Sodium in PDB 7p4l: Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)

The structure of Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1), PDB code: 7p4l was solved by S.Nishio, K.Tunyasuvunakool, J.Jumper, D.De Sanctis, L.Jovine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.32 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	262.51, 111.33, 68.51, 90, 100.71, 90
R / Rfree (%)	19.9 / 24.3

The structure of Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) also contains other interesting chemical elements:

Calcium	(Ca)	31 atoms
Chlorine	(Cl)	21 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) (pdb code 7p4l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1), PDB code: 7p4l:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)


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 Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na612 b:34.5 occ:1.00 OE2 A:GLU250 2.2 51.4 1.0 OE2 B:GLU250 2.3 56.7 1.0 O A:HOH827 2.3 50.6 1.0 O B:HOH843 2.3 41.3 1.0 O C:HOH795 2.4 47.9 1.0 OE2 C:GLU250 2.4 66.9 1.0 CD A:GLU250 3.0 59.2 1.0 OE1 A:GLU250 3.2 57.4 1.0 CD C:GLU250 3.2 57.0 1.0 CD B:GLU250 3.2 47.6 1.0 OE1 C:GLU250 3.2 56.9 1.0 OE1 B:GLU250 3.5 64.8 1.0 O B:HOH830 4.0 40.3 1.0 O C:HOH782 4.1 38.6 1.0 O A:HOH771 4.2 33.5 1.0 OE1 A:GLN247 4.3 69.8 1.0 OE1 C:GLN247 4.4 63.0 1.0 CG A:GLU250 4.5 41.9 1.0 OE1 B:GLN247 4.5 64.5 1.0 CG B:GLU250 4.6 48.4 1.0 CG C:GLU250 4.6 46.1 1.0

Sodium binding site 2 out of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)


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 Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na613 b:55.8 occ:1.00 O A:SER387 2.6 47.6 1.0 O B:ASP197 2.7 49.2 1.0 C A:SER387 3.7 38.5 1.0 C B:ASP197 3.8 38.2 1.0 CB A:SER387 4.2 35.9 1.0 CA A:SER387 4.3 36.8 1.0 CA B:ALA198 4.4 40.1 1.0 N B:ALA198 4.5 34.7 1.0 OD2 B:ASP197 4.6 60.3 1.0 CB B:ASP197 4.6 41.6 1.0 O A:HOH763 4.7 65.4 1.0 N A:SER388 4.7 31.1 1.0 CA B:ASP197 4.7 34.8 1.0 CB A:SER388 4.7 42.3 1.0 C B:ALA198 4.7 42.3 1.0 O B:HOH824 4.7 47.4 1.0 O B:GLY199 4.8 45.2 1.0 O A:HOH828 4.8 60.8 1.0 N B:GLY199 4.9 46.6 1.0 CA A:SER388 5.0 45.9 1.0 OG A:SER387 5.0 55.1 1.0 CG B:ASP197 5.0 55.9 1.0

Sodium binding site 3 out of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)


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 Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na614 b:60.8 occ:1.00 OE1 C:GLN499 2.6 68.5 1.0 OE1 A:GLU108 2.6 70.6 1.0 OE2 C:GLU507 3.2 75.2 1.0 CD A:GLU108 3.4 71.8 1.0 OE2 A:GLU108 3.5 68.4 1.0 CD C:GLN499 3.6 47.0 1.0 NE2 C:GLN499 3.9 55.3 1.0 CD C:GLU507 4.3 68.0 1.0 OE1 C:GLU507 4.5 79.2 1.0 O A:HOH811 4.6 45.1 1.0 CG A:GLU108 4.9 50.7 1.0 O A:TYR107 4.9 55.0 1.0

Sodium binding site 4 out of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na615 b:54.5 occ:1.00 OD2 A:ASP263 2.1 63.4 1.0 O C:HOH733 2.3 49.5 1.0 O A:HOH797 2.4 66.9 1.0 O C:HOH753 2.5 53.8 1.0 O A:HOH772 2.6 58.2 1.0 CG A:ASP263 3.1 70.0 1.0 OD1 A:ASP263 3.4 84.4 1.0 O B:HOH822 4.3 46.4 1.0 OD1 C:ASP260 4.3 54.5 1.0 CB A:ASP263 4.4 46.8 1.0 O A:GLY259 4.4 37.5 1.0 CB C:ASP263 4.5 57.2 1.0 O C:ASP260 4.5 41.8 1.0 CG C:ASP260 4.5 54.6 1.0 CB C:ASP260 4.6 38.6 1.0 OD1 A:ASP260 4.7 51.3 1.0 C A:GLY259 4.7 40.2 1.0 CA C:ASP260 4.9 50.5 1.0 OD2 C:ASP263 4.9 66.4 1.0 OD2 C:ASP267 4.9 67.3 1.0

Sodium binding site 5 out of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na616 b:41.7 occ:1.00 OD1 A:ASP319 2.2 37.4 1.0 O A:SER85 2.2 36.7 1.0 O A:THR320 2.3 40.2 1.0 OD1 A:ASP84 2.4 43.6 1.0 O A:HOH807 2.5 38.4 1.0 O A:HOH825 2.7 40.1 1.0 N A:THR320 3.2 34.2 1.0 OG1 A:THR320 3.2 65.2 1.0 C A:THR320 3.3 40.8 1.0 C A:SER85 3.4 37.6 1.0 CG A:ASP84 3.4 38.2 1.0 CG A:ASP319 3.4 39.9 1.0 CA A:CA608 3.4 50.0 1.0 C A:ASP319 3.6 29.1 1.0 N A:SER85 3.6 39.9 1.0 CA A:THR320 3.7 43.6 1.0 OD2 A:ASP84 3.8 38.3 1.0 CA A:SER85 4.0 37.0 1.0 CA A:ASP319 4.0 31.8 1.0 CB A:THR320 4.1 53.0 1.0 O A:ASP319 4.1 46.3 1.0 O A:HOH901 4.2 42.7 1.0 OD2 A:ASP319 4.3 42.7 1.0 CB A:ASP319 4.3 35.2 1.0 N A:LYS86 4.4 35.1 1.0 N A:PRO321 4.5 59.0 1.0 CB A:SER85 4.5 27.2 1.0 O A:GLU322 4.5 37.9 1.0 C A:ASP84 4.5 37.4 1.0 CB A:ASP84 4.6 27.1 1.0 CG A:LYS86 4.6 50.6 1.0 CA A:ASP84 4.7 32.3 1.0 O A:HOH881 4.7 50.7 1.0 CA A:LYS86 4.8 35.9 1.0 O A:HOH879 4.9 51.4 1.0 CA A:PRO321 4.9 43.9 1.0

Sodium binding site 6 out of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na612 b:70.3 occ:1.00 O C:ASP197 2.8 43.2 1.0 O B:SER387 3.0 53.4 1.0 C C:ASP197 3.7 34.5 1.0 CA C:ALA198 4.0 40.0 1.0 OD2 C:ASP197 4.2 74.5 1.0 C B:SER387 4.2 45.5 1.0 N C:ALA198 4.2 44.0 1.0 CB C:ASP197 4.5 41.9 1.0 C C:ALA198 4.6 44.1 1.0 CG C:ASP197 4.7 52.3 1.0 CA C:ASP197 4.7 44.7 1.0 N C:GLY199 4.8 35.5 1.0 CA B:SER387 4.9 42.6 1.0

Sodium binding site 7 out of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na613 b:58.7 occ:1.00 O B:HOH777 2.5 67.9 1.0 OE1 B:GLU108 2.7 81.8 1.0 OE1 A:GLN499 2.7 94.8 1.0 OE2 A:GLU507 3.3 82.1 1.0 OE2 B:GLU108 3.4 74.0 1.0 CD B:GLU108 3.4 77.5 1.0 O B:HOH708 3.5 66.5 1.0 CD A:GLN499 3.6 69.5 1.0 NE2 A:GLN499 3.7 57.5 1.0 CD A:GLU507 4.3 93.6 1.0 O B:HOH721 4.4 51.6 1.0 O B:TYR107 4.5 49.5 1.0 OE1 A:GLU507 4.5 98.6 1.0 O A:ALA498 4.6 55.0 1.0 CG B:GLU108 4.8 50.4 1.0

Sodium binding site 8 out of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na614 b:68.8 occ:1.00 OE2 B:GLU507 2.5 95.4 1.0 OE1 C:GLU108 2.7 72.0 1.0 OE1 B:GLN499 2.8 74.2 1.0 CD B:GLU507 3.4 95.6 1.0 CD C:GLU108 3.5 90.0 1.0 NE2 B:GLN499 3.5 55.2 1.0 CD B:GLN499 3.5 68.8 1.0 OE2 C:GLU108 3.6 93.2 1.0 OE1 B:GLU507 3.6 85.0 1.0 O C:TYR107 4.5 62.4 1.0 CG B:GLU507 4.8 69.1 1.0 O B:ALA498 4.8 68.2 1.0 CG C:GLU108 4.9 69.2 1.0

Sodium binding site 9 out of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na615 b:47.9 occ:1.00 O A:HOH739 2.3 52.5 1.0 O B:HOH822 2.4 46.4 1.0 O B:HOH750 2.4 48.1 1.0 OD2 B:ASP263 2.5 63.3 1.0 O A:HOH799 2.6 57.6 1.0 CG B:ASP263 3.3 52.5 1.0 O B:HOH782 3.4 54.7 1.0 OD1 B:ASP263 3.6 65.2 1.0 O B:HOH831 4.3 62.0 1.0 CB A:ASP263 4.3 46.8 1.0 O A:ASP260 4.3 45.6 1.0 O B:HOH759 4.4 50.8 1.0 OD1 A:ASP260 4.4 51.3 1.0 CB A:ASP260 4.6 43.8 1.0 CG A:ASP260 4.6 57.8 1.0 OD2 A:ASP267 4.7 78.9 1.0 CB B:ASP263 4.7 43.8 1.0 O B:GLY259 4.7 52.4 1.0 CA A:ASP260 4.7 41.0 1.0 OD1 B:ASP260 4.8 66.0 1.0 OD2 A:ASP263 4.9 63.4 1.0 C B:GLY259 5.0 43.2 1.0 C A:ASP260 5.0 43.8 1.0

Sodium binding site 10 out of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na616 b:41.2 occ:1.00 OD1 B:ASP319 2.2 38.9 1.0 O B:HOH771 2.2 37.3 1.0 O B:SER85 2.2 30.0 1.0 O B:THR320 2.3 50.5 1.0 OD1 B:ASP84 2.5 49.4 1.0 N B:THR320 3.3 38.4 1.0 C B:THR320 3.3 39.4 1.0 C B:SER85 3.4 39.5 1.0 CG B:ASP319 3.4 47.0 1.0 CG B:ASP84 3.5 46.1 1.0 N B:SER85 3.5 38.7 1.0 CA B:CA606 3.6 53.7 1.0 C B:ASP319 3.7 41.7 1.0 CG2 B:THR320 3.7 43.9 1.0 CA B:THR320 3.8 48.1 1.0 O B:HOH894 3.9 45.3 1.0 CA B:SER85 3.9 37.9 1.0 OD2 B:ASP84 4.1 57.8 1.0 CA B:ASP319 4.1 36.5 1.0 O B:ASP319 4.2 44.4 1.0 OD2 B:ASP319 4.3 43.9 1.0 CB B:SER85 4.3 34.2 1.0 O B:HOH753 4.3 54.4 1.0 O B:GLU322 4.4 45.2 1.0 CB B:THR320 4.4 45.6 1.0 CB B:ASP319 4.4 40.6 1.0 N B:PRO321 4.5 54.3 1.0 N B:LYS86 4.5 31.9 1.0 C B:ASP84 4.5 45.3 1.0 CB B:ASP84 4.7 38.2 1.0 CA B:ASP84 4.7 40.3 1.0 CG B:LYS86 4.8 39.3 1.0 CA B:PRO321 4.8 44.3 1.0 C B:PRO321 4.9 48.3 1.0 CA B:LYS86 4.9 36.5 1.0 N B:GLU322 4.9 49.6 1.0 O B:HOH885 4.9 46.3 1.0

D.Moi, S.Nishio, X.Li, C.Valansi, M.Langleib, N.G.Brukman, K.Flyak, C.Dessimoz, D.De Sanctis, K.Tunyasuvunakool, J.Jumper, M.Grana, H.Romero, P.S.Aguilar, L.Jovine, B.Podbilewicz. Discovery of Archaeal Fusexins Homologous to Eukaryotic HAP2/GCS1 Gamete Fusion Proteins Nat Commun V. 13 3880 2022.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-022-31564-1