Chlorine in PDB 5oy0: 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;

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

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
Calcium	(Ca)	6 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution, PDB code: 5oy0:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl6000 b:36.4 occ:1.00 NH2 A:ARG647 3.1 35.6 1.0 OG1 A:THR641 3.1 33.1 1.0 NH1 A:ARG647 3.3 35.7 1.0 NH2 A:ARG462 3.4 37.2 1.0 CD A:ARG462 3.6 35.2 1.0 N A:GLY644 3.7 42.4 1.0 CZ A:ARG647 3.7 37.3 1.0 CB A:ASN643 3.8 36.1 1.0 ND2 A:ASN643 3.8 40.8 1.0 CE1 B:TYR632 3.9 33.9 1.0 O B:TYR632 4.0 36.0 1.0 CD1 B:TYR632 4.0 34.5 1.0 CA A:GLY644 4.1 34.1 1.0 C A:ASN643 4.1 37.4 1.0 CB A:THR641 4.2 32.6 1.0 CG A:ASN643 4.2 40.4 1.0 CD B:PRO634 4.2 40.6 1.0 CZ A:ARG462 4.3 43.3 1.0 CA B:ASN633 4.3 36.6 1.0 NE A:ARG462 4.4 34.8 1.0 C B:ASN633 4.5 44.9 1.0 C B:TYR632 4.5 36.4 1.0 CA A:ASN643 4.6 33.6 1.0 N B:PRO634 4.6 46.4 1.0 CG2 A:THR641 4.6 32.7 1.0 N B:ASN633 4.6 36.4 1.0 O A:ASN643 4.7 39.0 1.0 CG A:ARG462 4.8 36.8 1.0 CG B:PRO634 4.8 43.4 1.0 NE A:ARG647 5.0 36.5 1.0 CZ B:TYR632 5.0 33.8 1.0

Chlorine binding site 2 out of 3 in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 b:Cl6000 b:53.5 occ:1.00 OG1 a:THR641 2.9 56.6 1.0 O a:HOH8005 2.9 51.3 1.0 NH2 a:ARG647 3.1 58.2 1.0 O b:TYR632 3.6 59.1 1.0 N a:GLY644 3.7 57.1 1.0 NH1 a:ARG647 3.7 56.5 1.0 CD a:ARG462 3.7 58.8 1.0 CZ a:ARG647 3.9 57.8 1.0 CA b:ASN633 3.9 57.6 1.0 CD1 b:TYR632 4.0 52.5 1.0 CB a:THR641 4.0 55.8 1.0 CA a:GLY644 4.0 59.6 1.0 CE1 b:TYR632 4.1 54.7 1.0 NE a:ARG462 4.1 70.2 1.0 CB a:ASN643 4.1 56.5 1.0 CD b:PRO634 4.2 59.1 1.0 ND2 a:ASN643 4.2 57.8 1.0 C a:ASN643 4.2 56.4 1.0 C b:TYR632 4.3 60.9 1.0 CG2 a:THR641 4.3 55.6 1.0 N b:ASN633 4.5 55.6 1.0 CG a:ASN643 4.5 58.5 1.0 C b:ASN633 4.6 59.6 1.0 N b:PRO634 4.7 58.2 1.0 CA a:ASN643 4.7 55.0 1.0 O a:ASN643 4.9 56.9 1.0 CB b:ASN633 4.9 57.3 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 2:Cl6000 b:74.6 occ:1.00 OG1 1:THR641 3.2 68.0 1.0 NE 1:ARG462 3.2 62.9 1.0 CD 1:ARG462 3.5 69.8 1.0 O 2:TYR632 3.5 70.6 1.0 CD1 2:TYR632 3.6 67.1 1.0 CE1 2:TYR632 3.6 66.5 1.0 ND2 1:ASN643 3.7 65.2 1.0 NH1 1:ARG647 3.7 64.8 1.0 CB 1:ASN643 3.7 60.7 1.0 CA 2:ASN633 3.8 73.1 1.0 NH2 1:ARG647 3.9 65.0 1.0 N 1:GLY644 4.1 67.5 1.0 C 2:TYR632 4.1 70.5 1.0 CG 1:ASN643 4.1 68.6 1.0 CB 1:THR641 4.2 55.9 1.0 CZ 1:ARG462 4.2 53.0 1.0 CG2 1:THR641 4.2 50.7 1.0 N 2:ASN633 4.2 70.4 1.0 CZ 1:ARG647 4.3 69.2 1.0 C 2:ASN633 4.3 75.5 1.0 C 1:ASN643 4.3 72.2 1.0 CD 2:PRO634 4.4 75.5 1.0 NH2 1:ARG462 4.5 46.1 1.0 CA 1:ASN643 4.6 67.1 1.0 CA 1:GLY644 4.6 65.3 1.0 N 2:PRO634 4.7 76.4 1.0 CG 2:TYR632 4.7 68.1 1.0 CZ 2:TYR632 4.7 66.8 1.0 CB 2:ASN633 4.8 72.4 1.0 CG 1:ARG462 4.9 68.8 1.0 O 1:ASN643 5.0 75.2 1.0 OD1 1:ASP459 5.0 67.7 1.0

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