Iodine in PDB 5mhe: Crystal Structure of Anti-T4 Fab Fragment with T4
Protein crystallography data
The structure of Crystal Structure of Anti-T4 Fab Fragment with T4, PDB code: 5mhe
was solved by
T.Parkkinen,
J.Rouvinen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.84 /
1.90
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
131.730,
55.330,
61.160,
90.00,
97.77,
90.00
|
R / Rfree (%)
|
17.8 /
22.7
|
Iodine Binding Sites:
The binding sites of Iodine atom in the Crystal Structure of Anti-T4 Fab Fragment with T4
(pdb code 5mhe). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the
Crystal Structure of Anti-T4 Fab Fragment with T4, PDB code: 5mhe:
Jump to Iodine binding site number:
1;
2;
3;
4;
Iodine binding site 1 out
of 4 in 5mhe
Go back to
Iodine Binding Sites List in 5mhe
Iodine binding site 1 out
of 4 in the Crystal Structure of Anti-T4 Fab Fragment with T4
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of Crystal Structure of Anti-T4 Fab Fragment with T4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:I301
b:40.7
occ:1.00
|
I3
|
H:T44301
|
0.0
|
40.7
|
1.0
|
C3
|
H:T44301
|
2.1
|
36.6
|
1.0
|
HG
|
L:LEU95
|
3.0
|
28.0
|
1.0
|
C2
|
H:T44301
|
3.0
|
32.2
|
1.0
|
H2
|
H:T44301
|
3.1
|
38.7
|
1.0
|
C4
|
H:T44301
|
3.1
|
29.9
|
1.0
|
O4
|
H:T44301
|
3.3
|
31.4
|
1.0
|
HD21
|
L:LEU95
|
3.5
|
29.6
|
1.0
|
HD1
|
H:TYR109
|
3.6
|
34.0
|
1.0
|
HD1
|
L:TYR93
|
3.6
|
34.2
|
1.0
|
C1'
|
H:T44301
|
3.7
|
30.8
|
1.0
|
CD1
|
L:TYR93
|
3.7
|
28.5
|
1.0
|
HD11
|
L:LEU95
|
3.8
|
38.0
|
1.0
|
CG
|
L:LEU95
|
3.8
|
23.3
|
1.0
|
H2'
|
H:T44301
|
3.9
|
31.1
|
1.0
|
HE1
|
H:TYR109
|
3.9
|
36.0
|
1.0
|
HD21
|
H:LEU47
|
3.9
|
47.6
|
1.0
|
CE1
|
L:TYR93
|
3.9
|
30.8
|
1.0
|
C2'
|
H:T44301
|
4.0
|
25.9
|
1.0
|
HE1
|
L:TYR93
|
4.0
|
36.9
|
1.0
|
H
|
L:LEU95
|
4.0
|
39.1
|
1.0
|
CD2
|
L:LEU95
|
4.0
|
24.7
|
1.0
|
HD2
|
H:TYR59
|
4.1
|
36.5
|
1.0
|
CD2
|
H:TYR59
|
4.1
|
30.4
|
1.0
|
HD23
|
L:LEU95
|
4.2
|
29.6
|
1.0
|
HD22
|
H:LEU47
|
4.2
|
47.6
|
1.0
|
CD1
|
H:TYR109
|
4.2
|
28.4
|
1.0
|
CD1
|
L:LEU95
|
4.3
|
31.7
|
1.0
|
CG
|
L:TYR93
|
4.3
|
31.7
|
1.0
|
HB3
|
L:TYR93
|
4.3
|
36.2
|
1.0
|
C1
|
H:T44301
|
4.4
|
35.9
|
1.0
|
CE1
|
H:TYR109
|
4.4
|
30.0
|
1.0
|
HB3
|
H:TYR59
|
4.4
|
33.6
|
1.0
|
C6'
|
H:T44301
|
4.4
|
28.2
|
1.0
|
CG
|
H:TYR59
|
4.4
|
34.9
|
1.0
|
CD2
|
H:LEU47
|
4.5
|
39.6
|
1.0
|
C5
|
H:T44301
|
4.5
|
34.9
|
1.0
|
HD12
|
L:LEU95
|
4.5
|
38.0
|
1.0
|
CE2
|
H:TYR59
|
4.5
|
34.0
|
1.0
|
HA
|
L:PRO94
|
4.6
|
31.2
|
1.0
|
HB3
|
H:ALA50
|
4.6
|
31.9
|
1.0
|
CZ
|
L:TYR93
|
4.7
|
36.1
|
1.0
|
HE2
|
H:TYR59
|
4.7
|
40.8
|
1.0
|
HD23
|
H:LEU47
|
4.7
|
47.6
|
1.0
|
CB
|
H:TYR59
|
4.8
|
28.0
|
1.0
|
HA
|
L:TYR93
|
4.8
|
29.4
|
1.0
|
HB2
|
H:TYR59
|
4.8
|
33.6
|
1.0
|
N
|
L:LEU95
|
4.8
|
32.6
|
1.0
|
H6'
|
H:T44301
|
4.8
|
33.9
|
1.0
|
CB
|
L:TYR93
|
4.8
|
30.1
|
1.0
|
C3'
|
H:T44301
|
4.9
|
28.0
|
1.0
|
C6
|
H:T44301
|
4.9
|
28.9
|
1.0
|
HD22
|
L:LEU95
|
4.9
|
29.6
|
1.0
|
HB2
|
H:ALA50
|
5.0
|
31.9
|
1.0
|
CD2
|
L:TYR93
|
5.0
|
28.8
|
1.0
|
|
Iodine binding site 2 out
of 4 in 5mhe
Go back to
Iodine Binding Sites List in 5mhe
Iodine binding site 2 out
of 4 in the Crystal Structure of Anti-T4 Fab Fragment with T4
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of Crystal Structure of Anti-T4 Fab Fragment with T4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:I301
b:32.4
occ:1.00
|
I3'
|
H:T44301
|
0.0
|
32.4
|
1.0
|
C3'
|
H:T44301
|
2.1
|
28.0
|
1.0
|
HE2
|
H:MET111
|
2.9
|
33.4
|
1.0
|
H2'
|
H:T44301
|
3.0
|
31.1
|
1.0
|
C2'
|
H:T44301
|
3.0
|
25.9
|
1.0
|
C4'
|
H:T44301
|
3.1
|
29.7
|
1.0
|
O4'
|
H:T44301
|
3.3
|
33.9
|
1.0
|
HA3
|
H:GLY99
|
3.4
|
35.2
|
1.0
|
HA
|
H:TYR109
|
3.5
|
33.9
|
1.0
|
CE
|
H:MET111
|
3.6
|
27.8
|
1.0
|
HD11
|
L:LEU95
|
3.6
|
38.0
|
1.0
|
HE1
|
H:MET111
|
3.7
|
33.4
|
1.0
|
SD
|
H:MET111
|
3.7
|
49.7
|
1.0
|
HG3
|
H:MET111
|
3.7
|
44.4
|
1.0
|
HA2
|
H:GLY99
|
3.7
|
35.2
|
1.0
|
HB3
|
H:SER35
|
3.8
|
35.4
|
1.0
|
HO4'
|
H:T44301
|
3.9
|
40.7
|
1.0
|
HD12
|
L:LEU95
|
4.0
|
38.0
|
1.0
|
CA
|
H:GLY99
|
4.1
|
29.3
|
1.0
|
HG
|
H:SER35
|
4.1
|
43.2
|
0.0
|
CD1
|
L:LEU95
|
4.2
|
31.7
|
1.0
|
O
|
H:ALA110
|
4.2
|
32.2
|
1.0
|
C
|
H:TYR109
|
4.3
|
26.6
|
1.0
|
CG
|
H:MET111
|
4.3
|
37.0
|
1.0
|
HD13
|
L:LEU95
|
4.3
|
38.0
|
1.0
|
CA
|
H:TYR109
|
4.3
|
28.3
|
1.0
|
C1'
|
H:T44301
|
4.3
|
30.8
|
1.0
|
C5'
|
H:T44301
|
4.4
|
20.5
|
1.0
|
HE3
|
H:MET111
|
4.4
|
33.4
|
1.0
|
HD1
|
H:TYR109
|
4.5
|
34.0
|
1.0
|
N
|
H:ALA110
|
4.5
|
27.6
|
1.0
|
C
|
H:ALA110
|
4.5
|
28.8
|
1.0
|
OG
|
H:SER35
|
4.6
|
36.0
|
1.0
|
CB
|
H:SER35
|
4.6
|
29.5
|
1.0
|
O
|
H:TYR109
|
4.6
|
17.8
|
1.0
|
H
|
H:ASP100
|
4.7
|
35.2
|
1.0
|
HB3
|
H:TYR109
|
4.7
|
36.7
|
1.0
|
HA
|
H:MET111
|
4.7
|
28.4
|
1.0
|
H
|
H:ALA110
|
4.7
|
33.1
|
1.0
|
N
|
H:GLY99
|
4.9
|
27.7
|
1.0
|
C6'
|
H:T44301
|
4.9
|
28.2
|
1.0
|
HB3
|
H:TYR33
|
4.9
|
34.6
|
1.0
|
HB2
|
H:SER35
|
4.9
|
35.4
|
1.0
|
HG2
|
H:MET111
|
4.9
|
44.4
|
1.0
|
HB2
|
H:ALA50
|
5.0
|
31.9
|
1.0
|
N
|
H:MET111
|
5.0
|
25.4
|
1.0
|
|
Iodine binding site 3 out
of 4 in 5mhe
Go back to
Iodine Binding Sites List in 5mhe
Iodine binding site 3 out
of 4 in the Crystal Structure of Anti-T4 Fab Fragment with T4
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of Crystal Structure of Anti-T4 Fab Fragment with T4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:I301
b:40.5
occ:1.00
|
I5
|
H:T44301
|
0.0
|
40.5
|
1.0
|
C5
|
H:T44301
|
2.2
|
34.9
|
1.0
|
H6
|
H:T44301
|
3.1
|
34.8
|
1.0
|
C6
|
H:T44301
|
3.1
|
28.9
|
1.0
|
C4
|
H:T44301
|
3.2
|
29.9
|
1.0
|
HE1
|
H:TYR33
|
3.2
|
37.6
|
1.0
|
O4
|
H:T44301
|
3.4
|
31.4
|
1.0
|
HB3
|
H:ASN52
|
3.5
|
41.0
|
1.0
|
HA
|
H:THR58
|
3.6
|
33.4
|
1.0
|
HA
|
H:ILE51
|
3.6
|
35.9
|
1.0
|
HD1
|
H:TYR33
|
3.6
|
35.1
|
1.0
|
HB2
|
H:SER57
|
3.7
|
44.0
|
1.0
|
H
|
H:ASN52
|
3.8
|
34.0
|
1.0
|
H6'
|
H:T44301
|
3.8
|
33.9
|
1.0
|
N
|
H:ASN52
|
3.8
|
28.3
|
1.0
|
CE1
|
H:TYR33
|
4.0
|
31.4
|
1.0
|
C
|
H:ILE51
|
4.0
|
31.8
|
1.0
|
HB2
|
H:TYR59
|
4.0
|
33.6
|
1.0
|
O
|
H:SER57
|
4.0
|
33.8
|
1.0
|
HB3
|
H:ALA50
|
4.0
|
31.9
|
1.0
|
C1'
|
H:T44301
|
4.0
|
30.8
|
1.0
|
O
|
H:ALA50
|
4.0
|
28.2
|
1.0
|
CA
|
H:ILE51
|
4.1
|
29.9
|
1.0
|
C6'
|
H:T44301
|
4.1
|
28.2
|
1.0
|
N
|
H:ILE51
|
4.1
|
28.5
|
1.0
|
C
|
H:SER57
|
4.1
|
38.7
|
1.0
|
CA
|
H:THR58
|
4.1
|
27.8
|
1.0
|
HB1
|
H:ALA50
|
4.1
|
31.9
|
1.0
|
CD1
|
H:TYR33
|
4.2
|
29.2
|
1.0
|
C
|
H:ALA50
|
4.2
|
30.1
|
1.0
|
HB3
|
H:TYR59
|
4.2
|
33.6
|
1.0
|
N
|
H:THR58
|
4.2
|
31.4
|
1.0
|
C
|
H:THR58
|
4.2
|
36.9
|
1.0
|
HB3
|
H:SER57
|
4.2
|
44.0
|
1.0
|
H
|
H:TYR59
|
4.2
|
33.8
|
1.0
|
N
|
H:TYR59
|
4.3
|
28.2
|
1.0
|
CB
|
H:ASN52
|
4.3
|
34.2
|
1.0
|
CB
|
H:SER57
|
4.4
|
36.6
|
1.0
|
C1
|
H:T44301
|
4.4
|
35.9
|
1.0
|
HA
|
H:ASN52
|
4.4
|
38.7
|
1.0
|
CA
|
H:ASN52
|
4.5
|
32.3
|
1.0
|
C3
|
H:T44301
|
4.5
|
36.6
|
1.0
|
H
|
H:ILE51
|
4.5
|
34.2
|
1.0
|
CB
|
H:TYR59
|
4.5
|
28.0
|
1.0
|
CB
|
H:ALA50
|
4.5
|
26.6
|
1.0
|
O
|
H:ILE51
|
4.6
|
29.5
|
1.0
|
H
|
H:THR58
|
4.6
|
37.7
|
1.0
|
O
|
H:THR58
|
4.8
|
31.7
|
1.0
|
O
|
H:HOH403
|
4.9
|
51.9
|
1.0
|
CA
|
H:SER57
|
4.9
|
35.2
|
1.0
|
HB2
|
H:ASN52
|
4.9
|
41.0
|
1.0
|
C2
|
H:T44301
|
4.9
|
32.2
|
1.0
|
|
Iodine binding site 4 out
of 4 in 5mhe
Go back to
Iodine Binding Sites List in 5mhe
Iodine binding site 4 out
of 4 in the Crystal Structure of Anti-T4 Fab Fragment with T4
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of Crystal Structure of Anti-T4 Fab Fragment with T4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:I301
b:31.6
occ:1.00
|
I5'
|
H:T44301
|
0.0
|
31.6
|
1.0
|
C5'
|
H:T44301
|
2.1
|
20.5
|
1.0
|
H6'
|
H:T44301
|
2.8
|
33.9
|
1.0
|
HO4'
|
H:T44301
|
3.0
|
40.7
|
1.0
|
C4'
|
H:T44301
|
3.0
|
29.7
|
1.0
|
C6'
|
H:T44301
|
3.1
|
28.2
|
1.0
|
O4'
|
H:T44301
|
3.2
|
33.9
|
1.0
|
HD2
|
H:TYR107
|
3.2
|
43.6
|
1.0
|
HB3
|
H:TYR107
|
3.3
|
39.7
|
1.0
|
CD2
|
H:TYR107
|
3.3
|
36.3
|
1.0
|
HB2
|
H:ASP100
|
3.4
|
41.2
|
1.0
|
OD2
|
H:ASP100
|
3.5
|
31.8
|
1.0
|
HE1
|
H:TYR109
|
3.6
|
36.0
|
1.0
|
CG
|
H:TYR107
|
3.6
|
39.3
|
1.0
|
CE1
|
H:TYR109
|
3.7
|
30.0
|
1.0
|
CZ
|
H:TYR33
|
3.7
|
32.4
|
1.0
|
CE1
|
H:TYR33
|
3.7
|
31.4
|
1.0
|
CE2
|
H:TYR33
|
3.8
|
37.7
|
1.0
|
CE2
|
H:TYR107
|
3.8
|
37.5
|
1.0
|
CD1
|
H:TYR33
|
3.8
|
29.2
|
1.0
|
CD2
|
H:TYR33
|
3.9
|
27.2
|
1.0
|
CZ
|
H:TYR109
|
3.9
|
29.7
|
1.0
|
CG
|
H:TYR33
|
3.9
|
29.2
|
1.0
|
CB
|
H:TYR107
|
3.9
|
33.1
|
1.0
|
HE2
|
H:TYR107
|
4.1
|
45.0
|
1.0
|
HE1
|
H:TYR33
|
4.1
|
37.6
|
1.0
|
CD1
|
H:TYR109
|
4.1
|
28.4
|
1.0
|
CB
|
H:ASP100
|
4.1
|
34.3
|
1.0
|
CG
|
H:ASP100
|
4.1
|
34.1
|
1.0
|
OH
|
H:TYR109
|
4.2
|
33.4
|
1.0
|
HE2
|
H:TYR33
|
4.2
|
45.2
|
1.0
|
OH
|
H:TYR33
|
4.3
|
39.0
|
1.0
|
HD1
|
H:TYR33
|
4.3
|
35.1
|
1.0
|
C3'
|
H:T44301
|
4.3
|
28.0
|
1.0
|
CD1
|
H:TYR107
|
4.4
|
38.7
|
1.0
|
HD1
|
H:TYR109
|
4.4
|
34.0
|
1.0
|
HB2
|
H:TYR107
|
4.4
|
39.7
|
1.0
|
HD2
|
H:TYR33
|
4.4
|
32.7
|
1.0
|
C1'
|
H:T44301
|
4.4
|
30.8
|
1.0
|
HB3
|
H:ASP100
|
4.5
|
41.2
|
1.0
|
HH
|
H:TYR33
|
4.5
|
46.8
|
0.0
|
CZ
|
H:TYR107
|
4.5
|
39.6
|
1.0
|
O
|
H:HOH403
|
4.5
|
51.9
|
1.0
|
H
|
H:ASP100
|
4.6
|
35.2
|
1.0
|
CE2
|
H:TYR109
|
4.6
|
26.4
|
1.0
|
HB2
|
H:TYR33
|
4.6
|
34.6
|
1.0
|
HH
|
H:TYR109
|
4.6
|
40.1
|
0.0
|
H
|
H:TYR109
|
4.7
|
27.9
|
1.0
|
CE1
|
H:TYR107
|
4.8
|
39.6
|
1.0
|
CB
|
H:TYR33
|
4.8
|
28.8
|
1.0
|
CG
|
H:TYR109
|
4.8
|
25.5
|
1.0
|
HB3
|
H:TYR33
|
4.8
|
34.6
|
1.0
|
HA
|
H:TYR109
|
4.8
|
33.9
|
1.0
|
C2'
|
H:T44301
|
4.8
|
25.9
|
1.0
|
HD1
|
H:TYR107
|
4.9
|
46.5
|
1.0
|
CD2
|
H:TYR109
|
5.0
|
30.2
|
1.0
|
|
Reference:
T.Parkkinen,
J.Rouvinen.
Crystal Structures of Anti-T4 Fab Fragment To Be Published.
Page generated: Sun Aug 11 21:28:56 2024
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