Zinc 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:

Sodium

(Na)

3 atoms

The binding sites of Zinc 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 Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Zinc-Bound Pseudecin From Pseudechis Porphyriacus, PDB code: 2epf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Zinc-Bound Pseudecin From Pseudechis Porphyriacus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn301 b:29.1 occ:1.00 NE2 A:HIS51 2.1 23.6 1.0 NE2 A:HIS106 2.1 25.9 1.0 CE1 A:HIS51 3.0 23.3 1.0 CE1 A:HIS106 3.0 26.4 1.0 CD2 A:HIS51 3.1 23.7 1.0 CD2 A:HIS106 3.2 22.9 1.0 ND1 A:HIS51 4.1 23.2 1.0 ND1 A:HIS106 4.1 25.6 1.0 CG A:HIS51 4.2 23.8 1.0 CG A:HIS106 4.2 23.2 1.0 O A:GLU66 4.8 18.4 1.0 O A:HOH369 4.9 16.7 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Zinc-Bound Pseudecin From Pseudechis Porphyriacus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 A:Zn305 b:56.4 occ:1.00 NE2 A:HIS206 2.0 40.3 1.0 O A:HOH307 2.7 30.9 1.0 O A:HOH308 2.7 43.6 1.0 CD2 A:HIS206 2.9 39.5 1.0 CE1 A:HIS206 3.1 40.7 1.0 CG A:HIS206 4.1 37.7 1.0 ND1 A:HIS206 4.1 39.9 1.0 CB A:ASN207 4.8 32.8 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Zinc-Bound Pseudecin From Pseudechis Porphyriacus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 B:Zn302 b:33.8 occ:1.00 O B:HOH303 1.9 21.9 1.0 NE2 B:HIS51 2.0 24.3 1.0 NE2 B:HIS106 2.3 28.1 1.0 CE1 B:HIS51 2.9 25.2 1.0 CD2 B:HIS51 3.1 25.5 1.0 CD2 B:HIS106 3.2 26.0 1.0 CE1 B:HIS106 3.2 29.1 1.0 ND1 B:HIS51 4.1 24.7 1.0 CG B:HIS51 4.2 25.7 1.0 ND1 B:HIS106 4.3 27.2 1.0 CG B:HIS106 4.3 24.8 1.0 CD2 C:LEU184 4.7 35.4 1.0 O B:HOH306 4.7 15.3 1.0 O B:GLU66 4.7 25.0 1.0 NZ C:LYS187 4.8 45.3 1.0 CG2 B:ILE68 4.8 23.7 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Zinc-Bound Pseudecin From Pseudechis Porphyriacus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Zinc-Bound Pseudecin From Pseudechis Porphyriacus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn303 b:39.6 occ:1.00 NE2 C:HIS106 2.0 32.1 1.0 NE2 C:HIS51 2.0 29.6 1.0 O B:HOH304 2.7 41.7 1.0 CE1 C:HIS106 2.9 30.7 1.0 CD2 C:HIS51 3.0 30.9 1.0 CD2 C:HIS106 3.1 29.8 1.0 CE1 C:HIS51 3.1 29.8 1.0 ND1 C:HIS106 4.1 30.5 1.0 CG C:HIS51 4.1 31.5 1.0 ND1 C:HIS51 4.1 30.1 1.0 CG C:HIS106 4.2 29.7 1.0 CG1 C:ILE68 4.5 28.8 1.0 O C:GLU66 4.7 26.7 1.0 CD2 B:LEU184 4.8 41.9 1.0 O C:HOH310 4.8 22.1 1.0 CD1 C:ILE68 4.9 27.7 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Zinc-Bound Pseudecin From Pseudechis Porphyriacus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Zinc-Bound Pseudecin From Pseudechis Porphyriacus within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn304 b:49.4 occ:1.00 NE2 D:HIS51 2.0 36.2 1.0 NE2 D:HIS106 2.2 50.5 1.0 O D:HOH310 2.5 33.5 1.0 CE1 D:HIS106 2.9 50.8 1.0 O D:HOH328 2.9 45.8 1.0 CE1 D:HIS51 3.0 35.9 1.0 CD2 D:HIS51 3.0 36.0 1.0 CD2 D:HIS106 3.3 50.1 1.0 ND1 D:HIS106 4.1 51.2 1.0 ND1 D:HIS51 4.1 36.2 1.0 CG D:HIS51 4.2 36.9 1.0 CG D:HIS106 4.3 49.9 1.0 O D:GLU66 4.7 37.5 1.0 O D:HOH315 4.9 29.1 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