Sodium in PDB 5iiz: Xanthomonas Campestris Peroxiredoxin Q - Structure F0
Protein crystallography data
The structure of Xanthomonas Campestris Peroxiredoxin Q - Structure F0, PDB code: 5iiz
was solved by
A.Perkins,
D.Parsonage,
K.J.Nelson,
L.B.Poole,
A.Karplus,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
34.46 /
1.05
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
35.400,
51.360,
39.955,
90.00,
103.27,
90.00
|
|
R / Rfree (%)
|
13.5 /
15.3
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Xanthomonas Campestris Peroxiredoxin Q - Structure F0
(pdb code 5iiz). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the
Xanthomonas Campestris Peroxiredoxin Q - Structure F0, PDB code: 5iiz:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 5iiz
Go back to
Sodium Binding Sites List in 5iiz
Sodium binding site 1 out
of 5 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F0
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Xanthomonas Campestris Peroxiredoxin Q - Structure F0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na201
b:12.7
occ:0.80
|
O
|
A:HOH451
|
2.3
|
43.7
|
1.0
|
|
O
|
A:HOH353
|
2.3
|
17.1
|
1.0
|
|
OG
|
A:SER18
|
2.4
|
12.9
|
1.0
|
|
O
|
A:HOH458
|
2.4
|
24.8
|
1.0
|
|
O
|
A:HOH462
|
2.5
|
27.5
|
1.0
|
|
O
|
A:HOH356
|
2.5
|
10.6
|
1.0
|
|
HB2
|
A:SER18
|
3.3
|
12.5
|
1.0
|
|
H
|
A:SER18
|
3.4
|
10.1
|
1.0
|
|
CB
|
A:SER18
|
3.4
|
10.4
|
1.0
|
|
O
|
A:HOH469
|
3.9
|
31.8
|
1.0
|
|
N
|
A:SER18
|
4.1
|
8.4
|
1.0
|
|
HB3
|
A:SER18
|
4.1
|
12.5
|
1.0
|
|
O
|
A:SER95
|
4.1
|
8.2
|
1.0
|
|
O
|
A:HOH323
|
4.4
|
10.7
|
1.0
|
|
CA
|
A:SER18
|
4.4
|
8.3
|
1.0
|
|
NA
|
A:NA204
|
4.4
|
26.6
|
0.6
|
|
O
|
A:PRO16
|
4.4
|
11.0
|
1.0
|
|
H
|
A:GLY97
|
4.7
|
10.0
|
1.0
|
|
O
|
A:HOH325
|
4.7
|
23.9
|
1.0
|
|
HA
|
A:LEU17
|
4.8
|
9.8
|
1.0
|
|
HA
|
A:SER18
|
4.8
|
10.0
|
1.0
|
|
Sodium binding site 2 out
of 5 in 5iiz
Go back to
Sodium Binding Sites List in 5iiz
Sodium binding site 2 out
of 5 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F0
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Xanthomonas Campestris Peroxiredoxin Q - Structure F0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na202
b:57.9
occ:0.50
|
O
|
A:HOH486
|
2.0
|
41.2
|
1.0
|
|
O
|
A:HOH409
|
2.3
|
15.8
|
1.0
|
|
O
|
A:ALA137
|
2.4
|
9.7
|
1.0
|
|
O
|
A:HOH395
|
2.6
|
41.2
|
1.0
|
|
O
|
A:HOH439
|
2.7
|
13.6
|
1.0
|
|
H
|
A:ALA137
|
3.4
|
9.2
|
1.0
|
|
C
|
A:ALA137
|
3.6
|
7.5
|
1.0
|
|
HG3
|
A:GLN136
|
3.6
|
12.0
|
1.0
|
|
O
|
A:HOH515
|
3.8
|
39.4
|
1.0
|
|
HE21
|
A:GLN136
|
3.9
|
15.3
|
1.0
|
|
HA
|
A:TRP138
|
4.0
|
8.7
|
1.0
|
|
N
|
A:ALA137
|
4.1
|
7.7
|
1.0
|
|
HB3
|
A:ALA137
|
4.2
|
11.2
|
1.0
|
|
HG2
|
A:GLN136
|
4.3
|
12.0
|
1.0
|
|
O
|
A:HOH401
|
4.4
|
22.9
|
1.0
|
|
CG
|
A:GLN136
|
4.4
|
10.0
|
1.0
|
|
CA
|
A:ALA137
|
4.4
|
8.1
|
1.0
|
|
N
|
A:TRP138
|
4.6
|
6.8
|
1.0
|
|
NE2
|
A:GLN136
|
4.6
|
12.8
|
1.0
|
|
O
|
A:HOH514
|
4.6
|
32.3
|
0.7
|
|
CA
|
A:TRP138
|
4.7
|
7.2
|
1.0
|
|
CB
|
A:ALA137
|
4.8
|
9.3
|
1.0
|
|
HA
|
A:GLN136
|
4.9
|
9.6
|
1.0
|
|
Sodium binding site 3 out
of 5 in 5iiz
Go back to
Sodium Binding Sites List in 5iiz
Sodium binding site 3 out
of 5 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F0
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Xanthomonas Campestris Peroxiredoxin Q - Structure F0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na203
b:19.9
occ:1.00
|
HD23
|
A:LEU128
|
2.8
|
13.0
|
0.5
|
|
O
|
A:HOH406
|
2.8
|
16.6
|
1.0
|
|
O
|
A:SER129
|
2.9
|
8.6
|
1.0
|
|
O
|
A:HIS33
|
2.9
|
9.1
|
1.0
|
|
O
|
A:HIS30
|
3.2
|
11.5
|
1.0
|
|
HB3
|
A:HIS30
|
3.4
|
13.7
|
1.0
|
|
HA
|
A:PRO130
|
3.4
|
12.2
|
1.0
|
|
HB2
|
A:LEU35
|
3.5
|
11.4
|
1.0
|
|
HG
|
A:LEU128
|
3.5
|
12.6
|
0.5
|
|
CD2
|
A:LEU128
|
3.6
|
10.8
|
0.5
|
|
HB3
|
A:LEU35
|
3.6
|
11.4
|
1.0
|
|
HA
|
A:ALA31
|
3.7
|
13.2
|
1.0
|
|
HB3
|
A:LEU128
|
3.7
|
11.0
|
0.5
|
|
C
|
A:HIS30
|
3.7
|
10.0
|
1.0
|
|
HB2
|
A:HIS30
|
3.8
|
13.7
|
1.0
|
|
HD21
|
A:LEU128
|
3.8
|
13.0
|
0.5
|
|
H
|
A:GLY132
|
3.8
|
14.2
|
1.0
|
|
C
|
A:SER129
|
3.9
|
8.4
|
1.0
|
|
HB3
|
A:LEU128
|
3.9
|
13.3
|
0.5
|
|
HA2
|
A:GLY132
|
4.0
|
15.9
|
1.0
|
|
CB
|
A:HIS30
|
4.0
|
11.4
|
1.0
|
|
O
|
A:LEU128
|
4.0
|
7.6
|
0.5
|
|
CG
|
A:LEU128
|
4.0
|
10.5
|
0.5
|
|
CB
|
A:LEU35
|
4.0
|
9.5
|
1.0
|
|
H
|
A:HIS33
|
4.1
|
13.0
|
1.0
|
|
CA
|
A:PRO130
|
4.1
|
10.1
|
1.0
|
|
C
|
A:HIS33
|
4.1
|
8.6
|
1.0
|
|
HB2
|
A:LEU128
|
4.3
|
11.0
|
0.5
|
|
N
|
A:ALA31
|
4.3
|
10.7
|
1.0
|
|
HD22
|
A:LEU35
|
4.3
|
15.2
|
1.0
|
|
HA
|
A:TRP34
|
4.3
|
9.8
|
1.0
|
|
H
|
A:LEU35
|
4.3
|
9.5
|
1.0
|
|
C
|
A:PRO130
|
4.3
|
10.8
|
1.0
|
|
HD22
|
A:LEU128
|
4.4
|
13.0
|
0.5
|
|
N
|
A:PRO130
|
4.4
|
9.3
|
1.0
|
|
CA
|
A:ALA31
|
4.4
|
11.0
|
1.0
|
|
CB
|
A:LEU128
|
4.4
|
11.1
|
0.5
|
|
N
|
A:GLY132
|
4.4
|
11.8
|
1.0
|
|
C
|
A:LEU128
|
4.4
|
8.6
|
0.5
|
|
N
|
A:LEU35
|
4.5
|
7.9
|
1.0
|
|
CB
|
A:LEU128
|
4.5
|
9.2
|
0.5
|
|
O
|
A:PRO130
|
4.5
|
11.8
|
1.0
|
|
CA
|
A:HIS30
|
4.5
|
10.7
|
1.0
|
|
O
|
A:LEU128
|
4.5
|
8.4
|
0.5
|
|
H
|
A:GLY32
|
4.5
|
13.2
|
1.0
|
|
HD23
|
A:LEU35
|
4.5
|
15.2
|
1.0
|
|
CA
|
A:GLY132
|
4.7
|
13.2
|
1.0
|
|
C
|
A:LEU128
|
4.7
|
8.3
|
0.5
|
|
C
|
A:TRP34
|
4.7
|
7.9
|
1.0
|
|
HD23
|
A:LEU128
|
4.7
|
11.3
|
0.5
|
|
O
|
A:LEU27
|
4.8
|
8.9
|
1.0
|
|
N
|
A:HIS33
|
4.8
|
10.8
|
1.0
|
|
CD2
|
A:LEU35
|
4.8
|
12.7
|
1.0
|
|
CA
|
A:TRP34
|
4.9
|
8.2
|
1.0
|
|
N
|
A:SER129
|
4.9
|
8.8
|
1.0
|
|
HD2
|
A:HIS33
|
4.9
|
14.7
|
1.0
|
|
H
|
A:ALA31
|
4.9
|
12.8
|
1.0
|
|
CA
|
A:LEU35
|
4.9
|
8.2
|
1.0
|
|
N
|
A:GLY32
|
4.9
|
11.0
|
1.0
|
|
N
|
A:TRP34
|
5.0
|
8.6
|
1.0
|
|
CA
|
A:SER129
|
5.0
|
8.9
|
1.0
|
|
Sodium binding site 4 out
of 5 in 5iiz
Go back to
Sodium Binding Sites List in 5iiz
Sodium binding site 4 out
of 5 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F0
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Xanthomonas Campestris Peroxiredoxin Q - Structure F0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na204
b:26.6
occ:0.60
|
OG
|
A:SER18
|
2.6
|
12.9
|
1.0
|
|
OE1
|
A:GLN24
|
2.9
|
23.7
|
1.0
|
|
O
|
A:HOH469
|
3.0
|
31.8
|
1.0
|
|
HG3
|
A:GLN24
|
3.2
|
22.2
|
1.0
|
|
HB3
|
A:SER18
|
3.3
|
12.5
|
1.0
|
|
O
|
A:HOH496
|
3.3
|
46.5
|
1.0
|
|
CB
|
A:SER18
|
3.4
|
10.4
|
1.0
|
|
CD
|
A:GLN24
|
3.5
|
22.0
|
1.0
|
|
HA
|
A:SER18
|
3.5
|
10.0
|
1.0
|
|
CG
|
A:GLN24
|
3.7
|
18.5
|
1.0
|
|
HG2
|
A:GLN24
|
3.7
|
22.2
|
1.0
|
|
O
|
A:HOH458
|
3.8
|
24.8
|
1.0
|
|
O
|
A:HOH377
|
3.9
|
13.9
|
1.0
|
|
CA
|
A:SER18
|
4.0
|
8.3
|
1.0
|
|
HB2
|
A:SER18
|
4.2
|
12.5
|
1.0
|
|
NA
|
A:NA201
|
4.4
|
12.7
|
0.8
|
|
O
|
A:HOH353
|
4.6
|
17.1
|
1.0
|
|
NE2
|
A:GLN24
|
4.6
|
23.7
|
1.0
|
|
N
|
A:SER18
|
4.7
|
8.4
|
1.0
|
|
HE22
|
A:GLN24
|
4.9
|
28.4
|
1.0
|
|
H
|
A:SER18
|
4.9
|
10.1
|
1.0
|
|
O
|
A:HOH519
|
4.9
|
41.8
|
1.0
|
|
HG21
|
A:VAL77
|
4.9
|
12.9
|
1.0
|
|
O
|
A:THR23
|
5.0
|
11.2
|
1.0
|
|
Sodium binding site 5 out
of 5 in 5iiz
Go back to
Sodium Binding Sites List in 5iiz
Sodium binding site 5 out
of 5 in the Xanthomonas Campestris Peroxiredoxin Q - Structure F0
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Xanthomonas Campestris Peroxiredoxin Q - Structure F0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na205
b:13.0
occ:1.00
|
HG1
|
A:THR125
|
2.4
|
8.2
|
0.9
|
|
OE2
|
A:GLU51
|
2.6
|
8.5
|
1.0
|
|
HG2
|
A:ARG123
|
2.7
|
8.8
|
1.0
|
|
HB2
|
A:TYR38
|
2.7
|
9.0
|
1.0
|
|
OG1
|
A:THR125
|
2.8
|
6.8
|
0.9
|
|
O
|
A:PHE39
|
2.9
|
6.7
|
1.0
|
|
H
|
A:SER124
|
3.0
|
7.3
|
1.0
|
|
O
|
A:SER124
|
3.0
|
7.4
|
1.0
|
|
HB
|
A:THR125
|
3.1
|
8.5
|
0.1
|
|
HD2
|
A:TYR38
|
3.2
|
8.9
|
1.0
|
|
HG3
|
A:ARG123
|
3.3
|
8.8
|
1.0
|
|
H
|
A:PHE39
|
3.4
|
6.6
|
1.0
|
|
CG
|
A:ARG123
|
3.4
|
7.3
|
1.0
|
|
C
|
A:SER124
|
3.4
|
5.6
|
1.0
|
|
CD
|
A:GLU51
|
3.4
|
7.5
|
1.0
|
|
N
|
A:SER124
|
3.4
|
6.1
|
1.0
|
|
OE1
|
A:GLU51
|
3.5
|
8.7
|
1.0
|
|
HG21
|
A:VAL141
|
3.5
|
14.8
|
1.0
|
|
HG11
|
A:VAL141
|
3.7
|
13.9
|
1.0
|
|
CB
|
A:TYR38
|
3.7
|
7.5
|
1.0
|
|
N
|
A:PHE39
|
3.8
|
5.5
|
1.0
|
|
HA
|
A:TYR38
|
3.8
|
7.4
|
1.0
|
|
C
|
A:PHE39
|
3.9
|
6.1
|
1.0
|
|
CA
|
A:SER124
|
4.0
|
6.2
|
1.0
|
|
HD3
|
A:ARG123
|
4.0
|
9.6
|
1.0
|
|
CD2
|
A:TYR38
|
4.0
|
7.4
|
1.0
|
|
HB
|
A:VAL141
|
4.0
|
12.7
|
1.0
|
|
CB
|
A:THR125
|
4.0
|
7.1
|
0.1
|
|
N
|
A:THR125
|
4.1
|
6.0
|
1.0
|
|
C
|
A:ARG123
|
4.1
|
6.6
|
1.0
|
|
CA
|
A:TYR38
|
4.1
|
6.2
|
1.0
|
|
HA
|
A:ARG123
|
4.1
|
8.0
|
1.0
|
|
CB
|
A:THR125
|
4.1
|
5.7
|
0.9
|
|
NE2
|
A:HIS146
|
4.2
|
8.6
|
1.0
|
|
C
|
A:TYR38
|
4.2
|
6.0
|
1.0
|
|
HD2
|
A:HIS146
|
4.2
|
10.0
|
1.0
|
|
CD
|
A:ARG123
|
4.3
|
8.0
|
1.0
|
|
HA
|
A:SER124
|
4.3
|
7.5
|
1.0
|
|
HA
|
A:THR125
|
4.3
|
6.6
|
0.9
|
|
HB3
|
A:TYR38
|
4.3
|
9.0
|
1.0
|
|
CG2
|
A:VAL141
|
4.3
|
12.3
|
1.0
|
|
CG
|
A:TYR38
|
4.3
|
6.7
|
1.0
|
|
HA
|
A:THR125
|
4.4
|
7.6
|
0.1
|
|
CA
|
A:THR125
|
4.4
|
5.5
|
0.9
|
|
CA
|
A:THR125
|
4.4
|
6.4
|
0.1
|
|
CG1
|
A:VAL141
|
4.5
|
11.6
|
1.0
|
|
HB3
|
A:TYR40
|
4.5
|
9.2
|
1.0
|
|
CA
|
A:ARG123
|
4.5
|
6.7
|
1.0
|
|
CD2
|
A:HIS146
|
4.5
|
8.3
|
1.0
|
|
CB
|
A:VAL141
|
4.5
|
10.6
|
1.0
|
|
CA
|
A:PHE39
|
4.5
|
5.8
|
1.0
|
|
CB
|
A:ARG123
|
4.5
|
6.9
|
1.0
|
|
HH11
|
A:ARG123
|
4.6
|
11.7
|
1.0
|
|
HD2
|
A:ARG123
|
4.6
|
9.6
|
1.0
|
|
H
|
A:THR125
|
4.6
|
7.1
|
0.1
|
|
HB
|
A:THR125
|
4.6
|
6.8
|
0.9
|
|
HG23
|
A:VAL141
|
4.6
|
14.8
|
1.0
|
|
H
|
A:THR125
|
4.6
|
7.1
|
0.9
|
|
HE2
|
A:PHE55
|
4.6
|
9.9
|
1.0
|
|
HG22
|
A:THR125
|
4.7
|
8.5
|
0.1
|
|
HG1
|
A:THR125
|
4.7
|
9.8
|
0.1
|
|
HA
|
A:TYR40
|
4.7
|
8.7
|
1.0
|
|
HB2
|
A:PHE39
|
4.7
|
7.3
|
1.0
|
|
OG1
|
A:THR125
|
4.8
|
8.2
|
0.1
|
|
CG2
|
A:THR125
|
4.8
|
7.1
|
0.1
|
|
CG
|
A:GLU51
|
4.8
|
7.9
|
1.0
|
|
HG12
|
A:VAL141
|
4.9
|
13.9
|
1.0
|
|
HB3
|
A:ARG123
|
4.9
|
8.3
|
1.0
|
|
O
|
A:ARG123
|
4.9
|
7.5
|
1.0
|
|
N
|
A:TYR40
|
4.9
|
6.7
|
1.0
|
|
HG21
|
A:THR125
|
4.9
|
8.5
|
0.1
|
|
HG23
|
A:THR125
|
5.0
|
8.0
|
0.9
|
|
Reference:
A.Perkins,
D.Parsonage,
K.J.Nelson,
O.M.Ogba,
P.H.Cheong,
L.B.Poole,
P.A.Karplus.
Peroxiredoxin Catalysis at Atomic Resolution. Structure V. 24 1668 2016.
ISSN: ISSN 0969-2126
PubMed: 27594682
DOI: 10.1016/J.STR.2016.07.012
Page generated: Mon Oct 7 21:37:36 2024
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