Sodium in PDB 2epf: Crystal Structure of Zinc-Bound Pseudecin From Pseudechis Porphyriacus

The structure of Crystal Structure of Zinc-Bound Pseudecin From Pseudechis Porphyriacus, PDB code: 2epf 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)	38.72 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.077, 62.344, 246.943, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 27.7

The structure of Crystal Structure of Zinc-Bound Pseudecin From Pseudechis Porphyriacus also contains other interesting chemical elements:

Zinc

(Zn)

5 atoms

The binding sites of Sodium atom in the Crystal Structure of Zinc-Bound Pseudecin From Pseudechis Porphyriacus (pdb code 2epf). 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 Zinc-Bound Pseudecin From Pseudechis Porphyriacus, PDB code: 2epf:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Zinc-Bound 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 Zinc-Bound Pseudecin From Pseudechis Porphyriacus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:28.0 occ:1.00 O A:SER72 2.3 17.2 1.0 O A:SER127 2.3 20.6 1.0 O A:HOH309 2.6 27.1 1.0 O A:HOH379 2.6 28.8 1.0 OE1 A:GLN73 3.0 24.4 1.0 CD A:GLN73 3.4 23.8 1.0 C A:SER127 3.5 20.1 1.0 C A:SER72 3.5 17.1 1.0 CA A:SER128 3.6 19.5 1.0 NE2 A:GLN73 3.7 24.0 1.0 O A:HOH317 3.8 20.6 1.0 N A:SER128 4.0 20.0 1.0 CB A:SER128 4.2 19.6 1.0 CA A:GLN73 4.3 18.0 1.0 CG A:GLN73 4.3 20.8 1.0 N A:GLN73 4.3 17.4 1.0 CE1 A:TYR130 4.4 18.5 1.0 CA A:SER72 4.5 16.6 1.0 CB A:SER72 4.6 16.6 1.0 C A:SER128 4.6 18.9 1.0 CA A:SER127 4.7 20.9 1.0 CB A:GLN73 4.9 18.1 1.0 OG A:SER72 4.9 16.9 1.0 OH A:TYR130 5.0 20.1 1.0 CB A:SER127 5.0 20.8 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Zinc-Bound 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 Zinc-Bound Pseudecin From Pseudechis Porphyriacus within 5.0Å range: probe atom residue distance (Å) B Occ C:Na307 b:39.7 occ:1.00 O C:HOH308 2.4 46.5 1.0 OE1 C:GLN73 2.5 38.2 1.0 O C:SER127 2.6 35.7 1.0 O C:SER72 2.7 34.1 1.0 CD C:GLN73 3.5 37.7 1.0 O C:HOH332 3.6 38.5 1.0 C C:SER127 3.6 35.6 1.0 CA C:SER128 3.7 34.6 1.0 C C:SER72 3.9 34.0 1.0 CG C:GLN73 3.9 36.0 1.0 N C:SER128 4.1 34.9 1.0 CB C:SER128 4.1 34.7 1.0 NE2 C:GLN73 4.6 38.5 1.0 N C:GLN73 4.7 34.1 1.0 CB C:SER72 4.7 33.9 1.0 CA C:GLN73 4.7 34.8 1.0 CA C:SER72 4.8 33.9 1.0 CA C:SER127 4.9 36.1 1.0 C C:SER128 4.9 34.4 1.0 CB C:GLN73 4.9 35.0 1.0 CE1 C:TYR130 5.0 33.5 1.0 OG C:SER72 5.0 35.0 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Zinc-Bound 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 Zinc-Bound Pseudecin From Pseudechis Porphyriacus within 5.0Å range: probe atom residue distance (Å) B Occ D:Na308 b:41.1 occ:1.00 O D:SER127 2.4 38.2 1.0 OE1 D:GLN73 2.6 39.9 1.0 O D:SER72 2.6 35.4 1.0 CD D:GLN73 3.0 39.8 1.0 NE2 D:GLN73 3.0 39.5 1.0 O D:HOH313 3.0 35.9 1.0 O D:HOH311 3.3 36.2 1.0 C D:SER127 3.5 38.4 1.0 C D:SER72 3.7 35.5 1.0 CA D:SER128 3.7 37.5 1.0 O D:HOH317 3.9 32.8 1.0 N D:SER128 4.0 37.9 1.0 CA D:GLN73 4.2 38.0 1.0 CG D:GLN73 4.3 39.1 1.0 CE1 D:TYR130 4.4 39.3 1.0 N D:GLN73 4.4 36.7 1.0 CB D:SER128 4.5 37.3 1.0 CB D:GLN73 4.5 38.1 1.0 CA D:SER127 4.7 38.8 1.0 C D:SER128 4.7 37.3 1.0 OH D:TYR130 4.8 40.3 1.0 CA D:SER72 4.8 34.8 1.0 CB D:SER72 5.0 34.5 1.0 CB D:SER127 5.0 39.1 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