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Iodine in PDB 5ksr: Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).

Enzymatic activity of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).

All present enzymatic activity of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).:
3.1.3.5;

Protein crystallography data

The structure of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger)., PDB code: 5ksr 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.De Aparicio, J.Iulek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.25 / 1.96
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 172.336, 84.170, 87.310, 90.00, 96.62, 90.00
R / Rfree (%) 19.6 / 23.8

Other elements in 5ksr:

The structure of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger). also contains other interesting chemical elements:

Manganese (Mn) 4 atoms
Chlorine (Cl) 4 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger). (pdb code 5ksr). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger)., PDB code: 5ksr:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 5ksr

Go back to Iodine Binding Sites List in 5ksr
Iodine binding site 1 out of 6 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).


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 - Xfsure-Tb (Tetramer Bigger). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:20.2
occ:1.00
 O A:HOH689 3.5 23.7 1.0
O B:HOH660 3.6 22.7 1.0
N A:ASN44 3.8 14.2 1.0
N B:ASN44 3.8 13.7 1.0
ND2 A:ASN44 4.0 22.4 1.0
CG A:ASN44 4.1 21.3 1.0
ND2 B:ASN44 4.2 20.0 1.0
CD1 A:TYR103 4.2 17.0 1.0
CD1 B:TYR103 4.2 17.4 1.0
CB A:ASN44 4.3 16.0 1.0
CG B:ASN44 4.3 19.4 1.0
CA B:SER43 4.4 23.5 1.0
CB B:ASN44 4.4 11.7 1.0
CB A:TYR103 4.4 19.2 1.0
CA A:SER43 4.4 20.9 1.0
CB B:TYR103 4.5 28.0 1.0
CG A:TYR103 4.6 17.1 1.0
C A:SER43 4.6 19.0 1.0
C B:SER43 4.6 20.7 1.0
CG B:TYR103 4.6 18.8 1.0
CA A:ASN44 4.6 14.5 1.0
CA B:ASN44 4.7 13.2 1.0
OD1 A:ASN44 4.7 20.1 1.0
OD1 B:ASN44 4.8 21.4 1.0
OG B:SER43 4.8 19.6 1.0
O A:TYR103 4.8 13.9 1.0
CA A:TYR103 5.0 15.3 1.0
O B:TYR103 5.0 14.4 1.0

Iodine binding site 2 out of 6 in 5ksr

Go back to Iodine Binding Sites List in 5ksr
Iodine binding site 2 out of 6 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).


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 - Xfsure-Tb (Tetramer Bigger). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:39.2
occ:0.69
 NE2 A:GLN242 3.8 44.3 1.0
N A:TYR241 3.8 32.2 1.0
NE2 B:HIS235 3.9 27.3 1.0
N A:GLN242 4.0 38.5 1.0
CE1 B:HIS235 4.1 27.0 1.0
CB A:TYR241 4.1 36.1 1.0
NE2 B:GLN242 4.2 40.7 1.0
O A:HOH635 4.4 24.7 1.0
CA A:TYR241 4.4 35.6 1.0
CG A:GLN242 4.4 45.9 1.0
O B:HOH693 4.5 34.5 1.0
C A:ARG240 4.5 30.4 1.0
O A:THR239 4.5 24.6 1.0
CD2 A:TYR241 4.6 34.0 1.0
CD A:GLN242 4.6 48.1 1.0
CB A:GLN242 4.6 44.2 1.0
I B:IOD502 4.7 40.1 0.8
CA A:ARG240 4.7 27.6 1.0
C A:TYR241 4.7 37.9 1.0
CE1 A:HIS235 4.9 29.3 1.0
CG A:TYR241 4.9 35.9 1.0
CA A:GLN242 5.0 41.8 1.0

Iodine binding site 3 out of 6 in 5ksr

Go back to Iodine Binding Sites List in 5ksr
Iodine binding site 3 out of 6 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).


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 - Xfsure-Tb (Tetramer Bigger). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I502

b:40.1
occ:0.76
 O A:HOH734 3.4 50.8 1.0
N B:TYR241 3.7 31.1 1.0
NE2 A:HIS235 3.7 27.3 1.0
NE2 B:GLN242 3.9 40.7 1.0
N B:GLN242 3.9 35.1 1.0
CE1 A:HIS235 4.0 29.3 1.0
CB B:TYR241 4.1 29.8 1.0
CG B:GLN242 4.2 42.5 1.0
CA B:TYR241 4.3 33.3 1.0
O B:HOH635 4.4 22.7 1.0
NE2 A:GLN242 4.4 44.3 1.0
C B:ARG240 4.4 29.6 1.0
CD B:GLN242 4.4 46.1 1.0
O B:THR239 4.6 24.3 1.0
CB B:GLN242 4.6 39.2 1.0
C B:TYR241 4.6 35.7 1.0
CA B:ARG240 4.6 26.6 1.0
CD2 B:TYR241 4.6 27.1 1.0
O A:HOH722 4.6 39.5 1.0
I A:IOD503 4.7 39.2 0.7
CG B:TYR241 4.9 29.8 1.0
CA B:GLN242 4.9 35.6 1.0
CE1 B:HIS235 4.9 27.0 1.0
CD2 A:HIS235 5.0 25.6 1.0

Iodine binding site 4 out of 6 in 5ksr

Go back to Iodine Binding Sites List in 5ksr
Iodine binding site 4 out of 6 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I502

b:25.9
occ:0.82
 O D:HOH656 3.7 29.7 1.0
N C:ASN44 3.9 23.8 1.0
N D:ASN44 3.9 20.7 1.0
ND2 C:ASN44 3.9 26.1 1.0
O C:HOH647 3.9 40.7 1.0
ND2 D:ASN44 4.1 26.8 1.0
CG C:ASN44 4.1 27.0 1.0
CD1 D:TYR103 4.2 29.6 1.0
CD1 C:TYR103 4.2 26.1 1.0
CG D:ASN44 4.3 31.8 1.0
CB C:ASN44 4.3 22.4 1.0
CA D:SER43 4.4 29.7 1.0
CB D:ASN44 4.4 17.4 1.0
CA C:SER43 4.5 29.2 1.0
CB C:TYR103 4.5 23.5 1.0
CB D:TYR103 4.6 25.3 1.0
CG D:TYR103 4.6 28.5 1.0
CG C:TYR103 4.6 24.2 1.0
C D:SER43 4.6 25.5 1.0
C C:SER43 4.7 26.8 1.0
CA C:ASN44 4.7 21.5 1.0
OD1 C:ASN44 4.8 29.6 1.0
CA D:ASN44 4.8 21.2 1.0
OD1 D:ASN44 4.8 36.0 1.0
O C:TYR103 4.8 19.6 1.0
O D:TYR103 4.9 19.5 1.0
CE1 D:TYR103 4.9 30.8 1.0
OG D:SER43 4.9 33.6 1.0
OG C:SER43 4.9 27.3 1.0
O C:ALA42 4.9 33.3 1.0
CE1 C:TYR103 5.0 25.0 1.0
CB D:SER43 5.0 29.7 1.0
CA C:TYR103 5.0 20.1 1.0

Iodine binding site 5 out of 6 in 5ksr

Go back to Iodine Binding Sites List in 5ksr
Iodine binding site 5 out of 6 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I503

b:32.6
occ:0.67
 NE2 C:GLN242 3.6 42.7 1.0
NE2 D:HIS235 3.8 28.3 1.0
N C:TYR241 3.8 29.6 1.0
CE1 D:HIS235 4.0 27.1 1.0
N C:GLN242 4.0 34.1 1.0
CG C:GLN242 4.1 44.1 1.0
NE2 D:GLN242 4.1 38.7 1.0
CB C:TYR241 4.2 34.0 1.0
O D:HOH720 4.2 52.5 1.0
CD C:GLN242 4.3 46.1 1.0
O C:HOH650 4.4 23.6 1.0
CA C:TYR241 4.4 32.3 1.0
CD2 C:TYR241 4.5 27.8 1.0
C C:ARG240 4.6 28.6 1.0
CB C:GLN242 4.6 41.6 1.0
O C:THR239 4.6 26.6 1.0
CA C:ARG240 4.7 28.8 1.0
C C:TYR241 4.7 34.1 1.0
O D:HOH700 4.8 46.3 1.0
I D:IOD502 4.8 31.5 0.7
CG C:TYR241 4.9 33.0 1.0
CA C:GLN242 5.0 37.4 1.0

Iodine binding site 6 out of 6 in 5ksr

Go back to Iodine Binding Sites List in 5ksr
Iodine binding site 6 out of 6 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I502

b:31.5
occ:0.72
 NE2 D:GLN242 3.7 38.7 1.0
N D:TYR241 3.8 25.6 1.0
N D:GLN242 3.9 34.2 1.0
CE1 C:HIS235 3.9 26.7 1.0
CG D:GLN242 4.0 39.2 1.0
NE2 C:HIS235 4.0 28.6 1.0
O C:HOH731 4.2 49.6 1.0
CB D:TYR241 4.2 31.5 1.0
NE2 C:GLN242 4.2 42.7 1.0
CD D:GLN242 4.3 42.0 1.0
CA D:TYR241 4.4 28.8 1.0
CB D:GLN242 4.5 37.1 1.0
CD2 D:TYR241 4.5 28.4 1.0
C D:ARG240 4.5 25.8 1.0
O D:HOH628 4.6 21.9 1.0
O D:THR239 4.6 24.8 1.0
C D:TYR241 4.7 31.8 1.0
CA D:ARG240 4.7 26.4 1.0
O C:HOH671 4.7 41.9 1.0
CA D:GLN242 4.8 34.8 1.0
I C:IOD503 4.8 32.6 0.7
CG D:TYR241 4.9 29.6 1.0

Reference:

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
Page generated: Sun Dec 13 19:40:00 2020

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