Sodium in PDB 2ddb: Crystal Structure of Pseudecin From Pseudechis Porphyriacus

The structure of Crystal Structure of Pseudecin From Pseudechis Porphyriacus, PDB code: 2ddb was solved by N.Suzuki, Y.Yamazaki, Z.Fujimoto, T.Morita, H.Mizuno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.27 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.707, 61.668, 251.224, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.8

The binding sites of Sodium atom in the Crystal Structure of Pseudecin From Pseudechis Porphyriacus (pdb code 2ddb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Pseudecin From Pseudechis Porphyriacus, PDB code: 2ddb:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Pseudecin From Pseudechis Porphyriacus


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 Pseudecin From Pseudechis Porphyriacus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:15.0 occ:1.00 O A:HOH977 2.2 21.5 1.0 O A:SER127 2.3 14.4 1.0 O A:SER72 2.3 14.3 1.0 O B:HOH976 2.3 16.2 1.0 OE1 A:GLN73 2.5 19.5 1.0 O A:HOH774 2.6 27.9 1.0 CD A:GLN73 3.2 17.6 1.0 C A:SER127 3.5 15.0 1.0 C A:SER72 3.5 14.6 1.0 O A:HOH422 3.5 22.0 1.0 NE2 A:GLN73 3.7 20.8 1.0 CA A:SER128 3.9 14.4 1.0 O A:HOH929 4.0 16.0 1.0 OE2 B:GLU87 4.1 19.8 1.0 CA A:GLN73 4.1 14.5 1.0 N A:SER128 4.1 14.5 1.0 CG A:GLN73 4.2 14.2 1.0 N A:GLN73 4.2 14.5 1.0 CE1 A:TYR130 4.4 11.5 1.0 O C:HOH767 4.4 25.2 1.0 CE1 B:HIS106 4.4 17.6 1.0 ND1 B:HIS106 4.6 18.3 1.0 CB A:SER128 4.6 14.9 1.0 CA A:SER127 4.6 15.0 1.0 CA A:SER72 4.6 14.1 1.0 CB A:GLN73 4.6 14.6 1.0 OH A:TYR130 4.8 13.4 1.0 CB A:SER72 4.8 14.7 1.0 CB A:SER127 4.9 15.4 1.0 C A:SER128 5.0 13.8 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Pseudecin From Pseudechis Porphyriacus


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 Pseudecin From Pseudechis Porphyriacus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:20.8 occ:1.00 O B:SER72 2.3 16.4 1.0 O B:SER127 2.3 22.9 1.0 O B:HOH957 2.3 32.6 1.0 OE1 B:GLN73 2.4 21.0 1.0 O A:HOH568 2.5 34.6 1.0 O B:HOH601 3.3 33.1 1.0 CD B:GLN73 3.3 20.2 1.0 C B:SER72 3.5 17.1 1.0 C B:SER127 3.5 23.4 1.0 CA B:SER128 3.8 21.7 1.0 O B:HOH942 3.9 18.0 1.0 NE2 B:GLN73 4.0 22.1 1.0 N B:SER128 4.1 22.5 1.0 CE1 A:HIS106 4.2 20.6 1.0 OE2 A:GLU87 4.2 22.1 1.0 CA B:GLN73 4.2 18.0 1.0 N B:GLN73 4.2 17.0 1.0 CG B:GLN73 4.3 17.6 1.0 CB B:SER128 4.3 21.8 1.0 ND1 A:HIS106 4.5 20.0 1.0 CA B:SER72 4.6 16.6 1.0 CE1 B:TYR130 4.6 21.6 1.0 CB B:SER72 4.6 16.5 1.0 CA B:SER127 4.7 24.0 1.0 CB B:GLN73 4.7 18.4 1.0 C B:SER128 4.9 21.1 1.0 CB B:SER127 4.9 24.1 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Pseudecin From Pseudechis Porphyriacus


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 Pseudecin From Pseudechis Porphyriacus within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:20.4 occ:1.00 O C:SER72 2.3 16.6 1.0 O C:SER127 2.4 18.0 1.0 OE1 C:GLN73 2.4 19.4 1.0 O1 C:GOL326 2.4 26.1 1.0 O C:HOH1000 2.4 24.2 1.0 O2 C:GOL326 2.6 25.8 1.0 CD C:GLN73 3.2 18.1 1.0 C2 C:GOL326 3.4 27.2 1.0 C1 C:GOL326 3.4 26.8 1.0 C C:SER72 3.5 16.7 1.0 C C:SER127 3.5 18.9 1.0 O C:HOH501 3.6 30.7 1.0 CA C:SER128 3.8 18.5 1.0 NE2 C:GLN73 3.9 19.4 1.0 O C:HOH861 3.9 14.5 1.0 N C:SER128 4.1 18.3 1.0 CA C:GLN73 4.1 17.3 1.0 N C:GLN73 4.2 17.0 1.0 CG C:GLN73 4.2 16.4 1.0 CE1 D:HIS106 4.3 25.8 1.0 OE2 D:GLU87 4.3 24.8 1.0 CE1 C:TYR130 4.4 16.2 1.0 CB C:SER128 4.4 19.0 1.0 ND1 D:HIS106 4.5 25.4 1.0 CA C:SER72 4.6 16.2 1.0 CB C:GLN73 4.7 17.4 1.0 CA C:SER127 4.7 19.6 1.0 CB C:SER72 4.8 16.8 1.0 C3 C:GOL326 4.8 27.1 1.0 C C:SER128 4.9 18.1 1.0 OH C:TYR130 5.0 17.8 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Pseudecin From Pseudechis Porphyriacus


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 Pseudecin From Pseudechis Porphyriacus within 5.0Å range: probe atom residue distance (Å) B Occ D:Na304 b:18.9 occ:1.00 O D:SER127 2.2 22.2 1.0 O D:HOH941 2.3 21.4 1.0 O D:SER72 2.3 17.4 1.0 OE1 D:GLN73 2.5 22.5 1.0 O3 D:GOL327 2.6 24.2 1.0 O2 D:GOL327 2.7 28.0 1.0 C D:SER127 3.4 22.2 1.0 CD D:GLN73 3.4 21.1 1.0 C D:SER72 3.5 17.1 1.0 O D:HOH504 3.6 29.8 1.0 C3 D:GOL327 3.6 28.2 1.0 C2 D:GOL327 3.7 28.9 1.0 CA D:SER128 3.7 21.1 1.0 O D:HOH862 3.9 16.2 1.0 N D:SER128 4.0 21.6 1.0 NE2 D:GLN73 4.0 23.2 1.0 CA D:GLN73 4.3 18.0 1.0 N D:GLN73 4.3 17.7 1.0 CE1 D:TYR130 4.3 18.6 1.0 CB D:SER128 4.4 20.9 1.0 CG D:GLN73 4.4 18.2 1.0 OE2 C:GLU87 4.4 19.6 1.0 CE1 C:HIS106 4.5 18.9 1.0 CA D:SER72 4.6 17.0 1.0 CA D:SER127 4.6 23.1 1.0 O B:HOH681 4.6 34.8 1.0 CB D:SER72 4.7 16.7 1.0 ND1 C:HIS106 4.7 17.6 1.0 C D:SER128 4.7 21.0 1.0 OH D:TYR130 4.8 18.7 1.0 C1 D:GOL327 4.8 31.1 1.0 CB D:GLN73 4.9 18.5 1.0 CB D:SER127 4.9 22.9 1.0

N.Suzuki, Y.Yamazaki, R.L.Brown, Z.Fujimoto, T.Morita, H.Mizuno. Structures of Pseudechetoxin and Pseudecin, Two Snake-Venom Cysteine-Rich Secretory Proteins That Target Cyclic Nucleotide-Gated Ion Channels: Implications For Movement of the C-Terminal Cysteine-Rich Domain Acta Crystallogr.,Sect.D V. 64 1034 2008.
ISSN: ISSN 0907-4449
PubMed: 18931410
DOI: 10.1107/S0907444908023512