Sodium in PDB 6pul: Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru
Protein crystallography data
The structure of Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru, PDB code: 6pul
was solved by
W.Awad,
A.N.Keller,
J.Rossjohn,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.49 /
1.84
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
216.548,
70.029,
143.252,
90.00,
104.30,
90.00
|
R / Rfree (%)
|
15.6 /
18.4
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru
(pdb code 6pul). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the
Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru, PDB code: 6pul:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 6pul
Go back to
Sodium Binding Sites List in 6pul
Sodium binding site 1 out
of 5 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na302
b:39.7
occ:0.80
|
O
|
E:HOH423
|
2.3
|
41.6
|
1.0
|
O
|
E:TYR64
|
2.3
|
38.1
|
1.0
|
O
|
E:HOH427
|
2.4
|
44.0
|
1.0
|
OH
|
E:TYR47
|
2.5
|
43.8
|
1.0
|
O
|
E:HOH482
|
2.5
|
45.3
|
1.0
|
O
|
E:PRO61
|
2.6
|
44.7
|
1.0
|
C
|
E:PRO61
|
3.5
|
45.7
|
1.0
|
C
|
E:TYR64
|
3.5
|
40.1
|
1.0
|
CZ
|
E:TYR47
|
3.5
|
40.2
|
1.0
|
CE2
|
E:TYR47
|
3.6
|
34.8
|
1.0
|
N
|
E:TYR64
|
3.7
|
40.3
|
1.0
|
OD1
|
E:ASN65
|
4.0
|
39.3
|
0.4
|
N
|
E:GLY63
|
4.1
|
45.1
|
1.0
|
CA
|
E:ASN62
|
4.1
|
48.7
|
1.0
|
CB
|
E:PRO61
|
4.1
|
42.6
|
1.0
|
CA
|
E:TYR64
|
4.2
|
38.5
|
1.0
|
N
|
E:ASN62
|
4.2
|
45.3
|
1.0
|
CA
|
E:PRO61
|
4.3
|
39.5
|
1.0
|
NZ
|
E:LYS57
|
4.3
|
68.3
|
1.0
|
C
|
E:ASN62
|
4.5
|
49.3
|
1.0
|
CG
|
E:ASN65
|
4.5
|
44.0
|
0.4
|
N
|
E:ASN65
|
4.5
|
40.6
|
0.6
|
N
|
E:ASN65
|
4.5
|
40.4
|
0.4
|
C
|
E:GLY63
|
4.7
|
44.3
|
1.0
|
CA
|
E:ASN65
|
4.8
|
40.5
|
0.6
|
CE1
|
E:TYR47
|
4.8
|
43.7
|
1.0
|
CB
|
E:TYR64
|
4.8
|
35.3
|
1.0
|
ND2
|
E:ASN65
|
4.8
|
50.0
|
0.4
|
CA
|
E:ASN65
|
4.8
|
40.5
|
0.4
|
OD1
|
E:ASN62
|
4.9
|
52.4
|
1.0
|
CA
|
E:GLY63
|
5.0
|
45.9
|
1.0
|
|
Sodium binding site 2 out
of 5 in 6pul
Go back to
Sodium Binding Sites List in 6pul
Sodium binding site 2 out
of 5 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na103
b:62.8
occ:1.00
|
OH
|
F:TYR78
|
2.6
|
51.6
|
1.0
|
O
|
F:THR71
|
2.6
|
51.7
|
1.0
|
OD2
|
F:ASP76
|
2.6
|
55.5
|
1.0
|
CB
|
F:ASP76
|
3.2
|
49.4
|
1.0
|
CG
|
F:ASP76
|
3.3
|
54.3
|
1.0
|
CZ
|
F:TYR78
|
3.5
|
47.1
|
1.0
|
N
|
F:THR73
|
3.5
|
51.9
|
1.0
|
CE2
|
F:TYR78
|
3.5
|
42.6
|
1.0
|
CG2
|
F:THR73
|
3.6
|
59.4
|
1.0
|
OG1
|
F:THR73
|
3.6
|
56.2
|
1.0
|
O
|
F:HOH294
|
3.6
|
53.1
|
1.0
|
C
|
F:THR71
|
3.7
|
43.0
|
1.0
|
CA
|
F:PRO72
|
3.8
|
46.3
|
1.0
|
C
|
F:PRO72
|
3.9
|
49.7
|
1.0
|
CB
|
F:THR73
|
4.0
|
60.0
|
1.0
|
CE
|
F:LYS41
|
4.2
|
49.6
|
1.0
|
N
|
F:PRO72
|
4.3
|
42.2
|
1.0
|
CA
|
F:THR73
|
4.3
|
53.8
|
1.0
|
O
|
F:HOH252
|
4.4
|
50.6
|
1.0
|
OD1
|
F:ASP76
|
4.5
|
56.1
|
1.0
|
NZ
|
F:LYS41
|
4.5
|
50.3
|
1.0
|
CA
|
F:ASP76
|
4.6
|
45.7
|
1.0
|
O
|
F:PRO72
|
4.7
|
48.0
|
1.0
|
CE1
|
F:TYR78
|
4.8
|
43.1
|
1.0
|
O
|
F:HOH277
|
4.8
|
50.0
|
1.0
|
CD2
|
F:TYR78
|
4.8
|
39.5
|
1.0
|
O
|
F:HOH292
|
4.9
|
56.5
|
1.0
|
CA
|
F:THR71
|
4.9
|
40.5
|
1.0
|
N
|
F:THR71
|
4.9
|
45.0
|
1.0
|
|
Sodium binding site 3 out
of 5 in 6pul
Go back to
Sodium Binding Sites List in 6pul
Sodium binding site 3 out
of 5 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na104
b:46.0
occ:1.00
|
O
|
F:LEU87
|
2.3
|
38.2
|
1.0
|
O
|
F:HOH299
|
2.4
|
44.8
|
1.0
|
O
|
F:HOH304
|
2.4
|
49.1
|
1.0
|
O
|
F:HIS84
|
2.4
|
33.7
|
1.0
|
O
|
F:HOH278
|
2.5
|
48.4
|
1.0
|
OD1
|
F:ASN83
|
2.5
|
40.0
|
1.0
|
C
|
F:HIS84
|
3.4
|
36.0
|
1.0
|
CG
|
F:ASN83
|
3.4
|
40.7
|
1.0
|
C
|
F:LEU87
|
3.5
|
36.3
|
1.0
|
ND2
|
F:ASN83
|
3.8
|
46.6
|
1.0
|
N
|
F:HIS84
|
3.9
|
32.7
|
1.0
|
CA
|
F:VAL85
|
4.1
|
32.5
|
1.0
|
N
|
F:LEU87
|
4.1
|
34.9
|
1.0
|
N
|
F:VAL85
|
4.1
|
34.1
|
1.0
|
CA
|
F:LEU87
|
4.2
|
32.4
|
1.0
|
CB
|
F:LEU87
|
4.2
|
34.8
|
1.0
|
CA
|
F:HIS84
|
4.3
|
31.9
|
1.0
|
C
|
F:VAL85
|
4.3
|
35.4
|
1.0
|
O
|
F:VAL85
|
4.4
|
35.0
|
1.0
|
O
|
F:HOH343
|
4.5
|
69.9
|
1.0
|
N
|
F:SER88
|
4.6
|
36.7
|
1.0
|
C
|
F:SER88
|
4.7
|
38.5
|
1.0
|
CB
|
F:ASN83
|
4.7
|
36.2
|
1.0
|
CA
|
F:SER88
|
4.7
|
40.6
|
1.0
|
O
|
F:HOH303
|
4.8
|
54.1
|
1.0
|
C
|
F:ASN83
|
4.8
|
34.4
|
1.0
|
O
|
F:SER88
|
4.9
|
44.1
|
1.0
|
N
|
F:GLN89
|
5.0
|
37.7
|
1.0
|
CA
|
F:ASN83
|
5.0
|
35.2
|
1.0
|
|
Sodium binding site 4 out
of 5 in 6pul
Go back to
Sodium Binding Sites List in 6pul
Sodium binding site 4 out
of 5 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Na302
b:39.0
occ:1.00
|
O
|
G:TYR64
|
2.4
|
35.5
|
1.0
|
O
|
G:HOH510
|
2.5
|
38.1
|
1.0
|
O
|
G:HOH524
|
2.5
|
44.2
|
1.0
|
O
|
G:HOH498
|
2.5
|
39.2
|
1.0
|
OH
|
G:TYR47
|
2.5
|
34.5
|
1.0
|
O
|
G:PRO61
|
2.6
|
31.9
|
1.0
|
CZ
|
G:TYR47
|
3.5
|
36.1
|
1.0
|
C
|
G:PRO61
|
3.5
|
30.1
|
1.0
|
C
|
G:TYR64
|
3.6
|
35.6
|
1.0
|
CE2
|
G:TYR47
|
3.7
|
34.2
|
1.0
|
N
|
G:TYR64
|
3.9
|
34.6
|
1.0
|
CA
|
G:ASN62
|
4.1
|
38.0
|
1.0
|
N
|
G:GLY63
|
4.2
|
35.8
|
1.0
|
ND2
|
G:ASN65
|
4.2
|
43.6
|
0.7
|
CB
|
G:PRO61
|
4.2
|
35.6
|
1.0
|
N
|
G:ASN62
|
4.2
|
33.6
|
1.0
|
NZ
|
G:LYS57
|
4.3
|
65.2
|
1.0
|
CA
|
G:TYR64
|
4.3
|
29.7
|
1.0
|
CA
|
G:PRO61
|
4.4
|
34.2
|
1.0
|
C
|
G:ASN62
|
4.5
|
37.7
|
1.0
|
CG
|
G:ASN65
|
4.5
|
48.8
|
0.7
|
O
|
G:HOH682
|
4.6
|
40.0
|
1.0
|
N
|
G:ASN65
|
4.6
|
35.4
|
1.0
|
OD1
|
G:ASN65
|
4.7
|
57.9
|
0.7
|
OD1
|
G:ASN62
|
4.8
|
39.9
|
1.0
|
CE1
|
G:TYR47
|
4.8
|
35.5
|
1.0
|
CA
|
G:ASN65
|
4.8
|
37.1
|
0.3
|
CA
|
G:ASN65
|
4.9
|
37.0
|
0.7
|
C
|
G:GLY63
|
4.9
|
36.8
|
1.0
|
CB
|
G:TYR64
|
5.0
|
29.5
|
1.0
|
CE
|
G:LYS57
|
5.0
|
63.3
|
1.0
|
|
Sodium binding site 5 out
of 5 in 6pul
Go back to
Sodium Binding Sites List in 6pul
Sodium binding site 5 out
of 5 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na501
b:70.2
occ:1.00
|
O
|
H:HOH660
|
2.4
|
61.7
|
1.0
|
O
|
H:HOH657
|
2.5
|
63.3
|
1.0
|
O
|
H:LEU87
|
2.5
|
64.1
|
1.0
|
O
|
H:HOH656
|
2.6
|
73.5
|
1.0
|
O
|
H:HIS84
|
2.6
|
56.1
|
1.0
|
OD1
|
H:ASN83
|
2.8
|
73.1
|
1.0
|
C
|
H:HIS84
|
3.5
|
55.1
|
1.0
|
CG
|
H:ASN83
|
3.6
|
73.1
|
1.0
|
C
|
H:LEU87
|
3.7
|
64.0
|
1.0
|
ND2
|
H:ASN83
|
3.8
|
73.4
|
1.0
|
CA
|
H:VAL85
|
4.0
|
54.8
|
1.0
|
N
|
H:HIS84
|
4.2
|
51.6
|
1.0
|
N
|
H:VAL85
|
4.2
|
50.3
|
1.0
|
N
|
H:LEU87
|
4.2
|
52.9
|
1.0
|
C
|
H:VAL85
|
4.3
|
58.9
|
1.0
|
O
|
H:VAL85
|
4.3
|
60.1
|
1.0
|
CA
|
H:LEU87
|
4.4
|
61.6
|
1.0
|
CA
|
H:HIS84
|
4.5
|
52.5
|
1.0
|
CB
|
H:LEU87
|
4.5
|
58.2
|
1.0
|
O
|
H:HOH648
|
4.7
|
64.2
|
1.0
|
N
|
H:SER88
|
4.8
|
68.2
|
1.0
|
O
|
H:SER88
|
4.8
|
77.3
|
1.0
|
C
|
H:SER88
|
4.9
|
74.8
|
1.0
|
CB
|
H:ASN83
|
5.0
|
63.0
|
1.0
|
CA
|
H:SER88
|
5.0
|
74.1
|
1.0
|
|
Reference:
W.Awad,
A.N.Keller,
J.Rossjohn.
The Molecular Basis Underpinning the Potency and Specificity of Mait Cell Antigens To Be Published.
Page generated: Tue Oct 8 12:46:50 2024
|