Sodium in PDB 2p6z: Enzymatic and Structural Characterisation of Amphinase, A Novel Cytotoxic Ribonuclease From Rana Pipiens Oocytes

The structure of Enzymatic and Structural Characterisation of Amphinase, A Novel Cytotoxic Ribonuclease From Rana Pipiens Oocytes, PDB code: 2p6z was solved by U.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.20 / 1.93
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	29.795, 44.607, 46.054, 116.56, 83.19, 103.68
R / Rfree (%)	14.6 / 19.1

The binding sites of Sodium atom in the Enzymatic and Structural Characterisation of Amphinase, A Novel Cytotoxic Ribonuclease From Rana Pipiens Oocytes (pdb code 2p6z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Enzymatic and Structural Characterisation of Amphinase, A Novel Cytotoxic Ribonuclease From Rana Pipiens Oocytes, PDB code: 2p6z:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Enzymatic and Structural Characterisation of Amphinase, A Novel Cytotoxic Ribonuclease From Rana Pipiens Oocytes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Enzymatic and Structural Characterisation of Amphinase, A Novel Cytotoxic Ribonuclease From Rana Pipiens Oocytes within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:39.5 occ:1.00 O A:HOH647 2.4 31.7 1.0 O A:HOH629 2.4 35.5 1.0 O A:THR93 2.5 13.5 1.0 OE1 A:GLN73 2.9 18.3 1.0 OG1 A:THR93 3.0 16.2 1.0 C A:THR93 3.4 13.7 1.0 O A:HOH536 3.7 18.5 1.0 O A:HOH553 4.0 30.4 1.0 CB A:THR93 4.0 14.3 1.0 CD A:GLN73 4.0 15.6 1.0 CA A:THR93 4.1 14.1 1.0 N A:THR93 4.3 13.8 1.0 N A:ASN94 4.3 13.4 1.0 NE2 A:GLN73 4.5 16.5 1.0 CA A:ASN94 4.5 13.1 1.0 OG1 A:THR92 4.7 16.6 1.0

Sodium binding site 2 out of 3 in the Enzymatic and Structural Characterisation of Amphinase, A Novel Cytotoxic Ribonuclease From Rana Pipiens Oocytes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Enzymatic and Structural Characterisation of Amphinase, A Novel Cytotoxic Ribonuclease From Rana Pipiens Oocytes within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:32.8 occ:1.00 O B:HOH643 2.2 19.4 1.0 O B:HOH531 2.5 24.5 1.0 O B:HOH514 2.6 11.9 1.0 O6 B:CIT502 2.6 14.4 1.0 O7 B:CIT502 2.6 8.7 1.0 O B:ILE44 2.7 9.6 1.0 C6 B:CIT502 3.5 11.3 1.0 C3 B:CIT502 3.6 10.4 1.0 C B:ILE44 3.8 8.6 1.0 O A:HOH615 3.9 29.7 1.0 O A:HOH544 3.9 14.3 1.0 CB B:LYS42 4.1 12.1 1.0 CG2 B:ILE44 4.2 7.5 1.0 O A:HOH518 4.2 22.7 1.0 C4 B:CIT502 4.4 9.8 1.0 CD B:LYS42 4.4 18.7 1.0 CG B:LYS42 4.5 14.5 1.0 OD1 B:ASN45 4.5 8.5 1.0 O B:HOH605 4.5 14.2 0.5 N B:ILE44 4.6 8.7 1.0 O1 B:CIT502 4.7 11.4 1.0 O5 B:CIT502 4.7 13.5 1.0 NZ B:LYS14 4.7 6.3 1.0 CA B:ILE44 4.7 8.4 1.0 N B:ASN45 4.7 8.5 1.0 O3 B:CIT502 4.8 8.6 1.0 CA B:ASN45 4.8 8.5 1.0 C2 B:CIT502 4.8 9.8 1.0 C1 B:CIT502 4.8 11.0 1.0 CB B:ASN45 4.8 7.7 1.0 C5 B:CIT502 4.9 9.6 1.0

Sodium binding site 3 out of 3 in the Enzymatic and Structural Characterisation of Amphinase, A Novel Cytotoxic Ribonuclease From Rana Pipiens Oocytes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Enzymatic and Structural Characterisation of Amphinase, A Novel Cytotoxic Ribonuclease From Rana Pipiens Oocytes within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:33.4 occ:1.00 O B:HOH541 2.2 29.7 1.0 O B:HOH526 2.4 11.8 1.0 O1 B:CIT503 2.4 10.2 0.5 O B:HOH567 2.6 27.9 1.0 OG1 B:THR71 2.7 12.9 0.5 O7 B:CIT503 3.0 17.8 0.5 OG1 B:THR71 3.4 14.6 0.5 C1 B:CIT503 3.4 12.9 0.5 CG2 B:THR71 3.6 14.9 0.5 C2 B:CIT503 3.8 15.9 0.5 C3 B:CIT503 3.9 17.1 0.5 CB B:THR71 4.0 13.8 0.5 O B:ILE58 4.0 11.1 1.0 CB B:THR71 4.1 14.2 0.5 O5 B:CIT503 4.1 18.0 0.5 N B:THR71 4.2 13.1 1.0 O B:HOH621 4.2 38.3 1.0 O B:GLU57 4.3 11.2 1.0 CA B:ILE58 4.3 11.4 1.0 O B:SER69 4.3 10.6 1.0 C6 B:CIT503 4.5 17.4 0.5 O2 B:CIT503 4.5 12.6 0.5 C B:ILE58 4.5 11.3 1.0 O B:HOH520 4.6 17.0 1.0 CA B:THR71 4.7 13.8 0.5 CA B:THR71 4.7 14.2 0.5 C B:SER70 5.0 11.9 1.0

U.P.Singh, W.Ardelt, S.K.Saxena, D.E.Holloway, E.Vidunas, H.S.Lee, A.Saxena, K.Shogen, K.R.Acharya. Enzymatic and Structural Characterisation of Amphinase, A Novel Cytotoxic Ribonuclease From Rana Pipiens Oocytes. J.Mol.Biol. V. 371 93 2007.
ISSN: ISSN 0022-2836
PubMed: 17560606
DOI: 10.1016/J.JMB.2007.04.071