Sodium in PDB 4fdz: Eutl From Clostridium Perfringens, Crystallized Under Reducing Conditions

The structure of Eutl From Clostridium Perfringens, Crystallized Under Reducing Conditions, PDB code: 4fdz was solved by M.C.Thompson, D.Cascio, C.S.Crowley, J.S.Kopstein, T.O.Yeates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.82 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.970, 87.970, 252.460, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 17.7

The binding sites of Sodium atom in the Eutl From Clostridium Perfringens, Crystallized Under Reducing Conditions (pdb code 4fdz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Eutl From Clostridium Perfringens, Crystallized Under Reducing Conditions, PDB code: 4fdz:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Eutl From Clostridium Perfringens, Crystallized Under Reducing Conditions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Eutl From Clostridium Perfringens, Crystallized Under Reducing Conditions within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:12.9 occ:1.00 OD1 B:ASN74 2.4 17.8 1.0 OD1 A:ASN74 2.4 21.1 1.0 OD1 C:ASN74 2.5 18.1 1.0 O C:HOH540 2.5 48.6 1.0 O A:HOH404 2.6 39.0 1.0 O B:HOH545 2.6 48.7 1.0 CG B:ASN74 3.5 16.2 1.0 CG A:ASN74 3.5 17.9 1.0 CG C:ASN74 3.5 16.0 1.0 HA A:ASN74 3.8 17.9 1.0 HA B:ASN74 3.9 16.6 1.0 HA C:ASN74 4.0 15.0 1.0 HB3 B:ASN74 4.0 16.8 1.0 HB3 A:ASN74 4.1 18.5 1.0 HB3 C:ASN74 4.2 15.7 1.0 CB B:ASN74 4.2 14.0 1.0 CB A:ASN74 4.3 15.4 1.0 O B:HOH596 4.3 43.5 1.0 CB C:ASN74 4.3 13.1 1.0 ND2 B:ASN74 4.4 14.8 1.0 HD22 B:ASN74 4.4 17.8 1.0 HD22 C:ASN74 4.4 18.4 1.0 ND2 C:ASN74 4.5 15.3 1.0 O A:HOH408 4.5 35.5 1.0 ND2 A:ASN74 4.5 15.0 1.0 HD22 A:ASN74 4.5 18.0 1.0 CA A:ASN74 4.6 14.9 1.0 CA B:ASN74 4.6 13.9 1.0 O B:HOH606 4.6 42.4 1.0 CA C:ASN74 4.7 12.5 1.0

Sodium binding site 2 out of 3 in the Eutl From Clostridium Perfringens, Crystallized Under Reducing Conditions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Eutl From Clostridium Perfringens, Crystallized Under Reducing Conditions within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:26.2 occ:1.00 O B:HOH445 2.4 25.2 1.0 O B:HOH469 2.4 27.1 1.0 O B:ALA168 2.5 18.7 1.0 O B:LEU165 2.5 20.3 1.0 O B:HOH603 2.5 26.1 1.0 O B:HOH602 2.5 25.6 1.0 HA B:ASP169 3.2 22.3 1.0 H B:VAL170 3.4 19.8 1.0 C B:ALA168 3.5 19.9 1.0 C B:LEU165 3.7 19.1 1.0 H B:ALA168 4.0 23.7 1.0 CA B:ASP169 4.0 18.6 1.0 HA B:LYS166 4.0 22.7 1.0 O C:HOH451 4.1 26.4 1.0 N B:VAL170 4.1 16.5 1.0 N B:ASP169 4.1 18.6 1.0 HA B:LEU165 4.2 21.1 1.0 N B:ALA168 4.3 19.7 1.0 HG22 B:VAL170 4.3 19.4 1.0 O B:LYS166 4.3 20.3 1.0 C B:LYS166 4.4 20.0 1.0 O B:VAL170 4.5 21.0 1.0 CA B:ALA168 4.5 18.7 1.0 CA B:LYS166 4.5 18.9 1.0 CA B:LEU165 4.5 17.6 1.0 N B:LYS166 4.6 17.8 1.0 C B:ASP169 4.6 17.5 1.0 HB3 B:LEU165 4.8 19.5 1.0 OE2 C:GLU22 4.8 24.9 1.0 O C:HOH541 4.9 37.4 1.0 HG23 B:VAL170 4.9 19.4 1.0 OD1 B:ASP169 4.9 24.9 1.0 N B:ALA167 5.0 18.8 1.0 H B:ASP169 5.0 22.3 1.0

Sodium binding site 3 out of 3 in the Eutl From Clostridium Perfringens, Crystallized Under Reducing Conditions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Eutl From Clostridium Perfringens, Crystallized Under Reducing Conditions within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:87.7 occ:1.00 O C:HOH524 3.3 36.9 1.0 O C:HOH497 3.4 32.3 1.0 O A:HOH397 3.6 33.4 1.0 O A:HOH483 4.0 50.7 1.0 O A:HOH484 4.2 51.6 1.0 O C:LEU165 4.3 20.2 1.0 OE2 A:GLU22 4.4 39.8 1.0 HA C:ASP169 4.7 36.7 1.0 O C:ALA168 4.8 26.9 1.0 HA C:LYS166 4.8 23.8 1.0 O A:HOH361 4.8 28.8 1.0

M.C.Thompson, D.Cascio, D.J.Leibly, T.O.Yeates. An Allosteric Model For Control of Pore Opening By Substrate Binding in the Eutl Microcompartment Shell Protein. Protein Sci. V. 24 956 2015.
ISSN: ISSN 0961-8368
PubMed: 25752492
DOI: 10.1002/PRO.2672