Sodium in PDB 8g8d: Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide
Protein crystallography data
The structure of Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide, PDB code: 8g8d
was solved by
A.Niyongabo,
B.M.Janus,
G.Ofek,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
37.98 /
2.02
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
41.069,
115.513,
231.322,
90,
90,
90
|
|
R / Rfree (%)
|
19.8 /
23.4
|
Other elements in 8g8d:
The structure of Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide
(pdb code 8g8d). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the
Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide, PDB code: 8g8d:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 10 in 8g8d
Go back to
Sodium Binding Sites List in 8g8d
Sodium binding site 1 out
of 10 in the Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na301
b:35.5
occ:1.00
|
OG1
|
H:THR58
|
2.7
|
26.3
|
1.0
|
|
O
|
H:ASN56
|
2.7
|
20.3
|
1.0
|
|
HG1
|
H:THR58
|
2.8
|
31.6
|
1.0
|
|
H
|
H:ASN52
|
3.0
|
27.9
|
1.0
|
|
HA
|
H:ILE51
|
3.2
|
26.1
|
1.0
|
|
H
|
H:THR58
|
3.3
|
23.4
|
1.0
|
|
CZ2
|
H:TRP50
|
3.3
|
25.7
|
1.0
|
|
CE2
|
H:TRP50
|
3.3
|
23.5
|
1.0
|
|
N
|
H:THR58
|
3.4
|
19.5
|
1.0
|
|
CH2
|
H:TRP50
|
3.4
|
23.4
|
1.0
|
|
HB
|
H:THR58
|
3.4
|
34.8
|
1.0
|
|
HA
|
H:PRO57
|
3.4
|
27.4
|
1.0
|
|
HB2
|
H:ASN52
|
3.5
|
33.0
|
1.0
|
|
CD2
|
H:TRP50
|
3.5
|
20.5
|
1.0
|
|
CB
|
H:THR58
|
3.5
|
29.0
|
1.0
|
|
CZ3
|
H:TRP50
|
3.5
|
22.7
|
1.0
|
|
HD21
|
H:ASN56
|
3.5
|
36.1
|
1.0
|
|
C
|
H:PRO57
|
3.5
|
22.7
|
1.0
|
|
N
|
H:ASN52
|
3.6
|
23.2
|
1.0
|
|
CE3
|
H:TRP50
|
3.6
|
22.4
|
1.0
|
|
O
|
H:TRP50
|
3.6
|
20.0
|
1.0
|
|
C
|
H:ASN56
|
3.6
|
23.8
|
1.0
|
|
HZ2
|
H:TRP50
|
3.7
|
30.9
|
1.0
|
|
HH2
|
H:TRP50
|
3.8
|
28.1
|
1.0
|
|
CA
|
H:PRO57
|
3.8
|
22.8
|
1.0
|
|
HB3
|
H:ASN56
|
3.9
|
34.1
|
1.0
|
|
CA
|
H:ILE51
|
4.0
|
21.7
|
1.0
|
|
HZ3
|
H:TRP50
|
4.0
|
27.3
|
1.0
|
|
CA
|
H:THR58
|
4.0
|
20.1
|
1.0
|
|
NE1
|
H:TRP50
|
4.0
|
22.6
|
1.0
|
|
C
|
H:ILE51
|
4.1
|
21.6
|
1.0
|
|
N
|
H:PRO57
|
4.1
|
22.6
|
1.0
|
|
ND2
|
H:ASN56
|
4.1
|
30.1
|
1.0
|
|
HE3
|
H:TRP50
|
4.1
|
27.0
|
1.0
|
|
O
|
H:PRO57
|
4.1
|
24.8
|
1.0
|
|
C
|
H:TRP50
|
4.1
|
20.4
|
1.0
|
|
HZ3
|
P:LYS665
|
4.2
|
49.7
|
1.0
|
|
CB
|
H:ASN52
|
4.2
|
27.5
|
1.0
|
|
CG
|
H:TRP50
|
4.3
|
19.9
|
1.0
|
|
N
|
H:ILE51
|
4.3
|
20.1
|
1.0
|
|
HB3
|
H:ASN52
|
4.3
|
33.0
|
1.0
|
|
HE1
|
H:TRP50
|
4.4
|
27.2
|
1.0
|
|
CA
|
H:ASN52
|
4.4
|
25.1
|
1.0
|
|
HA
|
H:THR58
|
4.5
|
24.2
|
1.0
|
|
CD1
|
H:TRP50
|
4.5
|
21.9
|
1.0
|
|
HD22
|
H:ASN56
|
4.5
|
36.1
|
1.0
|
|
CB
|
H:ASN56
|
4.6
|
28.4
|
1.0
|
|
CA
|
H:ASN56
|
4.7
|
25.2
|
1.0
|
|
HA
|
H:ASN52
|
4.7
|
30.2
|
1.0
|
|
CG
|
H:ASN56
|
4.7
|
29.1
|
1.0
|
|
OE2
|
P:GLU662
|
4.8
|
39.4
|
1.0
|
|
HG13
|
H:ILE51
|
4.8
|
25.5
|
1.0
|
|
CG2
|
H:THR58
|
4.8
|
21.4
|
1.0
|
|
HZ2
|
P:LYS665
|
4.9
|
49.7
|
1.0
|
|
NZ
|
P:LYS665
|
4.9
|
41.4
|
1.0
|
|
HG21
|
H:THR58
|
4.9
|
25.8
|
1.0
|
|
Sodium binding site 2 out
of 10 in 8g8d
Go back to
Sodium Binding Sites List in 8g8d
Sodium binding site 2 out
of 10 in the Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na302
b:40.8
occ:1.00
|
HB2
|
H:SER7
|
2.5
|
41.0
|
1.0
|
|
OG
|
H:SER7
|
2.5
|
33.6
|
1.0
|
|
O
|
H:GLY8
|
2.8
|
27.2
|
1.0
|
|
CB
|
H:SER7
|
3.0
|
34.2
|
1.0
|
|
HG21
|
H:THR107
|
3.0
|
28.0
|
1.0
|
|
OE1
|
H:GLU10
|
3.2
|
52.8
|
1.0
|
|
HG22
|
H:VAL20
|
3.2
|
42.0
|
1.0
|
|
HA
|
H:VAL20
|
3.2
|
33.1
|
1.0
|
|
HG13
|
H:VAL20
|
3.6
|
53.4
|
1.0
|
|
HB3
|
H:SER7
|
3.7
|
41.0
|
1.0
|
|
H
|
H:GLY8
|
3.7
|
38.3
|
1.0
|
|
N
|
H:GLY8
|
3.7
|
31.9
|
1.0
|
|
C
|
H:SER7
|
3.8
|
32.2
|
1.0
|
|
CG2
|
H:THR107
|
3.8
|
23.3
|
1.0
|
|
C
|
H:GLY8
|
3.9
|
28.6
|
1.0
|
|
HG23
|
H:THR107
|
3.9
|
28.0
|
1.0
|
|
CA
|
H:SER7
|
4.0
|
32.1
|
1.0
|
|
HB2
|
H:GLU10
|
4.0
|
52.4
|
1.0
|
|
O
|
H:LYS19
|
4.1
|
27.1
|
1.0
|
|
H
|
H:SER21
|
4.1
|
33.0
|
1.0
|
|
CG2
|
H:VAL20
|
4.1
|
35.0
|
1.0
|
|
CA
|
H:VAL20
|
4.2
|
27.6
|
1.0
|
|
O
|
H:SER7
|
4.2
|
24.5
|
1.0
|
|
HG22
|
H:THR107
|
4.2
|
28.0
|
1.0
|
|
O
|
H:HOH531
|
4.3
|
58.6
|
1.0
|
|
CG1
|
H:VAL20
|
4.4
|
44.4
|
1.0
|
|
CA
|
H:GLY8
|
4.4
|
29.2
|
1.0
|
|
CD
|
H:GLU10
|
4.4
|
57.0
|
1.0
|
|
CB
|
H:VAL20
|
4.4
|
30.3
|
1.0
|
|
HA
|
H:SER7
|
4.6
|
38.6
|
1.0
|
|
O
|
H:HOH506
|
4.6
|
55.2
|
1.0
|
|
HG21
|
H:VAL20
|
4.7
|
42.0
|
1.0
|
|
HG23
|
H:VAL20
|
4.7
|
42.0
|
1.0
|
|
HG1
|
H:THR107
|
4.7
|
38.0
|
1.0
|
|
H
|
H:SER7
|
4.7
|
33.5
|
1.0
|
|
OG1
|
H:THR107
|
4.8
|
31.7
|
1.0
|
|
N
|
H:SER21
|
4.8
|
27.5
|
1.0
|
|
O
|
H:HOH453
|
4.9
|
37.1
|
1.0
|
|
N
|
H:SER7
|
4.9
|
27.9
|
1.0
|
|
C
|
H:LYS19
|
4.9
|
26.7
|
1.0
|
|
HA3
|
H:GLY8
|
4.9
|
35.0
|
1.0
|
|
CB
|
H:GLU10
|
4.9
|
43.6
|
1.0
|
|
CB
|
H:THR107
|
4.9
|
23.4
|
1.0
|
|
HG11
|
H:VAL20
|
4.9
|
53.4
|
1.0
|
|
N
|
H:VAL20
|
5.0
|
22.4
|
1.0
|
|
HG12
|
H:VAL20
|
5.0
|
53.4
|
1.0
|
|
Sodium binding site 3 out
of 10 in 8g8d
Go back to
Sodium Binding Sites List in 8g8d
Sodium binding site 3 out
of 10 in the Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na303
b:60.9
occ:1.00
|
HG3
|
H:GLU10
|
2.2
|
70.6
|
1.0
|
|
HG2
|
H:GLU10
|
2.2
|
70.6
|
1.0
|
|
H
|
H:LEU11
|
2.4
|
27.6
|
1.0
|
|
CG
|
H:GLU10
|
2.6
|
58.8
|
1.0
|
|
O
|
H:LEU11
|
3.1
|
22.8
|
1.0
|
|
HA
|
H:GLU10
|
3.2
|
51.7
|
1.0
|
|
N
|
H:LEU11
|
3.2
|
23.0
|
1.0
|
|
O
|
H:HOH493
|
3.3
|
43.0
|
1.0
|
|
HD3
|
H:LYS12
|
3.5
|
43.7
|
1.0
|
|
CD
|
H:GLU10
|
3.6
|
57.0
|
1.0
|
|
CB
|
H:GLU10
|
3.7
|
43.6
|
1.0
|
|
CA
|
H:GLU10
|
3.7
|
43.1
|
1.0
|
|
OE2
|
H:GLU10
|
3.7
|
63.6
|
1.0
|
|
C
|
H:LEU11
|
3.9
|
24.8
|
1.0
|
|
C
|
H:GLU10
|
4.0
|
31.5
|
1.0
|
|
HD2
|
H:LYS12
|
4.0
|
43.7
|
1.0
|
|
HB3
|
H:LEU11
|
4.0
|
27.8
|
1.0
|
|
CA
|
H:LEU11
|
4.1
|
27.7
|
1.0
|
|
HB3
|
H:GLU10
|
4.1
|
52.4
|
1.0
|
|
CD
|
H:LYS12
|
4.2
|
36.4
|
1.0
|
|
HZ3
|
H:LYS12
|
4.3
|
53.6
|
1.0
|
|
HB2
|
H:GLU10
|
4.4
|
52.4
|
1.0
|
|
HZ2
|
H:LYS12
|
4.4
|
53.6
|
1.0
|
|
CB
|
H:LEU11
|
4.6
|
23.1
|
1.0
|
|
NZ
|
H:LYS12
|
4.7
|
44.6
|
1.0
|
|
OE1
|
H:GLU10
|
4.7
|
52.8
|
1.0
|
|
HG2
|
H:LYS12
|
4.9
|
32.7
|
1.0
|
|
HA
|
H:LEU11
|
4.9
|
33.2
|
1.0
|
|
O
|
H:SER9
|
4.9
|
27.8
|
1.0
|
|
Sodium binding site 4 out
of 10 in 8g8d
Go back to
Sodium Binding Sites List in 8g8d
Sodium binding site 4 out
of 10 in the Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Na301
b:56.7
occ:1.00
|
HG1
|
L:THR5
|
2.1
|
75.0
|
1.0
|
|
HG21
|
L:THR5
|
2.1
|
77.7
|
1.0
|
|
O
|
L:GLN24
|
2.6
|
44.9
|
1.0
|
|
OG1
|
L:THR5
|
2.7
|
62.5
|
1.0
|
|
HB3
|
L:LEU4
|
2.8
|
67.7
|
1.0
|
|
CG2
|
L:THR5
|
2.9
|
64.7
|
1.0
|
|
H
|
L:THR5
|
3.0
|
59.0
|
1.0
|
|
HG22
|
L:THR5
|
3.0
|
77.7
|
1.0
|
|
HD21
|
L:LEU4
|
3.1
|
81.1
|
1.0
|
|
HA2
|
L:GLY25
|
3.3
|
50.1
|
1.0
|
|
CB
|
L:THR5
|
3.3
|
47.9
|
1.0
|
|
C
|
L:GLN24
|
3.4
|
45.9
|
1.0
|
|
HB3
|
L:GLN24
|
3.4
|
57.0
|
1.0
|
|
N
|
L:THR5
|
3.6
|
49.2
|
1.0
|
|
HG2
|
L:GLN24
|
3.7
|
67.3
|
1.0
|
|
HG23
|
L:THR5
|
3.7
|
77.7
|
1.0
|
|
HG
|
L:LEU4
|
3.7
|
71.7
|
1.0
|
|
CB
|
L:LEU4
|
3.7
|
56.4
|
1.0
|
|
O
|
L:HOH446
|
3.7
|
61.9
|
1.0
|
|
CD2
|
L:LEU4
|
3.9
|
67.5
|
1.0
|
|
CG
|
L:LEU4
|
4.0
|
59.8
|
1.0
|
|
CA
|
L:GLY25
|
4.0
|
41.8
|
1.0
|
|
N
|
L:GLY25
|
4.0
|
47.0
|
1.0
|
|
CA
|
L:THR5
|
4.1
|
55.6
|
1.0
|
|
CB
|
L:GLN24
|
4.1
|
47.5
|
1.0
|
|
HB
|
L:THR5
|
4.1
|
57.5
|
1.0
|
|
OE1
|
L:GLN24
|
4.2
|
79.8
|
1.0
|
|
HB2
|
L:LEU4
|
4.2
|
67.7
|
1.0
|
|
CG
|
L:GLN24
|
4.2
|
56.0
|
1.0
|
|
HD23
|
L:LEU4
|
4.2
|
81.1
|
1.0
|
|
HA3
|
L:GLY25
|
4.3
|
50.1
|
1.0
|
|
CA
|
L:GLN24
|
4.3
|
51.6
|
1.0
|
|
C
|
L:LEU4
|
4.5
|
53.6
|
1.0
|
|
CD
|
L:GLN24
|
4.6
|
56.7
|
1.0
|
|
H
|
L:LEU4
|
4.6
|
69.6
|
1.0
|
|
H
|
L:GLN24
|
4.6
|
55.4
|
1.0
|
|
HD22
|
L:LEU4
|
4.6
|
81.1
|
1.0
|
|
CA
|
L:LEU4
|
4.6
|
47.6
|
1.0
|
|
H
|
L:GLY25
|
4.8
|
56.4
|
1.0
|
|
HA
|
L:THR5
|
4.8
|
66.8
|
1.0
|
|
HB2
|
L:GLN24
|
5.0
|
57.0
|
1.0
|
|
Sodium binding site 5 out
of 10 in 8g8d
Go back to
Sodium Binding Sites List in 8g8d
Sodium binding site 5 out
of 10 in the Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Na302
b:64.4
occ:1.00
|
HG21
|
L:THR162
|
2.1
|
88.0
|
1.0
|
|
OG1
|
L:THR162
|
2.1
|
82.9
|
1.0
|
|
OG
|
L:SER175
|
2.2
|
58.0
|
1.0
|
|
HB3
|
H:PHE166
|
2.4
|
61.1
|
1.0
|
|
HG23
|
L:THR162
|
2.4
|
88.0
|
1.0
|
|
CG2
|
L:THR162
|
2.4
|
73.4
|
1.0
|
|
CB
|
L:THR162
|
2.6
|
75.5
|
1.0
|
|
HD2
|
H:PRO167
|
2.7
|
65.8
|
1.0
|
|
HB
|
L:THR162
|
2.7
|
90.6
|
1.0
|
|
O
|
H:PRO167
|
3.1
|
45.2
|
1.0
|
|
H
|
L:SER175
|
3.2
|
73.8
|
1.0
|
|
CB
|
H:PHE166
|
3.3
|
50.9
|
1.0
|
|
CB
|
L:SER175
|
3.4
|
52.0
|
1.0
|
|
HD2
|
H:PHE166
|
3.4
|
69.3
|
1.0
|
|
HG22
|
L:THR162
|
3.4
|
88.0
|
1.0
|
|
O
|
L:HOH408
|
3.4
|
48.5
|
1.0
|
|
CD
|
H:PRO167
|
3.5
|
54.8
|
1.0
|
|
HB3
|
L:SER175
|
3.5
|
62.2
|
1.0
|
|
N
|
L:SER175
|
3.6
|
61.5
|
1.0
|
|
HB2
|
H:PHE166
|
3.6
|
61.1
|
1.0
|
|
N
|
H:PRO167
|
3.7
|
55.4
|
1.0
|
|
HB2
|
H:PRO167
|
3.8
|
66.7
|
1.0
|
|
CA
|
L:SER175
|
3.9
|
62.3
|
1.0
|
|
CD2
|
H:PHE166
|
4.0
|
57.7
|
1.0
|
|
HE1
|
L:TYR177
|
4.0
|
86.4
|
1.0
|
|
HA
|
L:ALA174
|
4.0
|
79.4
|
1.0
|
|
C
|
H:PRO167
|
4.0
|
44.5
|
1.0
|
|
CA
|
L:THR162
|
4.0
|
83.0
|
1.0
|
|
CG
|
H:PHE166
|
4.0
|
56.1
|
1.0
|
|
O
|
L:SER175
|
4.1
|
62.0
|
1.0
|
|
HH
|
L:TYR177
|
4.1
|
69.5
|
1.0
|
|
HB2
|
L:SER175
|
4.1
|
62.2
|
1.0
|
|
H
|
L:THR162
|
4.1
|
91.3
|
1.0
|
|
HD3
|
H:PRO167
|
4.2
|
65.8
|
1.0
|
|
C
|
H:PHE166
|
4.2
|
52.6
|
1.0
|
|
HG2
|
H:PRO167
|
4.2
|
70.4
|
1.0
|
|
CA
|
H:PRO167
|
4.3
|
55.4
|
1.0
|
|
CA
|
H:PHE166
|
4.3
|
53.0
|
1.0
|
|
CG
|
H:PRO167
|
4.3
|
58.6
|
1.0
|
|
CB
|
H:PRO167
|
4.3
|
55.5
|
1.0
|
|
C
|
L:SER175
|
4.3
|
61.4
|
1.0
|
|
C
|
L:ALA174
|
4.4
|
64.6
|
1.0
|
|
HA
|
H:PHE166
|
4.4
|
63.6
|
1.0
|
|
N
|
L:THR162
|
4.5
|
76.2
|
1.0
|
|
HA
|
L:THR162
|
4.6
|
99.7
|
1.0
|
|
CA
|
L:ALA174
|
4.7
|
66.1
|
1.0
|
|
C
|
L:THR162
|
4.7
|
86.3
|
1.0
|
|
CE1
|
L:TYR177
|
4.8
|
72.0
|
1.0
|
|
HA
|
L:SER175
|
4.8
|
74.8
|
1.0
|
|
HB1
|
L:ALA174
|
4.9
|
81.5
|
1.0
|
|
OH
|
L:TYR177
|
4.9
|
57.9
|
1.0
|
|
Sodium binding site 6 out
of 10 in 8g8d
Go back to
Sodium Binding Sites List in 8g8d
Sodium binding site 6 out
of 10 in the Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Na303
b:104.9
occ:1.00
|
HB3
|
L:SER187
|
2.2
|
96.7
|
1.0
|
|
OG
|
L:SER187
|
2.3
|
110.4
|
1.0
|
|
CB
|
L:SER187
|
2.5
|
80.8
|
1.0
|
|
HA
|
L:GLN184
|
2.6
|
89.5
|
1.0
|
|
HB2
|
L:SER187
|
2.6
|
96.7
|
1.0
|
|
OE1
|
L:GLU183
|
2.6
|
94.8
|
1.0
|
|
CD
|
L:GLU183
|
3.2
|
94.8
|
1.0
|
|
OE2
|
L:GLU183
|
3.2
|
95.5
|
1.0
|
|
CA
|
L:GLN184
|
3.5
|
74.7
|
1.0
|
|
O
|
L:HOH407
|
3.6
|
65.4
|
1.0
|
|
O
|
L:GLU183
|
3.7
|
75.5
|
1.0
|
|
HG2
|
L:GLN184
|
3.7
|
117.7
|
1.0
|
|
N
|
L:GLN184
|
3.8
|
76.3
|
1.0
|
|
C
|
L:GLU183
|
4.0
|
76.1
|
1.0
|
|
CA
|
L:SER187
|
4.0
|
74.5
|
1.0
|
|
HG3
|
L:GLN184
|
4.2
|
117.7
|
1.0
|
|
CG
|
L:GLN184
|
4.2
|
98.0
|
1.0
|
|
CB
|
L:GLN184
|
4.2
|
79.3
|
1.0
|
|
H
|
L:GLN184
|
4.3
|
91.5
|
1.0
|
|
HB3
|
L:GLN184
|
4.4
|
95.2
|
1.0
|
|
HE1
|
L:HIS188
|
4.4
|
96.5
|
1.0
|
|
HB3
|
L:GLU183
|
4.5
|
102.8
|
1.0
|
|
CG
|
L:GLU183
|
4.5
|
89.8
|
1.0
|
|
H
|
L:SER187
|
4.5
|
98.2
|
1.0
|
|
C
|
L:GLN184
|
4.5
|
69.9
|
1.0
|
|
HA
|
L:SER187
|
4.5
|
89.2
|
1.0
|
|
O
|
L:GLN184
|
4.5
|
66.0
|
1.0
|
|
C
|
L:SER187
|
4.6
|
74.8
|
1.0
|
|
O
|
L:SER187
|
4.6
|
78.0
|
1.0
|
|
HD1
|
L:HIS188
|
4.7
|
111.0
|
1.0
|
|
HG2
|
L:GLU183
|
4.7
|
107.6
|
1.0
|
|
N
|
L:SER187
|
4.7
|
81.8
|
1.0
|
|
CE1
|
L:HIS188
|
4.8
|
80.4
|
1.0
|
|
CB
|
L:GLU183
|
4.9
|
85.8
|
1.0
|
|
ND1
|
L:HIS188
|
4.9
|
92.5
|
1.0
|
|
Sodium binding site 7 out
of 10 in 8g8d
Go back to
Sodium Binding Sites List in 8g8d
Sodium binding site 7 out
of 10 in the Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na301
b:44.6
occ:1.00
|
H
|
A:VAL150
|
2.5
|
28.5
|
1.0
|
|
O
|
A:VAL150
|
3.1
|
23.3
|
1.0
|
|
HB2
|
A:PRO149
|
3.1
|
30.4
|
1.0
|
|
HA
|
A:PRO149
|
3.2
|
28.2
|
1.0
|
|
N
|
A:VAL150
|
3.3
|
23.7
|
1.0
|
|
HG22
|
A:VAL150
|
3.3
|
47.6
|
1.0
|
|
HD23
|
A:LEU178
|
3.4
|
36.1
|
1.0
|
|
OE1
|
A:GLU148
|
3.4
|
42.8
|
1.0
|
|
O
|
A:HOH494
|
3.5
|
37.4
|
1.0
|
|
HB3
|
A:PRO149
|
3.6
|
30.4
|
1.0
|
|
CB
|
A:PRO149
|
3.6
|
25.3
|
1.0
|
|
CA
|
A:PRO149
|
3.7
|
23.5
|
1.0
|
|
HD21
|
A:LEU178
|
3.8
|
36.1
|
1.0
|
|
HD22
|
A:LEU178
|
3.8
|
36.1
|
1.0
|
|
O
|
A:HOH464
|
3.9
|
37.2
|
1.0
|
|
CD2
|
A:LEU178
|
3.9
|
30.1
|
1.0
|
|
C
|
A:PRO149
|
4.0
|
19.2
|
1.0
|
|
C
|
A:VAL150
|
4.0
|
28.3
|
1.0
|
|
OH
|
A:TYR145
|
4.2
|
22.0
|
1.0
|
|
HB2
|
A:ALA168
|
4.2
|
34.4
|
1.0
|
|
CA
|
A:VAL150
|
4.2
|
28.9
|
1.0
|
|
HB3
|
A:GLU148
|
4.2
|
33.6
|
1.0
|
|
CG2
|
A:VAL150
|
4.3
|
39.7
|
1.0
|
|
HH
|
A:TYR145
|
4.5
|
26.4
|
1.0
|
|
CD
|
A:GLU148
|
4.5
|
39.6
|
1.0
|
|
HG23
|
A:VAL150
|
4.6
|
47.6
|
1.0
|
|
H
|
A:ALA168
|
4.8
|
36.6
|
1.0
|
|
CB
|
A:VAL150
|
4.8
|
28.6
|
1.0
|
|
HA
|
A:GLU148
|
4.8
|
28.9
|
1.0
|
|
HG21
|
A:VAL150
|
4.9
|
47.6
|
1.0
|
|
HG13
|
A:VAL150
|
4.9
|
31.1
|
1.0
|
|
Sodium binding site 8 out
of 10 in 8g8d
Go back to
Sodium Binding Sites List in 8g8d
Sodium binding site 8 out
of 10 in the Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na302
b:45.0
occ:1.00
|
HH
|
A:TYR100E
|
1.9
|
42.5
|
1.0
|
|
O
|
A:HOH531
|
2.2
|
52.4
|
1.0
|
|
O
|
C:HOH711
|
2.5
|
42.6
|
1.0
|
|
OH
|
A:TYR100E
|
2.7
|
35.4
|
1.0
|
|
HB3
|
C:ASN671
|
2.7
|
34.7
|
1.0
|
|
HE1
|
A:TYR100E
|
2.8
|
32.3
|
1.0
|
|
O
|
B:HOH425
|
3.0
|
25.6
|
1.0
|
|
CE1
|
A:TYR100E
|
3.4
|
27.1
|
1.0
|
|
CZ
|
A:TYR100E
|
3.5
|
29.6
|
1.0
|
|
CB
|
C:ASN671
|
3.6
|
28.9
|
1.0
|
|
HE2
|
B:TYR31
|
3.7
|
40.3
|
1.0
|
|
HB2
|
C:ASN671
|
3.7
|
34.7
|
1.0
|
|
HD22
|
C:ASN671
|
3.9
|
29.9
|
1.0
|
|
HB3
|
B:TRP30
|
4.0
|
49.0
|
1.0
|
|
HB2
|
B:TRP30
|
4.1
|
49.0
|
1.0
|
|
CG
|
B:TRP30
|
4.2
|
48.2
|
1.0
|
|
HG21
|
C:ILE675
|
4.2
|
49.4
|
1.0
|
|
CG
|
C:ASN671
|
4.3
|
29.6
|
1.0
|
|
ND2
|
C:ASN671
|
4.3
|
24.9
|
1.0
|
|
CB
|
B:TRP30
|
4.3
|
40.8
|
1.0
|
|
O
|
C:HOH707
|
4.4
|
37.3
|
1.0
|
|
CE2
|
B:TYR31
|
4.4
|
33.6
|
1.0
|
|
CD2
|
B:TRP30
|
4.5
|
48.3
|
1.0
|
|
C
|
C:ASN671
|
4.6
|
30.5
|
1.0
|
|
CD1
|
B:TRP30
|
4.6
|
41.9
|
1.0
|
|
CA
|
C:ASN671
|
4.7
|
31.6
|
1.0
|
|
OH
|
B:TYR31
|
4.7
|
30.6
|
1.0
|
|
O
|
C:ASN671
|
4.7
|
30.5
|
1.0
|
|
CD1
|
A:TYR100E
|
4.7
|
27.9
|
1.0
|
|
HB
|
C:ILE675
|
4.8
|
45.7
|
1.0
|
|
CE2
|
A:TYR100E
|
4.8
|
34.1
|
1.0
|
|
CE3
|
B:TRP30
|
4.9
|
49.8
|
1.0
|
|
HA
|
C:TRP672
|
4.9
|
39.3
|
1.0
|
|
HE3
|
B:TRP30
|
4.9
|
59.8
|
1.0
|
|
HD1
|
B:TRP30
|
4.9
|
50.2
|
1.0
|
|
O
|
B:HOH473
|
4.9
|
40.3
|
1.0
|
|
N
|
C:TRP672
|
5.0
|
26.3
|
1.0
|
|
CZ
|
B:TYR31
|
5.0
|
30.0
|
1.0
|
|
HD21
|
C:ASN671
|
5.0
|
29.9
|
1.0
|
|
CE2
|
B:TRP30
|
5.0
|
48.0
|
1.0
|
|
Sodium binding site 9 out
of 10 in 8g8d
Go back to
Sodium Binding Sites List in 8g8d
Sodium binding site 9 out
of 10 in the Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na301
b:67.9
occ:1.00
|
OG1
|
B:THR105
|
2.2
|
59.9
|
1.0
|
|
OG1
|
B:THR9
|
2.7
|
72.3
|
1.0
|
|
HG3
|
B:LYS103
|
2.7
|
73.7
|
1.0
|
|
HG1
|
B:THR9
|
2.8
|
86.8
|
1.0
|
|
O
|
B:LYS103
|
2.9
|
52.1
|
1.0
|
|
H
|
B:VAL11
|
3.1
|
71.1
|
1.0
|
|
O
|
B:VAL11
|
3.2
|
60.9
|
1.0
|
|
H
|
B:THR105
|
3.3
|
64.7
|
1.0
|
|
CB
|
B:THR105
|
3.3
|
57.6
|
1.0
|
|
HB
|
B:THR105
|
3.3
|
69.2
|
1.0
|
|
HG2
|
B:LYS103
|
3.4
|
73.7
|
1.0
|
|
N
|
B:THR105
|
3.4
|
53.9
|
1.0
|
|
CG
|
B:LYS103
|
3.5
|
61.4
|
1.0
|
|
C
|
B:LYS103
|
3.6
|
48.8
|
1.0
|
|
HB3
|
B:LYS103
|
3.7
|
61.1
|
1.0
|
|
N
|
B:VAL11
|
3.8
|
59.2
|
1.0
|
|
HA
|
B:THR9
|
3.8
|
77.1
|
1.0
|
|
CB
|
B:THR9
|
3.8
|
57.9
|
1.0
|
|
C
|
B:LEU104
|
3.8
|
58.1
|
1.0
|
|
HA
|
B:LEU104
|
3.9
|
66.3
|
1.0
|
|
CA
|
B:THR105
|
3.9
|
56.2
|
1.0
|
|
HZ2
|
B:LYS103
|
4.0
|
86.5
|
1.0
|
|
HB
|
B:THR9
|
4.0
|
69.5
|
1.0
|
|
C
|
B:VAL11
|
4.0
|
64.6
|
1.0
|
|
CB
|
B:LYS103
|
4.1
|
50.9
|
1.0
|
|
N
|
B:LEU104
|
4.2
|
50.2
|
1.0
|
|
CA
|
B:LEU104
|
4.2
|
55.2
|
1.0
|
|
CA
|
B:THR9
|
4.2
|
64.2
|
1.0
|
|
HA
|
B:THR105
|
4.3
|
67.5
|
1.0
|
|
HE2
|
B:LYS103
|
4.4
|
74.7
|
1.0
|
|
C
|
B:THR9
|
4.5
|
59.3
|
1.0
|
|
O
|
B:LEU104
|
4.5
|
54.0
|
1.0
|
|
CA
|
B:LYS103
|
4.5
|
50.4
|
1.0
|
|
CG2
|
B:THR105
|
4.5
|
67.1
|
1.0
|
|
CA
|
B:VAL11
|
4.6
|
64.8
|
1.0
|
|
HG22
|
B:THR105
|
4.6
|
80.5
|
1.0
|
|
HB3
|
B:SER12
|
4.7
|
74.7
|
1.0
|
|
HA
|
B:SER12
|
4.7
|
77.8
|
1.0
|
|
CD
|
B:LYS103
|
4.7
|
64.7
|
1.0
|
|
NZ
|
B:LYS103
|
4.7
|
72.0
|
1.0
|
|
HG21
|
B:THR105
|
4.8
|
80.5
|
1.0
|
|
CE
|
B:LYS103
|
4.8
|
62.2
|
1.0
|
|
H
|
B:LEU104
|
4.9
|
60.2
|
1.0
|
|
N
|
B:SER12
|
5.0
|
60.3
|
1.0
|
|
HB2
|
B:LYS103
|
5.0
|
61.1
|
1.0
|
|
Sodium binding site 10 out
of 10 in 8g8d
Go back to
Sodium Binding Sites List in 8g8d
Sodium binding site 10 out
of 10 in the Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of Crystal Structure of DH1346 Fab in Complex with Hiv Proximal Mper Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na302
b:49.1
occ:1.00
|
HG3
|
B:GLU183
|
2.3
|
90.6
|
1.0
|
|
H
|
B:GLU183
|
2.4
|
42.2
|
1.0
|
|
HD2
|
B:PRO182
|
2.5
|
43.4
|
1.0
|
|
O
|
B:HOH466
|
2.8
|
54.8
|
1.0
|
|
HB
|
B:THR181
|
2.9
|
47.9
|
1.0
|
|
CG
|
B:GLU183
|
3.1
|
75.5
|
1.0
|
|
HB2
|
B:GLU183
|
3.2
|
55.6
|
1.0
|
|
N
|
B:GLU183
|
3.3
|
35.1
|
1.0
|
|
CD
|
B:PRO182
|
3.4
|
36.2
|
1.0
|
|
HB2
|
B:PRO182
|
3.5
|
40.9
|
1.0
|
|
CB
|
B:GLU183
|
3.6
|
46.3
|
1.0
|
|
CD
|
B:GLU183
|
3.6
|
109.5
|
1.0
|
|
N
|
B:PRO182
|
3.7
|
40.5
|
1.0
|
|
CB
|
B:THR181
|
3.7
|
39.9
|
1.0
|
|
HG1
|
B:THR181
|
3.8
|
41.0
|
1.0
|
|
HG2
|
B:GLU183
|
3.8
|
90.6
|
1.0
|
|
HG2
|
B:PRO182
|
3.9
|
51.6
|
1.0
|
|
OG1
|
B:THR181
|
3.9
|
34.3
|
1.0
|
|
OE2
|
B:GLU183
|
4.0
|
110.5
|
1.0
|
|
CG
|
B:PRO182
|
4.0
|
43.0
|
1.0
|
|
CA
|
B:GLU183
|
4.0
|
39.0
|
1.0
|
|
CB
|
B:PRO182
|
4.0
|
34.1
|
1.0
|
|
HD3
|
B:PRO182
|
4.1
|
43.4
|
1.0
|
|
OD1
|
B:ASN128
|
4.1
|
47.5
|
1.0
|
|
OE1
|
B:GLU183
|
4.2
|
92.5
|
1.0
|
|
C
|
B:PRO182
|
4.2
|
32.1
|
1.0
|
|
CA
|
B:PRO182
|
4.2
|
33.0
|
1.0
|
|
C
|
B:THR181
|
4.3
|
39.3
|
1.0
|
|
HB3
|
B:GLU183
|
4.5
|
55.6
|
1.0
|
|
O
|
B:HOH448
|
4.5
|
44.2
|
1.0
|
|
HA
|
B:GLU183
|
4.6
|
46.8
|
1.0
|
|
CA
|
B:THR181
|
4.6
|
33.9
|
1.0
|
|
HG21
|
B:THR181
|
4.6
|
49.4
|
1.0
|
|
H
|
B:GLN184
|
4.7
|
42.9
|
1.0
|
|
CG2
|
B:THR181
|
4.7
|
41.1
|
1.0
|
|
HA
|
B:THR181
|
4.8
|
40.7
|
1.0
|
|
HD22
|
B:ASN128
|
4.8
|
67.8
|
1.0
|
|
HB3
|
B:PRO182
|
5.0
|
40.9
|
1.0
|
|
HG3
|
B:PRO182
|
5.0
|
51.6
|
1.0
|
|
HG22
|
B:THR181
|
5.0
|
49.4
|
1.0
|
|
Reference:
B.M.Janus,
A.Astavans,
G.Ofek.
Vaccine Induction of Heterologous Hiv-1 Neutralizing Antibody B Cell Lineages in Humans Cell(Cambridge,Mass.) 2024.
ISSN: ISSN 0092-8674
Page generated: Wed Oct 9 12:02:24 2024
|
