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Calcium in PDB 5oy0: Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution

Enzymatic activity of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution

All present enzymatic activity of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution:
1.97.1.12;

Protein crystallography data

The structure of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution, PDB code: 5oy0 was solved by N.Nelson, T.Malavath, I.Caspy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.48 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 212.170, 137.622, 225.095, 90.00, 116.74, 90.00
R / Rfree (%) 22.8 / 26.4

Other elements in 5oy0:

The structure of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution also contains other interesting chemical elements:

Magnesium (Mg) 287 atoms
Iron (Fe) 36 atoms
Chlorine (Cl) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution (pdb code 5oy0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution, PDB code: 5oy0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5oy0

Go back to Calcium Binding Sites List in 5oy0
Calcium binding site 1 out of 6 in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca6001

b:80.0
occ:1.00
 O B:HOH8045 2.4 76.0 1.0
OE2 B:GLU201 2.4 64.7 1.0
O B:HOH8026 2.5 74.5 1.0
CD2 B:HIS206 2.6 83.8 1.0
O B:HOH8004 2.7 65.8 1.0
CD B:GLU201 3.0 66.8 1.0
OE2 B:GLU134 3.0 69.3 1.0
O B:HOH8040 3.0 63.0 1.0
OE1 B:GLU201 3.1 67.9 1.0
NE2 B:HIS206 3.3 83.1 1.0
CG B:HIS206 3.6 81.4 1.0
OG1 B:THR130 3.9 69.4 1.0
CD B:GLU134 4.0 64.6 1.0
CG B:GLU201 4.2 65.2 1.0
CB B:HIS206 4.2 78.0 1.0
OE1 B:GLU134 4.3 67.9 1.0
O B:GLY128 4.3 62.5 1.0
CA B:HIS206 4.3 71.6 1.0
O B:VAL207 4.3 71.8 1.0
N B:VAL207 4.4 69.8 1.0
CE1 B:HIS206 4.4 82.7 1.0
ND1 B:HIS206 4.6 84.7 1.0
C B:VAL207 4.8 69.0 1.0
C B:HIS206 4.8 68.8 1.0

Calcium binding site 2 out of 6 in 5oy0

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Calcium binding site 2 out of 6 in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1001

b:44.7
occ:1.00
 O 0:PHE156 2.3 46.2 1.0
O L:PRO70 2.4 36.9 1.0
O A:HOH8043 2.4 33.2 1.0
O L:HOH8020 2.5 49.0 1.0
OD1 L:ASP73 2.5 57.1 1.0
O 0:HOH8029 2.5 36.0 1.0
O 0:HOH8017 2.6 32.9 1.0
CG L:ASP73 3.3 49.7 1.0
C 0:PHE156 3.5 46.1 1.0
C L:PRO70 3.6 38.9 1.0
OD2 L:ASP73 3.6 50.3 1.0
CA 0:ASN157 4.3 46.1 1.0
CA L:PRO70 4.3 37.0 1.0
N 0:ASN157 4.3 46.0 1.0
CA 0:PHE156 4.5 46.1 1.0
CB 0:PHE156 4.5 45.6 1.0
NE2 A:GLN468 4.5 42.0 1.0
N L:LEU71 4.6 42.3 1.0
C 0:ASN157 4.6 47.2 1.0
CB L:ASP73 4.7 38.1 1.0
O L:ASP73 4.7 54.9 1.0
CA L:LEU71 4.7 40.4 1.0
N L:ASP73 4.8 37.3 1.0
OD1 A:ASP469 4.8 37.3 1.0
OXT 0:ASN157 4.8 47.9 1.0
C L:ASP73 4.9 53.5 1.0
CB L:PRO70 4.9 35.7 1.0
OD2 A:ASP469 4.9 34.7 1.0

Calcium binding site 3 out of 6 in 5oy0

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Calcium binding site 3 out of 6 in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Ca6001

b:61.3
occ:1.00
 O b:HOH8022 2.3 57.6 1.0
O b:HOH8088 2.4 49.6 1.0
ND1 b:HIS206 2.5 49.6 1.0
O b:HOH8017 2.6 49.7 1.0
OE2 b:GLU201 2.7 49.6 1.0
O b:HOH8103 2.9 56.7 1.0
OE1 b:GLU201 2.9 48.2 1.0
CD b:GLU201 3.0 51.3 1.0
CE1 b:HIS206 3.3 49.1 1.0
CG b:HIS206 3.5 52.8 1.0
OE2 b:GLU134 3.6 48.4 1.0
CB b:HIS206 3.9 57.1 1.0
CA b:HIS206 4.1 54.8 1.0
N b:VAL207 4.1 49.5 1.0
OG1 b:THR130 4.1 49.9 1.0
O b:VAL207 4.3 47.7 1.0
CG b:GLU201 4.3 54.3 1.0
O b:GLY128 4.4 46.0 1.0
NE2 b:HIS206 4.5 49.5 1.0
C b:HIS206 4.6 50.3 1.0
CD2 b:HIS206 4.6 49.6 1.0
C b:VAL207 4.6 48.3 1.0
CD b:GLU134 4.6 44.6 1.0
O b:HOH8125 4.8 50.0 1.0
OE1 b:GLU134 5.0 53.7 1.0

Calcium binding site 4 out of 6 in 5oy0

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Calcium binding site 4 out of 6 in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
l:Ca1001

b:55.7
occ:1.00
 O l:PRO70 2.3 51.4 1.0
O L:HOH8007 2.4 42.1 1.0
O a:HOH8012 2.4 49.3 1.0
OD1 l:ASP73 2.5 57.3 1.0
O L:PHE156 2.5 60.9 1.0
O L:HOH8013 2.5 50.8 1.0
O l:HOH8003 2.5 49.6 1.0
CG l:ASP73 3.2 58.0 1.0
OD2 l:ASP73 3.3 54.6 1.0
C l:PRO70 3.4 50.9 1.0
C L:PHE156 3.5 57.1 1.0
CA L:ASN157 3.9 59.7 1.0
CA l:PRO70 4.1 50.6 1.0
N L:ASN157 4.2 57.3 1.0
O l:HOH8016 4.5 50.0 1.0
CB l:PRO70 4.5 49.5 1.0
OD1 a:ASP469 4.5 53.0 1.0
N l:LEU71 4.5 51.5 1.0
CB L:ASN157 4.6 60.1 1.0
NE2 a:GLN468 4.6 52.5 1.0
CB L:PHE156 4.6 54.9 1.0
NH1 l:ARG72 4.6 53.6 1.0
CB l:ASP73 4.6 55.6 1.0
CA L:PHE156 4.6 55.7 1.0
OD2 a:ASP469 4.8 51.2 1.0
O L:HOH8028 4.8 57.4 1.0
CA l:LEU71 4.8 51.1 1.0
N l:ASP73 4.8 54.6 1.0
C L:ASN157 4.9 61.6 1.0

Calcium binding site 5 out of 6 in 5oy0

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Calcium binding site 5 out of 6 in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca6001

b:0.6
occ:1.00
 ND1 2:HIS206 2.7 0.3 1.0
OE2 2:GLU134 2.9 0.8 1.0
CE1 2:HIS206 3.1 0.0 1.0
OE1 2:GLU201 3.2 0.4 1.0
OE2 2:GLU201 3.2 0.7 1.0
CD 2:GLU201 3.4 0.9 1.0
OG1 2:THR130 3.4 0.0 1.0
CD 2:GLU134 3.8 0.9 1.0
CG 2:HIS206 4.0 0.4 1.0
OE1 2:GLU134 4.1 0.3 1.0
O 2:GLY128 4.1 0.3 1.0
O 2:VAL207 4.2 0.0 1.0
NE2 2:HIS206 4.4 0.2 1.0
O1D 2:CLA1211 4.4 0.6 1.0
N 2:VAL207 4.4 0.5 1.0
CG 2:GLU201 4.5 0.6 1.0
C 2:VAL207 4.6 0.3 1.0
CB 2:HIS206 4.6 0.3 1.0
CA 2:HIS206 4.7 0.3 1.0
CB 2:THR130 4.7 0.4 1.0
CD2 2:HIS206 4.8 0.4 1.0
CG2 2:THR130 4.8 0.1 1.0

Calcium binding site 6 out of 6 in 5oy0

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Calcium binding site 6 out of 6 in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Ca1001

b:56.1
occ:1.00
 O 0:PRO70 2.5 64.3 1.0
OD1 0:ASP73 2.5 75.1 1.0
O 1:HOH8011 2.6 55.6 1.0
O l:PHE156 2.6 78.8 1.0
O l:HOH8002 2.9 59.9 1.0
OD2 0:ASP73 3.0 78.4 1.0
CG 0:ASP73 3.1 72.8 1.0
C 0:PRO70 3.6 59.0 1.0
C l:PHE156 3.8 78.9 1.0
CA 0:PRO70 4.1 60.8 1.0
CA l:ASN157 4.2 82.0 1.0
OD1 1:ASP469 4.3 48.1 1.0
NE2 1:GLN468 4.3 54.3 1.0
C l:ASN157 4.4 83.1 1.0
O l:ASN157 4.4 82.4 1.0
N l:ASN157 4.5 80.3 1.0
CB 0:PRO70 4.5 53.3 1.0
CB 0:ASP73 4.6 63.3 1.0
N 0:LEU71 4.7 61.9 1.0
OD2 1:ASP469 4.7 46.7 1.0
NH1 0:ARG72 4.8 53.7 1.0
CB l:PHE156 4.9 75.7 1.0
CG 1:ASP469 4.9 47.4 1.0
CA l:PHE156 4.9 77.3 1.0

Reference:

T.Malavath, I.Caspy, S.Y.Netzer-El, D.Klaiman, N.Nelson. Structure and Function of Wild-Type and Subunit-Depleted Photosystem I in Synechocystis. Biochim. Biophys. Acta V.1859 645 2018.
ISSN: ISSN 0006-3002
PubMed: 29414678
DOI: 10.1016/J.BBABIO.2018.02.002
Page generated: Wed Jul 9 09:23:02 2025

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