Magnesium in PDB 6s2y: Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B
Protein crystallography data
The structure of Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B, PDB code: 6s2y
was solved by
A.Agostini,
E.Meneghin,
L.Gewehr,
D.Pedron,
D.M.Palm,
D.Carbonera,
H.Paulsen,
E.Jaenicke,
E.Collini,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.63 /
2.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
73.310,
82.900,
122.220,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
24.3 /
27.7
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B
(pdb code 6s2y). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B, PDB code: 6s2y:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6s2y
Go back to
Magnesium Binding Sites List in 6s2y
Magnesium binding site 1 out
of 4 in the Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1001
b:23.8
occ:1.00
|
MG
|
A:CHL1001
|
0.0
|
23.8
|
1.0
|
NA
|
A:CHL1001
|
2.0
|
23.9
|
1.0
|
ND
|
A:CHL1001
|
2.0
|
22.5
|
1.0
|
NB
|
A:CHL1001
|
2.0
|
24.7
|
1.0
|
NC
|
A:CHL1001
|
2.1
|
24.1
|
1.0
|
O
|
A:PRO36
|
2.3
|
22.1
|
1.0
|
C4D
|
A:CHL1001
|
2.9
|
23.4
|
1.0
|
C1A
|
A:CHL1001
|
3.0
|
24.0
|
1.0
|
C4A
|
A:CHL1001
|
3.0
|
22.7
|
1.0
|
C4B
|
A:CHL1001
|
3.0
|
24.0
|
1.0
|
C1B
|
A:CHL1001
|
3.1
|
22.6
|
1.0
|
C1C
|
A:CHL1001
|
3.1
|
23.2
|
1.0
|
C4C
|
A:CHL1001
|
3.1
|
24.2
|
1.0
|
C1D
|
A:CHL1001
|
3.1
|
23.3
|
1.0
|
CHB
|
A:CHL1001
|
3.3
|
22.1
|
1.0
|
CHC
|
A:CHL1001
|
3.4
|
22.1
|
1.0
|
CHA
|
A:CHL1001
|
3.4
|
24.0
|
1.0
|
C
|
A:PRO36
|
3.5
|
20.7
|
1.0
|
CHD
|
A:CHL1001
|
3.5
|
23.8
|
1.0
|
C9
|
B:CHL1001
|
3.9
|
39.2
|
1.0
|
C3D
|
A:CHL1001
|
4.1
|
22.7
|
1.0
|
C8
|
B:CHL1001
|
4.2
|
38.8
|
1.0
|
C3B
|
A:CHL1001
|
4.3
|
25.0
|
1.0
|
CA
|
A:ALA37
|
4.3
|
21.5
|
1.0
|
N
|
A:ALA37
|
4.3
|
19.9
|
1.0
|
C3A
|
A:CHL1001
|
4.3
|
23.2
|
1.0
|
C2A
|
A:CHL1001
|
4.3
|
23.5
|
1.0
|
C2D
|
A:CHL1001
|
4.3
|
22.1
|
1.0
|
C2B
|
A:CHL1001
|
4.4
|
24.7
|
1.0
|
C2C
|
A:CHL1001
|
4.4
|
24.0
|
1.0
|
C7
|
B:CHL1001
|
4.4
|
37.3
|
1.0
|
C3C
|
A:CHL1001
|
4.4
|
23.7
|
1.0
|
CA
|
A:PRO36
|
4.5
|
21.2
|
1.0
|
CD
|
A:PRO36
|
4.5
|
20.1
|
1.0
|
CB
|
A:ALA37
|
4.6
|
20.6
|
1.0
|
CB
|
A:PRO36
|
4.6
|
19.2
|
1.0
|
N
|
A:PRO36
|
4.6
|
20.5
|
1.0
|
CBD
|
A:CHL1001
|
4.8
|
24.3
|
1.0
|
CG2
|
A:VAL35
|
4.9
|
17.1
|
1.0
|
CG
|
A:PRO36
|
4.9
|
21.3
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6s2y
Go back to
Magnesium Binding Sites List in 6s2y
Magnesium binding site 2 out
of 4 in the Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1001
b:25.5
occ:1.00
|
MG
|
B:CHL1001
|
0.0
|
25.5
|
1.0
|
NA
|
B:CHL1001
|
2.0
|
24.6
|
1.0
|
ND
|
B:CHL1001
|
2.0
|
24.4
|
1.0
|
NB
|
B:CHL1001
|
2.1
|
25.0
|
1.0
|
NC
|
B:CHL1001
|
2.1
|
25.0
|
1.0
|
O
|
B:PRO36
|
2.3
|
26.0
|
1.0
|
C4D
|
B:CHL1001
|
2.9
|
24.3
|
1.0
|
C1A
|
B:CHL1001
|
3.0
|
26.2
|
1.0
|
C4A
|
B:CHL1001
|
3.0
|
24.6
|
1.0
|
C4B
|
B:CHL1001
|
3.0
|
24.5
|
1.0
|
C1B
|
B:CHL1001
|
3.1
|
25.4
|
1.0
|
C1C
|
B:CHL1001
|
3.1
|
25.9
|
1.0
|
C4C
|
B:CHL1001
|
3.1
|
25.2
|
1.0
|
C1D
|
B:CHL1001
|
3.1
|
24.1
|
1.0
|
CHB
|
B:CHL1001
|
3.3
|
24.0
|
1.0
|
CHC
|
B:CHL1001
|
3.4
|
26.4
|
1.0
|
CHA
|
B:CHL1001
|
3.4
|
24.8
|
1.0
|
C
|
B:PRO36
|
3.5
|
26.8
|
1.0
|
CHD
|
B:CHL1001
|
3.5
|
23.4
|
1.0
|
C9
|
A:CHL1001
|
3.9
|
41.7
|
1.0
|
C3D
|
B:CHL1001
|
4.1
|
25.5
|
1.0
|
C8
|
A:CHL1001
|
4.1
|
44.2
|
1.0
|
C2A
|
B:CHL1001
|
4.3
|
25.1
|
1.0
|
C6
|
A:CHL1001
|
4.3
|
40.7
|
1.0
|
C3A
|
B:CHL1001
|
4.3
|
24.8
|
1.0
|
C3B
|
B:CHL1001
|
4.3
|
26.4
|
1.0
|
N
|
B:ALA37
|
4.3
|
30.1
|
1.0
|
C2D
|
B:CHL1001
|
4.3
|
24.8
|
1.0
|
CA
|
B:ALA37
|
4.3
|
33.1
|
1.0
|
C2C
|
B:CHL1001
|
4.4
|
27.1
|
1.0
|
C2B
|
B:CHL1001
|
4.4
|
25.7
|
1.0
|
CD
|
B:PRO36
|
4.4
|
26.5
|
1.0
|
C3C
|
B:CHL1001
|
4.4
|
24.3
|
1.0
|
CA
|
B:PRO36
|
4.4
|
27.4
|
1.0
|
N
|
B:PRO36
|
4.5
|
29.1
|
1.0
|
CB
|
B:ALA37
|
4.6
|
29.0
|
1.0
|
CB
|
B:PRO36
|
4.6
|
27.9
|
1.0
|
C7
|
A:CHL1001
|
4.8
|
43.4
|
1.0
|
CG2
|
B:VAL35
|
4.8
|
29.1
|
1.0
|
CBD
|
B:CHL1001
|
4.9
|
26.2
|
1.0
|
CG
|
B:PRO36
|
4.9
|
27.7
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6s2y
Go back to
Magnesium Binding Sites List in 6s2y
Magnesium binding site 3 out
of 4 in the Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1001
b:21.1
occ:1.00
|
MG
|
C:CHL1001
|
0.0
|
21.1
|
1.0
|
NA
|
C:CHL1001
|
2.0
|
21.0
|
1.0
|
NB
|
C:CHL1001
|
2.0
|
22.5
|
1.0
|
ND
|
C:CHL1001
|
2.0
|
19.7
|
1.0
|
NC
|
C:CHL1001
|
2.1
|
22.5
|
1.0
|
O
|
C:PRO36
|
2.3
|
19.4
|
1.0
|
C4D
|
C:CHL1001
|
2.9
|
18.8
|
1.0
|
C1A
|
C:CHL1001
|
3.0
|
20.6
|
1.0
|
C4A
|
C:CHL1001
|
3.0
|
19.3
|
1.0
|
C1B
|
C:CHL1001
|
3.0
|
21.4
|
1.0
|
C4B
|
C:CHL1001
|
3.0
|
22.0
|
1.0
|
C1C
|
C:CHL1001
|
3.1
|
20.8
|
1.0
|
C4C
|
C:CHL1001
|
3.1
|
20.0
|
1.0
|
C1D
|
C:CHL1001
|
3.1
|
19.7
|
1.0
|
CHB
|
C:CHL1001
|
3.3
|
18.8
|
1.0
|
CHC
|
C:CHL1001
|
3.4
|
20.9
|
1.0
|
CHA
|
C:CHL1001
|
3.4
|
19.2
|
1.0
|
C
|
C:PRO36
|
3.5
|
17.2
|
1.0
|
CHD
|
C:CHL1001
|
3.5
|
19.2
|
1.0
|
C7
|
D:CHL1001
|
3.6
|
39.9
|
1.0
|
C8
|
D:CHL1001
|
3.7
|
40.1
|
1.0
|
C9
|
D:CHL1001
|
3.8
|
36.7
|
1.0
|
C3D
|
C:CHL1001
|
4.1
|
19.3
|
1.0
|
C2A
|
C:CHL1001
|
4.3
|
21.8
|
1.0
|
C3B
|
C:CHL1001
|
4.3
|
21.3
|
1.0
|
C3A
|
C:CHL1001
|
4.3
|
20.3
|
1.0
|
N
|
C:ALA37
|
4.3
|
17.4
|
1.0
|
C2B
|
C:CHL1001
|
4.3
|
21.8
|
1.0
|
C2C
|
C:CHL1001
|
4.3
|
21.3
|
1.0
|
C2D
|
C:CHL1001
|
4.4
|
21.2
|
1.0
|
CA
|
C:ALA37
|
4.4
|
20.3
|
1.0
|
C3C
|
C:CHL1001
|
4.4
|
20.1
|
1.0
|
CD
|
C:PRO36
|
4.4
|
18.1
|
1.0
|
CA
|
C:PRO36
|
4.5
|
18.6
|
1.0
|
N
|
C:PRO36
|
4.6
|
18.8
|
1.0
|
CB
|
C:ALA37
|
4.6
|
20.3
|
1.0
|
CB
|
C:PRO36
|
4.6
|
16.9
|
1.0
|
CG2
|
C:VAL35
|
4.8
|
19.2
|
1.0
|
CBD
|
C:CHL1001
|
4.9
|
20.1
|
1.0
|
CG
|
C:PRO36
|
4.9
|
17.0
|
1.0
|
C6
|
D:CHL1001
|
5.0
|
36.5
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6s2y
Go back to
Magnesium Binding Sites List in 6s2y
Magnesium binding site 4 out
of 4 in the Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1001
b:23.6
occ:1.00
|
MG
|
D:CHL1001
|
0.0
|
23.6
|
1.0
|
NA
|
D:CHL1001
|
2.0
|
23.8
|
1.0
|
ND
|
D:CHL1001
|
2.0
|
21.3
|
1.0
|
NB
|
D:CHL1001
|
2.0
|
22.5
|
1.0
|
NC
|
D:CHL1001
|
2.1
|
21.5
|
1.0
|
O
|
D:PRO36
|
2.2
|
21.5
|
1.0
|
C4D
|
D:CHL1001
|
2.9
|
20.2
|
1.0
|
C4A
|
D:CHL1001
|
3.0
|
22.9
|
1.0
|
C1A
|
D:CHL1001
|
3.0
|
23.7
|
1.0
|
C1B
|
D:CHL1001
|
3.0
|
22.1
|
1.0
|
C4B
|
D:CHL1001
|
3.0
|
21.0
|
1.0
|
C4C
|
D:CHL1001
|
3.1
|
20.5
|
1.0
|
C1C
|
D:CHL1001
|
3.1
|
19.4
|
1.0
|
C1D
|
D:CHL1001
|
3.1
|
19.9
|
1.0
|
CHB
|
D:CHL1001
|
3.3
|
22.7
|
1.0
|
C
|
D:PRO36
|
3.4
|
21.1
|
1.0
|
CHC
|
D:CHL1001
|
3.4
|
22.1
|
1.0
|
CHA
|
D:CHL1001
|
3.4
|
21.8
|
1.0
|
CHD
|
D:CHL1001
|
3.5
|
19.5
|
1.0
|
C8
|
C:CHL1001
|
3.7
|
42.4
|
1.0
|
C7
|
C:CHL1001
|
3.8
|
42.8
|
1.0
|
C9
|
C:CHL1001
|
4.0
|
40.0
|
1.0
|
C3D
|
D:CHL1001
|
4.1
|
20.0
|
1.0
|
N
|
D:ALA37
|
4.2
|
21.8
|
1.0
|
CA
|
D:ALA37
|
4.2
|
24.6
|
1.0
|
C3B
|
D:CHL1001
|
4.3
|
20.3
|
1.0
|
C3A
|
D:CHL1001
|
4.3
|
24.0
|
1.0
|
C2A
|
D:CHL1001
|
4.3
|
22.1
|
1.0
|
C2B
|
D:CHL1001
|
4.3
|
19.2
|
1.0
|
C2D
|
D:CHL1001
|
4.4
|
19.3
|
1.0
|
CA
|
D:PRO36
|
4.4
|
23.1
|
1.0
|
C2C
|
D:CHL1001
|
4.4
|
20.1
|
1.0
|
C3C
|
D:CHL1001
|
4.4
|
19.6
|
1.0
|
CD
|
D:PRO36
|
4.4
|
23.7
|
1.0
|
CB
|
D:ALA37
|
4.5
|
21.2
|
1.0
|
N
|
D:PRO36
|
4.5
|
22.7
|
1.0
|
CB
|
D:PRO36
|
4.5
|
23.5
|
1.0
|
CG2
|
D:VAL35
|
4.8
|
19.9
|
1.0
|
C10
|
C:CHL1001
|
4.8
|
40.0
|
1.0
|
CBD
|
D:CHL1001
|
4.9
|
21.6
|
1.0
|
CG
|
D:PRO36
|
4.9
|
25.1
|
1.0
|
|
Reference:
A.Agostini,
E.Meneghin,
L.Gewehr,
D.Pedron,
D.M.Palm,
D.Carbonera,
H.Paulsen,
E.Jaenicke,
E.Collini.
How Water-Mediated Hydrogen Bonds Affect Chlorophyll A/B Selectivity in Water-Soluble Chlorophyll Protein. Sci Rep V. 9 18255 2019.
ISSN: ESSN 2045-2322
PubMed: 31796824
DOI: 10.1038/S41598-019-54520-4
Page generated: Tue Oct 1 17:37:11 2024
|