Sodium in PDB 8xf2: Crystal Structure of the Reassembled C-Phycocyanin Hexamer From Thermoleptolyngbya Sp. O-77

The structure of Crystal Structure of the Reassembled C-Phycocyanin Hexamer From Thermoleptolyngbya Sp. O-77, PDB code: 8xf2 was solved by H.K.Nguyen, T.Teramoto, Y.Kakuta, K.S.Yoon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.00 / 1.98
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	107.729, 115.069, 186.989, 90, 90, 90
R / Rfree (%)	18.3 / 22.1

The binding sites of Sodium atom in the Crystal Structure of the Reassembled C-Phycocyanin Hexamer From Thermoleptolyngbya Sp. O-77 (pdb code 8xf2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Reassembled C-Phycocyanin Hexamer From Thermoleptolyngbya Sp. O-77, PDB code: 8xf2:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Reassembled C-Phycocyanin Hexamer From Thermoleptolyngbya Sp. O-77


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Reassembled C-Phycocyanin Hexamer From Thermoleptolyngbya Sp. O-77 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:45.3 occ:1.00 O L:HOH373 2.2 56.4 1.0 O I:HOH431 2.2 42.7 1.0 O L:HOH321 2.3 51.6 1.0 O L:HOH438 2.3 44.9 1.0 O L:HOH417 2.4 40.8 1.0 O I:HOH321 2.4 32.4 1.0 OE2 A:GLU117 3.6 46.1 1.0 OE1 L:GLU87 3.8 53.8 1.0 OE2 L:GLU87 4.1 42.9 1.0 CD L:GLU87 4.3 43.3 1.0 OXT I:SER162 4.3 29.5 1.0 O L:HOH357 4.4 23.9 1.0 O I:SER162 4.4 26.8 1.0 CD A:GLU117 4.5 44.0 1.0 OG1 A:THR121 4.5 25.9 1.0 OG L:SER49 4.6 28.9 1.0 O L:HOH309 4.6 44.7 1.0 C I:SER162 4.8 32.4 1.0 OE1 A:GLU117 4.8 51.6 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Reassembled C-Phycocyanin Hexamer From Thermoleptolyngbya Sp. O-77


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Reassembled C-Phycocyanin Hexamer From Thermoleptolyngbya Sp. O-77 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na203 b:40.9 occ:1.00 O I:HOH425 2.2 47.4 1.0 O A:HOH431 2.2 36.5 1.0 O D:HOH456 2.2 43.8 1.0 O D:HOH312 2.2 42.2 1.0 O D:HOH392 2.3 34.9 1.0 O A:HOH315 2.3 33.8 1.0 OE1 I:GLU117 3.8 39.5 1.0 OXT A:SER162 4.0 23.1 1.0 O I:HOH416 4.0 40.3 1.0 OE2 D:GLU87 4.1 43.7 1.0 OE1 D:GLU87 4.2 47.1 1.0 O A:SER162 4.2 27.5 1.0 OG D:SER49 4.4 21.9 1.0 O D:HOH357 4.4 22.5 1.0 O D:HOH415 4.4 36.8 1.0 CD D:GLU87 4.5 42.7 1.0 C A:SER162 4.5 30.6 1.0 OG1 I:THR121 4.6 25.2 1.0 CD I:GLU117 4.7 47.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Reassembled C-Phycocyanin Hexamer From Thermoleptolyngbya Sp. O-77


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Reassembled C-Phycocyanin Hexamer From Thermoleptolyngbya Sp. O-77 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na202 b:45.9 occ:1.00 O C:HOH315 2.2 51.3 1.0 O E:HOH304 2.2 54.4 1.0 O B:HOH310 2.2 52.9 1.0 O B:HOH354 2.3 42.7 1.0 O B:HOH365 2.3 39.4 1.0 O C:HOH326 2.5 39.5 1.0 OE2 E:GLU117 3.3 47.5 1.0 OE2 B:GLU87 3.8 56.8 1.0 O C:SER162 4.0 35.6 1.0 O B:HOH351 4.1 41.9 1.0 OXT C:SER162 4.1 37.4 1.0 O E:HOH310 4.2 39.2 1.0 OE1 B:GLU87 4.3 46.8 1.0 CD E:GLU117 4.4 43.8 1.0 C C:SER162 4.5 36.2 1.0 CD B:GLU87 4.5 52.4 1.0 O B:HOH391 4.6 28.0 1.0 OG B:SER49 4.7 28.1 1.0 OE1 E:GLU117 4.7 49.5 1.0 OG1 E:THR121 4.8 28.4 1.0

H.K.Nguyen, T.Minato, T.Teramoto, S.Ogo, Y.Kakuta, K.S.Yoon. Disassembly and Reassembly of the Non-Conventional Thermophilic C-Phycocyanin. J.Biosci.Bioeng. V. 137 179 2024.
ISSN: ISSN 1389-1723
PubMed: 38238241
DOI: 10.1016/J.JBIOSC.2023.12.015