Chlorine in PDB 6ndf: Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium
Protein crystallography data
The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium, PDB code: 6ndf
was solved by
J.Stetefeld,
M.D.Mcdougall,
P.C.Loewen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.50 /
3.05
|
Space group
|
P 41
|
Cell size a, b, c (Å), α, β, γ (°)
|
132.395,
132.395,
252.991,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
25.7 /
31.7
|
Other elements in 6ndf:
The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium
(pdb code 6ndf). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the
Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium, PDB code: 6ndf:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Chlorine binding site 1 out
of 9 in 6ndf
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Chlorine Binding Sites List in 6ndf
Chlorine binding site 1 out
of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl403
b:82.1
occ:1.00
|
NH2
|
C:ARG339
|
2.9
|
0.4
|
1.0
|
NH2
|
O:ARG339
|
3.9
|
0.3
|
1.0
|
CZ
|
C:ARG339
|
4.2
|
0.8
|
1.0
|
NE
|
C:ARG339
|
4.8
|
0.2
|
1.0
|
CZ
|
O:ARG339
|
4.8
|
0.5
|
1.0
|
|
Chlorine binding site 2 out
of 9 in 6ndf
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Chlorine Binding Sites List in 6ndf
Chlorine binding site 2 out
of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cl202
b:73.5
occ:1.00
|
N
|
E:LYS59
|
3.2
|
72.0
|
1.0
|
N
|
E:TYR60
|
3.7
|
80.5
|
1.0
|
CA
|
E:LEU58
|
3.8
|
74.0
|
1.0
|
CB
|
E:LYS59
|
3.9
|
94.5
|
1.0
|
C
|
E:LEU58
|
4.0
|
65.7
|
1.0
|
CA
|
E:LYS59
|
4.0
|
85.5
|
1.0
|
CD2
|
E:LEU58
|
4.0
|
72.2
|
1.0
|
OD1
|
F:ASP321
|
4.0
|
77.6
|
1.0
|
CB
|
E:LEU58
|
4.3
|
82.4
|
1.0
|
CD2
|
E:TYR60
|
4.3
|
83.3
|
1.0
|
C
|
E:LYS59
|
4.4
|
88.0
|
1.0
|
CB
|
E:TYR60
|
4.7
|
68.5
|
1.0
|
CA
|
E:TYR60
|
4.7
|
67.5
|
1.0
|
O
|
E:TYR60
|
4.7
|
71.1
|
1.0
|
CG
|
E:LEU58
|
4.8
|
75.1
|
1.0
|
O
|
E:THR57
|
5.0
|
67.2
|
1.0
|
CG
|
E:TYR60
|
5.0
|
71.5
|
1.0
|
|
Chlorine binding site 3 out
of 9 in 6ndf
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Chlorine Binding Sites List in 6ndf
Chlorine binding site 3 out
of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cl201
b:75.8
occ:1.00
|
N
|
G:GLY7
|
3.4
|
89.9
|
1.0
|
NH2
|
C:ARG260
|
3.5
|
0.7
|
1.0
|
CA
|
G:GLY7
|
3.6
|
86.3
|
1.0
|
NH1
|
C:ARG260
|
3.9
|
79.2
|
1.0
|
CZ
|
C:ARG260
|
4.2
|
87.8
|
1.0
|
CE
|
C:LYS261
|
4.2
|
73.2
|
1.0
|
C
|
G:GLY7
|
4.3
|
92.8
|
1.0
|
O
|
G:TRP8
|
4.5
|
46.1
|
1.0
|
C
|
G:PRO6
|
4.6
|
94.5
|
1.0
|
O
|
G:GLY7
|
4.6
|
99.0
|
1.0
|
NZ
|
C:LYS261
|
4.9
|
86.0
|
1.0
|
N
|
G:TRP8
|
5.0
|
72.0
|
1.0
|
|
Chlorine binding site 4 out
of 9 in 6ndf
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Chlorine Binding Sites List in 6ndf
Chlorine binding site 4 out
of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Cl201
b:77.4
occ:1.00
|
N
|
H:LYS59
|
3.1
|
76.7
|
1.0
|
N
|
H:TYR60
|
3.6
|
69.8
|
1.0
|
CA
|
H:LEU58
|
3.8
|
69.7
|
1.0
|
OD2
|
I:ASP321
|
3.9
|
71.7
|
1.0
|
CB
|
H:LYS59
|
3.9
|
88.1
|
1.0
|
C
|
H:LEU58
|
3.9
|
68.3
|
1.0
|
CA
|
H:LYS59
|
3.9
|
80.3
|
1.0
|
CD2
|
H:LEU58
|
4.0
|
76.5
|
1.0
|
CB
|
H:LEU58
|
4.2
|
76.7
|
1.0
|
CD2
|
H:TYR60
|
4.2
|
78.4
|
1.0
|
C
|
H:LYS59
|
4.3
|
82.3
|
1.0
|
CA
|
H:TYR60
|
4.6
|
62.5
|
1.0
|
CB
|
H:TYR60
|
4.6
|
66.7
|
1.0
|
O
|
H:TYR60
|
4.6
|
58.0
|
1.0
|
OG
|
H:SER17
|
4.7
|
76.7
|
1.0
|
CG
|
H:LEU58
|
4.7
|
73.0
|
1.0
|
CG
|
I:ASP321
|
4.8
|
79.8
|
1.0
|
CG
|
H:TYR60
|
4.9
|
68.0
|
1.0
|
OD1
|
I:ASP321
|
4.9
|
89.4
|
1.0
|
C
|
H:TYR60
|
5.0
|
59.6
|
1.0
|
CG
|
H:LYS59
|
5.0
|
89.0
|
1.0
|
|
Chlorine binding site 5 out
of 9 in 6ndf
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Chlorine Binding Sites List in 6ndf
Chlorine binding site 5 out
of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Cl202
b:87.1
occ:1.00
|
NH2
|
J:ARG73
|
3.6
|
0.1
|
1.0
|
CD
|
J:ARG75
|
3.8
|
99.1
|
1.0
|
NH1
|
J:ARG75
|
3.9
|
0.2
|
1.0
|
NE
|
J:ARG75
|
4.4
|
91.8
|
1.0
|
CZ
|
J:ARG75
|
4.5
|
0.1
|
1.0
|
CG
|
J:ARG75
|
4.6
|
93.4
|
1.0
|
CZ
|
J:ARG73
|
4.9
|
0.3
|
1.0
|
CB
|
J:ARG75
|
4.9
|
90.7
|
1.0
|
|
Chlorine binding site 6 out
of 9 in 6ndf
Go back to
Chlorine Binding Sites List in 6ndf
Chlorine binding site 6 out
of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Cl201
b:92.2
occ:1.00
|
NH2
|
K:ARG14
|
3.1
|
0.1
|
1.0
|
NH1
|
K:ARG14
|
3.7
|
1.0
|
1.0
|
CZ
|
K:ARG14
|
3.9
|
0.8
|
1.0
|
|
Chlorine binding site 7 out
of 9 in 6ndf
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Chlorine Binding Sites List in 6ndf
Chlorine binding site 7 out
of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Cl403
b:77.6
occ:1.00
|
NH2
|
L:ARG260
|
3.7
|
1.0
|
1.0
|
NH1
|
L:ARG260
|
3.9
|
81.1
|
1.0
|
CZ
|
L:ARG260
|
4.3
|
94.8
|
1.0
|
CE
|
L:LYS261
|
4.4
|
76.7
|
1.0
|
NZ
|
L:LYS261
|
5.0
|
91.9
|
1.0
|
|
Chlorine binding site 8 out
of 9 in 6ndf
Go back to
Chlorine Binding Sites List in 6ndf
Chlorine binding site 8 out
of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 8 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Cl201
b:71.4
occ:1.00
|
NE2
|
M:GLN102
|
3.0
|
52.1
|
1.0
|
NH1
|
N:ARG91
|
3.1
|
67.3
|
1.0
|
OE1
|
M:GLN102
|
3.8
|
87.9
|
1.0
|
CD
|
M:GLN102
|
3.8
|
66.5
|
1.0
|
CZ
|
N:ARG91
|
4.0
|
74.8
|
1.0
|
NH2
|
N:ARG91
|
4.2
|
63.0
|
1.0
|
OE1
|
M:GLU100
|
4.5
|
55.0
|
1.0
|
CE2
|
N:TYR94
|
4.9
|
58.9
|
1.0
|
OE2
|
M:GLU100
|
5.0
|
42.2
|
1.0
|
|
Chlorine binding site 9 out
of 9 in 6ndf
Go back to
Chlorine Binding Sites List in 6ndf
Chlorine binding site 9 out
of 9 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 9 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Cl403
b:75.9
occ:1.00
|
NH2
|
R:ARG339
|
4.1
|
0.5
|
1.0
|
|
Reference:
J.Stetefeld,
M.D.Mcdougall,
P.C.Loewen.
Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Strontium Bound To Be Published.
Page generated: Mon Jul 29 11:55:38 2024
|