Iodine in PDB 5fob: Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice)
Protein crystallography data
The structure of Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice), PDB code: 5fob
was solved by
F.Forneris,
J.Wu,
X.Xue,
P.Gros,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.356 /
2.60
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.891,
83.311,
127.377,
75.03,
76.20,
68.50
|
R / Rfree (%)
|
19.8 /
22.95
|
Other elements in 5fob:
The structure of Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice) also contains other interesting chemical elements:
Iodine Binding Sites:
The binding sites of Iodine atom in the Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice)
(pdb code 5fob). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the
Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice), PDB code: 5fob:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
7;
Iodine binding site 1 out
of 7 in 5fob
Go back to
Iodine Binding Sites List in 5fob
Iodine binding site 1 out
of 7 in the Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice)
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 Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I1677
b:55.5
occ:0.72
|
NZ
|
A:LYS155
|
1.7
|
69.9
|
1.0
|
CD
|
A:LYS155
|
2.3
|
51.6
|
1.0
|
CE
|
A:LYS155
|
2.4
|
74.8
|
1.0
|
ND2
|
A:ASN153
|
3.2
|
42.4
|
1.0
|
CG
|
A:ASN153
|
3.6
|
50.9
|
1.0
|
N
|
A:GLU39
|
3.7
|
73.7
|
1.0
|
CG
|
A:LYS155
|
3.8
|
61.9
|
1.0
|
CB
|
A:ASN153
|
3.8
|
46.1
|
1.0
|
OG
|
A:SER38
|
3.8
|
1.0
|
1.0
|
CA
|
A:SER38
|
4.0
|
82.3
|
1.0
|
N
|
A:HIS154
|
4.1
|
52.0
|
1.0
|
N
|
A:LYS155
|
4.2
|
56.1
|
1.0
|
CB
|
A:SER38
|
4.3
|
88.5
|
1.0
|
C
|
A:SER38
|
4.4
|
86.6
|
1.0
|
CB
|
A:LYS155
|
4.4
|
67.7
|
1.0
|
OD1
|
A:ASN153
|
4.4
|
60.3
|
1.0
|
CB
|
A:GLU39
|
4.5
|
84.7
|
1.0
|
CB
|
A:HIS154
|
4.6
|
46.7
|
1.0
|
O
|
A:GLU37
|
4.6
|
69.4
|
1.0
|
CA
|
A:GLU39
|
4.7
|
79.5
|
1.0
|
CA
|
A:HIS154
|
4.7
|
54.6
|
1.0
|
C
|
A:HIS154
|
4.8
|
58.9
|
1.0
|
C
|
A:ASN153
|
4.9
|
51.1
|
1.0
|
CA
|
A:ASN153
|
4.9
|
45.1
|
1.0
|
CA
|
A:LYS155
|
4.9
|
58.4
|
1.0
|
ND1
|
A:HIS154
|
4.9
|
64.1
|
1.0
|
|
Iodine binding site 2 out
of 7 in 5fob
Go back to
Iodine Binding Sites List in 5fob
Iodine binding site 2 out
of 7 in the Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice)
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 Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I1678
b:65.0
occ:0.76
|
NH1
|
A:ARG304
|
3.5
|
63.9
|
1.0
|
CD1
|
A:LEU308
|
3.9
|
51.8
|
1.0
|
CG
|
A:ARG304
|
4.0
|
44.9
|
1.0
|
CA
|
A:LYS305
|
4.1
|
60.0
|
1.0
|
N
|
A:LYS305
|
4.1
|
51.3
|
1.0
|
O1
|
A:GOL1668
|
4.3
|
98.5
|
1.0
|
CB
|
A:LYS305
|
4.3
|
61.8
|
1.0
|
CD
|
A:ARG304
|
4.3
|
52.4
|
1.0
|
C
|
A:ARG304
|
4.3
|
54.4
|
1.0
|
CB
|
A:ARG304
|
4.4
|
43.9
|
1.0
|
O
|
A:ARG304
|
4.5
|
55.4
|
1.0
|
CZ
|
A:ARG304
|
4.6
|
62.0
|
1.0
|
CG
|
A:LYS305
|
4.7
|
75.7
|
1.0
|
OE1
|
A:GLU248
|
4.7
|
0.0
|
1.0
|
NE
|
A:ARG304
|
4.9
|
59.3
|
1.0
|
CG
|
A:LEU308
|
4.9
|
47.5
|
1.0
|
|
Iodine binding site 3 out
of 7 in 5fob
Go back to
Iodine Binding Sites List in 5fob
Iodine binding site 3 out
of 7 in the Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice)
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 Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I1679
b:65.1
occ:0.68
|
CG
|
A:GLN613
|
3.8
|
47.0
|
1.0
|
CB
|
A:GLN613
|
3.8
|
36.1
|
1.0
|
CB
|
A:ASP557
|
3.8
|
65.7
|
1.0
|
CD1
|
A:TRP617
|
3.8
|
60.8
|
1.0
|
O
|
A:HOH2092
|
3.8
|
50.3
|
1.0
|
N
|
A:SER558
|
3.9
|
60.7
|
1.0
|
N
|
A:SER614
|
4.0
|
43.3
|
1.0
|
C
|
A:ASP557
|
4.0
|
61.1
|
1.0
|
NE1
|
A:TRP617
|
4.0
|
64.3
|
1.0
|
CA
|
A:SER558
|
4.1
|
61.7
|
1.0
|
O
|
A:ASP557
|
4.2
|
57.7
|
1.0
|
C
|
A:GLN613
|
4.3
|
48.7
|
1.0
|
CA
|
A:SER614
|
4.3
|
46.7
|
1.0
|
CB
|
A:SER614
|
4.5
|
41.7
|
1.0
|
CA
|
A:ASP557
|
4.6
|
63.7
|
1.0
|
C
|
A:SER558
|
4.6
|
61.4
|
1.0
|
CA
|
A:GLN613
|
4.7
|
41.0
|
1.0
|
O
|
A:GLN613
|
4.7
|
59.0
|
1.0
|
O
|
A:SER558
|
4.9
|
71.1
|
1.0
|
CG
|
A:ASP557
|
5.0
|
71.4
|
1.0
|
|
Iodine binding site 4 out
of 7 in 5fob
Go back to
Iodine Binding Sites List in 5fob
Iodine binding site 4 out
of 7 in the Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice)
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 Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I2678
b:83.1
occ:0.79
|
CG
|
B:GLU1032
|
3.0
|
0.0
|
1.0
|
CA
|
B:GLU1032
|
3.4
|
0.3
|
1.0
|
CB
|
B:GLU1032
|
3.6
|
0.5
|
1.0
|
C
|
B:GLU1032
|
3.6
|
0.0
|
1.0
|
O
|
B:GLU1032
|
3.6
|
0.7
|
1.0
|
CE1
|
A:PHE62
|
3.6
|
92.5
|
1.0
|
CB
|
B:TRP1034
|
3.8
|
95.8
|
1.0
|
CD1
|
B:TRP1034
|
3.9
|
88.3
|
1.0
|
N
|
B:TRP1034
|
4.1
|
96.6
|
1.0
|
CD1
|
A:PHE62
|
4.1
|
81.1
|
1.0
|
CD
|
A:PRO63
|
4.2
|
85.7
|
1.0
|
CG
|
B:TRP1034
|
4.3
|
90.5
|
1.0
|
CD
|
B:GLU1032
|
4.3
|
0.6
|
1.0
|
N
|
B:GLN1033
|
4.4
|
94.9
|
1.0
|
CG
|
A:PRO63
|
4.5
|
88.5
|
1.0
|
OE2
|
B:GLU1032
|
4.5
|
0.9
|
1.0
|
CA
|
B:TRP1034
|
4.5
|
96.8
|
1.0
|
CZ
|
A:PHE62
|
4.6
|
89.7
|
1.0
|
N
|
B:GLU1032
|
4.7
|
0.2
|
1.0
|
CD2
|
A:PHE105
|
4.8
|
90.8
|
1.0
|
|
Iodine binding site 5 out
of 7 in 5fob
Go back to
Iodine Binding Sites List in 5fob
Iodine binding site 5 out
of 7 in the Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice)
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I2679
b:67.4
occ:0.62
|
O
|
B:HOH2007
|
2.2
|
28.9
|
1.0
|
ND2
|
B:ASN760
|
2.4
|
95.8
|
1.0
|
CG
|
B:ASN760
|
3.6
|
79.9
|
1.0
|
N
|
B:ALA757
|
3.7
|
55.9
|
1.0
|
CE
|
C:LYS60
|
3.7
|
73.8
|
1.0
|
O
|
B:HOH2005
|
3.9
|
37.4
|
1.0
|
O
|
B:HOH2006
|
4.0
|
53.3
|
1.0
|
CB
|
B:ASN760
|
4.0
|
68.1
|
1.0
|
CA
|
B:ILE756
|
4.2
|
62.3
|
1.0
|
CB
|
B:ALA757
|
4.3
|
59.5
|
1.0
|
CG2
|
B:ILE756
|
4.3
|
51.6
|
1.0
|
CG
|
C:LYS60
|
4.4
|
62.3
|
1.0
|
C
|
B:ILE756
|
4.4
|
61.2
|
1.0
|
NZ
|
C:LYS60
|
4.5
|
89.5
|
1.0
|
CA
|
B:ALA757
|
4.6
|
57.5
|
1.0
|
OD1
|
B:ASN760
|
4.6
|
75.0
|
1.0
|
CD
|
C:LYS60
|
4.6
|
58.0
|
1.0
|
CB
|
B:ILE756
|
4.6
|
59.4
|
1.0
|
CG1
|
B:ILE756
|
4.8
|
60.6
|
1.0
|
|
Iodine binding site 6 out
of 7 in 5fob
Go back to
Iodine Binding Sites List in 5fob
Iodine binding site 6 out
of 7 in the Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice)
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I2680
b:68.1
occ:0.68
|
NZ
|
B:LYS1139
|
1.9
|
89.9
|
1.0
|
CE
|
B:LYS1139
|
2.6
|
90.5
|
1.0
|
O
|
B:HOH2058
|
3.0
|
51.1
|
1.0
|
O
|
B:HOH2054
|
3.0
|
35.3
|
1.0
|
CD2
|
B:LEU1133
|
4.0
|
49.5
|
1.0
|
CD
|
B:LYS1139
|
4.0
|
86.9
|
1.0
|
CB
|
B:GLU1120
|
4.2
|
49.4
|
1.0
|
CG
|
B:GLU1120
|
4.2
|
51.2
|
1.0
|
CB
|
B:TRP1077
|
4.2
|
46.7
|
1.0
|
OE2
|
B:GLU1120
|
4.3
|
65.0
|
1.0
|
CD1
|
B:LEU1143
|
4.4
|
40.6
|
1.0
|
CD1
|
B:ILE1130
|
4.4
|
46.2
|
1.0
|
CD2
|
B:LEU1143
|
4.4
|
45.3
|
1.0
|
CD1
|
B:TRP1077
|
4.5
|
40.4
|
1.0
|
CG
|
B:TRP1077
|
4.6
|
55.3
|
1.0
|
CD
|
B:GLU1120
|
4.7
|
63.4
|
1.0
|
CG
|
B:LEU1143
|
4.9
|
53.8
|
1.0
|
CG
|
B:LEU1133
|
5.0
|
57.0
|
1.0
|
|
Iodine binding site 7 out
of 7 in 5fob
Go back to
Iodine Binding Sites List in 5fob
Iodine binding site 7 out
of 7 in the Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice)
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 7 of Crystal Structure of Human Complement C3B in Complex with Smallpox Inhibitor of Complement (Spice) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I2681
b:75.4
occ:0.82
|
CD
|
B:LYS1105
|
3.4
|
74.8
|
1.0
|
N
|
B:ASN1163
|
3.4
|
75.3
|
1.0
|
OG
|
B:SER1164
|
3.8
|
60.7
|
1.0
|
N
|
B:SER1164
|
3.8
|
64.7
|
1.0
|
CG
|
B:LYS1105
|
3.9
|
67.5
|
1.0
|
OD1
|
B:ASN1163
|
3.9
|
85.8
|
1.0
|
CG1
|
B:VAL1162
|
4.1
|
64.1
|
1.0
|
CA
|
B:VAL1162
|
4.1
|
74.2
|
1.0
|
CB
|
B:ASN1163
|
4.1
|
87.8
|
1.0
|
C
|
B:VAL1162
|
4.2
|
75.4
|
1.0
|
CA
|
B:ASN1163
|
4.2
|
79.3
|
1.0
|
CB
|
B:SER1164
|
4.3
|
61.1
|
1.0
|
CE
|
B:LYS1105
|
4.4
|
82.7
|
1.0
|
C
|
B:ASN1163
|
4.5
|
70.7
|
1.0
|
CG
|
B:ASN1163
|
4.5
|
93.7
|
1.0
|
O
|
B:GLN1161
|
4.6
|
84.5
|
1.0
|
CD1
|
B:LEU1109
|
4.7
|
63.2
|
1.0
|
CB
|
B:VAL1162
|
4.7
|
71.8
|
1.0
|
CA
|
B:SER1164
|
4.7
|
62.5
|
1.0
|
NZ
|
B:LYS1105
|
5.0
|
91.8
|
1.0
|
|
Reference:
F.Forneris,
J.Wu,
X.Xue,
D.Ricklin,
Z.Lin,
G.Sfyroera,
A.Tzekou,
E.Volokhina,
J.C.Granneman,
R.Hauhart,
P.Bertram,
M.K.Liszewski,
J.P.Atkinson,
J.D.Lambris,
P.Gros.
Regulators of Complement Activity Mediate Inhibitory Mechanisms Through A Common C3B-Binding Mode. Embo J. V. 35 1133 2016.
ISSN: ISSN 0261-4189
PubMed: 27013439
DOI: 10.15252/EMBJ.201593673
Page generated: Sun Aug 11 20:58:05 2024
|