Magnesium in PDB 5v2c: Re-Refinement of Crystal Structure of Photosystem II Complex
Enzymatic activity of Re-Refinement of Crystal Structure of Photosystem II Complex
All present enzymatic activity of Re-Refinement of Crystal Structure of Photosystem II Complex:
1.10.3.9;
Protein crystallography data
The structure of Re-Refinement of Crystal Structure of Photosystem II Complex, PDB code: 5v2c
was solved by
J.Wang,
J.M.Wiwczar,
G.W.Brudvig,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
178.62 /
1.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
122.190,
228.510,
286.400,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
9.2 /
16.3
|
Other elements in 5v2c:
The structure of Re-Refinement of Crystal Structure of Photosystem II Complex also contains other interesting chemical elements:
Magnesium Binding Sites:
Magnesium binding site 1 out
of 74 in 5v2c
Go back to
Magnesium Binding Sites List in 5v2c
Magnesium binding site 1 out
of 74 in the Re-Refinement of Crystal Structure of Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg606
b:20.2
occ:1.00
|
MG
|
A:CLA606
|
0.0
|
20.2
|
1.0
|
ND
|
A:CLA606
|
2.0
|
17.6
|
1.0
|
NB
|
A:CLA606
|
2.0
|
18.7
|
1.0
|
NA
|
A:CLA606
|
2.0
|
18.6
|
1.0
|
NC
|
A:CLA606
|
2.1
|
19.2
|
1.0
|
NE2
|
A:HIS198
|
2.2
|
20.4
|
1.0
|
C4D
|
A:CLA606
|
3.0
|
18.1
|
1.0
|
C4A
|
A:CLA606
|
3.0
|
17.9
|
1.0
|
C4B
|
A:CLA606
|
3.0
|
18.3
|
1.0
|
C1A
|
A:CLA606
|
3.1
|
17.6
|
1.0
|
C1C
|
A:CLA606
|
3.1
|
16.8
|
1.0
|
C1B
|
A:CLA606
|
3.1
|
17.1
|
1.0
|
CE1
|
A:HIS198
|
3.1
|
17.5
|
1.0
|
C1D
|
A:CLA606
|
3.1
|
17.2
|
1.0
|
C4C
|
A:CLA606
|
3.2
|
16.0
|
1.0
|
CD2
|
A:HIS198
|
3.2
|
21.3
|
1.0
|
CHC
|
A:CLA606
|
3.4
|
17.7
|
1.0
|
CHB
|
A:CLA606
|
3.4
|
15.4
|
1.0
|
CHA
|
A:CLA606
|
3.4
|
17.1
|
1.0
|
CHD
|
A:CLA606
|
3.5
|
16.8
|
1.0
|
CE
|
A:MET183
|
4.0
|
20.3
|
1.0
|
C3D
|
A:CLA606
|
4.2
|
17.9
|
1.0
|
ND1
|
A:HIS198
|
4.2
|
18.8
|
1.0
|
C3B
|
A:CLA606
|
4.3
|
15.8
|
1.0
|
CG
|
A:HIS198
|
4.3
|
18.3
|
1.0
|
C2D
|
A:CLA606
|
4.4
|
15.4
|
1.0
|
C2B
|
A:CLA606
|
4.4
|
18.1
|
1.0
|
C3A
|
A:CLA606
|
4.4
|
18.3
|
1.0
|
C2C
|
A:CLA606
|
4.4
|
14.8
|
1.0
|
C2A
|
A:CLA606
|
4.4
|
18.1
|
1.0
|
C3C
|
A:CLA606
|
4.4
|
15.4
|
1.0
|
CAB
|
D:CLA404
|
4.5
|
17.8
|
1.0
|
CBD
|
A:CLA606
|
4.9
|
17.8
|
1.0
|
|
Magnesium binding site 2 out
of 74 in 5v2c
Go back to
Magnesium Binding Sites List in 5v2c
Magnesium binding site 2 out
of 74 in the Re-Refinement of Crystal Structure of Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg607
b:20.9
occ:1.00
|
MG
|
A:CLA607
|
0.0
|
20.9
|
1.0
|
NB
|
A:CLA607
|
2.0
|
19.7
|
1.0
|
ND
|
A:CLA607
|
2.0
|
18.7
|
1.0
|
NC
|
A:CLA607
|
2.0
|
19.8
|
1.0
|
NA
|
A:CLA607
|
2.1
|
20.5
|
1.0
|
O
|
A:HOH850
|
2.3
|
20.4
|
1.0
|
C4D
|
A:CLA607
|
3.0
|
19.1
|
1.0
|
C4B
|
A:CLA607
|
3.0
|
20.2
|
1.0
|
C1B
|
A:CLA607
|
3.0
|
19.9
|
1.0
|
C4A
|
A:CLA607
|
3.0
|
19.9
|
1.0
|
C1C
|
A:CLA607
|
3.0
|
18.9
|
1.0
|
C1A
|
A:CLA607
|
3.0
|
18.7
|
1.0
|
C4C
|
A:CLA607
|
3.1
|
18.7
|
1.0
|
C1D
|
A:CLA607
|
3.1
|
19.1
|
1.0
|
CHB
|
A:CLA607
|
3.4
|
19.8
|
1.0
|
CHC
|
A:CLA607
|
3.4
|
17.2
|
1.0
|
CHA
|
A:CLA607
|
3.5
|
18.9
|
1.0
|
CHD
|
A:CLA607
|
3.5
|
20.5
|
1.0
|
CBB
|
D:PHO401
|
3.8
|
29.3
|
1.0
|
O
|
A:HOH852
|
4.2
|
18.4
|
1.0
|
C3D
|
A:CLA607
|
4.2
|
19.0
|
1.0
|
C3B
|
A:CLA607
|
4.3
|
21.2
|
1.0
|
C2B
|
A:CLA607
|
4.3
|
18.1
|
1.0
|
C2C
|
A:CLA607
|
4.3
|
17.9
|
1.0
|
C3C
|
A:CLA607
|
4.4
|
17.3
|
1.0
|
C2D
|
A:CLA607
|
4.4
|
19.1
|
1.0
|
C3A
|
A:CLA607
|
4.4
|
19.2
|
1.0
|
C2A
|
A:CLA607
|
4.4
|
17.4
|
1.0
|
CG2
|
D:ILE178
|
4.7
|
20.0
|
1.0
|
CE2
|
A:PHE206
|
4.7
|
21.2
|
1.0
|
CBA
|
A:CLA607
|
4.8
|
19.3
|
1.0
|
CBD
|
A:CLA607
|
4.9
|
21.5
|
1.0
|
C20
|
D:PHO401
|
5.0
|
21.1
|
1.0
|
|
Magnesium binding site 3 out
of 74 in 5v2c
Go back to
Magnesium Binding Sites List in 5v2c
Magnesium binding site 3 out
of 74 in the Re-Refinement of Crystal Structure of Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg609
b:24.6
occ:1.00
|
MG
|
A:CLA609
|
0.0
|
24.6
|
1.0
|
NA
|
A:CLA609
|
2.0
|
24.7
|
1.0
|
ND
|
A:CLA609
|
2.0
|
23.3
|
1.0
|
NB
|
A:CLA609
|
2.0
|
23.5
|
1.0
|
NC
|
A:CLA609
|
2.1
|
25.4
|
1.0
|
NE2
|
A:HIS118
|
2.1
|
22.9
|
1.0
|
C4A
|
A:CLA609
|
3.0
|
24.5
|
1.0
|
C4D
|
A:CLA609
|
3.0
|
24.6
|
1.0
|
C1A
|
A:CLA609
|
3.0
|
27.4
|
1.0
|
C1B
|
A:CLA609
|
3.0
|
21.9
|
1.0
|
CE1
|
A:HIS118
|
3.0
|
28.1
|
1.0
|
C4B
|
A:CLA609
|
3.0
|
24.3
|
1.0
|
C1C
|
A:CLA609
|
3.1
|
24.8
|
1.0
|
C4C
|
A:CLA609
|
3.1
|
20.5
|
1.0
|
C1D
|
A:CLA609
|
3.1
|
20.8
|
1.0
|
CD2
|
A:HIS118
|
3.2
|
22.3
|
1.0
|
CHB
|
A:CLA609
|
3.4
|
19.2
|
1.0
|
CHC
|
A:CLA609
|
3.5
|
24.2
|
1.0
|
CHA
|
A:CLA609
|
3.5
|
23.7
|
1.0
|
CHD
|
A:CLA609
|
3.5
|
22.1
|
1.0
|
ND1
|
A:HIS118
|
4.2
|
22.9
|
1.0
|
C3D
|
A:CLA609
|
4.2
|
22.2
|
1.0
|
CG1
|
I:VAL8
|
4.2
|
28.0
|
1.0
|
CG
|
A:HIS118
|
4.3
|
20.0
|
1.0
|
C3A
|
A:CLA609
|
4.3
|
23.1
|
1.0
|
C2D
|
A:CLA609
|
4.4
|
24.3
|
1.0
|
C3B
|
A:CLA609
|
4.4
|
23.1
|
1.0
|
C2B
|
A:CLA609
|
4.4
|
23.2
|
1.0
|
C2A
|
A:CLA609
|
4.4
|
24.8
|
1.0
|
C3C
|
A:CLA609
|
4.4
|
24.9
|
1.0
|
C2C
|
A:CLA609
|
4.4
|
20.1
|
1.0
|
CG2
|
I:VAL12
|
4.5
|
29.8
|
1.0
|
CMA
|
A:CLA609
|
4.9
|
24.5
|
1.0
|
CBD
|
A:CLA609
|
4.9
|
25.6
|
1.0
|
CBA
|
A:CLA609
|
5.0
|
29.2
|
1.0
|
|
Magnesium binding site 4 out
of 74 in 5v2c
Go back to
Magnesium Binding Sites List in 5v2c
Magnesium binding site 4 out
of 74 in the Re-Refinement of Crystal Structure of Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:35.0
occ:1.00
|
MG
|
B:CLA602
|
0.0
|
35.0
|
1.0
|
NC
|
B:CLA602
|
2.0
|
31.2
|
1.0
|
ND
|
B:CLA602
|
2.0
|
32.9
|
1.0
|
NA
|
B:CLA602
|
2.0
|
39.4
|
1.0
|
NB
|
B:CLA602
|
2.1
|
32.2
|
1.0
|
O
|
B:HOH727
|
2.3
|
37.2
|
1.0
|
C4D
|
B:CLA602
|
3.0
|
37.5
|
1.0
|
C1C
|
B:CLA602
|
3.0
|
35.4
|
1.0
|
C4A
|
B:CLA602
|
3.0
|
35.9
|
1.0
|
C1A
|
B:CLA602
|
3.0
|
41.7
|
1.0
|
C4B
|
B:CLA602
|
3.1
|
31.8
|
1.0
|
C4C
|
B:CLA602
|
3.1
|
30.6
|
1.0
|
C1B
|
B:CLA602
|
3.1
|
32.8
|
1.0
|
C1D
|
B:CLA602
|
3.1
|
36.2
|
1.0
|
CHC
|
B:CLA602
|
3.4
|
35.1
|
1.0
|
CHB
|
B:CLA602
|
3.4
|
31.1
|
1.0
|
CHA
|
B:CLA602
|
3.5
|
32.1
|
1.0
|
CHD
|
B:CLA602
|
3.5
|
30.8
|
1.0
|
C10
|
B:CLA602
|
3.7
|
58.9
|
1.0
|
C12
|
B:CLA602
|
4.0
|
50.6
|
1.0
|
C3D
|
B:CLA602
|
4.2
|
32.6
|
1.0
|
O
|
B:TRP185
|
4.3
|
37.4
|
1.0
|
C11
|
B:CLA602
|
4.3
|
53.8
|
1.0
|
C2C
|
B:CLA602
|
4.3
|
27.1
|
1.0
|
C3C
|
B:CLA602
|
4.4
|
32.0
|
1.0
|
C2D
|
B:CLA602
|
4.4
|
39.8
|
1.0
|
C3B
|
B:CLA602
|
4.4
|
29.0
|
1.0
|
C3A
|
B:CLA602
|
4.4
|
39.1
|
1.0
|
C2A
|
B:CLA602
|
4.4
|
38.2
|
1.0
|
C2B
|
B:CLA602
|
4.4
|
29.4
|
1.0
|
C14
|
B:CLA602
|
4.5
|
92.8
|
1.0
|
CE2
|
B:PHE190
|
4.5
|
33.9
|
1.0
|
CZ
|
B:PHE190
|
4.7
|
30.2
|
1.0
|
C8
|
B:CLA602
|
4.8
|
71.7
|
1.0
|
CBB
|
B:CLA603
|
4.8
|
29.9
|
1.0
|
C13
|
B:CLA602
|
4.9
|
64.9
|
1.0
|
CBA
|
B:CLA602
|
4.9
|
52.2
|
1.0
|
CBD
|
B:CLA602
|
4.9
|
40.7
|
1.0
|
|
Magnesium binding site 5 out
of 74 in 5v2c
Go back to
Magnesium Binding Sites List in 5v2c
Magnesium binding site 5 out
of 74 in the Re-Refinement of Crystal Structure of Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:27.7
occ:1.00
|
MG
|
B:CLA603
|
0.0
|
27.7
|
1.0
|
ND
|
B:CLA603
|
2.0
|
22.2
|
1.0
|
NB
|
B:CLA603
|
2.0
|
27.3
|
1.0
|
NA
|
B:CLA603
|
2.1
|
26.4
|
1.0
|
NC
|
B:CLA603
|
2.1
|
29.1
|
1.0
|
ND1
|
B:HIS201
|
2.2
|
28.3
|
1.0
|
CE1
|
B:HIS201
|
2.9
|
29.0
|
1.0
|
C4D
|
B:CLA603
|
3.0
|
25.2
|
1.0
|
C4A
|
B:CLA603
|
3.0
|
27.1
|
1.0
|
C1B
|
B:CLA603
|
3.1
|
29.0
|
1.0
|
C4B
|
B:CLA603
|
3.1
|
27.6
|
1.0
|
C1A
|
B:CLA603
|
3.1
|
25.4
|
1.0
|
C1C
|
B:CLA603
|
3.1
|
27.5
|
1.0
|
C4C
|
B:CLA603
|
3.1
|
25.4
|
1.0
|
C1D
|
B:CLA603
|
3.1
|
24.4
|
1.0
|
CG
|
B:HIS201
|
3.4
|
25.6
|
1.0
|
CHB
|
B:CLA603
|
3.4
|
25.4
|
1.0
|
CHC
|
B:CLA603
|
3.5
|
25.6
|
1.0
|
CHA
|
B:CLA603
|
3.5
|
23.1
|
1.0
|
CHD
|
B:CLA603
|
3.5
|
23.5
|
1.0
|
CZ
|
H:PHE41
|
3.7
|
30.0
|
1.0
|
CB
|
B:HIS201
|
3.9
|
23.9
|
1.0
|
NE2
|
B:HIS201
|
4.2
|
29.2
|
1.0
|
CE2
|
H:PHE41
|
4.2
|
24.6
|
1.0
|
C3D
|
B:CLA603
|
4.2
|
23.2
|
1.0
|
C3A
|
B:CLA603
|
4.4
|
26.1
|
1.0
|
C2D
|
B:CLA603
|
4.4
|
23.0
|
1.0
|
C2B
|
B:CLA603
|
4.4
|
29.0
|
1.0
|
C3B
|
B:CLA603
|
4.4
|
25.8
|
1.0
|
CD2
|
B:HIS201
|
4.4
|
23.1
|
1.0
|
C2C
|
B:CLA603
|
4.4
|
27.6
|
1.0
|
C3C
|
B:CLA603
|
4.4
|
27.3
|
1.0
|
C2A
|
B:CLA603
|
4.4
|
27.9
|
1.0
|
CA
|
B:HIS201
|
4.5
|
25.2
|
1.0
|
CE1
|
H:PHE41
|
4.8
|
28.1
|
1.0
|
CBD
|
B:CLA603
|
4.9
|
25.1
|
1.0
|
CMA
|
B:CLA603
|
5.0
|
26.8
|
1.0
|
|
Magnesium binding site 6 out
of 74 in 5v2c
Go back to
Magnesium Binding Sites List in 5v2c
Magnesium binding site 6 out
of 74 in the Re-Refinement of Crystal Structure of Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:24.1
occ:1.00
|
MG
|
B:CLA604
|
0.0
|
24.1
|
1.0
|
NB
|
B:CLA604
|
2.0
|
21.3
|
1.0
|
NA
|
B:CLA604
|
2.1
|
22.1
|
1.0
|
ND
|
B:CLA604
|
2.1
|
21.9
|
1.0
|
NC
|
B:CLA604
|
2.1
|
23.7
|
1.0
|
NE2
|
B:HIS202
|
2.1
|
21.0
|
1.0
|
C4B
|
B:CLA604
|
3.0
|
22.3
|
1.0
|
C4D
|
B:CLA604
|
3.0
|
22.2
|
1.0
|
C1B
|
B:CLA604
|
3.0
|
23.9
|
1.0
|
C1A
|
B:CLA604
|
3.0
|
24.5
|
1.0
|
C4A
|
B:CLA604
|
3.1
|
22.2
|
1.0
|
C1C
|
B:CLA604
|
3.1
|
21.6
|
1.0
|
C4C
|
B:CLA604
|
3.1
|
20.5
|
1.0
|
CE1
|
B:HIS202
|
3.1
|
26.4
|
1.0
|
C1D
|
B:CLA604
|
3.1
|
21.9
|
1.0
|
CD2
|
B:HIS202
|
3.2
|
25.1
|
1.0
|
CHC
|
B:CLA604
|
3.4
|
21.3
|
1.0
|
CHB
|
B:CLA604
|
3.4
|
23.4
|
1.0
|
CHA
|
B:CLA604
|
3.5
|
21.1
|
1.0
|
CHD
|
B:CLA604
|
3.5
|
23.0
|
1.0
|
ND1
|
B:HIS202
|
4.3
|
23.9
|
1.0
|
C3D
|
B:CLA604
|
4.3
|
22.6
|
1.0
|
CG
|
B:HIS202
|
4.3
|
20.6
|
1.0
|
C3B
|
B:CLA604
|
4.3
|
20.9
|
1.0
|
C2A
|
B:CLA604
|
4.4
|
24.1
|
1.0
|
C2D
|
B:CLA604
|
4.4
|
22.0
|
1.0
|
C2B
|
B:CLA604
|
4.4
|
19.9
|
1.0
|
C3A
|
B:CLA604
|
4.4
|
24.4
|
1.0
|
C2C
|
B:CLA604
|
4.4
|
23.2
|
1.0
|
C3C
|
B:CLA604
|
4.4
|
21.9
|
1.0
|
C6
|
B:CLA606
|
4.4
|
32.8
|
1.0
|
C4
|
B:CLA606
|
4.5
|
33.0
|
1.0
|
C5
|
B:CLA606
|
4.6
|
26.4
|
1.0
|
C7
|
B:CLA606
|
4.8
|
34.5
|
1.0
|
CBA
|
B:CLA604
|
4.9
|
20.9
|
1.0
|
NE2
|
B:HIS201
|
4.9
|
29.2
|
1.0
|
CD2
|
B:HIS201
|
4.9
|
23.1
|
1.0
|
CBD
|
B:CLA604
|
5.0
|
24.1
|
1.0
|
|
Magnesium binding site 7 out
of 74 in 5v2c
Go back to
Magnesium Binding Sites List in 5v2c
Magnesium binding site 7 out
of 74 in the Re-Refinement of Crystal Structure of Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg605
b:22.0
occ:1.00
|
MG
|
B:CLA605
|
0.0
|
22.0
|
1.0
|
NB
|
B:CLA605
|
2.0
|
20.7
|
1.0
|
ND
|
B:CLA605
|
2.0
|
20.1
|
1.0
|
NA
|
B:CLA605
|
2.0
|
19.9
|
1.0
|
NC
|
B:CLA605
|
2.0
|
21.2
|
1.0
|
NE2
|
B:HIS455
|
2.1
|
19.9
|
1.0
|
C4D
|
B:CLA605
|
3.0
|
19.6
|
1.0
|
C4A
|
B:CLA605
|
3.0
|
19.2
|
1.0
|
C4B
|
B:CLA605
|
3.0
|
19.9
|
1.0
|
C1B
|
B:CLA605
|
3.0
|
19.5
|
1.0
|
C1A
|
B:CLA605
|
3.1
|
17.9
|
1.0
|
C1C
|
B:CLA605
|
3.1
|
20.2
|
1.0
|
C4C
|
B:CLA605
|
3.1
|
18.7
|
1.0
|
CD2
|
B:HIS455
|
3.1
|
21.8
|
1.0
|
C1D
|
B:CLA605
|
3.1
|
18.3
|
1.0
|
CE1
|
B:HIS455
|
3.2
|
22.4
|
1.0
|
CHB
|
B:CLA605
|
3.4
|
18.5
|
1.0
|
CHC
|
B:CLA605
|
3.4
|
19.6
|
1.0
|
CHD
|
B:CLA605
|
3.5
|
17.7
|
1.0
|
CHA
|
B:CLA605
|
3.5
|
18.1
|
1.0
|
C14
|
B:CLA613
|
4.2
|
31.7
|
1.0
|
C3D
|
B:CLA605
|
4.2
|
17.8
|
1.0
|
CG
|
B:HIS455
|
4.3
|
18.5
|
1.0
|
ND1
|
B:HIS455
|
4.3
|
20.6
|
1.0
|
C3B
|
B:CLA605
|
4.3
|
19.8
|
1.0
|
C2B
|
B:CLA605
|
4.3
|
18.5
|
1.0
|
C3A
|
B:CLA605
|
4.4
|
20.6
|
1.0
|
C2D
|
B:CLA605
|
4.4
|
18.2
|
1.0
|
C2A
|
B:CLA605
|
4.4
|
20.1
|
1.0
|
C3C
|
B:CLA605
|
4.4
|
20.2
|
1.0
|
C2C
|
B:CLA605
|
4.4
|
19.8
|
1.0
|
C13
|
B:CLA613
|
4.7
|
25.3
|
1.0
|
C15
|
B:CLA613
|
4.8
|
28.1
|
1.0
|
CBD
|
B:CLA605
|
5.0
|
17.7
|
1.0
|
|
Magnesium binding site 8 out
of 74 in 5v2c
Go back to
Magnesium Binding Sites List in 5v2c
Magnesium binding site 8 out
of 74 in the Re-Refinement of Crystal Structure of Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg606
b:22.7
occ:1.00
|
MG
|
B:CLA606
|
0.0
|
22.7
|
1.0
|
ND
|
B:CLA606
|
2.0
|
21.0
|
1.0
|
NB
|
B:CLA606
|
2.0
|
22.7
|
1.0
|
NA
|
B:CLA606
|
2.1
|
21.8
|
1.0
|
NC
|
B:CLA606
|
2.1
|
24.6
|
1.0
|
NE2
|
B:HIS100
|
2.2
|
21.4
|
1.0
|
C4D
|
B:CLA606
|
3.0
|
21.5
|
1.0
|
C4A
|
B:CLA606
|
3.0
|
21.6
|
1.0
|
C4B
|
B:CLA606
|
3.0
|
21.9
|
1.0
|
C1A
|
B:CLA606
|
3.0
|
18.2
|
1.0
|
C1B
|
B:CLA606
|
3.1
|
21.9
|
1.0
|
C1C
|
B:CLA606
|
3.1
|
21.8
|
1.0
|
C1D
|
B:CLA606
|
3.1
|
20.9
|
1.0
|
C4C
|
B:CLA606
|
3.1
|
20.7
|
1.0
|
CE1
|
B:HIS100
|
3.1
|
25.4
|
1.0
|
CD2
|
B:HIS100
|
3.2
|
19.7
|
1.0
|
CHC
|
B:CLA606
|
3.4
|
19.5
|
1.0
|
CHB
|
B:CLA606
|
3.4
|
25.3
|
1.0
|
CHA
|
B:CLA606
|
3.4
|
18.9
|
1.0
|
CHD
|
B:CLA606
|
3.5
|
23.0
|
1.0
|
C1
|
B:CLA605
|
4.1
|
30.9
|
1.0
|
C2
|
B:CLA605
|
4.2
|
40.6
|
1.0
|
C3D
|
B:CLA606
|
4.3
|
20.1
|
1.0
|
ND1
|
B:HIS100
|
4.3
|
21.6
|
1.0
|
CG
|
B:HIS100
|
4.3
|
19.4
|
1.0
|
C3B
|
B:CLA606
|
4.3
|
24.9
|
1.0
|
C3A
|
B:CLA606
|
4.4
|
21.1
|
1.0
|
C2D
|
B:CLA606
|
4.4
|
19.2
|
1.0
|
C2C
|
B:CLA606
|
4.4
|
20.4
|
1.0
|
C2B
|
B:CLA606
|
4.4
|
21.8
|
1.0
|
C2A
|
B:CLA606
|
4.4
|
20.4
|
1.0
|
C3C
|
B:CLA606
|
4.4
|
22.1
|
1.0
|
CBD
|
B:CLA606
|
4.9
|
19.4
|
1.0
|
O1A
|
B:CLA605
|
4.9
|
24.2
|
1.0
|
O2A
|
B:CLA605
|
4.9
|
27.1
|
1.0
|
|
Magnesium binding site 9 out
of 74 in 5v2c
Go back to
Magnesium Binding Sites List in 5v2c
Magnesium binding site 9 out
of 74 in the Re-Refinement of Crystal Structure of Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg607
b:26.2
occ:1.00
|
MG
|
B:CLA607
|
0.0
|
26.2
|
1.0
|
NB
|
B:CLA607
|
2.0
|
25.2
|
1.0
|
ND
|
B:CLA607
|
2.0
|
27.2
|
1.0
|
NC
|
B:CLA607
|
2.0
|
25.6
|
1.0
|
NA
|
B:CLA607
|
2.1
|
25.5
|
1.0
|
ND1
|
B:HIS157
|
2.2
|
27.4
|
1.0
|
CE1
|
B:HIS157
|
3.0
|
34.0
|
1.0
|
C4D
|
B:CLA607
|
3.0
|
28.6
|
1.0
|
C1B
|
B:CLA607
|
3.0
|
24.7
|
1.0
|
C4B
|
B:CLA607
|
3.0
|
24.4
|
1.0
|
C4C
|
B:CLA607
|
3.1
|
23.0
|
1.0
|
C1A
|
B:CLA607
|
3.1
|
23.5
|
1.0
|
C1C
|
B:CLA607
|
3.1
|
25.6
|
1.0
|
C4A
|
B:CLA607
|
3.1
|
22.4
|
1.0
|
C1D
|
B:CLA607
|
3.1
|
24.0
|
1.0
|
CG
|
B:HIS157
|
3.3
|
27.3
|
1.0
|
CHB
|
B:CLA607
|
3.4
|
23.0
|
1.0
|
CHC
|
B:CLA607
|
3.4
|
25.8
|
1.0
|
CHA
|
B:CLA607
|
3.5
|
25.1
|
1.0
|
CHD
|
B:CLA607
|
3.5
|
27.2
|
1.0
|
CB
|
B:HIS157
|
3.9
|
27.0
|
1.0
|
C11
|
B:P6G651
|
3.9
|
50.4
|
1.0
|
O10
|
B:P6G651
|
4.0
|
53.8
|
1.0
|
NE2
|
B:HIS157
|
4.2
|
30.9
|
1.0
|
C3D
|
B:CLA607
|
4.2
|
28.6
|
1.0
|
C3B
|
B:CLA607
|
4.3
|
20.4
|
1.0
|
C2B
|
B:CLA607
|
4.3
|
21.8
|
1.0
|
C2D
|
B:CLA607
|
4.4
|
27.1
|
1.0
|
C3C
|
B:CLA607
|
4.4
|
24.6
|
1.0
|
CD2
|
B:HIS157
|
4.4
|
28.0
|
1.0
|
C12
|
B:P6G651
|
4.4
|
49.2
|
1.0
|
C2C
|
B:CLA607
|
4.4
|
26.2
|
1.0
|
C3A
|
B:CLA607
|
4.4
|
19.8
|
1.0
|
C2A
|
B:CLA607
|
4.4
|
21.5
|
1.0
|
C9
|
B:P6G651
|
4.6
|
49.8
|
1.0
|
CD
|
B:PRO164
|
4.9
|
29.3
|
1.0
|
CBD
|
B:CLA607
|
5.0
|
32.1
|
1.0
|
|
Magnesium binding site 10 out
of 74 in 5v2c
Go back to
Magnesium Binding Sites List in 5v2c
Magnesium binding site 10 out
of 74 in the Re-Refinement of Crystal Structure of Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg608
b:19.9
occ:1.00
|
MG
|
B:CLA608
|
0.0
|
19.9
|
1.0
|
NB
|
B:CLA608
|
2.0
|
16.6
|
1.0
|
ND
|
B:CLA608
|
2.0
|
17.1
|
1.0
|
NA
|
B:CLA608
|
2.1
|
18.4
|
1.0
|
NC
|
B:CLA608
|
2.1
|
21.6
|
1.0
|
O
|
B:HOH991
|
2.2
|
18.4
|
1.0
|
C4D
|
B:CLA608
|
3.0
|
20.2
|
1.0
|
C1B
|
B:CLA608
|
3.0
|
19.2
|
1.0
|
C4B
|
B:CLA608
|
3.0
|
18.6
|
1.0
|
C4A
|
B:CLA608
|
3.1
|
20.9
|
1.0
|
C1A
|
B:CLA608
|
3.1
|
18.9
|
1.0
|
C1C
|
B:CLA608
|
3.1
|
19.9
|
1.0
|
C4C
|
B:CLA608
|
3.1
|
17.9
|
1.0
|
C1D
|
B:CLA608
|
3.1
|
18.4
|
1.0
|
CHB
|
B:CLA608
|
3.4
|
18.0
|
1.0
|
CHC
|
B:CLA608
|
3.4
|
18.7
|
1.0
|
CHA
|
B:CLA608
|
3.5
|
20.7
|
1.0
|
C12
|
B:LMG621
|
3.5
|
38.5
|
1.0
|
CHD
|
B:CLA608
|
3.5
|
18.4
|
1.0
|
O
|
B:HOH751
|
4.2
|
18.0
|
1.0
|
C3D
|
B:CLA608
|
4.2
|
19.2
|
1.0
|
C14
|
B:LMG621
|
4.3
|
30.6
|
1.0
|
C3B
|
B:CLA608
|
4.4
|
20.1
|
1.0
|
C2C
|
B:CLA608
|
4.4
|
20.5
|
1.0
|
C2B
|
B:CLA608
|
4.4
|
18.3
|
1.0
|
C3C
|
B:CLA608
|
4.4
|
19.0
|
1.0
|
C2D
|
B:CLA608
|
4.4
|
20.2
|
1.0
|
C2A
|
B:CLA608
|
4.4
|
19.3
|
1.0
|
C3A
|
B:CLA608
|
4.4
|
19.9
|
1.0
|
C11
|
B:LMG621
|
4.4
|
32.8
|
1.0
|
SD
|
B:MET37
|
4.5
|
19.5
|
1.0
|
C13
|
B:LMG621
|
4.5
|
31.6
|
1.0
|
CD2
|
B:PHE61
|
4.6
|
21.9
|
1.0
|
O9
|
B:LMG621
|
4.6
|
43.2
|
1.0
|
CE
|
B:MET37
|
4.8
|
21.0
|
1.0
|
CB
|
B:PHE61
|
4.9
|
15.4
|
1.0
|
CBA
|
B:CLA608
|
4.9
|
18.4
|
1.0
|
C10
|
B:LMG621
|
4.9
|
36.6
|
1.0
|
CG
|
B:PHE61
|
4.9
|
20.1
|
1.0
|
CBD
|
B:CLA608
|
4.9
|
20.0
|
1.0
|
|
Reference:
J.M.Wiwczar,
A.M.Lafountain,
J.Wang,
H.A.Frank,
G.W.Brudvig.
Chlorophyll A with A Farnesyl Tail in Thermophilic Cyanobacteria. Photosyn. Res. V. 134 175 2017.
ISSN: ISSN 1573-5079
PubMed: 28741056
DOI: 10.1007/S11120-017-0425-4
Page generated: Mon Sep 30 05:57:17 2024
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