Calcium in PDB 7n8o: High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803
Enzymatic activity of High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803
All present enzymatic activity of High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803:
1.10.3.9;
Other elements in 7n8o:
The structure of High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803
(pdb code 7n8o). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803, PDB code: 7n8o:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 7n8o
Go back to
Calcium Binding Sites List in 7n8o
Calcium binding site 1 out
of 8 in the High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca401
b:5.5
occ:1.00
|
CA1
|
A:OEX401
|
0.0
|
5.5
|
1.0
|
O5
|
A:OEX401
|
2.1
|
5.5
|
1.0
|
O
|
A:HOH515
|
2.2
|
4.9
|
1.0
|
OD2
|
A:ASP170
|
2.3
|
0.4
|
1.0
|
O
|
A:HOH546
|
2.4
|
5.4
|
1.0
|
O2
|
A:OEX401
|
2.4
|
5.5
|
1.0
|
O1
|
A:OEX401
|
2.5
|
5.5
|
1.0
|
CG
|
A:ASP170
|
3.1
|
0.4
|
1.0
|
OD1
|
A:ASP170
|
3.4
|
0.4
|
1.0
|
OE1
|
A:GLU189
|
3.4
|
1.9
|
1.0
|
MN3
|
A:OEX401
|
3.4
|
5.5
|
1.0
|
MN2
|
A:OEX401
|
3.6
|
5.5
|
1.0
|
MN1
|
A:OEX401
|
3.8
|
5.5
|
1.0
|
O
|
A:ALA344
|
3.8
|
4.4
|
1.0
|
OE1
|
A:GLN165
|
3.8
|
1.1
|
1.0
|
MN4
|
A:OEX401
|
3.9
|
5.5
|
1.0
|
O4
|
A:OEX401
|
3.9
|
5.5
|
1.0
|
NH1
|
C:ARG344
|
4.2
|
2.7
|
1.0
|
C
|
A:ALA344
|
4.2
|
4.4
|
1.0
|
NH2
|
C:ARG344
|
4.3
|
2.7
|
1.0
|
CB
|
A:ASP170
|
4.3
|
0.4
|
1.0
|
O3
|
A:OEX401
|
4.4
|
5.5
|
1.0
|
CD
|
A:GLU189
|
4.4
|
1.9
|
1.0
|
O
|
A:HOH533
|
4.6
|
4.0
|
1.0
|
OE2
|
A:GLU189
|
4.7
|
1.9
|
1.0
|
CZ
|
C:ARG344
|
4.7
|
2.7
|
1.0
|
OH
|
A:TYR161
|
4.7
|
5.5
|
1.0
|
O
|
A:HOH556
|
4.8
|
5.2
|
1.0
|
CD
|
A:GLN165
|
4.8
|
1.1
|
1.0
|
O
|
A:HOH562
|
4.8
|
5.4
|
1.0
|
CB
|
A:GLN165
|
5.0
|
1.1
|
1.0
|
|
Calcium binding site 2 out
of 8 in 7n8o
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Calcium Binding Sites List in 7n8o
Calcium binding site 2 out
of 8 in the High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Ca104
b:17.6
occ:1.00
|
OD1
|
K:ASP22
|
2.2
|
11.2
|
1.0
|
OD2
|
K:ASP18
|
2.3
|
12.5
|
1.0
|
OD1
|
K:ASP18
|
2.4
|
12.5
|
1.0
|
OD2
|
K:ASP22
|
2.5
|
11.2
|
1.0
|
CG
|
K:ASP18
|
2.6
|
12.5
|
1.0
|
OE1
|
Y:GLU64
|
2.6
|
14.8
|
1.0
|
CG
|
K:ASP22
|
2.6
|
11.2
|
1.0
|
O
|
K:ASP18
|
3.7
|
12.5
|
1.0
|
CD
|
Y:GLU64
|
3.8
|
14.8
|
1.0
|
CB
|
K:ASP18
|
4.0
|
12.5
|
1.0
|
C
|
K:ASP18
|
4.0
|
12.5
|
1.0
|
CB
|
K:ASP22
|
4.1
|
11.2
|
1.0
|
NE2
|
C:HIS61
|
4.2
|
7.9
|
1.0
|
OE1
|
Y:GLN68
|
4.4
|
13.9
|
1.0
|
OE2
|
Y:GLU64
|
4.5
|
14.8
|
1.0
|
CA
|
K:ASP18
|
4.5
|
12.5
|
1.0
|
N
|
K:PRO19
|
4.6
|
11.6
|
1.0
|
CE1
|
C:HIS61
|
4.8
|
7.9
|
1.0
|
CA
|
K:PRO19
|
4.9
|
11.6
|
1.0
|
CD2
|
C:HIS61
|
4.9
|
7.9
|
1.0
|
CG
|
Y:GLU64
|
4.9
|
14.8
|
1.0
|
CA
|
K:ASP22
|
5.0
|
11.2
|
1.0
|
|
Calcium binding site 3 out
of 8 in 7n8o
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Calcium Binding Sites List in 7n8o
Calcium binding site 3 out
of 8 in the High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
U:Ca201
b:13.2
occ:1.00
|
OD1
|
U:ASP59
|
1.9
|
10.6
|
1.0
|
OD2
|
U:ASP59
|
2.2
|
10.6
|
1.0
|
O
|
B:SER386
|
2.3
|
11.6
|
1.0
|
CG
|
U:ASP59
|
2.3
|
10.6
|
1.0
|
O
|
U:HOH301
|
2.3
|
8.0
|
1.0
|
O
|
B:HOH736
|
2.4
|
8.3
|
1.0
|
OG
|
B:SER386
|
2.5
|
11.6
|
1.0
|
OD1
|
U:ASP62
|
2.5
|
11.2
|
1.0
|
OD2
|
U:ASP62
|
2.5
|
11.2
|
1.0
|
CG
|
U:ASP62
|
2.9
|
11.2
|
1.0
|
C
|
B:SER386
|
3.2
|
11.6
|
1.0
|
CB
|
B:SER386
|
3.6
|
11.6
|
1.0
|
CA
|
B:SER386
|
3.8
|
11.6
|
1.0
|
CB
|
U:ASP59
|
3.8
|
10.6
|
1.0
|
N
|
B:GLU387
|
4.2
|
12.7
|
1.0
|
CB
|
U:ASP62
|
4.4
|
11.2
|
1.0
|
N
|
U:ASP59
|
4.4
|
10.6
|
1.0
|
CG
|
B:GLU387
|
4.5
|
12.7
|
1.0
|
CA
|
B:GLU387
|
4.6
|
12.7
|
1.0
|
CA
|
U:ASP59
|
4.7
|
10.6
|
1.0
|
N
|
U:ASP62
|
5.0
|
11.2
|
1.0
|
|
Calcium binding site 4 out
of 8 in 7n8o
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Calcium Binding Sites List in 7n8o
Calcium binding site 4 out
of 8 in the High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Ca202
b:12.6
occ:1.00
|
O
|
V:HOH302
|
2.3
|
7.3
|
1.0
|
OE2
|
C:GLU70
|
2.3
|
5.9
|
1.0
|
O
|
V:HOH304
|
2.4
|
7.4
|
1.0
|
OE1
|
C:GLU70
|
2.4
|
5.9
|
1.0
|
OE1
|
V:GLU128
|
2.5
|
11.4
|
1.0
|
OE1
|
V:GLN64
|
2.6
|
6.6
|
1.0
|
OE2
|
V:GLU128
|
2.6
|
11.4
|
1.0
|
CD
|
C:GLU70
|
2.7
|
5.9
|
1.0
|
CD
|
V:GLU128
|
2.9
|
11.4
|
1.0
|
CD
|
V:GLN64
|
3.8
|
6.6
|
1.0
|
O
|
C:HOH704
|
3.9
|
30.0
|
1.0
|
NZ
|
C:LYS66
|
3.9
|
8.8
|
1.0
|
O
|
V:ASP60
|
4.1
|
9.6
|
1.0
|
CG
|
C:GLU70
|
4.2
|
5.9
|
1.0
|
NE2
|
C:HIS385
|
4.3
|
2.8
|
1.0
|
CG
|
V:GLU128
|
4.4
|
11.4
|
1.0
|
CE
|
C:LYS66
|
4.6
|
8.8
|
1.0
|
CG
|
V:GLN64
|
4.6
|
6.6
|
1.0
|
CE1
|
C:HIS385
|
4.7
|
2.8
|
1.0
|
NE2
|
V:GLN64
|
4.7
|
6.6
|
1.0
|
CA
|
V:THR61
|
4.8
|
7.9
|
1.0
|
O
|
V:THR61
|
4.8
|
7.9
|
1.0
|
O
|
V:HOH319
|
4.8
|
30.0
|
1.0
|
O
|
V:HOH307
|
4.9
|
5.6
|
1.0
|
CB
|
V:GLN64
|
4.9
|
6.6
|
1.0
|
CB
|
C:GLU70
|
5.0
|
5.9
|
1.0
|
|
Calcium binding site 5 out
of 8 in 7n8o
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Calcium Binding Sites List in 7n8o
Calcium binding site 5 out
of 8 in the High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Ca401
b:5.5
occ:1.00
|
CA1
|
a:OEX401
|
0.0
|
5.5
|
1.0
|
O5
|
a:OEX401
|
2.1
|
5.5
|
1.0
|
O
|
a:HOH515
|
2.2
|
4.9
|
1.0
|
OD2
|
a:ASP170
|
2.3
|
0.4
|
1.0
|
O
|
a:HOH546
|
2.4
|
5.4
|
1.0
|
O2
|
a:OEX401
|
2.4
|
5.5
|
1.0
|
O1
|
a:OEX401
|
2.5
|
5.5
|
1.0
|
CG
|
a:ASP170
|
3.1
|
0.4
|
1.0
|
OD1
|
a:ASP170
|
3.4
|
0.4
|
1.0
|
OE1
|
a:GLU189
|
3.4
|
1.9
|
1.0
|
MN3
|
a:OEX401
|
3.4
|
5.5
|
1.0
|
MN2
|
a:OEX401
|
3.6
|
5.5
|
1.0
|
MN1
|
a:OEX401
|
3.8
|
5.5
|
1.0
|
O
|
a:ALA344
|
3.8
|
4.4
|
1.0
|
OE1
|
a:GLN165
|
3.8
|
1.1
|
1.0
|
MN4
|
a:OEX401
|
3.9
|
5.5
|
1.0
|
O4
|
a:OEX401
|
3.9
|
5.5
|
1.0
|
NH1
|
c:ARG344
|
4.2
|
2.7
|
1.0
|
C
|
a:ALA344
|
4.2
|
4.4
|
1.0
|
NH2
|
c:ARG344
|
4.3
|
2.7
|
1.0
|
CB
|
a:ASP170
|
4.3
|
0.4
|
1.0
|
O3
|
a:OEX401
|
4.4
|
5.5
|
1.0
|
CD
|
a:GLU189
|
4.4
|
1.9
|
1.0
|
O
|
a:HOH533
|
4.6
|
4.0
|
1.0
|
OE2
|
a:GLU189
|
4.7
|
1.9
|
1.0
|
CZ
|
c:ARG344
|
4.7
|
2.7
|
1.0
|
OH
|
a:TYR161
|
4.7
|
5.5
|
1.0
|
O
|
a:HOH555
|
4.8
|
5.2
|
1.0
|
CD
|
a:GLN165
|
4.8
|
1.1
|
1.0
|
O
|
a:HOH562
|
4.8
|
5.4
|
1.0
|
CB
|
a:GLN165
|
5.0
|
1.1
|
1.0
|
|
Calcium binding site 6 out
of 8 in 7n8o
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Calcium Binding Sites List in 7n8o
Calcium binding site 6 out
of 8 in the High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
k:Ca104
b:17.6
occ:1.00
|
OD1
|
k:ASP22
|
2.2
|
11.2
|
1.0
|
OD2
|
k:ASP18
|
2.3
|
12.5
|
1.0
|
OD1
|
k:ASP18
|
2.4
|
12.5
|
1.0
|
OD2
|
k:ASP22
|
2.5
|
11.2
|
1.0
|
CG
|
k:ASP18
|
2.6
|
12.5
|
1.0
|
OE1
|
y:GLU64
|
2.6
|
14.8
|
1.0
|
CG
|
k:ASP22
|
2.6
|
11.2
|
1.0
|
O
|
k:ASP18
|
3.7
|
12.5
|
1.0
|
CD
|
y:GLU64
|
3.8
|
14.8
|
1.0
|
CB
|
k:ASP18
|
4.0
|
12.5
|
1.0
|
C
|
k:ASP18
|
4.0
|
12.5
|
1.0
|
CB
|
k:ASP22
|
4.1
|
11.2
|
1.0
|
NE2
|
c:HIS61
|
4.2
|
7.9
|
1.0
|
OE1
|
y:GLN68
|
4.4
|
13.9
|
1.0
|
OE2
|
y:GLU64
|
4.5
|
14.8
|
1.0
|
CA
|
k:ASP18
|
4.5
|
12.5
|
1.0
|
N
|
k:PRO19
|
4.6
|
11.6
|
1.0
|
CE1
|
c:HIS61
|
4.8
|
7.9
|
1.0
|
CA
|
k:PRO19
|
4.9
|
11.6
|
1.0
|
CD2
|
c:HIS61
|
4.9
|
7.9
|
1.0
|
CG
|
y:GLU64
|
4.9
|
14.8
|
1.0
|
CA
|
k:ASP22
|
5.0
|
11.2
|
1.0
|
|
Calcium binding site 7 out
of 8 in 7n8o
Go back to
Calcium Binding Sites List in 7n8o
Calcium binding site 7 out
of 8 in the High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
u:Ca201
b:13.2
occ:1.00
|
OD1
|
u:ASP59
|
1.9
|
10.6
|
1.0
|
OD2
|
u:ASP59
|
2.2
|
10.6
|
1.0
|
O
|
b:SER386
|
2.3
|
11.6
|
1.0
|
CG
|
u:ASP59
|
2.3
|
10.6
|
1.0
|
O
|
u:HOH301
|
2.3
|
8.0
|
1.0
|
O
|
b:HOH736
|
2.4
|
8.3
|
1.0
|
OG
|
b:SER386
|
2.5
|
11.6
|
1.0
|
OD1
|
u:ASP62
|
2.5
|
11.2
|
1.0
|
OD2
|
u:ASP62
|
2.5
|
11.2
|
1.0
|
CG
|
u:ASP62
|
2.9
|
11.2
|
1.0
|
C
|
b:SER386
|
3.2
|
11.6
|
1.0
|
CB
|
b:SER386
|
3.6
|
11.6
|
1.0
|
CA
|
b:SER386
|
3.8
|
11.6
|
1.0
|
CB
|
u:ASP59
|
3.8
|
10.6
|
1.0
|
N
|
b:GLU387
|
4.2
|
12.7
|
1.0
|
CB
|
u:ASP62
|
4.4
|
11.2
|
1.0
|
N
|
u:ASP59
|
4.4
|
10.6
|
1.0
|
CG
|
b:GLU387
|
4.5
|
12.7
|
1.0
|
CA
|
b:GLU387
|
4.6
|
12.7
|
1.0
|
CA
|
u:ASP59
|
4.7
|
10.6
|
1.0
|
N
|
u:ASP62
|
5.0
|
11.2
|
1.0
|
|
Calcium binding site 8 out
of 8 in 7n8o
Go back to
Calcium Binding Sites List in 7n8o
Calcium binding site 8 out
of 8 in the High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
v:Ca202
b:12.6
occ:1.00
|
O
|
v:HOH302
|
2.3
|
7.3
|
1.0
|
OE2
|
c:GLU70
|
2.3
|
5.9
|
1.0
|
O
|
v:HOH304
|
2.4
|
7.4
|
1.0
|
OE1
|
c:GLU70
|
2.4
|
5.9
|
1.0
|
OE1
|
v:GLU128
|
2.5
|
11.4
|
1.0
|
OE1
|
v:GLN64
|
2.6
|
6.6
|
1.0
|
OE2
|
v:GLU128
|
2.6
|
11.4
|
1.0
|
CD
|
c:GLU70
|
2.7
|
5.9
|
1.0
|
CD
|
v:GLU128
|
2.9
|
11.4
|
1.0
|
CD
|
v:GLN64
|
3.8
|
6.6
|
1.0
|
O
|
c:HOH704
|
3.9
|
30.0
|
1.0
|
NZ
|
c:LYS66
|
3.9
|
8.8
|
1.0
|
O
|
v:ASP60
|
4.1
|
9.6
|
1.0
|
CG
|
c:GLU70
|
4.2
|
5.9
|
1.0
|
NE2
|
c:HIS385
|
4.3
|
2.8
|
1.0
|
CG
|
v:GLU128
|
4.4
|
11.4
|
1.0
|
CE
|
c:LYS66
|
4.6
|
8.8
|
1.0
|
CG
|
v:GLN64
|
4.6
|
6.6
|
1.0
|
CE1
|
c:HIS385
|
4.7
|
2.8
|
1.0
|
NE2
|
v:GLN64
|
4.7
|
6.6
|
1.0
|
CA
|
v:THR61
|
4.8
|
7.9
|
1.0
|
O
|
v:THR61
|
4.8
|
7.9
|
1.0
|
O
|
v:HOH319
|
4.8
|
30.0
|
1.0
|
O
|
v:HOH307
|
4.9
|
5.6
|
1.0
|
CB
|
v:GLN64
|
4.9
|
6.6
|
1.0
|
CB
|
c:GLU70
|
5.0
|
5.9
|
1.0
|
|
Reference:
C.J.Gisriel,
J.Wang,
J.Liu,
D.A.Flesher,
K.M.Reiss,
H.Huang,
K.R.Yang,
W.H.Armstrong,
M.R.Gunner,
V.S.Batista,
R.J.Debus,
G.W.Brudvig.
High-Resolution Cryo-Em Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803 To Be Published.
Page generated: Fri Jul 19 02:10:20 2024
|