Calcium in PDB 6trd: Cryo- Em Structure of the Thermosynechococcus Elongatus Photosystem I in the Presence of Cytochrome C6
Enzymatic activity of Cryo- Em Structure of the Thermosynechococcus Elongatus Photosystem I in the Presence of Cytochrome C6
All present enzymatic activity of Cryo- Em Structure of the Thermosynechococcus Elongatus Photosystem I in the Presence of Cytochrome C6:
1.97.1.12;
Other elements in 6trd:
The structure of Cryo- Em Structure of the Thermosynechococcus Elongatus Photosystem I in the Presence of Cytochrome C6 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Cryo- Em Structure of the Thermosynechococcus Elongatus Photosystem I in the Presence of Cytochrome C6
(pdb code 6trd). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Cryo- Em Structure of the Thermosynechococcus Elongatus Photosystem I in the Presence of Cytochrome C6, PDB code: 6trd:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 6trd
Go back to
Calcium Binding Sites List in 6trd
Calcium binding site 1 out
of 6 in the Cryo- Em Structure of the Thermosynechococcus Elongatus Photosystem I in the Presence of Cytochrome C6
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Cryo- Em Structure of the Thermosynechococcus Elongatus Photosystem I in the Presence of Cytochrome C6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca801
b:9.5
occ:1.00
|
OE2
|
B:GLU200
|
2.4
|
9.1
|
1.0
|
OE1
|
B:GLU200
|
2.6
|
9.1
|
1.0
|
CD
|
B:GLU200
|
2.7
|
9.1
|
1.0
|
CD2
|
B:HIS205
|
2.8
|
10.1
|
1.0
|
NE2
|
B:HIS205
|
3.3
|
10.1
|
1.0
|
OD2
|
B:ASP133
|
3.7
|
8.2
|
1.0
|
CG
|
B:GLU200
|
4.0
|
9.1
|
1.0
|
CG
|
B:HIS205
|
4.0
|
10.1
|
1.0
|
N
|
B:VAL206
|
4.2
|
9.8
|
1.0
|
N
|
B:GLY207
|
4.2
|
9.9
|
1.0
|
O1D
|
B:CLA814
|
4.3
|
9.6
|
1.0
|
CG
|
B:ASP133
|
4.5
|
8.2
|
1.0
|
CE1
|
B:HIS205
|
4.5
|
10.1
|
1.0
|
OD1
|
B:ASP133
|
4.6
|
8.2
|
1.0
|
CA
|
B:HIS205
|
4.6
|
10.1
|
1.0
|
CA
|
B:GLY207
|
4.7
|
9.9
|
1.0
|
CB
|
B:HIS205
|
4.8
|
10.1
|
1.0
|
O
|
B:GLY127
|
4.8
|
7.3
|
1.0
|
ND1
|
B:HIS205
|
4.9
|
10.1
|
1.0
|
C
|
B:HIS205
|
4.9
|
10.1
|
1.0
|
|
Calcium binding site 2 out
of 6 in 6trd
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Calcium Binding Sites List in 6trd
Calcium binding site 2 out
of 6 in the Cryo- Em Structure of the Thermosynechococcus Elongatus Photosystem I in the Presence of Cytochrome C6
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Cryo- Em Structure of the Thermosynechococcus Elongatus Photosystem I in the Presence of Cytochrome C6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Ca202
b:8.8
occ:1.00
|
O
|
L:PRO67
|
2.2
|
1.5
|
1.0
|
O
|
l:PHE153
|
2.7
|
4.6
|
1.0
|
C
|
L:PRO67
|
3.4
|
1.5
|
1.0
|
CB
|
L:ASP70
|
3.5
|
5.1
|
1.0
|
OD2
|
L:ASP70
|
3.7
|
5.1
|
1.0
|
C
|
l:PHE153
|
3.9
|
4.6
|
1.0
|
CG
|
L:ASP70
|
4.1
|
5.1
|
1.0
|
N
|
L:ASP70
|
4.2
|
5.1
|
1.0
|
CA
|
L:PRO67
|
4.2
|
1.5
|
1.0
|
N
|
L:LEU68
|
4.3
|
2.5
|
1.0
|
CA
|
L:ASP70
|
4.5
|
5.1
|
1.0
|
CA
|
L:LEU68
|
4.5
|
2.5
|
1.0
|
CA
|
l:ASN154
|
4.5
|
2.6
|
1.0
|
N
|
l:ASN154
|
4.7
|
2.6
|
1.0
|
C
|
L:LEU68
|
4.7
|
2.5
|
1.0
|
N
|
L:ARG69
|
4.7
|
1.4
|
1.0
|
OD1
|
A:ASP473
|
4.8
|
1.1
|
1.0
|
NH1
|
L:ARG69
|
5.0
|
1.4
|
1.0
|
CA
|
l:PHE153
|
5.0
|
4.6
|
1.0
|
CB
|
L:PRO67
|
5.0
|
1.5
|
1.0
|
|
Calcium binding site 3 out
of 6 in 6trd
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Calcium Binding Sites List in 6trd
Calcium binding site 3 out
of 6 in the Cryo- Em Structure of the Thermosynechococcus Elongatus Photosystem I in the Presence of Cytochrome C6
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Cryo- Em Structure of the Thermosynechococcus Elongatus Photosystem I in the Presence of Cytochrome C6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
b:Ca801
b:9.7
occ:1.00
|
OE2
|
b:GLU200
|
2.4
|
5.7
|
1.0
|
OE1
|
b:GLU200
|
2.6
|
5.7
|
1.0
|
CD
|
b:GLU200
|
2.7
|
5.7
|
1.0
|
CD2
|
b:HIS205
|
2.8
|
7.1
|
1.0
|
NE2
|
b:HIS205
|
3.3
|
7.1
|
1.0
|
OD2
|
b:ASP133
|
3.7
|
4.7
|
1.0
|
CG
|
b:GLU200
|
4.0
|
5.7
|
1.0
|
CG
|
b:HIS205
|
4.0
|
7.1
|
1.0
|
N
|
b:VAL206
|
4.2
|
7.1
|
1.0
|
N
|
b:GLY207
|
4.2
|
6.2
|
1.0
|
O1D
|
b:CLA815
|
4.3
|
5.5
|
1.0
|
CG
|
b:ASP133
|
4.5
|
4.7
|
1.0
|
CE1
|
b:HIS205
|
4.5
|
7.1
|
1.0
|
OD1
|
b:ASP133
|
4.6
|
4.7
|
1.0
|
CA
|
b:HIS205
|
4.6
|
7.1
|
1.0
|
CA
|
b:GLY207
|
4.7
|
6.2
|
1.0
|
CB
|
b:HIS205
|
4.8
|
7.1
|
1.0
|
O
|
b:GLY127
|
4.8
|
4.4
|
1.0
|
ND1
|
b:HIS205
|
4.9
|
7.1
|
1.0
|
C
|
b:HIS205
|
4.9
|
7.1
|
1.0
|
|
Calcium binding site 4 out
of 6 in 6trd
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Calcium Binding Sites List in 6trd
Calcium binding site 4 out
of 6 in the Cryo- Em Structure of the Thermosynechococcus Elongatus Photosystem I in the Presence of Cytochrome C6
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Cryo- Em Structure of the Thermosynechococcus Elongatus Photosystem I in the Presence of Cytochrome C6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
l:Ca203
b:7.7
occ:1.00
|
O
|
l:PRO67
|
2.2
|
1.2
|
1.0
|
O
|
0:PHE153
|
2.6
|
2.8
|
1.0
|
C
|
l:PRO67
|
3.4
|
1.2
|
1.0
|
CB
|
l:ASP70
|
3.5
|
4.8
|
1.0
|
OD2
|
l:ASP70
|
3.7
|
4.8
|
1.0
|
C
|
0:PHE153
|
3.8
|
2.8
|
1.0
|
CG
|
l:ASP70
|
4.1
|
4.8
|
1.0
|
N
|
l:ASP70
|
4.2
|
4.8
|
1.0
|
CA
|
l:PRO67
|
4.2
|
1.2
|
1.0
|
N
|
l:LEU68
|
4.3
|
1.8
|
1.0
|
CA
|
0:ASN154
|
4.4
|
1.7
|
1.0
|
CA
|
l:ASP70
|
4.5
|
4.8
|
1.0
|
CA
|
l:LEU68
|
4.5
|
1.8
|
1.0
|
N
|
0:ASN154
|
4.5
|
1.7
|
1.0
|
C
|
l:LEU68
|
4.7
|
1.8
|
1.0
|
N
|
l:ARG69
|
4.7
|
1.5
|
1.0
|
OD1
|
a:ASP473
|
4.7
|
1.5
|
1.0
|
CA
|
0:PHE153
|
4.8
|
2.8
|
1.0
|
NH1
|
l:ARG69
|
5.0
|
1.5
|
1.0
|
CB
|
l:PRO67
|
5.0
|
1.2
|
1.0
|
|
Calcium binding site 5 out
of 6 in 6trd
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Calcium Binding Sites List in 6trd
Calcium binding site 5 out
of 6 in the Cryo- Em Structure of the Thermosynechococcus Elongatus Photosystem I in the Presence of Cytochrome C6
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Cryo- Em Structure of the Thermosynechococcus Elongatus Photosystem I in the Presence of Cytochrome C6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Ca801
b:7.7
occ:1.00
|
OE2
|
2:GLU200
|
2.4
|
7.9
|
1.0
|
OE1
|
2:GLU200
|
2.6
|
7.9
|
1.0
|
CD
|
2:GLU200
|
2.7
|
7.9
|
1.0
|
CD2
|
2:HIS205
|
2.8
|
7.4
|
1.0
|
NE2
|
2:HIS205
|
3.3
|
7.4
|
1.0
|
OD2
|
2:ASP133
|
3.7
|
6.2
|
1.0
|
CG
|
2:GLU200
|
4.0
|
7.9
|
1.0
|
CG
|
2:HIS205
|
4.0
|
7.4
|
1.0
|
N
|
2:VAL206
|
4.2
|
8.6
|
1.0
|
N
|
2:GLY207
|
4.2
|
8.7
|
1.0
|
O1D
|
2:CLA815
|
4.3
|
10.0
|
1.0
|
CG
|
2:ASP133
|
4.5
|
6.2
|
1.0
|
CE1
|
2:HIS205
|
4.5
|
7.4
|
1.0
|
OD1
|
2:ASP133
|
4.6
|
6.2
|
1.0
|
CA
|
2:HIS205
|
4.6
|
7.4
|
1.0
|
CA
|
2:GLY207
|
4.7
|
8.7
|
1.0
|
CB
|
2:HIS205
|
4.8
|
7.4
|
1.0
|
O
|
2:GLY127
|
4.8
|
5.3
|
1.0
|
ND1
|
2:HIS205
|
4.9
|
7.4
|
1.0
|
C
|
2:HIS205
|
4.9
|
7.4
|
1.0
|
|
Calcium binding site 6 out
of 6 in 6trd
Go back to
Calcium Binding Sites List in 6trd
Calcium binding site 6 out
of 6 in the Cryo- Em Structure of the Thermosynechococcus Elongatus Photosystem I in the Presence of Cytochrome C6
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Cryo- Em Structure of the Thermosynechococcus Elongatus Photosystem I in the Presence of Cytochrome C6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
0:Ca204
b:6.7
occ:1.00
|
O
|
0:PRO67
|
2.2
|
1.4
|
1.0
|
O
|
L:PHE153
|
2.9
|
2.4
|
1.0
|
C
|
0:PRO67
|
3.4
|
1.4
|
1.0
|
CB
|
0:ASP70
|
3.5
|
3.9
|
1.0
|
OD2
|
0:ASP70
|
3.7
|
3.9
|
1.0
|
CG
|
0:ASP70
|
4.1
|
3.9
|
1.0
|
C
|
L:PHE153
|
4.1
|
2.4
|
1.0
|
N
|
0:ASP70
|
4.2
|
3.9
|
1.0
|
CA
|
0:PRO67
|
4.2
|
1.4
|
1.0
|
N
|
0:LEU68
|
4.3
|
1.8
|
1.0
|
CA
|
0:ASP70
|
4.5
|
3.9
|
1.0
|
CA
|
0:LEU68
|
4.5
|
1.8
|
1.0
|
C
|
0:LEU68
|
4.7
|
1.8
|
1.0
|
N
|
0:ARG69
|
4.7
|
1.6
|
1.0
|
CA
|
L:ASN154
|
4.8
|
1.7
|
1.0
|
OD1
|
1:ASP473
|
4.9
|
1.5
|
1.0
|
N
|
L:ASN154
|
4.9
|
1.7
|
1.0
|
NH1
|
0:ARG69
|
5.0
|
1.6
|
1.0
|
CB
|
0:PRO67
|
5.0
|
1.4
|
1.0
|
|
Reference:
A.Koelsch,
C.Radon,
M.Golub,
A.Baumert,
J.Burger,
T.Miehlke,
F.Lisdat,
A.Feoktystov,
J.Pieper,
A.Zouni,
P.Wendler.
Current Limits of Structural Biology: the Transient Interaction Between Cytochrome C6 and Photosystem I Curr.Opin.Struct.Biol. V. 2 171 2020.
ISSN: ISSN 0959-440X
DOI: 10.1016/J.CRSTBI.2020.08.003
Page generated: Tue Jul 16 15:27:23 2024
|