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:
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
|