Iodine in PDB 5mhg: Crystal Structure of Anti-T4 Fab Fragment with Tetraiodobpa
Protein crystallography data
The structure of Crystal Structure of Anti-T4 Fab Fragment with Tetraiodobpa, PDB code: 5mhg
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)
|
20.09 /
2.80
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
131.767,
56.992,
61.993,
90.00,
98.39,
90.00
|
R / Rfree (%)
|
22.1 /
29.1
|
Iodine Binding Sites:
The binding sites of Iodine atom in the Crystal Structure of Anti-T4 Fab Fragment with Tetraiodobpa
(pdb code 5mhg). 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 Tetraiodobpa, PDB code: 5mhg:
Jump to Iodine binding site number:
1;
2;
3;
4;
Iodine binding site 1 out
of 4 in 5mhg
Go back to
Iodine Binding Sites List in 5mhg
Iodine binding site 1 out
of 4 in the Crystal Structure of Anti-T4 Fab Fragment with Tetraiodobpa
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 Tetraiodobpa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:I301
b:0.5
occ:1.00
|
I1
|
H:4IB301
|
0.0
|
0.5
|
1.0
|
C14
|
H:4IB301
|
2.1
|
78.0
|
1.0
|
C13
|
H:4IB301
|
3.0
|
80.9
|
1.0
|
H9
|
H:4IB301
|
3.0
|
97.0
|
1.0
|
C11
|
H:4IB301
|
3.1
|
71.7
|
1.0
|
H10
|
H:4IB301
|
3.2
|
94.3
|
1.0
|
O1
|
H:4IB301
|
3.2
|
78.6
|
1.0
|
CE2
|
L:TYR93
|
4.1
|
67.4
|
1.0
|
CD2
|
L:TYR93
|
4.3
|
71.8
|
1.0
|
C10
|
H:4IB301
|
4.4
|
72.1
|
1.0
|
C15
|
H:4IB301
|
4.4
|
71.3
|
1.0
|
CD1
|
H:TYR59
|
4.6
|
48.8
|
1.0
|
C12
|
H:4IB301
|
4.9
|
68.6
|
1.0
|
|
Iodine binding site 2 out
of 4 in 5mhg
Go back to
Iodine Binding Sites List in 5mhg
Iodine binding site 2 out
of 4 in the Crystal Structure of Anti-T4 Fab Fragment with Tetraiodobpa
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 Tetraiodobpa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:I301
b:81.2
occ:1.00
|
I2
|
H:4IB301
|
0.0
|
81.2
|
1.0
|
C15
|
H:4IB301
|
2.1
|
71.3
|
1.0
|
C12
|
H:4IB301
|
3.0
|
68.6
|
1.0
|
H11
|
H:4IB301
|
3.1
|
82.3
|
1.0
|
C11
|
H:4IB301
|
3.1
|
71.7
|
1.0
|
O1
|
H:4IB301
|
3.2
|
78.6
|
1.0
|
O
|
H:SER57
|
3.3
|
61.1
|
1.0
|
C
|
H:SER57
|
3.5
|
68.3
|
1.0
|
H10
|
H:4IB301
|
3.7
|
94.3
|
1.0
|
N
|
H:ASN52
|
3.7
|
62.1
|
1.0
|
CA
|
H:THR58
|
3.7
|
53.4
|
1.0
|
N
|
H:THR58
|
3.8
|
63.1
|
1.0
|
C
|
H:ILE51
|
3.8
|
60.6
|
1.0
|
O
|
H:ALA50
|
3.9
|
43.5
|
1.0
|
CA
|
H:ILE51
|
3.9
|
54.0
|
1.0
|
CB
|
H:SER57
|
4.0
|
72.5
|
1.0
|
C
|
H:THR58
|
4.0
|
53.5
|
1.0
|
CB
|
H:ASN52
|
4.0
|
63.5
|
1.0
|
C
|
H:ALA50
|
4.2
|
47.6
|
1.0
|
N
|
H:ILE51
|
4.2
|
53.7
|
1.0
|
CA
|
H:ASN52
|
4.3
|
62.4
|
1.0
|
N
|
H:TYR59
|
4.3
|
47.4
|
1.0
|
CE1
|
H:TYR33
|
4.3
|
69.3
|
1.0
|
C14
|
H:4IB301
|
4.4
|
78.0
|
1.0
|
C10
|
H:4IB301
|
4.4
|
72.1
|
1.0
|
CA
|
H:SER57
|
4.4
|
75.8
|
1.0
|
O
|
H:ILE51
|
4.4
|
57.2
|
1.0
|
CD1
|
H:TYR33
|
4.5
|
69.8
|
1.0
|
O
|
H:THR58
|
4.6
|
52.2
|
1.0
|
CG
|
H:ASN52
|
4.6
|
63.9
|
1.0
|
CB
|
H:TYR59
|
4.8
|
54.2
|
1.0
|
OD1
|
H:ASN52
|
4.9
|
69.6
|
1.0
|
C13
|
H:4IB301
|
4.9
|
80.9
|
1.0
|
|
Iodine binding site 3 out
of 4 in 5mhg
Go back to
Iodine Binding Sites List in 5mhg
Iodine binding site 3 out
of 4 in the Crystal Structure of Anti-T4 Fab Fragment with Tetraiodobpa
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 Tetraiodobpa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:I301
b:97.6
occ:1.00
|
I3
|
H:4IB301
|
0.0
|
97.6
|
1.0
|
C2
|
H:4IB301
|
2.1
|
83.4
|
1.0
|
C6
|
H:4IB301
|
3.0
|
74.2
|
1.0
|
H1
|
H:4IB301
|
3.0
|
89.0
|
1.0
|
C5
|
H:4IB301
|
3.1
|
80.6
|
1.0
|
O2
|
H:4IB301
|
3.2
|
74.2
|
1.0
|
H12
|
H:4IB301
|
3.5
|
89.0
|
1.0
|
CG
|
H:MET111
|
3.7
|
48.6
|
1.0
|
OG
|
H:SER35
|
3.9
|
52.7
|
1.0
|
CA
|
H:GLY99
|
4.0
|
58.6
|
1.0
|
SD
|
H:MET111
|
4.1
|
72.2
|
1.0
|
O
|
H:ALA110
|
4.3
|
51.7
|
1.0
|
C3
|
H:4IB301
|
4.4
|
64.5
|
1.0
|
C4
|
H:4IB301
|
4.4
|
81.1
|
1.0
|
CB
|
H:SER35
|
4.5
|
54.1
|
1.0
|
C
|
H:TYR109
|
4.5
|
66.2
|
1.0
|
O
|
H:TYR109
|
4.6
|
60.6
|
1.0
|
C
|
H:ALA110
|
4.7
|
54.5
|
1.0
|
CD1
|
L:LEU95
|
4.8
|
46.9
|
1.0
|
CE
|
H:MET111
|
4.8
|
49.9
|
1.0
|
N
|
H:GLY99
|
4.8
|
57.3
|
1.0
|
N
|
H:ALA110
|
4.8
|
67.0
|
1.0
|
CA
|
H:TYR109
|
4.8
|
60.6
|
1.0
|
C1
|
H:4IB301
|
4.9
|
75.8
|
1.0
|
|
Iodine binding site 4 out
of 4 in 5mhg
Go back to
Iodine Binding Sites List in 5mhg
Iodine binding site 4 out
of 4 in the Crystal Structure of Anti-T4 Fab Fragment with Tetraiodobpa
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 Tetraiodobpa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:I301
b:84.5
occ:1.00
|
I4
|
H:4IB301
|
0.0
|
84.5
|
1.0
|
C4
|
H:4IB301
|
2.1
|
81.1
|
1.0
|
C1
|
H:4IB301
|
3.0
|
75.8
|
1.0
|
C5
|
H:4IB301
|
3.1
|
80.6
|
1.0
|
H2
|
H:4IB301
|
3.1
|
91.0
|
1.0
|
O2
|
H:4IB301
|
3.2
|
74.2
|
1.0
|
H12
|
H:4IB301
|
3.4
|
89.0
|
1.0
|
CD2
|
H:TYR107
|
3.5
|
70.1
|
1.0
|
CG
|
H:TYR107
|
3.6
|
75.8
|
1.0
|
OD2
|
H:ASP100
|
3.8
|
66.2
|
1.0
|
CE2
|
H:TYR107
|
3.9
|
69.2
|
1.0
|
CE1
|
H:TYR109
|
4.0
|
68.7
|
1.0
|
CB
|
H:TYR107
|
4.0
|
75.8
|
1.0
|
CD1
|
H:TYR33
|
4.0
|
69.8
|
1.0
|
CE1
|
H:TYR33
|
4.0
|
69.3
|
1.0
|
CG
|
H:TYR33
|
4.1
|
66.2
|
1.0
|
CZ
|
H:TYR33
|
4.1
|
75.6
|
1.0
|
CD1
|
H:TYR107
|
4.2
|
74.0
|
1.0
|
CD1
|
H:TYR109
|
4.2
|
64.2
|
1.0
|
CD2
|
H:TYR33
|
4.2
|
68.4
|
1.0
|
CE2
|
H:TYR33
|
4.2
|
71.2
|
1.0
|
C2
|
H:4IB301
|
4.4
|
83.4
|
1.0
|
C3
|
H:4IB301
|
4.4
|
64.5
|
1.0
|
CB
|
H:ASP100
|
4.4
|
70.0
|
1.0
|
CZ
|
H:TYR107
|
4.4
|
70.7
|
1.0
|
CG
|
H:ASP100
|
4.5
|
69.3
|
1.0
|
CE1
|
H:TYR107
|
4.5
|
67.6
|
1.0
|
CZ
|
H:TYR109
|
4.7
|
65.6
|
1.0
|
OH
|
H:TYR33
|
4.8
|
73.3
|
1.0
|
CB
|
H:TYR33
|
4.8
|
63.7
|
1.0
|
C6
|
H:4IB301
|
4.9
|
74.2
|
1.0
|
|
Reference:
T.Parkkinen,
J.Rouvinen.
Crystal Structures of Anti-T4 Fab Fragment To Be Published.
Page generated: Sun Aug 11 21:29:42 2024
|