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Iodine in PDB 5kst: Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp).

Enzymatic activity of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp).

All present enzymatic activity of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp).:
3.1.3.5;

Protein crystallography data

The structure of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp)., PDB code: 5kst was solved by A.T.P.Machado, E.M.B.Fonseca, M.A.Dos Reis, A.M.Saraiva, C.A.Dos Santos, M.A.S.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) 77.96 / 2.76
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.001, 78.209, 82.158, 90.00, 96.74, 90.00
R / Rfree (%) 19.7 / 24.8

Other elements in 5kst:

The structure of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp). also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp). (pdb code 5kst). 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-Tsamp (Tetramer Smaller - Crystallization with 3'Amp)., PDB code: 5kst:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 5kst

Go back to Iodine Binding Sites List in 5kst
Iodine binding site 1 out of 6 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp).


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-Tsamp (Tetramer Smaller - Crystallization with 3'Amp). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:49.9
occ:0.56
 ND2 A:ASN44 3.5 36.1 1.0
N A:ASN44 3.6 37.1 1.0
N B:ASN44 3.6 49.0 1.0
CG A:ASN44 3.8 37.1 1.0
ND2 B:ASN44 3.8 41.1 1.0
CB A:ASN44 4.0 36.6 1.0
CG B:ASN44 4.1 42.4 1.0
CA B:SER43 4.1 42.7 1.0
CB B:ASN44 4.1 43.9 1.0
CA A:SER43 4.1 48.1 1.0
O A:TYR103 4.3 41.6 1.0
C A:SER43 4.3 47.5 1.0
O A:ALA42 4.3 46.5 1.0
C B:SER43 4.4 40.7 1.0
CD1 A:TYR103 4.4 47.6 1.0
OG B:SER43 4.4 43.5 1.0
CD1 B:TYR103 4.4 56.0 1.0
CA A:ASN44 4.4 37.0 1.0
CA B:ASN44 4.5 46.8 1.0
O B:ALA42 4.5 78.8 1.0
OD1 A:ASN44 4.5 39.0 1.0
CB A:TYR103 4.6 44.1 1.0
CA A:TYR103 4.6 41.5 1.0
OG A:SER43 4.6 46.9 1.0
O B:TYR103 4.7 46.5 1.0
CB B:TYR103 4.8 51.1 1.0
CB B:SER43 4.8 43.9 1.0
CG A:TYR103 4.8 46.5 1.0
C A:TYR103 4.9 40.9 1.0
OD1 B:ASN44 4.9 42.4 1.0
CA B:TYR103 4.9 48.6 1.0
CB A:SER43 4.9 47.5 1.0
CG B:TYR103 5.0 54.5 1.0

Iodine binding site 2 out of 6 in 5kst

Go back to Iodine Binding Sites List in 5kst
Iodine binding site 2 out of 6 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp).


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-Tsamp (Tetramer Smaller - Crystallization with 3'Amp). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:83.3
occ:0.57
 NH1 B:ARG240 3.3 46.9 1.0
NE2 A:HIS235 3.5 32.1 1.0
CE1 A:HIS235 3.5 32.6 1.0
N B:GLN242 3.6 74.2 1.0
N B:TYR241 3.6 42.5 1.0
CG B:GLN242 3.8 79.1 1.0
CB B:GLN242 4.0 77.7 1.0
CD B:GLN242 4.1 80.3 1.0
CB B:TYR241 4.2 43.0 1.0
CA B:TYR241 4.3 43.7 1.0
C B:ARG240 4.3 46.8 1.0
OE1 B:GLN242 4.4 80.5 1.0
CA B:GLN242 4.4 75.8 1.0
C B:TYR241 4.4 45.9 1.0
CA B:ARG240 4.4 45.4 1.0
I B:IOD301 4.5 0.4 0.9
CZ B:ARG240 4.6 47.7 1.0
O B:THR239 4.6 31.5 1.0
CD B:ARG240 4.6 45.9 1.0
ND1 A:HIS235 4.7 31.9 1.0
CD2 A:HIS235 4.8 31.3 1.0
NE2 B:GLN242 4.8 80.9 1.0
CG B:ARG240 4.8 45.6 1.0
CD2 B:TYR241 5.0 42.1 1.0

Iodine binding site 3 out of 6 in 5kst

Go back to Iodine Binding Sites List in 5kst
Iodine binding site 3 out of 6 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp).


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-Tsamp (Tetramer Smaller - Crystallization with 3'Amp). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I301

b:0.4
occ:0.86
 NE2 B:HIS235 3.3 41.3 1.0
CE1 B:HIS235 3.4 40.8 1.0
NH1 A:ARG240 3.7 50.7 1.0
N A:TYR241 3.7 33.8 1.0
N A:GLN242 3.8 43.5 1.0
CG A:GLN242 4.0 44.9 0.0
CB A:TYR241 4.2 37.1 1.0
CB A:GLN242 4.3 43.7 1.0
CA A:TYR241 4.3 36.3 1.0
O B:HOH429 4.3 64.5 1.0
CD A:GLN242 4.3 44.2 0.0
C A:ARG240 4.4 43.8 1.0
CA A:ARG240 4.5 42.1 1.0
O A:THR239 4.5 32.8 1.0
I A:IOD504 4.5 83.3 0.6
C A:TYR241 4.6 38.2 1.0
CD2 B:HIS235 4.6 39.6 1.0
OE1 A:GLN242 4.6 42.8 0.0
CA A:GLN242 4.7 44.4 1.0
ND1 B:HIS235 4.7 38.8 1.0
CE1 A:HIS235 4.7 32.6 1.0
CD2 A:TYR241 4.8 35.5 1.0
CD A:ARG240 4.9 43.6 1.0
NE2 A:HIS235 4.9 32.1 1.0
CZ A:ARG240 4.9 48.4 1.0
NE2 A:GLN242 4.9 45.3 0.0

Iodine binding site 4 out of 6 in 5kst

Go back to Iodine Binding Sites List in 5kst
Iodine binding site 4 out of 6 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp).


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-Tsamp (Tetramer Smaller - Crystallization with 3'Amp). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I502

b:0.1
occ:0.48
 NE2 C:GLN242 2.9 78.1 1.0
OE1 C:GLN242 2.9 79.4 1.0
CD C:GLN242 3.2 78.6 1.0
NE2 D:HIS235 3.3 43.4 1.0
CD1 C:TYR241 3.7 63.4 1.0
N C:TYR241 3.8 63.6 1.0
CE1 D:HIS235 3.8 42.6 1.0
CB C:TYR241 3.9 64.8 1.0
O C:THR239 4.0 37.2 1.0
O C:HOH610 4.0 20.8 1.0
CE1 C:HIS235 4.2 60.9 1.0
O D:HOH721 4.2 36.2 1.0
CG C:TYR241 4.3 64.4 1.0
CA C:TYR241 4.4 65.0 1.0
CD2 D:HIS235 4.5 43.3 1.0
N C:GLN242 4.5 78.2 1.0
CG C:GLN242 4.5 77.8 1.0
CE1 C:TYR241 4.7 63.1 1.0
C C:ARG240 4.7 68.2 1.0
O C:HOH653 4.8 27.8 1.0
CA C:ARG240 4.8 66.5 1.0
NE2 C:HIS235 4.9 60.0 1.0
C C:TYR241 5.0 65.5 1.0
ND1 C:HIS235 5.0 60.2 1.0

Iodine binding site 5 out of 6 in 5kst

Go back to Iodine Binding Sites List in 5kst
Iodine binding site 5 out of 6 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp).


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-Tsamp (Tetramer Smaller - Crystallization with 3'Amp). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I601

b:55.1
occ:0.53
 N C:ASN44 3.7 44.5 1.0
N D:ASN44 3.9 43.6 1.0
ND2 D:ASN44 4.0 44.4 1.0
CB C:ASN44 4.1 42.0 1.0
ND2 C:ASN44 4.1 42.3 1.0
CB D:ASN44 4.2 43.3 1.0
CG D:ASN44 4.2 43.9 1.0
CA D:SER43 4.3 44.2 1.0
CA C:SER43 4.3 38.6 1.0
CG C:ASN44 4.3 41.9 1.0
CD1 D:TYR103 4.3 65.5 1.0
O D:TYR103 4.4 59.1 1.0
O D:ALA42 4.4 61.6 1.0
CD1 C:TYR103 4.4 62.7 1.0
CB D:TYR103 4.4 62.6 1.0
CA D:TYR103 4.5 61.2 1.0
C C:SER43 4.5 37.3 1.0
CA C:ASN44 4.5 42.6 1.0
C D:SER43 4.5 44.7 1.0
OG C:SER43 4.6 40.6 1.0
CA D:ASN44 4.7 43.3 1.0
O C:ALA42 4.7 44.9 1.0
CA C:TYR103 4.7 54.2 1.0
CB C:TYR103 4.8 57.3 1.0
CG D:TYR103 4.8 64.8 1.0
O C:TYR103 4.8 52.9 1.0
C D:TYR103 4.8 60.5 1.0
OG D:SER43 4.8 42.6 1.0
CG C:TYR103 5.0 60.8 1.0
OD1 D:ASN44 5.0 44.6 1.0

Iodine binding site 6 out of 6 in 5kst

Go back to Iodine Binding Sites List in 5kst
Iodine binding site 6 out of 6 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp).


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-Tsamp (Tetramer Smaller - Crystallization with 3'Amp). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I603

b:78.9
occ:0.53
 N D:GLN242 3.1 69.5 1.0
N D:TYR241 3.1 56.1 1.0
CG D:GLN242 3.5 74.9 1.0
CB D:GLN242 3.6 72.0 1.0
CE1 C:HIS235 3.7 60.9 1.0
C D:ARG240 3.7 52.2 1.0
NE2 C:HIS235 3.7 60.0 1.0
CA D:TYR241 3.8 59.0 1.0
CA D:ARG240 3.8 50.9 1.0
C D:TYR241 3.9 61.4 1.0
CA D:GLN242 4.0 71.2 1.0
CB D:TYR241 4.0 61.0 1.0
CG D:ARG240 4.2 53.6 1.0
O D:THR239 4.3 36.1 1.0
CD D:GLN242 4.4 76.9 1.0
NE D:ARG240 4.4 57.7 1.0
CD D:ARG240 4.5 55.4 1.0
NE2 C:GLN242 4.6 78.1 1.0
CB D:ARG240 4.6 51.4 1.0
O D:ARG240 4.6 52.4 1.0
CD1 D:TYR241 4.7 58.9 1.0
ND1 C:HIS235 4.8 60.2 1.0
CG D:TYR241 4.9 60.1 1.0
O D:HOH711 4.9 30.7 1.0
OE1 D:GLN242 4.9 76.2 1.0
CD2 C:HIS235 4.9 58.5 1.0
N D:ARG240 4.9 49.4 1.0
NE2 D:GLN242 5.0 79.2 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 Aug 11 21:20:59 2024

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