Fluorine in PDB 3v4v: Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376
Protein crystallography data
The structure of Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376, PDB code: 3v4v
was solved by
Y.Yu,
J.Zhu,
T.A.Springer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
3.10
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
127.580,
123.530,
154.160,
90.00,
112.63,
90.00
|
R / Rfree (%)
|
19.7 /
23.1
|
Other elements in 3v4v:
The structure of Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376
(pdb code 3v4v). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376, PDB code: 3v4v:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 3v4v
Go back to
Fluorine Binding Sites List in 3v4v
Fluorine binding site 1 out
of 6 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376
![](/pictures/F/pdb/v4/3v4v-F-sphere_01.jpg) Mono view
![](/pictures/F/pdb/v4/3v4v-F-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F4000
b:96.8
occ:1.00
|
F06
|
B:0DU4000
|
0.0
|
96.8
|
1.0
|
C05
|
B:0DU4000
|
1.3
|
0.3
|
1.0
|
F08
|
B:0DU4000
|
2.1
|
0.2
|
1.0
|
F07
|
B:0DU4000
|
2.2
|
0.1
|
1.0
|
C04
|
B:0DU4000
|
2.2
|
81.5
|
1.0
|
C09
|
B:0DU4000
|
3.1
|
63.4
|
1.0
|
C03
|
B:0DU4000
|
3.2
|
0.7
|
1.0
|
CE1
|
A:TYR187
|
3.2
|
85.9
|
1.0
|
C10
|
B:0DU4000
|
3.4
|
69.7
|
1.0
|
CL1
|
B:0DU4000
|
3.4
|
0.0
|
1.0
|
C31
|
B:0DU4000
|
3.6
|
98.1
|
1.0
|
OH
|
A:TYR187
|
3.6
|
87.8
|
1.0
|
CZ
|
A:TYR187
|
3.7
|
0.9
|
1.0
|
CD1
|
A:TYR187
|
4.1
|
83.6
|
1.0
|
C11
|
B:0DU4000
|
4.2
|
51.6
|
1.0
|
C32
|
B:0DU4000
|
4.3
|
0.6
|
1.0
|
C02
|
B:0DU4000
|
4.4
|
88.6
|
1.0
|
C30
|
B:0DU4000
|
4.6
|
58.9
|
1.0
|
N34
|
B:0DU4000
|
4.8
|
63.1
|
1.0
|
CE2
|
A:TYR187
|
4.9
|
0.6
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 3v4v
Go back to
Fluorine Binding Sites List in 3v4v
Fluorine binding site 2 out
of 6 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376
![](/pictures/F/pdb/v4/3v4v-F-sphere_02.jpg) Mono view
![](/pictures/F/pdb/v4/3v4v-F-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F4000
b:0.1
occ:1.00
|
F07
|
B:0DU4000
|
0.0
|
0.1
|
1.0
|
C05
|
B:0DU4000
|
1.4
|
0.3
|
1.0
|
F08
|
B:0DU4000
|
2.2
|
0.2
|
1.0
|
F06
|
B:0DU4000
|
2.2
|
96.8
|
1.0
|
C04
|
B:0DU4000
|
2.3
|
81.5
|
1.0
|
C09
|
B:0DU4000
|
2.9
|
63.4
|
1.0
|
C10
|
B:0DU4000
|
2.9
|
69.7
|
1.0
|
C11
|
B:0DU4000
|
3.0
|
51.6
|
1.0
|
CL1
|
B:0DU4000
|
3.4
|
0.0
|
1.0
|
C03
|
B:0DU4000
|
3.5
|
0.7
|
1.0
|
C31
|
B:0DU4000
|
3.8
|
98.1
|
1.0
|
C12
|
B:0DU4000
|
3.9
|
96.9
|
1.0
|
C32
|
B:0DU4000
|
4.3
|
0.6
|
1.0
|
C30
|
B:0DU4000
|
4.5
|
58.9
|
1.0
|
C13
|
B:0DU4000
|
4.5
|
65.1
|
1.0
|
C02
|
B:0DU4000
|
4.7
|
88.6
|
1.0
|
O18
|
B:0DU4000
|
4.8
|
90.7
|
1.0
|
N34
|
B:0DU4000
|
5.0
|
63.1
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 3v4v
Go back to
Fluorine Binding Sites List in 3v4v
Fluorine binding site 3 out
of 6 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376
![](/pictures/F/pdb/v4/3v4v-F-sphere_03.jpg) Mono view
![](/pictures/F/pdb/v4/3v4v-F-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F4000
b:0.2
occ:1.00
|
F08
|
B:0DU4000
|
0.0
|
0.2
|
1.0
|
C05
|
B:0DU4000
|
1.3
|
0.3
|
1.0
|
F06
|
B:0DU4000
|
2.1
|
96.8
|
1.0
|
F07
|
B:0DU4000
|
2.2
|
0.1
|
1.0
|
C04
|
B:0DU4000
|
2.2
|
81.5
|
1.0
|
C03
|
B:0DU4000
|
2.6
|
0.7
|
1.0
|
C09
|
B:0DU4000
|
3.6
|
63.4
|
1.0
|
OH
|
A:TYR187
|
3.6
|
87.8
|
1.0
|
C02
|
B:0DU4000
|
3.9
|
88.6
|
1.0
|
CZ
|
A:TYR187
|
4.0
|
0.9
|
1.0
|
CE1
|
A:TYR187
|
4.2
|
85.9
|
1.0
|
C10
|
B:0DU4000
|
4.3
|
69.7
|
1.0
|
C32
|
B:0DU4000
|
4.6
|
0.6
|
1.0
|
C01
|
B:0DU4000
|
4.7
|
46.7
|
1.0
|
N34
|
B:0DU4000
|
4.8
|
63.1
|
1.0
|
CL1
|
B:0DU4000
|
4.8
|
0.0
|
1.0
|
C11
|
B:0DU4000
|
4.8
|
51.6
|
1.0
|
CE2
|
A:TYR187
|
4.9
|
0.6
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 3v4v
Go back to
Fluorine Binding Sites List in 3v4v
Fluorine binding site 4 out
of 6 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376
![](/pictures/F/pdb/v4/3v4v-F-sphere_04.jpg) Mono view
![](/pictures/F/pdb/v4/3v4v-F-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F4000
b:0.7
occ:1.00
|
F06
|
D:0DU4000
|
0.0
|
0.7
|
1.0
|
C05
|
D:0DU4000
|
1.3
|
0.3
|
1.0
|
F08
|
D:0DU4000
|
2.1
|
0.3
|
1.0
|
F07
|
D:0DU4000
|
2.2
|
0.3
|
1.0
|
C04
|
D:0DU4000
|
2.2
|
0.1
|
1.0
|
C09
|
D:0DU4000
|
3.0
|
92.7
|
1.0
|
C03
|
D:0DU4000
|
3.2
|
83.5
|
1.0
|
C11
|
D:0DU4000
|
3.2
|
97.9
|
1.0
|
C10
|
D:0DU4000
|
3.3
|
71.5
|
1.0
|
C12
|
D:0DU4000
|
4.2
|
70.1
|
1.0
|
C32
|
D:0DU4000
|
4.3
|
70.7
|
1.0
|
C31
|
D:0DU4000
|
4.3
|
77.0
|
1.0
|
C02
|
D:0DU4000
|
4.4
|
86.1
|
1.0
|
N34
|
D:0DU4000
|
4.8
|
86.1
|
1.0
|
CL1
|
D:0DU4000
|
5.0
|
0.7
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 3v4v
Go back to
Fluorine Binding Sites List in 3v4v
Fluorine binding site 5 out
of 6 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376
![](/pictures/F/pdb/v4/3v4v-F-sphere_05.jpg) Mono view
![](/pictures/F/pdb/v4/3v4v-F-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F4000
b:0.3
occ:1.00
|
F07
|
D:0DU4000
|
0.0
|
0.3
|
1.0
|
C05
|
D:0DU4000
|
1.4
|
0.3
|
1.0
|
F08
|
D:0DU4000
|
2.2
|
0.3
|
1.0
|
F06
|
D:0DU4000
|
2.2
|
0.7
|
1.0
|
C04
|
D:0DU4000
|
2.3
|
0.1
|
1.0
|
C03
|
D:0DU4000
|
2.6
|
83.5
|
1.0
|
OH
|
C:TYR187
|
3.5
|
91.6
|
1.0
|
C09
|
D:0DU4000
|
3.6
|
92.7
|
1.0
|
CZ
|
C:TYR187
|
4.0
|
0.8
|
1.0
|
C02
|
D:0DU4000
|
4.0
|
86.1
|
1.0
|
CE1
|
C:TYR187
|
4.2
|
92.5
|
1.0
|
C10
|
D:0DU4000
|
4.4
|
71.5
|
1.0
|
C32
|
D:0DU4000
|
4.7
|
70.7
|
1.0
|
C01
|
D:0DU4000
|
4.8
|
94.6
|
1.0
|
N34
|
D:0DU4000
|
4.8
|
86.1
|
1.0
|
CE2
|
C:TYR187
|
4.8
|
0.5
|
1.0
|
C11
|
D:0DU4000
|
4.9
|
97.9
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 3v4v
Go back to
Fluorine Binding Sites List in 3v4v
Fluorine binding site 6 out
of 6 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376
![](/pictures/F/pdb/v4/3v4v-F-sphere_06.jpg) Mono view
![](/pictures/F/pdb/v4/3v4v-F-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F4000
b:0.3
occ:1.00
|
F08
|
D:0DU4000
|
0.0
|
0.3
|
1.0
|
C05
|
D:0DU4000
|
1.3
|
0.3
|
1.0
|
F06
|
D:0DU4000
|
2.1
|
0.7
|
1.0
|
F07
|
D:0DU4000
|
2.2
|
0.3
|
1.0
|
C04
|
D:0DU4000
|
2.3
|
0.1
|
1.0
|
C09
|
D:0DU4000
|
2.9
|
92.7
|
1.0
|
C10
|
D:0DU4000
|
2.9
|
71.5
|
1.0
|
C31
|
D:0DU4000
|
3.3
|
77.0
|
1.0
|
CL1
|
D:0DU4000
|
3.3
|
0.7
|
1.0
|
C03
|
D:0DU4000
|
3.4
|
83.5
|
1.0
|
C11
|
D:0DU4000
|
3.5
|
97.9
|
1.0
|
C30
|
D:0DU4000
|
4.1
|
0.7
|
1.0
|
CE1
|
C:TYR187
|
4.1
|
92.5
|
1.0
|
C32
|
D:0DU4000
|
4.2
|
70.7
|
1.0
|
C12
|
D:0DU4000
|
4.3
|
70.1
|
1.0
|
OH
|
C:TYR187
|
4.4
|
91.6
|
1.0
|
C13
|
D:0DU4000
|
4.6
|
0.2
|
1.0
|
C02
|
D:0DU4000
|
4.6
|
86.1
|
1.0
|
CZ
|
C:TYR187
|
4.6
|
0.8
|
1.0
|
N34
|
D:0DU4000
|
4.9
|
86.1
|
1.0
|
O18
|
D:0DU4000
|
4.9
|
84.5
|
1.0
|
C20
|
D:0DU4000
|
4.9
|
0.5
|
1.0
|
CD1
|
C:TYR187
|
5.0
|
85.1
|
1.0
|
|
Reference:
Y.Yu,
J.Zhu,
L.Z.Mi,
T.Walz,
H.Sun,
J.Chen,
T.A.Springer.
Structural Specializations of A4B7, An Integrin That Mediates Rolling Adhesion J.Cell Biol. V. 196 131 2012.
ISSN: ISSN 0021-9525
PubMed: 22232704
DOI: 10.1083/JCB.201110023
Page generated: Wed Jul 31 23:12:48 2024
|