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Calcium in PDB 2axt: Crystal Structure of Photosystem II From Thermosynechococcus Elongatus

Protein crystallography data

The structure of Crystal Structure of Photosystem II From Thermosynechococcus Elongatus, PDB code: 2axt was solved by B.Loll, J.Kern, W.Saenger, A.Zouni, J.Biesiadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 127.692, 225.403, 306.106, 90.00, 90.00, 90.00
R / Rfree (%) 23.4 / 28.6

Other elements in 2axt:

The structure of Crystal Structure of Photosystem II From Thermosynechococcus Elongatus also contains other interesting chemical elements:

Manganese (Mn) 8 atoms
Magnesium (Mg) 70 atoms
Iron (Fe) 6 atoms
Neon (Ne) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus (pdb code 2axt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus, PDB code: 2axt:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2axt

Go back to Calcium Binding Sites List in 2axt
Calcium binding site 1 out of 4 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Photosystem II From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca565

b:62.6
occ:1.00
CA1 A:OEC565 0.0 62.6 1.0
OE1 A:GLU189 2.5 67.5 1.0
O A:ALA344 2.6 73.8 1.0
OE2 A:GLU189 3.2 65.8 1.0
CD A:GLU189 3.2 66.0 1.0
MN2 A:OEC565 3.2 63.0 1.0
MN3 A:OEC565 3.3 65.5 1.0
MN1 A:OEC565 3.4 63.8 1.0
OD2 A:ASP170 3.5 62.2 1.0
C A:ALA344 3.5 72.4 1.0
OXT A:ALA344 3.7 72.9 1.0
CG A:ASP170 4.1 63.1 1.0
NE2 A:GLN165 4.1 52.4 1.0
OD1 A:ASP170 4.2 65.4 1.0
MN4 A:OEC565 4.6 66.9 1.0
CG A:GLU189 4.7 64.0 1.0
OD1 A:ASP342 4.8 64.2 1.0
OE2 C:GLU354 4.8 64.6 1.0
OH A:TYR161 4.9 61.3 1.0
CA A:ALA344 4.9 71.8 1.0
OD2 A:ASP342 4.9 63.8 1.0
CD A:GLN165 5.0 52.9 1.0

Calcium binding site 2 out of 4 in 2axt

Go back to Calcium Binding Sites List in 2axt
Calcium binding site 2 out of 4 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Photosystem II From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca56

b:1.0
occ:1.00
OD1 K:ASP19 2.8 79.0 1.0
OD2 K:ASP23 2.9 71.9 1.0
OD2 K:ASP19 3.0 80.0 1.0
OD1 K:ASP23 3.2 72.0 1.0
CG K:ASP19 3.3 79.7 1.0
CG K:ASP23 3.3 72.1 1.0
N X:UNK2 3.5 97.8 1.0
CA X:UNK2 4.0 96.0 1.0
N X:UNK1 4.1 97.6 1.0
NE2 X:UNK6 4.1 76.3 1.0
CE1 C:HIS74 4.1 74.2 1.0
C X:UNK1 4.2 98.0 1.0
NE2 C:HIS74 4.3 74.5 1.0
CA X:UNK1 4.4 98.1 1.0
CB K:ASP23 4.7 68.6 1.0
ND1 C:HIS74 4.8 74.4 1.0
CB K:ASP19 4.9 77.7 1.0

Calcium binding site 3 out of 4 in 2axt

Go back to Calcium Binding Sites List in 2axt
Calcium binding site 3 out of 4 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Photosystem II From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca5565

b:64.2
occ:1.00
CA1 a:OEC5565 0.0 64.2 1.0
O a:ALA5344 2.5 78.7 1.0
OE1 a:GLU5189 2.7 69.3 1.0
MN3 a:OEC5565 3.2 71.1 1.0
MN2 a:OEC5565 3.3 67.5 1.0
MN1 a:OEC5565 3.3 63.4 1.0
OE2 a:GLU5189 3.3 68.2 1.0
OD2 a:ASP5170 3.3 69.0 1.0
CD a:GLU5189 3.4 67.2 1.0
C a:ALA5344 3.5 78.0 1.0
OXT a:ALA5344 3.7 77.8 1.0
CG a:ASP5170 3.9 66.3 1.0
OD1 a:ASP5170 4.0 67.1 1.0
NE2 a:GLN5165 4.2 61.0 1.0
MN4 a:OEC5565 4.6 87.9 1.0
OE2 c:GLU5354 4.7 64.8 1.0
OD1 a:ASP5342 4.8 67.3 1.0
CA a:ALA5344 4.9 77.0 1.0
CG a:GLU5189 4.9 64.5 1.0
OD2 a:ASP5342 4.9 65.7 1.0

Calcium binding site 4 out of 4 in 2axt

Go back to Calcium Binding Sites List in 2axt
Calcium binding site 4 out of 4 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Photosystem II From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
k:Ca5056

b:0.1
occ:1.00
OD1 k:ASP5019 2.6 88.6 1.0
OD2 k:ASP5019 2.7 87.1 1.0
OD2 k:ASP5023 2.8 83.5 1.0
CG k:ASP5019 3.0 88.0 1.0
OD1 k:ASP5023 3.2 83.1 1.0
CG k:ASP5023 3.3 83.1 1.0
N x:UNK5002 3.5 1.0 1.0
CA x:UNK5002 3.9 0.1 1.0
NE2 x:UNK5006 4.1 87.2 1.0
N x:UNK5001 4.2 99.9 1.0
C x:UNK5001 4.2 0.6 1.0
CE1 c:HIS5074 4.3 79.6 1.0
NE2 c:HIS5074 4.5 79.1 1.0
CA x:UNK5001 4.5 0.7 1.0
CB k:ASP5019 4.6 85.9 1.0
CB k:ASP5023 4.8 80.3 1.0
ND1 c:HIS5074 5.0 79.9 1.0

Reference:

B.Loll, J.Kern, W.Saenger, A.Zouni, J.Biesiadka. Towards Complete Cofactor Arrangement in the 3.0 A Resolution Structure of Photosystem II Nature V. 438 1040 2005.
ISSN: ISSN 0028-0836
PubMed: 16355230
DOI: 10.1038/NATURE04224
Page generated: Sat Dec 12 03:31:48 2020

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