44 5.0 34.1 1.0 CA B:ASN44 5.0 30.1 1.0 CA B:TYR103 5.0 25.6 1.0

Iodine binding site 3 out of 3 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa within 5.0Å range: probe atom residue distance (Å) B Occ B:I603 b:45.3 occ:0.75 N B:TYR241 3.9 27.1 1.0 NE2 A:HIS235 3.9 34.0 1.0 CG B:GLN242 4.0 64.2 1.0 CE1 A:HIS235 4.0 29.0 1.0 CD B:GLN242 4.2 70.0 1.0 N B:GLN242 4.2 47.0 1.0 NE2 B:GLN242 4.3 70.7 1.0 NE2 A:GLN242 4.4 61.9 1.0 CB B:TYR241 4.5 37.4 1.0 CB B:GLN242 4.5 56.7 1.0 O B:THR239 4.6 44.4 1.0 CA B:ARG240 4.6 31.9 1.0 CD1 B:TYR241 4.6 43.7 1.0 C B:ARG240 4.6 31.3 1.0 CA B:TYR241 4.6 41.4 1.0 OE1 B:GLN242 4.7 73.9 1.0 I A:IOD502 4.9 57.1 0.5 C B:TYR241 4.9 48.2 1.0 CG B:ARG240 4.9 39.4 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