Sodium in PDB 5tjf: The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis

The structure of The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis, PDB code: 5tjf was solved by M.Figueroa, J.Dagnino, F.Kerff, P.Chartier, M.Bunster, J.Martinez-Oyanedel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.18 / 2.30
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.410, 97.410, 63.830, 90.00, 90.00, 120.00
R / Rfree (%)	25.7 / 28.4

The structure of The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Sodium atom in the The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis (pdb code 5tjf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 17 binding sites of Sodium where determined in the The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis, PDB code: 5tjf:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 17 in the The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:30.8 occ:1.00 HG21 A:VAL66 2.5 35.5 1.0 OG1 A:THR78 2.7 26.5 1.0 HG23 A:VAL66 2.8 35.5 1.0 CG2 A:VAL66 2.9 35.5 1.0 HG22 A:VAL66 2.9 35.5 1.0 HG1 A:THR78 2.9 26.5 1.0 HG21 A:THR78 3.3 28.8 1.0 CB A:THR78 3.6 27.1 1.0 HA A:GLU75 3.7 41.2 1.0 HB A:THR78 3.7 27.1 1.0 O A:GLY74 3.8 29.1 1.0 CG2 A:THR78 3.9 28.8 1.0 H A:GLY74 4.0 27.5 1.0 C A:GLY74 4.1 26.0 1.0 HG23 A:THR78 4.2 28.8 1.0 CB A:VAL66 4.4 26.4 1.0 N A:GLU75 4.5 36.5 1.0 CA A:GLU75 4.5 41.2 1.0 O A:ALA72 4.6 28.6 1.0 O A:HOH464 4.6 31.9 1.0 N A:GLY74 4.6 27.5 1.0 HB A:VAL66 4.7 26.4 1.0 HG22 A:THR78 4.7 28.8 1.0 CA A:GLY74 4.8 31.2 1.0 HA2 A:GLY74 4.8 31.2 1.0 HG11 A:VAL66 4.8 39.8 1.0 H A:THR78 4.9 35.5 1.0 HB3 A:GLU75 4.9 39.5 1.0 O A:VAL66 5.0 23.3 1.0 H A:GLU75 5.0 36.5 1.0 CA A:THR78 5.0 28.1 1.0

Sodium binding site 2 out of 17 in the The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:35.1 occ:1.00 O A:HOH411 2.3 31.9 1.0 O A:HOH470 2.6 31.9 1.0 O A:HOH407 2.8 31.9 1.0 OG A:SER19 3.2 33.3 1.0 HB2 A:SER19 3.2 41.6 1.0 HB3 A:SER19 3.3 41.6 1.0 CB A:SER19 3.4 41.6 1.0 O A:HOH456 3.6 30.0 1.0 O A:HOH354 3.8 31.9 1.0 HG3 A:GLU22 4.3 45.1 1.0 O A:HOH365 4.7 31.9 1.0 H A:GLY21 4.8 41.5 1.0 H A:GLU22 4.9 43.0 1.0 O A:HOH405 4.9 30.0 1.0 O A:HOH398 5.0 31.9 1.0 CA A:SER19 5.0 25.6 1.0

Sodium binding site 3 out of 17 in the The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:29.0 occ:1.00 H A:SER124 2.4 33.8 1.0 OG A:SER124 2.9 39.8 1.0 HG A:SER124 3.0 39.8 1.0 H A:ILE123 3.1 34.9 1.0 HB3 A:SER124 3.2 39.1 1.0 N A:SER124 3.3 33.8 1.0 CB A:SER124 3.5 39.1 1.0 N A:ILE123 3.5 34.9 1.0 HB2 A:PRO122 3.8 26.6 1.0 HB A:ILE123 3.8 35.0 1.0 HA A:PRO122 3.8 28.6 1.0 CA A:SER124 4.0 35.3 1.0 HG12 A:ILE123 4.0 44.9 1.0 C A:PRO122 4.1 31.9 1.0 C A:ILE123 4.2 30.8 1.0 CA A:ILE123 4.2 35.8 1.0 CA A:PRO122 4.2 28.6 1.0 HB3 A:PRO122 4.3 26.6 1.0 CB A:PRO122 4.3 26.6 1.0 HB2 A:SER124 4.4 39.1 1.0 H A:GLY125 4.4 39.5 1.0 CB A:ILE123 4.4 35.0 1.0 HA A:SER124 4.6 35.3 1.0 CG1 A:ILE123 4.7 44.9 1.0 HH22 A:ARG62 4.9 30.9 1.0 O A:PRO122 5.0 21.4 1.0

Sodium binding site 4 out of 17 in the The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:30.0 occ:1.00 O A:HOH513 2.4 31.9 1.0 O B:HOH523 2.9 31.9 1.0 O B:HOH552 3.3 31.9 1.0 O B:HOH542 3.5 31.9 1.0 O A:HOH504 3.8 31.9 1.0 O B:HOH437 4.5 31.9 1.0 O B:HOH510 4.8 31.9 1.0 O B:HOH493 4.9 31.9 1.0

Sodium binding site 5 out of 17 in the The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:30.0 occ:1.00 OE1 A:GLN53 2.3 37.6 1.0 O A:HOH467 2.5 31.9 1.0 HB2 A:GLN53 3.0 30.9 1.0 HA A:GLN53 3.2 33.2 1.0 HB3 A:LYS52 3.5 30.0 1.0 CD A:GLN53 3.5 43.8 1.0 HE22 A:GLN56 3.6 36.2 1.0 H A:GLN53 3.6 26.7 1.0 CA A:GLN53 3.7 33.2 1.0 CB A:GLN53 3.7 30.9 1.0 N A:GLN53 3.7 26.7 1.0 HD12 A:LEU49 3.8 28.8 1.0 NE2 A:GLN56 3.8 36.2 1.0 HE21 A:GLN56 4.1 36.2 1.0 CG A:GLN53 4.2 38.0 1.0 CD A:GLN56 4.2 40.7 1.0 CB A:LYS52 4.4 30.0 1.0 C A:LYS52 4.4 26.6 1.0 OE1 A:GLN56 4.4 25.0 1.0 HD11 A:LEU49 4.5 28.8 1.0 HB2 A:LYS52 4.5 30.0 1.0 HB3 A:GLN53 4.5 30.9 1.0 NE2 A:GLN53 4.6 18.2 1.0 CD1 A:LEU49 4.6 28.8 1.0 HE22 A:GLN53 4.6 18.2 1.0 HG2 A:GLN53 4.7 38.0 1.0 HG3 A:GLN56 4.8 27.6 1.0 HG3 A:GLN53 4.9 38.0 1.0 O A:LYS52 4.9 25.9 1.0 O A:LEU49 5.0 26.6 1.0

Sodium binding site 6 out of 17 in the The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na204 b:28.0 occ:1.00 HG2 B:PRO68 3.2 27.3 1.0 HD2 B:PRO68 3.3 23.8 1.0 CD B:PRO68 3.8 23.8 1.0 CG B:PRO68 3.9 27.3 1.0 HD3 B:PRO68 3.9 23.8 1.0 HD2 B:ARG67 4.2 28.1 1.0 HG2 B:ARG67 4.3 32.1 1.0 HG3 B:PRO68 4.3 27.3 1.0 HB3 B:ARG67 4.8 27.9 1.0 HD3 B:ARG67 4.8 28.1 1.0 CD B:ARG67 4.9 28.1 1.0 CG B:ARG67 5.0 32.1 1.0 HB2 B:PRO68 5.0 30.4 1.0

Sodium binding site 7 out of 17 in the The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na205 b:35.8 occ:1.00 HB2 B:TYR62 3.3 34.0 1.0 HB3 B:TYR62 3.7 34.0 1.0 CB B:TYR62 4.0 34.0 1.0 O B:TYR62 4.2 27.9 1.0 HD2 B:TYR62 4.6 24.7 1.0 O B:LEU61 4.7 20.1 1.0 CG B:TYR62 4.8 30.2 1.0 CD2 B:TYR62 5.0 24.7 1.0

Sodium binding site 8 out of 17 in the The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na206 b:26.6 occ:1.00 O B:HOH437 2.1 31.9 1.0 OH B:TYR87 2.7 27.1 1.0 O B:HOH510 2.9 31.9 1.0 HE1 B:TYR87 3.6 28.3 1.0 CZ B:TYR87 3.8 28.5 1.0 HD3 B:ARG83 3.9 22.0 1.0 O B:HOH523 3.9 31.9 1.0 CE1 B:TYR87 4.1 28.3 1.0 O B:HOH493 4.2 31.9 1.0 O B:HOH435 4.3 31.9 1.0 HB1 A:ALA15 4.6 26.5 1.0 HB2 A:ALA15 4.8 26.5 1.0 CD B:ARG83 4.9 22.0 1.0

Sodium binding site 9 out of 17 in the The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na207 b:31.7 occ:1.00 O B:HOH342 2.3 31.9 1.0 O B:HOH383 2.3 27.6 1.0 OD2 B:ASP20 2.7 42.4 1.0 HH12 B:ARG17 2.7 66.2 1.0 O B:HOH461 2.8 31.9 1.0 HH22 B:ARG17 2.8 63.6 1.0 NH1 B:ARG17 3.2 66.2 1.0 NH2 B:ARG17 3.3 63.6 1.0 O B:HOH445 3.4 31.9 1.0 CZ B:ARG17 3.5 57.3 1.0 O B:HOH456 3.7 31.9 1.0 HH11 B:ARG17 3.7 66.2 1.0 CG B:ASP20 3.8 37.6 1.0 O B:HOH502 3.9 31.9 1.0 HH21 B:ARG17 4.0 63.6 1.0 HD22 B:ASN22 4.2 45.1 1.0 O B:HOH449 4.2 31.9 1.0 HB2 B:ASN22 4.3 35.6 1.0 OD1 B:ASP20 4.3 41.4 1.0 ND2 B:ASN22 4.4 45.1 1.0 HD21 B:ASN22 4.6 45.1 1.0 O B:HOH317 4.7 31.9 1.0 NE B:ARG17 4.7 42.6 1.0 NA B:NA211 4.8 30.0 1.0 CG B:ASN22 4.8 44.3 1.0 O B:HOH467 4.8 31.9 0.5 O B:HOH354 5.0 31.9 1.0

Sodium binding site 10 out of 17 in the The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of The Crystal Structure of Allophycocyanin From the Red Algae Gracilaria Chilensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na208 b:29.8 occ:1.00 H B:LEU36 2.1 20.9 1.0 H22 B:PEG202 2.1 35.6 1.0 H31 B:PEG202 2.5 31.5 1.0 HB2 B:GLU35 2.5 31.8 1.0 O B:GLN32 2.8 20.5 1.0 O B:HOH369 2.9 13.6 1.0 N B:LEU36 2.9 20.9 1.0 H B:GLU35 2.9 26.9 1.0 HA B:THR33 3.1 20.6 1.0 C2 B:PEG202 3.1 35.6 1.0 O B:HOH352 3.2 27.5 1.0 N B:GLU35 3.2 26.9 1.0 HB2 B:LEU36 3.2 25.4 1.0 CB B:GLU35 3.3 31.8 1.0 C3 B:PEG202 3.4 31.5 1.0 O2 B:PEG202 3.4 39.3 1.0 C B:THR33 3.4 20.8 1.0 CA B:GLU35 3.6 26.3 1.0 HB3 B:LEU36 3.6 25.4 1.0 O B:THR33 3.6 22.2 1.0 CA B:THR33 3.6 20.6 1.0 H21 B:PEG202 3.7 35.6 1.0 C B:GLU35 3.7 17.7 1.0 C B:GLN32 3.7 31.6 1.0 N B:GLY34 3.7 22.1 1.0 CB B:LEU36 3.7 25.4 1.0 HB3 B:GLU35 3.7 31.8 1.0 CA B:LEU36 3.9 22.6 1.0 H B:GLY34 3.9 22.1 1.0 H42 B:PEG202 3.9 29.8 1.0 C B:GLY34 4.0 24.3 1.0 N B:THR33 4.1 35.5 1.0 H32 B:PEG202 4.1 31.5 1.0 C1 B:PEG202 4.2 36.3 1.0 H11 B:PEG202 4.2 36.3 1.0 C4 B:PEG202 4.3 29.8 1.0 HA B:LEU36 4.3 22.6 1.0 CA B:GLY34 4.4 27.0 1.0 OE1 B:GLU35 4.4 29.4 1.0 O B:HOH336 4.5 31.9 1.0 CG B:GLU35 4.5 23.0 1.0 HA B:GLU35 4.5 26.3 1.0 HG3 B:GLU35 4.5 23.0 1.0 O1 B:PEG202 4.6 32.0 1.0 H B:ARG37 4.7 28.8 1.0 O B:GLY34 4.8 21.9 1.0 HA B:GLN32 4.8 25.2 1.0 O B:GLU35 4.8 16.7 1.0 H B:THR33 4.9 35.5 1.0 HA3 B:GLY34 4.9 27.0 1.0 CA B:GLN32 4.9 25.2 1.0 O4 B:PEG202 5.0 38.8 1.0 CD B:GLU35 5.0 29.3 1.0

J.Dagnino-Leone, M.Figueroa, C.Mella, M.A.Vorphal, F.Kerff, A.J.Vasquez, M.Bunster, J.Martinez-Oyanedel. Structural Models of the Different Trimers Present in the Core of Phycobilisomes From Gracilaria Chilensis Based on Crystal Structures and Sequences. Plos One V. 12 77540 2017.
ISSN: ESSN 1932-6203
PubMed: 28542288
DOI: 10.1371/JOURNAL.PONE.0177540