Atomistry » Iodine » PDB 5kkg-5nfi » 5kst
Atomistry »
  Iodine »
    PDB 5kkg-5nfi »
      5kst »

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

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy