Calcium in PDB 3wmm: Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form
Protein crystallography data
The structure of Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form, PDB code: 3wmm
was solved by
S.Niwa,
K.Takeda,
Z.-Y.Wang-Otomo,
K.Miki,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
47.99 /
3.01
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
227.341,
148.238,
161.792,
90.00,
117.59,
90.00
|
|
R / Rfree (%)
|
31.4 /
33.7
|
Other elements in 3wmm:
The structure of Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form also contains other interesting chemical elements:
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
17;
Binding sites:
The binding sites of Calcium atom in the Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form
(pdb code 3wmm). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 17 binding sites of Calcium where determined in the
Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form, PDB code: 3wmm:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 17 in 3wmm
Go back to
Calcium Binding Sites List in 3wmm
Calcium binding site 1 out
of 17 in the Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca505
b:93.3
occ:1.00
|
OE1
|
C:GLN183
|
2.1
|
0.8
|
1.0
|
|
NE2
|
C:GLN183
|
2.3
|
0.2
|
1.0
|
|
OE1
|
C:GLU230
|
2.3
|
54.4
|
1.0
|
|
CD
|
C:GLN183
|
2.3
|
0.9
|
1.0
|
|
OE2
|
C:GLU230
|
2.9
|
51.4
|
1.0
|
|
CD
|
C:GLU230
|
2.9
|
53.5
|
1.0
|
|
CG
|
C:GLN183
|
3.7
|
0.2
|
1.0
|
|
OE2
|
M:GLU96
|
3.7
|
67.5
|
1.0
|
|
OE1
|
M:GLU96
|
4.2
|
66.1
|
1.0
|
|
O
|
M:PRO181
|
4.3
|
44.9
|
1.0
|
|
CD
|
M:GLU96
|
4.3
|
72.2
|
1.0
|
|
CG
|
C:GLU230
|
4.4
|
53.9
|
1.0
|
|
CB
|
M:PRO181
|
4.6
|
47.1
|
1.0
|
|
CB
|
C:GLN183
|
4.8
|
0.4
|
1.0
|
|
CG
|
M:PRO176
|
4.8
|
66.1
|
1.0
|
|
CB
|
M:ASP184
|
4.9
|
53.9
|
1.0
|
|
CB
|
C:GLU230
|
5.0
|
63.2
|
1.0
|
|
CA
|
M:PRO181
|
5.0
|
44.7
|
1.0
|
|
C
|
M:PRO181
|
5.0
|
43.1
|
1.0
|
|
Calcium binding site 2 out
of 17 in 3wmm
Go back to
Calcium Binding Sites List in 3wmm
Calcium binding site 2 out
of 17 in the Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca104
b:0.4
occ:1.00
|
O
|
0:LEU46
|
2.2
|
0.6
|
1.0
|
|
O
|
A:TRP46
|
2.4
|
0.9
|
1.0
|
|
OD1
|
A:ASP49
|
2.4
|
0.6
|
1.0
|
|
OD1
|
A:ASN50
|
2.4
|
1.0
|
1.0
|
|
O
|
A:ILE51
|
2.6
|
0.0
|
1.0
|
|
OXT
|
0:LEU46
|
2.6
|
0.8
|
1.0
|
|
C
|
0:LEU46
|
2.7
|
0.1
|
1.0
|
|
NH2
|
B:ARG43
|
2.9
|
0.3
|
1.0
|
|
C
|
A:TRP46
|
3.1
|
0.4
|
1.0
|
|
N
|
A:ILE51
|
3.4
|
0.1
|
1.0
|
|
CA
|
A:TRP46
|
3.5
|
0.5
|
1.0
|
|
C
|
A:ILE51
|
3.6
|
0.5
|
1.0
|
|
CG
|
A:ASN50
|
3.6
|
0.7
|
1.0
|
|
CG
|
A:ASP49
|
3.6
|
0.8
|
1.0
|
|
N
|
A:ASN50
|
3.7
|
0.7
|
1.0
|
|
CZ
|
B:ARG43
|
3.8
|
0.6
|
1.0
|
|
CG1
|
A:ILE51
|
3.8
|
0.5
|
1.0
|
|
NH1
|
B:ARG43
|
3.8
|
0.8
|
1.0
|
|
O
|
A:ASN45
|
4.0
|
0.2
|
1.0
|
|
CA
|
A:ILE51
|
4.0
|
0.8
|
1.0
|
|
N
|
A:ASP49
|
4.2
|
0.8
|
1.0
|
|
N
|
A:LEU47
|
4.2
|
0.1
|
1.0
|
|
CA
|
0:LEU46
|
4.2
|
0.7
|
1.0
|
|
C
|
A:LEU47
|
4.3
|
0.9
|
1.0
|
|
CA
|
A:ASN50
|
4.3
|
0.9
|
1.0
|
|
C
|
A:ASN50
|
4.3
|
0.0
|
1.0
|
|
OD2
|
A:ASP49
|
4.4
|
0.8
|
1.0
|
|
CB
|
A:TRP46
|
4.4
|
1.0
|
1.0
|
|
O
|
A:LEU47
|
4.4
|
0.6
|
1.0
|
|
C
|
A:ASP49
|
4.4
|
0.8
|
1.0
|
|
N
|
A:ASP48
|
4.5
|
0.3
|
1.0
|
|
CB
|
A:ASN50
|
4.5
|
0.6
|
1.0
|
|
CB
|
A:ILE51
|
4.6
|
0.1
|
1.0
|
|
ND2
|
A:ASN50
|
4.6
|
0.5
|
1.0
|
|
C
|
A:ASP48
|
4.6
|
1.0
|
1.0
|
|
CA
|
A:ASP49
|
4.6
|
0.2
|
1.0
|
|
N
|
A:TRP46
|
4.6
|
0.9
|
1.0
|
|
CB
|
A:ASP49
|
4.6
|
0.6
|
1.0
|
|
CA
|
A:LEU47
|
4.7
|
0.9
|
1.0
|
|
N
|
A:PRO52
|
4.7
|
0.9
|
1.0
|
|
C
|
A:ASN45
|
4.8
|
0.4
|
1.0
|
|
CA
|
A:ASP48
|
4.8
|
0.5
|
1.0
|
|
CB
|
0:LEU46
|
4.8
|
0.3
|
1.0
|
|
N
|
0:LEU46
|
4.9
|
0.9
|
1.0
|
|
Calcium binding site 3 out
of 17 in 3wmm
Go back to
Calcium Binding Sites List in 3wmm
Calcium binding site 3 out
of 17 in the Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca101
b:0.6
occ:1.00
|
O
|
B:LEU46
|
2.2
|
0.3
|
1.0
|
|
OD1
|
D:ASP49
|
2.3
|
0.3
|
1.0
|
|
OXT
|
B:LEU46
|
2.4
|
0.7
|
1.0
|
|
OD1
|
D:ASN50
|
2.4
|
0.4
|
1.0
|
|
O
|
D:ILE51
|
2.5
|
0.6
|
1.0
|
|
C
|
B:LEU46
|
2.5
|
0.1
|
1.0
|
|
O
|
D:TRP46
|
2.5
|
0.2
|
1.0
|
|
C
|
D:TRP46
|
3.3
|
0.5
|
1.0
|
|
CG
|
D:ASN50
|
3.4
|
0.7
|
1.0
|
|
CG
|
D:ASP49
|
3.5
|
0.7
|
1.0
|
|
C
|
D:ILE51
|
3.6
|
0.8
|
1.0
|
|
N
|
D:ASN50
|
3.6
|
0.3
|
1.0
|
|
NH2
|
E:ARG43
|
3.8
|
0.5
|
1.0
|
|
CA
|
D:TRP46
|
3.8
|
0.5
|
1.0
|
|
CA
|
B:LEU46
|
3.9
|
0.9
|
1.0
|
|
C
|
D:ASN50
|
3.9
|
0.6
|
1.0
|
|
O
|
D:LEU47
|
4.0
|
0.3
|
1.0
|
|
N
|
D:ASP49
|
4.0
|
0.2
|
1.0
|
|
N
|
D:ILE51
|
4.0
|
0.5
|
1.0
|
|
C
|
D:LEU47
|
4.1
|
0.0
|
1.0
|
|
ND2
|
D:ASN50
|
4.2
|
0.3
|
1.0
|
|
CA
|
D:ASN50
|
4.2
|
0.1
|
1.0
|
|
OD2
|
D:ASP49
|
4.2
|
0.6
|
1.0
|
|
O
|
D:ASN50
|
4.2
|
0.2
|
1.0
|
|
N
|
D:LEU47
|
4.3
|
0.9
|
1.0
|
|
N
|
D:PRO52
|
4.3
|
0.7
|
1.0
|
|
N
|
B:LEU46
|
4.4
|
0.7
|
1.0
|
|
CB
|
D:ASN50
|
4.4
|
0.8
|
1.0
|
|
N
|
D:ASP48
|
4.4
|
0.6
|
1.0
|
|
CA
|
D:ILE51
|
4.5
|
0.8
|
1.0
|
|
CB
|
D:ASP49
|
4.5
|
0.2
|
1.0
|
|
CD
|
D:PRO52
|
4.5
|
0.3
|
1.0
|
|
CA
|
D:ASP49
|
4.6
|
0.7
|
1.0
|
|
C
|
D:ASP48
|
4.6
|
0.3
|
1.0
|
|
C
|
D:ASP49
|
4.6
|
0.0
|
1.0
|
|
O
|
D:ASN45
|
4.6
|
0.1
|
1.0
|
|
CA
|
D:ASP48
|
4.6
|
0.2
|
1.0
|
|
CZ
|
E:ARG43
|
4.7
|
0.5
|
1.0
|
|
CA
|
D:LEU47
|
4.8
|
0.7
|
1.0
|
|
CB
|
D:TRP46
|
4.8
|
0.9
|
1.0
|
|
N
|
D:TRP46
|
4.9
|
0.9
|
1.0
|
|
Calcium binding site 4 out
of 17 in 3wmm
Go back to
Calcium Binding Sites List in 3wmm
Calcium binding site 4 out
of 17 in the Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca101
b:0.3
occ:1.00
|
ND2
|
F:ASN50
|
1.9
|
0.8
|
1.0
|
|
CG
|
F:ASN50
|
2.1
|
0.6
|
1.0
|
|
O
|
E:LEU46
|
2.1
|
1.0
|
1.0
|
|
OD1
|
F:ASN50
|
2.4
|
0.9
|
1.0
|
|
O
|
F:TRP46
|
2.5
|
0.3
|
1.0
|
|
OXT
|
E:LEU46
|
2.6
|
0.1
|
1.0
|
|
OD1
|
F:ASP49
|
2.6
|
0.4
|
1.0
|
|
C
|
E:LEU46
|
2.7
|
0.5
|
1.0
|
|
O
|
F:ILE51
|
2.9
|
0.3
|
1.0
|
|
N
|
F:ASN50
|
3.1
|
1.0
|
1.0
|
|
CB
|
F:ASN50
|
3.1
|
0.8
|
1.0
|
|
CA
|
F:ASN50
|
3.2
|
0.8
|
1.0
|
|
C
|
F:ASN50
|
3.2
|
0.2
|
1.0
|
|
CA
|
F:TRP46
|
3.2
|
0.2
|
1.0
|
|
C
|
F:TRP46
|
3.2
|
0.7
|
1.0
|
|
O
|
F:ASN50
|
3.3
|
0.5
|
1.0
|
|
CG
|
F:ASP49
|
3.5
|
0.5
|
1.0
|
|
OD2
|
F:ASP49
|
3.8
|
1.0
|
1.0
|
|
N
|
F:ILE51
|
4.0
|
1.0
|
1.0
|
|
CB
|
F:TRP46
|
4.1
|
0.0
|
1.0
|
|
C
|
F:ILE51
|
4.1
|
0.2
|
1.0
|
|
CA
|
E:LEU46
|
4.2
|
0.8
|
1.0
|
|
N
|
F:TRP46
|
4.2
|
1.0
|
1.0
|
|
NH2
|
G:ARG43
|
4.2
|
0.8
|
1.0
|
|
C
|
F:ASP49
|
4.3
|
0.6
|
1.0
|
|
O
|
F:ASN45
|
4.3
|
0.9
|
1.0
|
|
N
|
F:ASP49
|
4.5
|
0.9
|
1.0
|
|
N
|
F:LEU47
|
4.5
|
0.8
|
1.0
|
|
NH1
|
G:ARG43
|
4.6
|
0.2
|
1.0
|
|
C
|
F:ASN45
|
4.6
|
0.9
|
1.0
|
|
N
|
E:LEU46
|
4.7
|
0.5
|
1.0
|
|
CB
|
F:ASP49
|
4.7
|
0.3
|
1.0
|
|
CA
|
F:ILE51
|
4.8
|
0.9
|
1.0
|
|
CA
|
F:ASP49
|
4.8
|
0.9
|
1.0
|
|
OH
|
G:TYR42
|
4.8
|
0.3
|
1.0
|
|
CB
|
E:LEU46
|
4.9
|
0.2
|
1.0
|
|
O
|
F:LEU47
|
4.9
|
0.3
|
1.0
|
|
C
|
F:LEU47
|
4.9
|
0.3
|
1.0
|
|
CZ
|
G:ARG43
|
4.9
|
0.3
|
1.0
|
|
Calcium binding site 5 out
of 17 in 3wmm
Go back to
Calcium Binding Sites List in 3wmm
Calcium binding site 5 out
of 17 in the Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Ca101
b:0.8
occ:1.00
|
O
|
G:LEU46
|
2.3
|
0.9
|
1.0
|
|
OD1
|
I:ASN50
|
2.4
|
0.4
|
1.0
|
|
OD1
|
I:ASP49
|
2.4
|
0.6
|
1.0
|
|
OXT
|
G:LEU46
|
2.4
|
0.9
|
1.0
|
|
O
|
I:TRP46
|
2.4
|
0.2
|
1.0
|
|
O
|
I:ILE51
|
2.5
|
0.3
|
1.0
|
|
C
|
G:LEU46
|
2.6
|
0.1
|
1.0
|
|
C
|
I:TRP46
|
3.4
|
0.8
|
1.0
|
|
CG
|
I:ASP49
|
3.5
|
0.8
|
1.0
|
|
CG
|
I:ASN50
|
3.5
|
0.7
|
1.0
|
|
C
|
I:ILE51
|
3.6
|
0.7
|
1.0
|
|
NH2
|
J:ARG43
|
3.7
|
1.0
|
1.0
|
|
CA
|
I:TRP46
|
3.7
|
0.9
|
1.0
|
|
N
|
I:ILE51
|
3.8
|
0.9
|
1.0
|
|
OD2
|
I:ASP49
|
3.9
|
0.8
|
1.0
|
|
N
|
I:ASN50
|
4.1
|
0.4
|
1.0
|
|
CA
|
G:LEU46
|
4.1
|
0.0
|
1.0
|
|
ND2
|
I:ASN50
|
4.2
|
0.4
|
1.0
|
|
C
|
I:ASN50
|
4.2
|
0.5
|
1.0
|
|
CA
|
I:ILE51
|
4.3
|
0.3
|
1.0
|
|
CG1
|
I:ILE51
|
4.3
|
0.7
|
1.0
|
|
O
|
I:ASN45
|
4.4
|
0.2
|
1.0
|
|
NE
|
J:ARG43
|
4.5
|
0.5
|
1.0
|
|
N
|
I:ASP49
|
4.5
|
0.8
|
1.0
|
|
CA
|
I:ASN50
|
4.5
|
0.3
|
1.0
|
|
CZ
|
J:ARG43
|
4.5
|
0.3
|
1.0
|
|
N
|
I:LEU47
|
4.5
|
1.0
|
1.0
|
|
CB
|
I:TRP46
|
4.6
|
0.4
|
1.0
|
|
CB
|
I:ASN50
|
4.6
|
0.5
|
1.0
|
|
N
|
I:PRO52
|
4.6
|
0.4
|
1.0
|
|
OH
|
J:TYR42
|
4.6
|
0.8
|
1.0
|
|
C
|
I:ASP49
|
4.7
|
0.4
|
1.0
|
|
N
|
G:LEU46
|
4.7
|
0.2
|
1.0
|
|
CB
|
I:ASP49
|
4.7
|
0.7
|
1.0
|
|
N
|
I:TRP46
|
4.8
|
0.4
|
1.0
|
|
CA
|
I:ASP49
|
4.8
|
0.5
|
1.0
|
|
O
|
I:LEU47
|
4.9
|
0.0
|
1.0
|
|
O
|
I:ASN50
|
4.9
|
0.8
|
1.0
|
|
C
|
I:LEU47
|
4.9
|
0.0
|
1.0
|
|
CB
|
I:ILE51
|
5.0
|
0.5
|
1.0
|
|
Calcium binding site 6 out
of 17 in 3wmm
Go back to
Calcium Binding Sites List in 3wmm
Calcium binding site 6 out
of 17 in the Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Ca101
b:0.5
occ:1.00
|
O
|
J:LEU46
|
2.2
|
0.3
|
1.0
|
|
OD1
|
K:ASN50
|
2.4
|
0.1
|
1.0
|
|
OD1
|
K:ASP49
|
2.4
|
0.7
|
1.0
|
|
O
|
K:TRP46
|
2.6
|
0.0
|
1.0
|
|
OXT
|
J:LEU46
|
2.6
|
0.9
|
1.0
|
|
O
|
K:ILE51
|
2.7
|
0.4
|
1.0
|
|
C
|
J:LEU46
|
2.7
|
0.8
|
1.0
|
|
CG
|
K:ASN50
|
3.3
|
0.8
|
1.0
|
|
C
|
K:TRP46
|
3.4
|
0.4
|
1.0
|
|
CA
|
K:TRP46
|
3.5
|
0.7
|
1.0
|
|
CG
|
K:ASP49
|
3.5
|
0.4
|
1.0
|
|
NH2
|
N:ARG43
|
3.7
|
0.1
|
1.0
|
|
N
|
K:ASN50
|
3.8
|
0.5
|
1.0
|
|
C
|
K:ILE51
|
3.9
|
0.1
|
1.0
|
|
ND2
|
K:ASN50
|
3.9
|
0.2
|
1.0
|
|
C
|
K:ASN50
|
3.9
|
0.0
|
1.0
|
|
OD2
|
K:ASP49
|
4.0
|
0.2
|
1.0
|
|
O
|
K:ASN50
|
4.0
|
0.9
|
1.0
|
|
CB
|
K:TRP46
|
4.2
|
0.3
|
1.0
|
|
CA
|
J:LEU46
|
4.2
|
0.7
|
1.0
|
|
CA
|
K:ASN50
|
4.2
|
0.6
|
1.0
|
|
N
|
K:ILE51
|
4.3
|
0.4
|
1.0
|
|
OH
|
N:TYR42
|
4.3
|
0.7
|
1.0
|
|
CB
|
K:ASN50
|
4.4
|
0.9
|
1.0
|
|
O
|
K:ASN45
|
4.4
|
0.7
|
1.0
|
|
CZ
|
N:ARG43
|
4.6
|
0.7
|
1.0
|
|
N
|
K:TRP46
|
4.6
|
0.5
|
1.0
|
|
N
|
J:LEU46
|
4.6
|
0.1
|
1.0
|
|
N
|
K:LEU47
|
4.6
|
0.7
|
1.0
|
|
CA
|
K:ILE51
|
4.7
|
0.3
|
1.0
|
|
N
|
K:ASP49
|
4.7
|
0.1
|
1.0
|
|
C
|
K:ASP49
|
4.8
|
0.3
|
1.0
|
|
CB
|
K:ASP49
|
4.8
|
0.0
|
1.0
|
|
NH1
|
N:ARG43
|
4.8
|
0.1
|
1.0
|
|
N
|
K:PRO52
|
4.9
|
0.5
|
1.0
|
|
C
|
K:ASN45
|
4.9
|
0.1
|
1.0
|
|
CA
|
K:ASP49
|
5.0
|
0.5
|
1.0
|
|
Calcium binding site 7 out
of 17 in 3wmm
Go back to
Calcium Binding Sites List in 3wmm
Calcium binding site 7 out
of 17 in the Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Ca101
b:0.9
occ:1.00
|
OXT
|
N:LEU46
|
1.8
|
0.8
|
1.0
|
|
O
|
O:ILE51
|
2.4
|
0.1
|
1.0
|
|
O
|
O:TRP46
|
2.4
|
0.3
|
1.0
|
|
OD1
|
O:ASN50
|
2.4
|
0.6
|
1.0
|
|
OD1
|
O:ASP49
|
2.4
|
0.3
|
1.0
|
|
C
|
N:LEU46
|
2.6
|
0.6
|
1.0
|
|
O
|
N:LEU46
|
2.8
|
0.1
|
1.0
|
|
CG
|
O:ASN50
|
3.2
|
0.5
|
1.0
|
|
N
|
O:ILE51
|
3.3
|
0.2
|
1.0
|
|
C
|
O:TRP46
|
3.3
|
0.7
|
1.0
|
|
C
|
O:ILE51
|
3.4
|
0.5
|
1.0
|
|
N
|
O:ASN50
|
3.5
|
0.7
|
1.0
|
|
CG
|
O:ASP49
|
3.7
|
0.8
|
1.0
|
|
C
|
O:ASN50
|
3.7
|
0.0
|
1.0
|
|
ND2
|
O:ASN50
|
3.8
|
0.5
|
1.0
|
|
CA
|
O:ILE51
|
3.9
|
0.8
|
1.0
|
|
CA
|
O:ASN50
|
3.9
|
0.7
|
1.0
|
|
CA
|
N:LEU46
|
4.0
|
0.4
|
1.0
|
|
O
|
O:LEU47
|
4.0
|
0.9
|
1.0
|
|
C
|
O:LEU47
|
4.1
|
0.3
|
1.0
|
|
CA
|
O:TRP46
|
4.1
|
1.0
|
1.0
|
|
OH
|
O:TYR55
|
4.1
|
0.9
|
1.0
|
|
NH2
|
P:ARG43
|
4.1
|
0.3
|
1.0
|
|
N
|
O:LEU47
|
4.1
|
0.5
|
1.0
|
|
CB
|
O:ASN50
|
4.1
|
0.3
|
1.0
|
|
CA
|
O:LEU47
|
4.3
|
0.3
|
1.0
|
|
OD2
|
O:ASP49
|
4.3
|
0.2
|
1.0
|
|
N
|
O:ASP49
|
4.4
|
0.2
|
1.0
|
|
O
|
O:ASN45
|
4.4
|
0.6
|
1.0
|
|
N
|
N:LEU46
|
4.4
|
0.4
|
1.0
|
|
N
|
O:PRO52
|
4.5
|
0.3
|
1.0
|
|
C
|
O:ASP49
|
4.5
|
0.9
|
1.0
|
|
O
|
O:ASN50
|
4.5
|
0.8
|
1.0
|
|
CG1
|
O:ILE51
|
4.6
|
1.0
|
1.0
|
|
N
|
O:ASP48
|
4.6
|
0.1
|
1.0
|
|
CA
|
O:ASP49
|
4.7
|
0.6
|
1.0
|
|
CB
|
N:LEU46
|
4.8
|
1.0
|
1.0
|
|
CB
|
O:ASP49
|
4.8
|
0.1
|
1.0
|
|
CB
|
O:ILE51
|
4.9
|
0.1
|
1.0
|
|
C
|
O:ASP48
|
4.9
|
1.0
|
1.0
|
|
C
|
N:TRP45
|
5.0
|
0.8
|
1.0
|
|
Calcium binding site 8 out
of 17 in 3wmm
Go back to
Calcium Binding Sites List in 3wmm
Calcium binding site 8 out
of 17 in the Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Ca101
b:0.6
occ:1.00
|
OD1
|
Q:ASN50
|
2.3
|
1.0
|
1.0
|
|
OXT
|
P:LEU46
|
2.4
|
0.7
|
1.0
|
|
O
|
Q:TRP46
|
2.4
|
0.7
|
1.0
|
|
O
|
P:LEU46
|
2.4
|
0.8
|
1.0
|
|
O
|
Q:ILE51
|
2.4
|
0.8
|
1.0
|
|
OD1
|
Q:ASP49
|
2.4
|
0.5
|
1.0
|
|
C
|
P:LEU46
|
2.7
|
0.7
|
1.0
|
|
CA
|
Q:TRP46
|
2.7
|
0.8
|
1.0
|
|
C
|
Q:TRP46
|
2.8
|
0.4
|
1.0
|
|
CG
|
Q:ASN50
|
2.9
|
0.0
|
1.0
|
|
ND2
|
Q:ASN50
|
3.3
|
0.8
|
1.0
|
|
N
|
Q:ASN50
|
3.4
|
0.1
|
1.0
|
|
N
|
Q:TRP46
|
3.5
|
0.3
|
1.0
|
|
C
|
Q:ILE51
|
3.6
|
0.2
|
1.0
|
|
C
|
Q:ASN50
|
3.6
|
0.7
|
1.0
|
|
CG
|
Q:ASP49
|
3.7
|
0.3
|
1.0
|
|
N
|
Q:ILE51
|
3.7
|
0.6
|
1.0
|
|
CB
|
Q:TRP46
|
3.9
|
0.8
|
1.0
|
|
CA
|
Q:ASN50
|
3.9
|
0.5
|
1.0
|
|
O
|
Q:ASN45
|
3.9
|
0.6
|
1.0
|
|
CB
|
Q:ASN50
|
4.0
|
0.2
|
1.0
|
|
C
|
Q:ASN45
|
4.0
|
0.0
|
1.0
|
|
O
|
Q:ASN50
|
4.0
|
0.2
|
1.0
|
|
N
|
Q:LEU47
|
4.1
|
0.5
|
1.0
|
|
N
|
Q:ASP49
|
4.1
|
0.2
|
1.0
|
|
CA
|
P:LEU46
|
4.2
|
0.9
|
1.0
|
|
CA
|
Q:ILE51
|
4.3
|
0.3
|
1.0
|
|
OD2
|
Q:ASP49
|
4.3
|
0.8
|
1.0
|
|
C
|
Q:ASP49
|
4.5
|
0.5
|
1.0
|
|
N
|
Q:PRO52
|
4.7
|
0.1
|
1.0
|
|
N
|
Q:ASP48
|
4.7
|
0.4
|
1.0
|
|
CA
|
Q:ASP49
|
4.7
|
0.5
|
1.0
|
|
CB
|
Q:ASP49
|
4.7
|
0.6
|
1.0
|
|
NH2
|
R:ARG43
|
4.8
|
0.3
|
1.0
|
|
CB
|
P:LEU46
|
4.8
|
0.2
|
1.0
|
|
C
|
Q:LEU47
|
4.8
|
0.7
|
1.0
|
|
N
|
P:LEU46
|
4.9
|
0.8
|
1.0
|
|
CB
|
Q:ILE51
|
4.9
|
0.5
|
1.0
|
|
CA
|
Q:LEU47
|
4.9
|
0.6
|
1.0
|
|
CD
|
Q:PRO52
|
5.0
|
0.4
|
1.0
|
|
Calcium binding site 9 out
of 17 in 3wmm
Go back to
Calcium Binding Sites List in 3wmm
Calcium binding site 9 out
of 17 in the Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Ca101
b:0.9
occ:1.00
|
OD1
|
S:ASP49
|
2.3
|
0.6
|
1.0
|
|
O
|
R:LEU46
|
2.3
|
0.5
|
1.0
|
|
O
|
S:ILE51
|
2.3
|
0.7
|
1.0
|
|
O
|
S:TRP46
|
2.4
|
0.7
|
1.0
|
|
OXT
|
R:LEU46
|
2.5
|
1.0
|
1.0
|
|
OD1
|
S:ASN50
|
2.5
|
0.5
|
1.0
|
|
C
|
R:LEU46
|
2.7
|
0.2
|
1.0
|
|
C
|
S:TRP46
|
3.2
|
0.0
|
1.0
|
|
CA
|
S:TRP46
|
3.4
|
0.7
|
1.0
|
|
CG
|
S:ASP49
|
3.5
|
0.4
|
1.0
|
|
C
|
S:ILE51
|
3.5
|
0.1
|
1.0
|
|
CG
|
S:ASN50
|
3.6
|
0.1
|
1.0
|
|
N
|
S:ILE51
|
3.8
|
0.2
|
1.0
|
|
N
|
S:ASN50
|
4.0
|
0.1
|
1.0
|
|
OD2
|
S:ASP49
|
4.0
|
0.3
|
1.0
|
|
CB
|
S:TRP46
|
4.1
|
0.9
|
1.0
|
|
CA
|
R:LEU46
|
4.2
|
0.4
|
1.0
|
|
O
|
S:ASN45
|
4.2
|
0.4
|
1.0
|
|
CA
|
S:ILE51
|
4.3
|
1.0
|
1.0
|
|
ND2
|
S:ASN50
|
4.3
|
0.7
|
1.0
|
|
C
|
S:ASN50
|
4.4
|
0.7
|
1.0
|
|
N
|
S:LEU47
|
4.4
|
0.5
|
1.0
|
|
N
|
S:PRO52
|
4.4
|
0.0
|
1.0
|
|
N
|
S:ASP49
|
4.5
|
0.2
|
1.0
|
|
CD
|
S:PRO52
|
4.5
|
0.4
|
1.0
|
|
N
|
S:TRP46
|
4.5
|
0.6
|
1.0
|
|
CA
|
S:ASN50
|
4.6
|
0.8
|
1.0
|
|
CG1
|
S:ILE51
|
4.6
|
0.9
|
1.0
|
|
NH2
|
T:ARG43
|
4.6
|
0.7
|
1.0
|
|
CB
|
S:ASP49
|
4.6
|
0.1
|
1.0
|
|
CB
|
S:ASN50
|
4.7
|
0.6
|
1.0
|
|
N
|
R:LEU46
|
4.8
|
0.0
|
1.0
|
|
C
|
S:ASN45
|
4.8
|
0.4
|
1.0
|
|
CA
|
S:ASP49
|
4.9
|
0.9
|
1.0
|
|
C
|
S:ASP49
|
4.9
|
0.8
|
1.0
|
|
C
|
S:LEU47
|
4.9
|
0.1
|
1.0
|
|
OH
|
T:TYR42
|
5.0
|
0.5
|
1.0
|
|
Calcium binding site 10 out
of 17 in 3wmm
Go back to
Calcium Binding Sites List in 3wmm
Calcium binding site 10 out
of 17 in the Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of the LH1-Rc Complex From Thermochromatium Tepidum in C2 Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
U:Ca101
b:0.1
occ:1.00
|
O
|
T:LEU46
|
2.4
|
0.4
|
1.0
|
|
OD1
|
U:ASN50
|
2.4
|
0.3
|
1.0
|
|
OD1
|
U:ASP49
|
2.4
|
0.4
|
1.0
|
|
OXT
|
T:LEU46
|
2.4
|
0.9
|
1.0
|
|
O
|
U:TRP46
|
2.4
|
0.4
|
1.0
|
|
O
|
U:ILE51
|
2.5
|
0.9
|
1.0
|
|
C
|
T:LEU46
|
2.7
|
0.1
|
1.0
|
|
C
|
U:TRP46
|
3.2
|
0.8
|
1.0
|
|
CA
|
U:TRP46
|
3.3
|
0.1
|
1.0
|
|
CG
|
U:ASN50
|
3.4
|
0.1
|
1.0
|
|
CG
|
U:ASP49
|
3.4
|
1.0
|
1.0
|
|
C
|
U:ILE51
|
3.6
|
0.2
|
1.0
|
|
O
|
U:ASN50
|
3.7
|
0.1
|
1.0
|
|
C
|
U:ASN50
|
3.7
|
0.3
|
1.0
|
|
N
|
U:ASN50
|
3.7
|
0.7
|
1.0
|
|
NH2
|
V:ARG43
|
3.8
|
0.2
|
1.0
|
|
OD2
|
U:ASP49
|
3.8
|
0.0
|
1.0
|
|
CB
|
U:TRP46
|
4.0
|
0.9
|
1.0
|
|
ND2
|
U:ASN50
|
4.1
|
1.0
|
1.0
|
|
N
|
U:ILE51
|
4.1
|
1.0
|
1.0
|
|
CA
|
U:ASN50
|
4.2
|
0.7
|
1.0
|
|
CA
|
T:LEU46
|
4.2
|
0.7
|
1.0
|
|
CB
|
U:ASN50
|
4.4
|
0.2
|
1.0
|
|
N
|
U:PRO52
|
4.5
|
0.7
|
1.0
|
|
CA
|
U:ILE51
|
4.5
|
1.0
|
1.0
|
|
N
|
U:LEU47
|
4.5
|
0.8
|
1.0
|
|
O
|
U:ASN45
|
4.5
|
0.0
|
1.0
|
|
N
|
U:TRP46
|
4.5
|
0.4
|
1.0
|
|
N
|
U:ASP49
|
4.6
|
0.8
|
1.0
|
|
CD
|
U:PRO52
|
4.7
|
0.8
|
1.0
|
|
CB
|
U:ASP49
|
4.7
|
0.1
|
1.0
|
|
C
|
U:ASP49
|
4.8
|
0.3
|
1.0
|
|
O
|
T:TRP45
|
4.9
|
0.3
|
1.0
|
|
N
|
T:LEU46
|
4.9
|
0.0
|
1.0
|
|
CB
|
T:LEU46
|
4.9
|
0.5
|
1.0
|
|
C
|
U:ASN45
|
5.0
|
0.5
|
1.0
|
|
CA
|
U:ASP49
|
5.0
|
0.4
|
1.0
|
|
Reference:
S.Niwa,
L.J.Yu,
K.Takeda,
Y.Hirano,
T.Kawakami,
Z.Y.Wang-Otomo,
K.Miki.
Structure of the LH1-Rc Complex From Thermochromatium Tepidum at 3.0 Angstrom Nature V. 508 228 2014.
ISSN: ISSN 0028-0836
PubMed: 24670637
DOI: 10.1038/NATURE13197
Page generated: Sat Jul 13 21:09:47 2024
|
