Magnesium in PDB 1ppr: Peridinin-Chlorophyll-Protein of Amphidinium Carterae
Protein crystallography data
The structure of Peridinin-Chlorophyll-Protein of Amphidinium Carterae, PDB code: 1ppr
was solved by
E.Hofmann,
W.Welte,
K.Diederichs,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
40.00 /
2.00
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
198.426,
116.296,
67.025,
90.00,
94.89,
90.00
|
|
R / Rfree (%)
|
17.9 /
20.1
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Peridinin-Chlorophyll-Protein of Amphidinium Carterae
(pdb code 1ppr). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Peridinin-Chlorophyll-Protein of Amphidinium Carterae, PDB code: 1ppr:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 1ppr
Go back to
Magnesium Binding Sites List in 1ppr
Magnesium binding site 1 out
of 6 in the Peridinin-Chlorophyll-Protein of Amphidinium Carterae
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Peridinin-Chlorophyll-Protein of Amphidinium Carterae within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg601
b:26.6
occ:1.00
|
MG
|
M:CLA601
|
0.0
|
26.6
|
1.0
|
|
O
|
M:HOH701
|
1.9
|
28.3
|
1.0
|
|
ND
|
M:CLA601
|
2.0
|
28.6
|
1.0
|
|
NB
|
M:CLA601
|
2.1
|
27.2
|
1.0
|
|
NC
|
M:CLA601
|
2.1
|
27.6
|
1.0
|
|
NA
|
M:CLA601
|
2.2
|
27.3
|
1.0
|
|
C4D
|
M:CLA601
|
3.0
|
28.1
|
1.0
|
|
C1B
|
M:CLA601
|
3.1
|
24.8
|
1.0
|
|
C1D
|
M:CLA601
|
3.1
|
29.8
|
1.0
|
|
C4C
|
M:CLA601
|
3.1
|
28.7
|
1.0
|
|
C4B
|
M:CLA601
|
3.1
|
26.2
|
1.0
|
|
C1C
|
M:CLA601
|
3.1
|
27.9
|
1.0
|
|
C4A
|
M:CLA601
|
3.2
|
26.4
|
1.0
|
|
C1A
|
M:CLA601
|
3.2
|
26.4
|
1.0
|
|
CHB
|
M:CLA601
|
3.5
|
25.2
|
1.0
|
|
CHD
|
M:CLA601
|
3.5
|
28.5
|
1.0
|
|
CHA
|
M:CLA601
|
3.5
|
29.0
|
1.0
|
|
CHC
|
M:CLA601
|
3.5
|
25.4
|
1.0
|
|
NE2
|
M:HIS66
|
4.0
|
26.9
|
1.0
|
|
C3D
|
M:CLA601
|
4.2
|
29.4
|
1.0
|
|
C22
|
M:PID612
|
4.3
|
26.3
|
1.0
|
|
C2B
|
M:CLA601
|
4.3
|
24.7
|
1.0
|
|
C2D
|
M:CLA601
|
4.3
|
30.0
|
1.0
|
|
C3B
|
M:CLA601
|
4.3
|
26.1
|
1.0
|
|
C3C
|
M:CLA601
|
4.3
|
28.6
|
1.0
|
|
C2C
|
M:CLA601
|
4.4
|
27.2
|
1.0
|
|
C3A
|
M:CLA601
|
4.5
|
24.4
|
1.0
|
|
C2A
|
M:CLA601
|
4.5
|
26.7
|
1.0
|
|
C23
|
M:PID612
|
4.7
|
26.5
|
1.0
|
|
CE1
|
M:HIS66
|
4.7
|
28.6
|
1.0
|
|
CD2
|
M:HIS66
|
4.7
|
28.4
|
1.0
|
|
CD1
|
M:LEU92
|
4.8
|
30.2
|
1.0
|
|
C19
|
M:PID614
|
5.0
|
32.2
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 1ppr
Go back to
Magnesium Binding Sites List in 1ppr
Magnesium binding site 2 out
of 6 in the Peridinin-Chlorophyll-Protein of Amphidinium Carterae
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Peridinin-Chlorophyll-Protein of Amphidinium Carterae within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg602
b:21.7
occ:1.00
|
MG
|
M:CLA602
|
0.0
|
21.7
|
1.0
|
|
O
|
M:HOH678
|
1.9
|
21.6
|
1.0
|
|
ND
|
M:CLA602
|
2.0
|
22.1
|
1.0
|
|
NB
|
M:CLA602
|
2.1
|
23.1
|
1.0
|
|
NC
|
M:CLA602
|
2.1
|
25.7
|
1.0
|
|
NA
|
M:CLA602
|
2.2
|
21.1
|
1.0
|
|
C4D
|
M:CLA602
|
3.0
|
23.8
|
1.0
|
|
C4B
|
M:CLA602
|
3.1
|
24.1
|
1.0
|
|
C1C
|
M:CLA602
|
3.1
|
24.1
|
1.0
|
|
C1B
|
M:CLA602
|
3.1
|
22.1
|
1.0
|
|
C4C
|
M:CLA602
|
3.1
|
24.6
|
1.0
|
|
C1D
|
M:CLA602
|
3.1
|
23.4
|
1.0
|
|
C4A
|
M:CLA602
|
3.2
|
21.0
|
1.0
|
|
C1A
|
M:CLA602
|
3.2
|
22.5
|
1.0
|
|
CHC
|
M:CLA602
|
3.4
|
25.0
|
1.0
|
|
CHB
|
M:CLA602
|
3.5
|
21.7
|
1.0
|
|
CHD
|
M:CLA602
|
3.5
|
24.6
|
1.0
|
|
CHA
|
M:CLA602
|
3.5
|
22.5
|
1.0
|
|
NE2
|
M:HIS229
|
4.1
|
22.9
|
1.0
|
|
C22
|
M:PID622
|
4.2
|
22.6
|
1.0
|
|
C3D
|
M:CLA602
|
4.3
|
20.9
|
1.0
|
|
C2B
|
M:CLA602
|
4.3
|
21.2
|
1.0
|
|
C3B
|
M:CLA602
|
4.3
|
24.2
|
1.0
|
|
C2C
|
M:CLA602
|
4.3
|
25.9
|
1.0
|
|
C2D
|
M:CLA602
|
4.3
|
21.9
|
1.0
|
|
C3C
|
M:CLA602
|
4.3
|
25.1
|
1.0
|
|
CIB
|
O:DGD625
|
4.4
|
36.4
|
1.0
|
|
C3A
|
M:CLA602
|
4.5
|
21.2
|
1.0
|
|
C2A
|
M:CLA602
|
4.6
|
21.3
|
1.0
|
|
C23
|
M:PID622
|
4.6
|
27.4
|
1.0
|
|
CM5
|
M:PID624
|
4.8
|
21.3
|
1.0
|
|
CD2
|
M:HIS229
|
4.8
|
24.1
|
1.0
|
|
CE1
|
M:HIS229
|
4.8
|
25.3
|
1.0
|
|
C19
|
M:PID624
|
4.8
|
20.1
|
1.0
|
|
CD1
|
M:LEU254
|
4.9
|
20.7
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 1ppr
Go back to
Magnesium Binding Sites List in 1ppr
Magnesium binding site 3 out
of 6 in the Peridinin-Chlorophyll-Protein of Amphidinium Carterae
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Peridinin-Chlorophyll-Protein of Amphidinium Carterae within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg601
b:30.6
occ:1.00
|
MG
|
N:CLA601
|
0.0
|
30.6
|
1.0
|
|
O
|
N:HOH699
|
1.9
|
31.7
|
1.0
|
|
ND
|
N:CLA601
|
2.0
|
31.8
|
1.0
|
|
NC
|
N:CLA601
|
2.1
|
29.2
|
1.0
|
|
NB
|
N:CLA601
|
2.1
|
29.6
|
1.0
|
|
NA
|
N:CLA601
|
2.2
|
30.5
|
1.0
|
|
C4D
|
N:CLA601
|
3.0
|
32.1
|
1.0
|
|
C1D
|
N:CLA601
|
3.1
|
33.6
|
1.0
|
|
C1C
|
N:CLA601
|
3.1
|
30.2
|
1.0
|
|
C1B
|
N:CLA601
|
3.1
|
28.9
|
1.0
|
|
C4C
|
N:CLA601
|
3.1
|
29.9
|
1.0
|
|
C4B
|
N:CLA601
|
3.1
|
30.9
|
1.0
|
|
C4A
|
N:CLA601
|
3.2
|
30.9
|
1.0
|
|
C1A
|
N:CLA601
|
3.2
|
29.4
|
1.0
|
|
CHC
|
N:CLA601
|
3.5
|
29.1
|
1.0
|
|
CHB
|
N:CLA601
|
3.5
|
28.4
|
1.0
|
|
CHD
|
N:CLA601
|
3.5
|
31.7
|
1.0
|
|
CHA
|
N:CLA601
|
3.5
|
32.9
|
1.0
|
|
NE2
|
N:HIS66
|
4.0
|
27.7
|
1.0
|
|
C3D
|
N:CLA601
|
4.2
|
32.8
|
1.0
|
|
C22
|
N:PID612
|
4.3
|
28.1
|
1.0
|
|
C2D
|
N:CLA601
|
4.3
|
33.2
|
1.0
|
|
C2C
|
N:CLA601
|
4.3
|
27.8
|
1.0
|
|
C3C
|
N:CLA601
|
4.3
|
30.4
|
1.0
|
|
C2B
|
N:CLA601
|
4.3
|
28.8
|
1.0
|
|
C3B
|
N:CLA601
|
4.4
|
29.3
|
1.0
|
|
C3A
|
N:CLA601
|
4.5
|
29.2
|
1.0
|
|
C2A
|
N:CLA601
|
4.5
|
29.2
|
1.0
|
|
C23
|
N:PID612
|
4.6
|
29.6
|
1.0
|
|
CE1
|
N:HIS66
|
4.7
|
27.6
|
1.0
|
|
CD2
|
N:HIS66
|
4.7
|
29.5
|
1.0
|
|
CD1
|
N:LEU92
|
4.8
|
34.8
|
1.0
|
|
C19
|
N:PID614
|
5.0
|
34.7
|
1.0
|
|
CBD
|
N:CLA601
|
5.0
|
33.8
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 1ppr
Go back to
Magnesium Binding Sites List in 1ppr
Magnesium binding site 4 out
of 6 in the Peridinin-Chlorophyll-Protein of Amphidinium Carterae
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Peridinin-Chlorophyll-Protein of Amphidinium Carterae within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg602
b:26.1
occ:1.00
|
MG
|
N:CLA602
|
0.0
|
26.1
|
1.0
|
|
O
|
N:HOH677
|
1.8
|
26.0
|
1.0
|
|
ND
|
N:CLA602
|
2.0
|
26.0
|
1.0
|
|
NB
|
N:CLA602
|
2.0
|
26.4
|
1.0
|
|
NC
|
N:CLA602
|
2.1
|
28.9
|
1.0
|
|
NA
|
N:CLA602
|
2.2
|
25.8
|
1.0
|
|
C4D
|
N:CLA602
|
3.0
|
26.8
|
1.0
|
|
C1B
|
N:CLA602
|
3.1
|
25.9
|
1.0
|
|
C4B
|
N:CLA602
|
3.1
|
26.9
|
1.0
|
|
C1C
|
N:CLA602
|
3.1
|
26.7
|
1.0
|
|
C1D
|
N:CLA602
|
3.1
|
24.9
|
1.0
|
|
C4C
|
N:CLA602
|
3.1
|
27.9
|
1.0
|
|
C4A
|
N:CLA602
|
3.2
|
24.1
|
1.0
|
|
C1A
|
N:CLA602
|
3.2
|
24.5
|
1.0
|
|
CHC
|
N:CLA602
|
3.4
|
27.3
|
1.0
|
|
CHB
|
N:CLA602
|
3.5
|
26.5
|
1.0
|
|
CHD
|
N:CLA602
|
3.5
|
26.7
|
1.0
|
|
CHA
|
N:CLA602
|
3.5
|
23.8
|
1.0
|
|
NE2
|
N:HIS229
|
4.1
|
26.2
|
1.0
|
|
C22
|
N:PID622
|
4.2
|
27.0
|
1.0
|
|
C3D
|
N:CLA602
|
4.2
|
26.3
|
1.0
|
|
C2B
|
N:CLA602
|
4.3
|
25.6
|
1.0
|
|
C3B
|
N:CLA602
|
4.3
|
25.0
|
1.0
|
|
C2D
|
N:CLA602
|
4.3
|
24.7
|
1.0
|
|
C2C
|
N:CLA602
|
4.3
|
28.9
|
1.0
|
|
C3C
|
N:CLA602
|
4.3
|
29.3
|
1.0
|
|
CIB
|
M:DGD625
|
4.4
|
40.1
|
1.0
|
|
C3A
|
N:CLA602
|
4.5
|
25.7
|
1.0
|
|
C2A
|
N:CLA602
|
4.6
|
25.2
|
1.0
|
|
C23
|
N:PID622
|
4.6
|
29.6
|
1.0
|
|
CM5
|
N:PID624
|
4.8
|
25.8
|
1.0
|
|
CE1
|
N:HIS229
|
4.8
|
27.7
|
1.0
|
|
CD2
|
N:HIS229
|
4.8
|
26.5
|
1.0
|
|
C19
|
N:PID624
|
4.8
|
25.5
|
1.0
|
|
CD1
|
N:LEU254
|
4.9
|
24.5
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 1ppr
Go back to
Magnesium Binding Sites List in 1ppr
Magnesium binding site 5 out
of 6 in the Peridinin-Chlorophyll-Protein of Amphidinium Carterae
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Peridinin-Chlorophyll-Protein of Amphidinium Carterae within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Mg601
b:24.8
occ:1.00
|
MG
|
O:CLA601
|
0.0
|
24.8
|
1.0
|
|
O
|
O:HOH708
|
2.0
|
26.3
|
1.0
|
|
ND
|
O:CLA601
|
2.0
|
25.0
|
1.0
|
|
NC
|
O:CLA601
|
2.1
|
24.3
|
1.0
|
|
NB
|
O:CLA601
|
2.1
|
22.9
|
1.0
|
|
NA
|
O:CLA601
|
2.2
|
25.8
|
1.0
|
|
C4D
|
O:CLA601
|
3.0
|
25.0
|
1.0
|
|
C1B
|
O:CLA601
|
3.1
|
23.1
|
1.0
|
|
C1C
|
O:CLA601
|
3.1
|
22.8
|
1.0
|
|
C4B
|
O:CLA601
|
3.1
|
22.6
|
1.0
|
|
C4C
|
O:CLA601
|
3.1
|
24.0
|
1.0
|
|
C1D
|
O:CLA601
|
3.1
|
27.0
|
1.0
|
|
C4A
|
O:CLA601
|
3.2
|
23.6
|
1.0
|
|
C1A
|
O:CLA601
|
3.2
|
24.7
|
1.0
|
|
CHC
|
O:CLA601
|
3.5
|
22.4
|
1.0
|
|
CHD
|
O:CLA601
|
3.5
|
25.0
|
1.0
|
|
CHB
|
O:CLA601
|
3.5
|
22.9
|
1.0
|
|
CHA
|
O:CLA601
|
3.5
|
24.9
|
1.0
|
|
NE2
|
O:HIS66
|
4.0
|
24.8
|
1.0
|
|
C3D
|
O:CLA601
|
4.2
|
27.2
|
1.0
|
|
C22
|
O:PID612
|
4.3
|
23.6
|
1.0
|
|
C2C
|
O:CLA601
|
4.3
|
21.7
|
1.0
|
|
C2B
|
O:CLA601
|
4.3
|
21.9
|
1.0
|
|
C3C
|
O:CLA601
|
4.3
|
24.6
|
1.0
|
|
C2D
|
O:CLA601
|
4.3
|
28.1
|
1.0
|
|
C3B
|
O:CLA601
|
4.3
|
22.5
|
1.0
|
|
C3A
|
O:CLA601
|
4.5
|
22.6
|
1.0
|
|
C2A
|
O:CLA601
|
4.5
|
23.6
|
1.0
|
|
C23
|
O:PID612
|
4.6
|
22.8
|
1.0
|
|
CD2
|
O:HIS66
|
4.7
|
25.2
|
1.0
|
|
CE1
|
O:HIS66
|
4.7
|
23.5
|
1.0
|
|
CD1
|
O:LEU92
|
4.8
|
28.8
|
1.0
|
|
CM5
|
O:PID614
|
5.0
|
26.2
|
1.0
|
|
C19
|
O:PID614
|
5.0
|
28.4
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 1ppr
Go back to
Magnesium Binding Sites List in 1ppr
Magnesium binding site 6 out
of 6 in the Peridinin-Chlorophyll-Protein of Amphidinium Carterae
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Peridinin-Chlorophyll-Protein of Amphidinium Carterae within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Mg602
b:21.3
occ:1.00
|
MG
|
O:CLA602
|
0.0
|
21.3
|
1.0
|
|
O
|
O:HOH685
|
2.0
|
21.7
|
1.0
|
|
ND
|
O:CLA602
|
2.0
|
21.0
|
1.0
|
|
NB
|
O:CLA602
|
2.1
|
21.4
|
1.0
|
|
NC
|
O:CLA602
|
2.1
|
23.8
|
1.0
|
|
NA
|
O:CLA602
|
2.2
|
20.9
|
1.0
|
|
C4D
|
O:CLA602
|
3.0
|
22.4
|
1.0
|
|
C1C
|
O:CLA602
|
3.1
|
20.3
|
1.0
|
|
C4B
|
O:CLA602
|
3.1
|
22.8
|
1.0
|
|
C1B
|
O:CLA602
|
3.1
|
20.9
|
1.0
|
|
C1D
|
O:CLA602
|
3.1
|
19.7
|
1.0
|
|
C4C
|
O:CLA602
|
3.1
|
19.8
|
1.0
|
|
C4A
|
O:CLA602
|
3.2
|
20.3
|
1.0
|
|
C1A
|
O:CLA602
|
3.2
|
19.2
|
1.0
|
|
CHC
|
O:CLA602
|
3.4
|
20.8
|
1.0
|
|
CHD
|
O:CLA602
|
3.5
|
21.8
|
1.0
|
|
CHB
|
O:CLA602
|
3.5
|
22.6
|
1.0
|
|
CHA
|
O:CLA602
|
3.5
|
20.7
|
1.0
|
|
NE2
|
O:HIS229
|
4.1
|
19.7
|
1.0
|
|
C22
|
O:PID622
|
4.2
|
23.7
|
1.0
|
|
C3D
|
O:CLA602
|
4.2
|
21.7
|
1.0
|
|
C2D
|
O:CLA602
|
4.3
|
21.5
|
1.0
|
|
C2B
|
O:CLA602
|
4.3
|
21.0
|
1.0
|
|
C3B
|
O:CLA602
|
4.3
|
21.8
|
1.0
|
|
C2C
|
O:CLA602
|
4.3
|
23.0
|
1.0
|
|
C3C
|
O:CLA602
|
4.3
|
23.1
|
1.0
|
|
CIB
|
N:DGD625
|
4.5
|
38.8
|
1.0
|
|
C3A
|
O:CLA602
|
4.5
|
20.7
|
1.0
|
|
C2A
|
O:CLA602
|
4.5
|
19.9
|
1.0
|
|
C23
|
O:PID622
|
4.6
|
26.5
|
1.0
|
|
CD2
|
O:HIS229
|
4.8
|
20.0
|
1.0
|
|
CM5
|
O:PID624
|
4.8
|
25.1
|
1.0
|
|
C19
|
O:PID624
|
4.9
|
21.7
|
1.0
|
|
CE1
|
O:HIS229
|
4.9
|
21.9
|
1.0
|
|
CD1
|
O:LEU254
|
4.9
|
23.1
|
1.0
|
|
Reference:
E.Hofmann,
P.M.Wrench,
F.P.Sharples,
R.G.Hiller,
W.Welte,
K.Diederichs.
Structural Basis of Light Harvesting By Carotenoids: Peridinin-Chlorophyll-Protein From Amphidinium Carterae. Science V. 272 1788 1996.
ISSN: ISSN 0036-8075
PubMed: 8650577
Page generated: Tue Aug 13 10:53:45 2024
|
