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Calcium in PDB 7rcv: 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 7rcv:

The structure of High-Resolution Structure of Photosystem II From the Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Magnesium (Mg) 70 atoms
Iron (Fe) 6 atoms
Manganese (Mn) 8 atoms

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 7rcv). 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: 7rcv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 7rcv

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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:8.9
occ:1.00
 CA1 A:OEX401 0.0 8.9 1.0
O2 A:OEX401 2.2 8.9 1.0
OD2 A:ASP170 2.3 3.1 1.0
O5 A:OEX401 2.3 8.9 1.0
O A:HOH560 2.4 9.5 1.0
O1 A:OEX401 2.6 8.9 1.0
O A:HOH517 2.7 8.7 1.0
CG A:ASP170 3.1 3.1 1.0
OD1 A:ASP170 3.4 3.1 1.0
MN3 A:OEX401 3.4 8.9 1.0
OE1 A:GLU189 3.5 4.2 1.0
MN2 A:OEX401 3.6 8.9 1.0
MN1 A:OEX401 3.9 8.9 1.0
MN4 A:OEX401 3.9 8.9 1.0
O4 A:OEX401 3.9 8.9 1.0
OE1 A:GLN165 4.0 3.0 1.0
O A:ALA344 4.1 9.1 1.0
C A:ALA344 4.1 9.1 1.0
NH1 C:ARG344 4.1 3.8 1.0
O3 A:OEX401 4.2 8.9 1.0
NH2 C:ARG344 4.2 3.8 1.0
CB A:ASP170 4.3 3.1 1.0
CD A:GLU189 4.5 4.2 1.0
O A:HOH512 4.6 9.9 1.0
CZ C:ARG344 4.6 3.8 1.0
OE2 A:GLU189 4.6 4.2 1.0
O A:HOH521 4.7 6.0 1.0
OH A:TYR161 4.8 2.9 1.0
O A:HOH589 4.9 11.0 1.0
CD A:GLN165 4.9 3.0 1.0
CB A:GLN165 5.0 3.0 1.0

Calcium binding site 2 out of 8 in 7rcv

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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:Ca103

b:26.9
occ:1.00
 OD2 K:ASP22 2.2 18.1 1.0
OD2 K:ASP18 2.3 20.4 1.0
OD1 K:ASP18 2.4 20.4 1.0
CG K:ASP18 2.5 20.4 1.0
OE1 Y:GLU64 2.5 23.0 1.0
OD1 K:ASP22 2.6 18.1 1.0
CG K:ASP22 2.7 18.1 1.0
O K:ASP18 3.1 20.4 1.0
C K:ASP18 3.5 20.4 1.0
CD Y:GLU64 3.7 23.0 1.0
CB K:ASP18 3.8 20.4 1.0
N K:PRO19 4.1 19.3 1.0
CA K:ASP18 4.2 20.4 1.0
CB K:ASP22 4.2 18.1 1.0
OE2 Y:GLU64 4.2 23.0 1.0
CA K:PRO19 4.3 19.3 1.0
NE2 C:HIS61 4.5 13.7 1.0
OE1 Y:GLN68 4.6 21.6 1.0
CG Y:GLU64 4.9 23.0 1.0
CA K:ASP22 5.0 18.1 1.0

Calcium binding site 3 out of 8 in 7rcv

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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:22.2
occ:1.00
 O U:HOH303 2.3 14.5 1.0
OD1 U:ASP59 2.4 15.9 1.0
O U:HOH306 2.4 13.6 1.0
O B:SER386 2.4 19.6 1.0
OD1 U:ASP62 2.5 17.0 1.0
OD2 U:ASP59 2.5 15.9 1.0
OD2 U:ASP62 2.6 17.0 1.0
CG U:ASP59 2.6 15.9 1.0
OG B:SER386 2.7 19.6 1.0
CG U:ASP62 2.8 17.0 1.0
C B:SER386 3.4 19.6 1.0
CB B:SER386 3.9 19.6 1.0
CB U:ASP59 3.9 15.9 1.0
CA B:SER386 4.0 19.6 1.0
CB U:ASP62 4.2 17.0 1.0
N B:GLU387 4.4 20.0 1.0
N U:ASP59 4.4 15.9 1.0
CA U:ASP59 4.7 15.9 1.0
CG B:GLU387 4.7 20.0 1.0
CA B:GLU387 4.8 20.0 1.0
N U:ASP62 4.8 17.0 1.0
CA U:ASP62 4.9 17.0 1.0

Calcium binding site 4 out of 8 in 7rcv

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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:21.3
occ:1.00
 OE1 V:GLN64 1.9 12.9 1.0
O V:HOH301 2.4 14.7 1.0
OE1 C:GLU70 2.4 11.4 1.0
O V:HOH302 2.5 14.1 1.0
OE1 V:GLU128 2.7 19.0 1.0
OE2 V:GLU128 2.8 19.0 1.0
CD V:GLN64 3.0 12.9 1.0
OE2 C:GLU70 3.1 11.4 1.0
CD C:GLU70 3.1 11.4 1.0
CD V:GLU128 3.1 19.0 1.0
CE1 C:HIS385 3.6 7.5 1.0
NE2 C:HIS385 3.7 7.5 1.0
NE2 V:GLN64 3.8 12.9 1.0
OE1 C:GLU381 4.0 9.8 1.0
CG V:GLN64 4.0 12.9 1.0
O V:HOH323 4.1 13.4 1.0
CB V:GLN64 4.2 12.9 1.0
O V:HOH319 4.4 13.4 1.0
CG C:GLU70 4.6 11.4 1.0
OE2 C:GLU381 4.6 9.8 1.0
CG V:GLU128 4.7 19.0 1.0
NZ C:LYS66 4.7 13.8 1.0
CD C:GLU381 4.7 9.8 1.0
O C:HOH637 4.7 12.9 1.0
O V:THR61 4.8 14.0 1.0
O V:HOH312 4.8 13.8 1.0
ND1 C:HIS385 4.9 7.5 1.0

Calcium binding site 5 out of 8 in 7rcv

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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:8.9
occ:1.00
 CA1 a:OEX401 0.0 8.9 1.0
O2 a:OEX401 2.2 8.9 1.0
OD2 a:ASP170 2.3 3.1 1.0
O5 a:OEX401 2.3 8.9 1.0
O a:HOH560 2.4 9.5 1.0
O1 a:OEX401 2.6 8.9 1.0
O a:HOH517 2.7 8.7 1.0
CG a:ASP170 3.1 3.1 1.0
OD1 a:ASP170 3.4 3.1 1.0
MN3 a:OEX401 3.4 8.9 1.0
OE1 a:GLU189 3.5 4.2 1.0
MN2 a:OEX401 3.6 8.9 1.0
MN1 a:OEX401 3.9 8.9 1.0
MN4 a:OEX401 3.9 8.9 1.0
O4 a:OEX401 3.9 8.9 1.0
OE1 a:GLN165 4.0 3.0 1.0
O a:ALA344 4.1 9.1 1.0
C a:ALA344 4.1 9.1 1.0
NH1 c:ARG344 4.1 3.8 1.0
O3 a:OEX401 4.2 8.9 1.0
NH2 c:ARG344 4.2 3.8 1.0
CB a:ASP170 4.3 3.1 1.0
CD a:GLU189 4.5 4.2 1.0
O a:HOH512 4.6 9.9 1.0
CZ c:ARG344 4.6 3.8 1.0
OE2 a:GLU189 4.6 4.2 1.0
O a:HOH521 4.7 6.0 1.0
OH a:TYR161 4.8 2.9 1.0
O a:HOH589 4.9 11.0 1.0
CD a:GLN165 4.9 3.0 1.0
CB a:GLN165 5.0 3.0 1.0

Calcium binding site 6 out of 8 in 7rcv

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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:Ca103

b:26.9
occ:1.00
 OD2 k:ASP22 2.2 18.1 1.0
OD2 k:ASP18 2.3 20.4 1.0
OD1 k:ASP18 2.4 20.4 1.0
CG k:ASP18 2.5 20.4 1.0
OE1 y:GLU64 2.5 23.0 1.0
OD1 k:ASP22 2.6 18.1 1.0
CG k:ASP22 2.7 18.1 1.0
O k:ASP18 3.1 20.4 1.0
C k:ASP18 3.5 20.4 1.0
CD y:GLU64 3.7 23.0 1.0
CB k:ASP18 3.8 20.4 1.0
N k:PRO19 4.1 19.3 1.0
CA k:ASP18 4.2 20.4 1.0
CB k:ASP22 4.2 18.1 1.0
OE2 y:GLU64 4.2 23.0 1.0
CA k:PRO19 4.3 19.3 1.0
NE2 c:HIS61 4.5 13.7 1.0
OE1 y:GLN68 4.6 21.6 1.0
CG y:GLU64 4.9 23.0 1.0
CA k:ASP22 5.0 18.1 1.0

Calcium binding site 7 out of 8 in 7rcv

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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:22.2
occ:1.00
 O u:HOH303 2.3 14.5 1.0
OD1 u:ASP59 2.4 15.9 1.0
O u:HOH306 2.4 13.6 1.0
O b:SER386 2.4 19.6 1.0
OD1 u:ASP62 2.5 17.0 1.0
OD2 u:ASP59 2.5 15.9 1.0
OD2 u:ASP62 2.6 17.0 1.0
CG u:ASP59 2.6 15.9 1.0
OG b:SER386 2.7 19.6 1.0
CG u:ASP62 2.8 17.0 1.0
C b:SER386 3.4 19.6 1.0
CB b:SER386 3.9 19.6 1.0
CB u:ASP59 3.9 15.9 1.0
CA b:SER386 4.0 19.6 1.0
CB u:ASP62 4.2 17.0 1.0
N b:GLU387 4.4 20.0 1.0
N u:ASP59 4.4 15.9 1.0
CA u:ASP59 4.7 15.9 1.0
CG b:GLU387 4.7 20.0 1.0
CA b:GLU387 4.8 20.0 1.0
N u:ASP62 4.8 17.0 1.0
CA u:ASP62 4.9 17.0 1.0

Calcium binding site 8 out of 8 in 7rcv

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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:21.3
occ:1.00
 OE1 v:GLN64 1.9 12.9 1.0
O v:HOH301 2.4 14.7 1.0
OE1 c:GLU70 2.4 11.4 1.0
O v:HOH302 2.5 14.1 1.0
OE1 v:GLU128 2.7 19.0 1.0
OE2 v:GLU128 2.8 19.0 1.0
CD v:GLN64 3.0 12.9 1.0
OE2 c:GLU70 3.1 11.4 1.0
CD c:GLU70 3.1 11.4 1.0
CD v:GLU128 3.1 19.0 1.0
CE1 c:HIS385 3.6 7.5 1.0
NE2 c:HIS385 3.7 7.5 1.0
NE2 v:GLN64 3.8 12.9 1.0
OE1 c:GLU381 4.0 9.8 1.0
CG v:GLN64 4.0 12.9 1.0
O v:HOH323 4.1 13.4 1.0
CB v:GLN64 4.2 12.9 1.0
O v:HOH319 4.4 13.4 1.0
CG c:GLU70 4.6 11.4 1.0
OE2 c:GLU381 4.6 9.8 1.0
CG v:GLU128 4.7 19.0 1.0
NZ c:LYS66 4.7 13.8 1.0
CD c:GLU381 4.7 9.8 1.0
O c:HOH637 4.7 12.9 1.0
O v:THR61 4.8 14.0 1.0
O v:HOH312 4.8 13.8 1.0
ND1 c:HIS385 4.9 7.5 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: Thu Jul 10 00:47:26 2025

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