Chlorine in PDB 5wjo: Crystal Structure of the Unliganded PG90 Tcr
Protein crystallography data
The structure of Crystal Structure of the Unliganded PG90 Tcr, PDB code: 5wjo
was solved by
A.Shahine,
S.Gras,
J.Rossjohn,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.18 /
2.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
41.150,
128.080,
169.680,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.8 /
23
|
Other elements in 5wjo:
The structure of Crystal Structure of the Unliganded PG90 Tcr also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of the Unliganded PG90 Tcr
(pdb code 5wjo). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the
Crystal Structure of the Unliganded PG90 Tcr, PDB code: 5wjo:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Chlorine binding site 1 out
of 9 in 5wjo
Go back to
Chlorine Binding Sites List in 5wjo
Chlorine binding site 1 out
of 9 in the Crystal Structure of the Unliganded PG90 Tcr
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Crystal Structure of the Unliganded PG90 Tcr within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl301
b:52.1
occ:1.00
|
NE
|
B:ARG214
|
3.3
|
29.1
|
1.0
|
N
|
B:GLY168
|
3.4
|
24.2
|
1.0
|
CD2
|
B:HIS212
|
3.5
|
27.4
|
1.0
|
CB
|
B:TRP165
|
3.7
|
15.4
|
1.0
|
CA
|
B:GLY168
|
3.7
|
23.5
|
1.0
|
CB
|
B:ARG214
|
3.8
|
15.8
|
1.0
|
NH1
|
B:ARG214
|
4.0
|
23.6
|
1.0
|
O
|
B:TRP165
|
4.0
|
22.4
|
1.0
|
NE2
|
B:HIS212
|
4.0
|
27.0
|
1.0
|
CZ
|
B:ARG214
|
4.1
|
38.3
|
1.0
|
CD
|
B:ARG214
|
4.1
|
25.7
|
1.0
|
C
|
B:TRP165
|
4.3
|
23.4
|
1.0
|
N
|
B:ASN167
|
4.5
|
25.3
|
1.0
|
C
|
B:ASN167
|
4.5
|
28.4
|
1.0
|
CG
|
B:ARG214
|
4.6
|
20.7
|
1.0
|
CG
|
B:HIS212
|
4.6
|
25.9
|
1.0
|
CA
|
B:TRP165
|
4.7
|
17.8
|
1.0
|
C
|
B:GLY168
|
4.8
|
26.5
|
1.0
|
CG
|
B:TRP165
|
4.8
|
14.8
|
1.0
|
CA
|
B:ASN167
|
4.8
|
25.1
|
1.0
|
N
|
B:ARG214
|
4.9
|
19.9
|
1.0
|
N
|
B:VAL166
|
4.9
|
22.3
|
1.0
|
CA
|
B:ARG214
|
5.0
|
18.4
|
1.0
|
|
Chlorine binding site 2 out
of 9 in 5wjo
Go back to
Chlorine Binding Sites List in 5wjo
Chlorine binding site 2 out
of 9 in the Crystal Structure of the Unliganded PG90 Tcr
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Crystal Structure of the Unliganded PG90 Tcr within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl302
b:58.3
occ:1.00
|
O
|
B:HOH406
|
3.1
|
27.1
|
1.0
|
NE2
|
B:GLN216
|
3.7
|
12.6
|
1.0
|
OE1
|
B:GLN216
|
4.1
|
22.6
|
1.0
|
CD1
|
B:ILE239
|
4.3
|
17.4
|
1.0
|
CZ2
|
B:TRP165
|
4.3
|
16.5
|
1.0
|
CD
|
B:GLN216
|
4.3
|
25.2
|
1.0
|
CH2
|
B:TRP165
|
4.6
|
16.7
|
1.0
|
|
Chlorine binding site 3 out
of 9 in 5wjo
Go back to
Chlorine Binding Sites List in 5wjo
Chlorine binding site 3 out
of 9 in the Crystal Structure of the Unliganded PG90 Tcr
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Crystal Structure of the Unliganded PG90 Tcr within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl303
b:49.6
occ:1.00
|
CD2
|
B:TYR220
|
3.5
|
18.0
|
1.0
|
N
|
B:ARG9
|
3.6
|
17.1
|
1.0
|
CE2
|
B:TYR220
|
3.6
|
18.3
|
1.0
|
N
|
B:TYR10
|
3.8
|
14.8
|
1.0
|
CB
|
B:PRO8
|
3.8
|
19.1
|
1.0
|
O
|
B:TYR10
|
3.9
|
20.4
|
1.0
|
CB
|
B:ARG9
|
4.1
|
18.1
|
1.0
|
CA
|
B:PRO8
|
4.2
|
17.5
|
1.0
|
C
|
B:PRO8
|
4.3
|
21.2
|
1.0
|
CA
|
B:ARG9
|
4.3
|
16.2
|
1.0
|
C
|
B:ARG9
|
4.5
|
18.3
|
1.0
|
CA
|
B:TYR10
|
4.7
|
14.7
|
1.0
|
C
|
B:TYR10
|
4.7
|
20.3
|
1.0
|
CG2
|
B:THR237
|
4.7
|
17.6
|
1.0
|
CG
|
B:TYR220
|
4.7
|
17.5
|
1.0
|
CZ
|
B:TYR220
|
4.9
|
25.5
|
1.0
|
OG1
|
B:THR237
|
4.9
|
19.3
|
1.0
|
|
Chlorine binding site 4 out
of 9 in 5wjo
Go back to
Chlorine Binding Sites List in 5wjo
Chlorine binding site 4 out
of 9 in the Crystal Structure of the Unliganded PG90 Tcr
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Crystal Structure of the Unliganded PG90 Tcr within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl304
b:66.3
occ:1.00
|
N
|
B:HIS172
|
3.2
|
25.1
|
1.0
|
N
|
B:SER173
|
3.4
|
26.2
|
1.0
|
CB
|
B:SER173
|
3.7
|
29.3
|
1.0
|
CA
|
B:VAL171
|
3.9
|
22.9
|
1.0
|
C
|
B:VAL171
|
4.1
|
26.9
|
1.0
|
CA
|
B:HIS172
|
4.1
|
25.4
|
1.0
|
CB
|
B:VAL171
|
4.2
|
26.8
|
1.0
|
CA
|
B:SER173
|
4.2
|
25.9
|
1.0
|
C
|
B:HIS172
|
4.2
|
30.0
|
1.0
|
O
|
B:HOH470
|
4.4
|
42.6
|
1.0
|
CB
|
B:HIS172
|
4.4
|
26.1
|
1.0
|
CG1
|
B:VAL171
|
4.5
|
27.0
|
1.0
|
O
|
B:GLU170
|
4.7
|
25.6
|
1.0
|
|
Chlorine binding site 5 out
of 9 in 5wjo
Go back to
Chlorine Binding Sites List in 5wjo
Chlorine binding site 5 out
of 9 in the Crystal Structure of the Unliganded PG90 Tcr
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Crystal Structure of the Unliganded PG90 Tcr within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl302
b:53.3
occ:1.00
|
NE2
|
C:GLN107
|
3.0
|
52.8
|
1.0
|
O
|
C:LEU106
|
3.9
|
25.0
|
1.0
|
CB
|
C:LYS105
|
4.1
|
22.3
|
1.0
|
O
|
C:ALA84
|
4.1
|
24.2
|
1.0
|
CG
|
C:LYS105
|
4.1
|
34.2
|
1.0
|
CD
|
C:GLN107
|
4.2
|
59.4
|
1.0
|
CG2
|
C:THR83
|
4.2
|
21.6
|
1.0
|
C
|
C:ALA84
|
4.2
|
24.3
|
1.0
|
CA
|
C:LYS105
|
4.3
|
19.6
|
1.0
|
N
|
C:ALA84
|
4.4
|
21.4
|
1.0
|
CA
|
C:ALA84
|
4.4
|
20.9
|
1.0
|
N
|
C:LEU106
|
4.4
|
19.6
|
1.0
|
C
|
C:LYS105
|
4.5
|
22.9
|
1.0
|
C
|
C:LEU106
|
4.6
|
24.8
|
1.0
|
CG2
|
C:VAL85
|
4.6
|
23.1
|
1.0
|
CG
|
C:GLN107
|
4.7
|
38.2
|
1.0
|
C
|
C:THR83
|
4.8
|
25.0
|
1.0
|
N
|
C:VAL85
|
4.8
|
20.4
|
1.0
|
CD
|
C:LYS105
|
4.8
|
42.4
|
1.0
|
|
Chlorine binding site 6 out
of 9 in 5wjo
Go back to
Chlorine Binding Sites List in 5wjo
Chlorine binding site 6 out
of 9 in the Crystal Structure of the Unliganded PG90 Tcr
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Crystal Structure of the Unliganded PG90 Tcr within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl303
b:58.5
occ:1.00
|
NH2
|
C:ARG16
|
3.0
|
46.9
|
1.0
|
O
|
C:ALA17
|
3.4
|
25.9
|
1.0
|
NH1
|
C:ARG16
|
3.4
|
45.3
|
1.0
|
CZ
|
C:ARG16
|
3.5
|
59.8
|
1.0
|
ND2
|
C:ASN19
|
3.5
|
23.8
|
1.0
|
C
|
C:ALA17
|
4.3
|
25.3
|
1.0
|
CB
|
C:ALA17
|
4.5
|
22.2
|
1.0
|
NE
|
C:ARG16
|
4.6
|
49.4
|
1.0
|
CG
|
C:ASN19
|
4.8
|
32.5
|
1.0
|
CA
|
C:ALA17
|
4.8
|
21.2
|
1.0
|
N
|
C:ALA17
|
4.8
|
21.7
|
1.0
|
|
Chlorine binding site 7 out
of 9 in 5wjo
Go back to
Chlorine Binding Sites List in 5wjo
Chlorine binding site 7 out
of 9 in the Crystal Structure of the Unliganded PG90 Tcr
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of Crystal Structure of the Unliganded PG90 Tcr within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl303
b:52.6
occ:1.00
|
O
|
D:HOH423
|
3.0
|
28.5
|
1.0
|
N
|
D:ARG9
|
3.3
|
22.9
|
1.0
|
CE2
|
D:TYR220
|
3.6
|
20.5
|
1.0
|
CD2
|
D:TYR220
|
3.6
|
20.1
|
1.0
|
CB
|
D:PRO8
|
3.7
|
24.0
|
1.0
|
O
|
D:HOH503
|
3.7
|
23.3
|
1.0
|
N
|
D:TYR10
|
3.8
|
20.6
|
1.0
|
CB
|
D:ARG9
|
3.8
|
22.4
|
1.0
|
CA
|
D:ARG9
|
4.0
|
21.9
|
1.0
|
CA
|
D:PRO8
|
4.0
|
22.6
|
1.0
|
C
|
D:PRO8
|
4.0
|
27.0
|
1.0
|
O
|
D:TYR10
|
4.0
|
24.3
|
1.0
|
C
|
D:ARG9
|
4.4
|
24.4
|
1.0
|
O
|
D:HOH412
|
4.7
|
28.1
|
1.0
|
O
|
D:HOH483
|
4.8
|
43.9
|
1.0
|
O
|
D:HOH499
|
4.8
|
42.8
|
1.0
|
CA
|
D:TYR10
|
4.8
|
20.2
|
1.0
|
C
|
D:TYR10
|
4.8
|
24.5
|
1.0
|
CZ
|
D:TYR220
|
4.9
|
25.9
|
1.0
|
CG
|
D:TYR220
|
4.9
|
19.4
|
1.0
|
CG2
|
D:THR237
|
5.0
|
25.2
|
1.0
|
|
Chlorine binding site 8 out
of 9 in 5wjo
Go back to
Chlorine Binding Sites List in 5wjo
Chlorine binding site 8 out
of 9 in the Crystal Structure of the Unliganded PG90 Tcr
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 8 of Crystal Structure of the Unliganded PG90 Tcr within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl304
b:41.3
occ:1.00
|
N
|
D:GLY168
|
3.1
|
21.1
|
1.0
|
CD2
|
D:HIS212
|
3.3
|
21.2
|
1.0
|
CA
|
D:GLY168
|
3.6
|
20.4
|
1.0
|
NE
|
D:ARG214
|
3.8
|
25.9
|
1.0
|
O
|
D:TRP165
|
3.8
|
22.4
|
1.0
|
CB
|
D:TRP165
|
3.8
|
14.8
|
1.0
|
N
|
D:ASN167
|
3.9
|
22.6
|
1.0
|
CB
|
D:ARG214
|
4.0
|
13.7
|
1.0
|
C
|
D:TRP165
|
4.1
|
22.1
|
1.0
|
NE2
|
D:HIS212
|
4.1
|
21.0
|
1.0
|
C
|
D:ASN167
|
4.1
|
25.7
|
1.0
|
CA
|
D:ASN167
|
4.3
|
22.5
|
1.0
|
CG
|
D:HIS212
|
4.4
|
19.8
|
1.0
|
NH1
|
D:ARG214
|
4.4
|
17.8
|
1.0
|
CZ
|
D:ARG214
|
4.6
|
29.9
|
1.0
|
CD
|
D:ARG214
|
4.6
|
26.3
|
1.0
|
N
|
D:VAL166
|
4.6
|
19.0
|
1.0
|
C
|
D:VAL166
|
4.6
|
25.6
|
1.0
|
CA
|
D:TRP165
|
4.6
|
16.4
|
1.0
|
O
|
D:HIS212
|
4.6
|
19.1
|
1.0
|
C
|
D:GLY168
|
4.7
|
23.6
|
1.0
|
CA
|
D:VAL166
|
4.8
|
18.8
|
1.0
|
N
|
D:ARG214
|
4.9
|
16.0
|
1.0
|
CB
|
D:HIS212
|
4.9
|
16.9
|
1.0
|
CG
|
D:ARG214
|
4.9
|
20.2
|
1.0
|
CG
|
D:TRP165
|
5.0
|
15.1
|
1.0
|
N
|
D:LYS169
|
5.0
|
18.6
|
1.0
|
|
Chlorine binding site 9 out
of 9 in 5wjo
Go back to
Chlorine Binding Sites List in 5wjo
Chlorine binding site 9 out
of 9 in the Crystal Structure of the Unliganded PG90 Tcr
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 9 of Crystal Structure of the Unliganded PG90 Tcr within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl305
b:49.0
occ:1.00
|
NE1
|
D:TRP245
|
3.4
|
19.9
|
1.0
|
CE1
|
D:HIS212
|
3.5
|
20.8
|
1.0
|
CB
|
D:GLU243
|
3.6
|
19.3
|
1.0
|
CD1
|
D:TRP245
|
3.6
|
20.1
|
1.0
|
ND1
|
D:HIS212
|
4.0
|
21.4
|
1.0
|
N
|
D:ALA244
|
4.0
|
17.9
|
1.0
|
CE2
|
D:TRP245
|
4.0
|
21.2
|
1.0
|
C
|
D:GLU243
|
4.1
|
22.6
|
1.0
|
CG
|
D:TRP245
|
4.3
|
17.9
|
1.0
|
CA
|
D:ALA244
|
4.3
|
16.9
|
1.0
|
O
|
D:GLU243
|
4.4
|
23.4
|
1.0
|
C
|
D:ALA244
|
4.4
|
20.3
|
1.0
|
N
|
D:TRP245
|
4.4
|
17.8
|
1.0
|
CA
|
D:GLU243
|
4.5
|
17.8
|
1.0
|
CD2
|
D:TRP245
|
4.5
|
16.9
|
1.0
|
CD
|
D:GLU243
|
4.5
|
43.3
|
1.0
|
O
|
D:HOH476
|
4.6
|
24.8
|
1.0
|
CG
|
D:GLU243
|
4.7
|
25.7
|
1.0
|
NE2
|
D:HIS212
|
4.7
|
21.0
|
1.0
|
CZ2
|
D:TRP245
|
4.7
|
20.5
|
1.0
|
OE1
|
D:GLU243
|
4.7
|
27.9
|
1.0
|
OE2
|
D:GLU243
|
4.8
|
39.6
|
1.0
|
|
Reference:
A.Shahine,
I.Van Rhijn,
T.Y.Cheng,
S.Iwany,
S.Gras,
D.B.Moody,
J.Rossjohn.
A Molecular Basis of Human T Cell Receptor Autoreactivity Toward Self-Phospholipids. Sci Immunol V. 2 2017.
ISSN: ESSN 2470-9468
PubMed: 29054999
DOI: 10.1126/SCIIMMUNOL.AAO1384
Page generated: Fri Jul 26 19:24:42 2024
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