Chlorine in PDB 6d64: Crystal Structure of Human CD1B in Complex with Popc
Protein crystallography data
The structure of Crystal Structure of Human CD1B in Complex with Popc, PDB code: 6d64
was solved by
A.E.Shahine,
J.Rossjohn,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.13 /
1.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.981,
80.032,
92.766,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.9 /
21.1
|
Other elements in 6d64:
The structure of Crystal Structure of Human CD1B in Complex with Popc also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of Human CD1B in Complex with Popc
(pdb code 6d64). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the
Crystal Structure of Human CD1B in Complex with Popc, PDB code: 6d64:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
Chlorine binding site 1 out
of 7 in 6d64
Go back to
Chlorine Binding Sites List in 6d64
Chlorine binding site 1 out
of 7 in the Crystal Structure of Human CD1B in Complex with Popc
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 Human CD1B in Complex with Popc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl419
b:20.8
occ:1.00
|
O
|
A:HOH627
|
2.8
|
27.1
|
1.0
|
O
|
A:HOH572
|
3.1
|
26.6
|
1.0
|
NE1
|
A:TRP40
|
3.4
|
20.8
|
1.0
|
CA
|
A:GLY45
|
3.8
|
17.1
|
1.0
|
O
|
A:HOH816
|
3.9
|
26.6
|
1.0
|
O
|
A:SER42
|
4.2
|
20.4
|
0.4
|
CA
|
A:SER42
|
4.2
|
18.4
|
0.6
|
CA
|
A:SER42
|
4.2
|
18.7
|
0.4
|
O
|
A:SER42
|
4.3
|
19.6
|
0.6
|
CE2
|
A:TRP40
|
4.3
|
19.2
|
1.0
|
CG2
|
A:ILE74
|
4.3
|
22.1
|
1.0
|
N
|
A:GLY45
|
4.3
|
18.0
|
1.0
|
CD1
|
A:TRP40
|
4.4
|
18.5
|
1.0
|
CZ2
|
A:TRP40
|
4.4
|
19.9
|
1.0
|
C
|
A:SER42
|
4.7
|
20.0
|
0.4
|
C
|
A:SER42
|
4.7
|
20.8
|
0.6
|
OG
|
A:SER42
|
4.7
|
18.1
|
0.6
|
CB
|
A:SER42
|
4.7
|
23.2
|
0.6
|
CG
|
A:ARG71
|
4.8
|
17.3
|
1.0
|
O
|
A:ASP41
|
4.8
|
16.6
|
1.0
|
CB
|
A:SER42
|
4.8
|
21.4
|
0.4
|
CD1
|
A:ILE74
|
4.9
|
25.1
|
1.0
|
CB
|
A:ILE74
|
4.9
|
18.3
|
1.0
|
O
|
A:HOH746
|
5.0
|
28.3
|
1.0
|
C
|
A:GLY45
|
5.0
|
20.2
|
1.0
|
|
Chlorine binding site 2 out
of 7 in 6d64
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Chlorine Binding Sites List in 6d64
Chlorine binding site 2 out
of 7 in the Crystal Structure of Human CD1B in Complex with Popc
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 Human CD1B in Complex with Popc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl420
b:28.0
occ:1.00
|
O
|
A:HOH648
|
3.1
|
28.4
|
1.0
|
N
|
A:LEU191
|
3.3
|
15.7
|
1.0
|
CA
|
A:TRP190
|
3.8
|
14.6
|
1.0
|
O
|
A:HOH669
|
3.8
|
38.7
|
1.0
|
CB
|
A:LEU191
|
4.0
|
14.9
|
1.0
|
CB
|
A:TRP190
|
4.0
|
17.8
|
1.0
|
C
|
A:TRP190
|
4.1
|
17.1
|
1.0
|
CG
|
A:LEU191
|
4.1
|
19.4
|
1.0
|
CA
|
A:LEU191
|
4.2
|
14.5
|
1.0
|
O
|
A:LEU191
|
4.4
|
22.0
|
1.0
|
O
|
A:ASN283
|
4.5
|
48.7
|
0.6
|
O
|
A:HOH858
|
4.6
|
52.1
|
1.0
|
CD1
|
A:LEU275
|
4.6
|
24.7
|
1.0
|
CD2
|
A:LEU275
|
4.7
|
21.0
|
1.0
|
CD1
|
A:LEU191
|
4.8
|
18.6
|
1.0
|
C
|
A:LEU191
|
4.8
|
19.8
|
1.0
|
O
|
A:HOH881
|
4.8
|
37.7
|
1.0
|
|
Chlorine binding site 3 out
of 7 in 6d64
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Chlorine Binding Sites List in 6d64
Chlorine binding site 3 out
of 7 in the Crystal Structure of Human CD1B in Complex with Popc
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 Human CD1B in Complex with Popc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl421
b:65.9
occ:1.00
|
OD2
|
A:ASP122
|
2.9
|
26.6
|
1.0
|
CD
|
A:ARG115
|
3.2
|
28.6
|
1.0
|
NE
|
A:ARG115
|
3.2
|
32.4
|
1.0
|
O
|
B:HOH386
|
3.6
|
37.1
|
1.0
|
O
|
A:HOH599
|
3.6
|
36.8
|
1.0
|
NZ
|
B:LYS60
|
3.7
|
37.6
|
1.0
|
OD1
|
A:ASP122
|
3.7
|
28.1
|
1.0
|
CG
|
A:ASP122
|
3.7
|
20.0
|
1.0
|
O
|
B:LYS60
|
3.8
|
25.1
|
1.0
|
NE1
|
B:TRP62
|
4.0
|
16.9
|
1.0
|
CZ2
|
B:TRP62
|
4.0
|
15.7
|
1.0
|
CE2
|
B:TRP62
|
4.2
|
12.9
|
1.0
|
CZ
|
A:ARG115
|
4.3
|
33.7
|
1.0
|
CG
|
A:ARG115
|
4.4
|
18.5
|
1.0
|
O
|
A:HOH579
|
4.4
|
33.5
|
1.0
|
CG
|
B:LYS60
|
4.4
|
36.9
|
1.0
|
CB
|
A:ARG115
|
4.6
|
15.8
|
1.0
|
NH1
|
A:ARG115
|
4.8
|
30.8
|
1.0
|
C
|
B:LYS60
|
5.0
|
16.7
|
1.0
|
|
Chlorine binding site 4 out
of 7 in 6d64
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Chlorine Binding Sites List in 6d64
Chlorine binding site 4 out
of 7 in the Crystal Structure of Human CD1B in Complex with Popc
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 Human CD1B in Complex with Popc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl422
b:27.9
occ:1.00
|
O
|
A:HOH920
|
4.0
|
49.9
|
1.0
|
O
|
A:HOH526
|
4.0
|
42.2
|
1.0
|
CG2
|
A:ILE160
|
4.0
|
26.5
|
1.0
|
CD1
|
A:ILE69
|
4.1
|
24.8
|
1.0
|
OG1
|
A:THR157
|
4.2
|
37.3
|
1.0
|
CG2
|
A:THR157
|
4.3
|
24.2
|
1.0
|
CB
|
A:ILE160
|
4.4
|
23.2
|
1.0
|
CD2
|
A:LEU161
|
4.4
|
18.9
|
1.0
|
CD1
|
A:ILE160
|
4.5
|
26.3
|
1.0
|
CA
|
A:THR157
|
4.6
|
32.1
|
1.0
|
CB
|
A:THR157
|
4.7
|
24.8
|
1.0
|
O
|
A:THR157
|
4.7
|
23.6
|
1.0
|
CG
|
A:LEU161
|
4.7
|
19.1
|
1.0
|
O
|
A:HOH820
|
4.9
|
31.4
|
1.0
|
|
Chlorine binding site 5 out
of 7 in 6d64
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Chlorine Binding Sites List in 6d64
Chlorine binding site 5 out
of 7 in the Crystal Structure of Human CD1B in Complex with Popc
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 Human CD1B in Complex with Popc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl423
b:19.0
occ:1.00
|
NE2
|
A:GLN228
|
2.4
|
57.0
|
1.0
|
OE1
|
A:GLN228
|
2.6
|
62.4
|
1.0
|
CD
|
A:GLN228
|
2.8
|
54.6
|
1.0
|
O
|
A:HOH519
|
3.1
|
39.5
|
1.0
|
O
|
A:HOH501
|
4.3
|
49.5
|
1.0
|
CG
|
A:GLN228
|
4.3
|
39.7
|
1.0
|
CB
|
A:GLN228
|
5.0
|
27.6
|
1.0
|
|
Chlorine binding site 6 out
of 7 in 6d64
Go back to
Chlorine Binding Sites List in 6d64
Chlorine binding site 6 out
of 7 in the Crystal Structure of Human CD1B in Complex with Popc
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 Human CD1B in Complex with Popc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl424
b:19.9
occ:1.00
|
O
|
A:PHE88
|
3.8
|
32.3
|
1.0
|
CA
|
A:PHE88
|
3.9
|
34.7
|
1.0
|
CD
|
A:LYS143
|
3.9
|
47.5
|
1.0
|
C
|
A:PHE88
|
4.0
|
38.9
|
1.0
|
CA
|
A:ARG140
|
4.1
|
20.0
|
1.0
|
CG
|
A:ARG140
|
4.2
|
28.4
|
1.0
|
CB
|
A:ARG140
|
4.2
|
25.1
|
1.0
|
CE
|
A:LYS143
|
4.3
|
54.9
|
1.0
|
O
|
A:ASP87
|
4.3
|
43.7
|
1.0
|
NE
|
A:ARG140
|
4.4
|
30.4
|
1.0
|
N
|
A:ARG140
|
4.6
|
22.3
|
1.0
|
CB
|
A:PHE88
|
4.6
|
35.3
|
1.0
|
CD2
|
A:PHE88
|
4.6
|
35.8
|
1.0
|
OG
|
A:SER139
|
4.7
|
43.0
|
1.0
|
N
|
A:GLN89
|
4.8
|
35.9
|
1.0
|
CG
|
A:PHE88
|
4.8
|
35.9
|
1.0
|
CD
|
A:ARG140
|
4.9
|
30.1
|
1.0
|
CG
|
A:GLN89
|
4.9
|
36.9
|
1.0
|
CB
|
A:GLN89
|
4.9
|
37.5
|
1.0
|
|
Chlorine binding site 7 out
of 7 in 6d64
Go back to
Chlorine Binding Sites List in 6d64
Chlorine binding site 7 out
of 7 in the Crystal Structure of Human CD1B in Complex with Popc
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 Human CD1B in Complex with Popc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl201
b:20.4
occ:1.00
|
N
|
B:GLY45
|
3.5
|
39.8
|
1.0
|
CB
|
B:ALA81
|
3.7
|
23.4
|
1.0
|
CB
|
B:GLU79
|
3.9
|
40.8
|
1.0
|
C
|
B:TYR80
|
4.0
|
36.3
|
1.0
|
C
|
B:GLU79
|
4.0
|
27.9
|
1.0
|
O
|
B:GLU79
|
4.1
|
33.8
|
1.0
|
N
|
B:TYR80
|
4.1
|
30.5
|
1.0
|
N
|
B:ALA81
|
4.1
|
28.5
|
1.0
|
N
|
B:ASN44
|
4.1
|
36.2
|
0.9
|
CA
|
B:GLY45
|
4.2
|
35.6
|
1.0
|
CA
|
B:TYR80
|
4.2
|
26.4
|
1.0
|
CA
|
B:ASN44
|
4.3
|
39.0
|
0.8
|
O
|
B:TYR80
|
4.3
|
31.2
|
1.0
|
C
|
B:ASN44
|
4.3
|
38.3
|
1.0
|
CB
|
B:LEU42
|
4.5
|
26.1
|
1.0
|
CA
|
B:ALA81
|
4.5
|
25.8
|
1.0
|
CA
|
B:GLU79
|
4.6
|
37.6
|
1.0
|
OE1
|
B:GLU79
|
4.7
|
76.1
|
1.0
|
CD
|
B:LYS96
|
4.7
|
58.0
|
1.0
|
O
|
B:LEU42
|
4.8
|
25.2
|
1.0
|
CG
|
B:LYS96
|
4.8
|
47.8
|
1.0
|
C
|
B:LYS43
|
4.9
|
31.7
|
1.0
|
CG
|
B:GLU79
|
5.0
|
57.5
|
1.0
|
CD
|
B:GLU79
|
5.0
|
68.1
|
1.0
|
C
|
B:LEU42
|
5.0
|
27.6
|
1.0
|
|
Reference:
A.Shahine,
P.Reinink,
J.F.Reijneveld,
S.Gras,
M.Holzheimer,
T.Y.Cheng,
A.J.Minnaard,
J.D.Altman,
S.Lenz,
J.Prandi,
J.Kubler-Kielb,
D.B.Moody,
J.Rossjohn,
I.Van Rhijn.
A T-Cell Receptor Escape Channel Allows Broad T-Cell Response to CD1B and Membrane Phospholipids. Nat Commun V. 10 56 2019.
ISSN: ESSN 2041-1723
PubMed: 30610190
DOI: 10.1038/S41467-018-07898-0
Page generated: Sat Jul 27 21:24:36 2024
|