Sodium in PDB 2gvk: Crystal Structure of A Dye-Decolorizing Peroxidase (Dyp) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.6 A Resolution

The structure of Crystal Structure of A Dye-Decolorizing Peroxidase (Dyp) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.6 A Resolution, PDB code: 2gvk was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.01 / 1.60
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	109.090, 109.090, 122.100, 90.00, 90.00, 120.00
R / Rfree (%)	16.4 / 19

The structure of Crystal Structure of A Dye-Decolorizing Peroxidase (Dyp) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.6 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of A Dye-Decolorizing Peroxidase (Dyp) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.6 A Resolution (pdb code 2gvk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of A Dye-Decolorizing Peroxidase (Dyp) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.6 A Resolution, PDB code: 2gvk:

Sodium binding site 1 out of 1 in the Crystal Structure of A Dye-Decolorizing Peroxidase (Dyp) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.6 A Resolution


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 A Dye-Decolorizing Peroxidase (Dyp) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.6 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na320 b:23.2 occ:1.00 OD1 A:ASP36 2.3 15.9 1.0 O A:PRO35 2.4 14.2 1.0 O A:HOH438 2.4 25.2 1.0 O A:HOH481 2.4 31.3 1.0 O A:HOH371 2.5 25.0 1.0 C A:PRO35 3.3 14.3 1.0 CG A:ASP36 3.5 14.7 1.0 CA A:ASP36 3.7 13.1 1.0 N A:ASP36 3.8 13.6 1.0 CB A:ASP36 4.2 13.3 1.0 CB A:PRO35 4.3 15.3 1.0 CA A:PRO35 4.4 15.0 1.0 OD2 A:ASP36 4.5 18.3 1.0 OD2 A:ASP39 4.6 19.7 1.0 O A:HOH357 4.8 18.6 1.0 CG A:PRO35 4.9 15.6 1.0

C.Zubieta, S.S.Krishna, M.Kapoor, P.Kozbial, D.Mcmullan, H.L.Axelrod, M.D.Miller, P.Abdubek, E.Ambing, T.Astakhova, D.Carlton, H.J.Chiu, T.Clayton, M.C.Deller, L.Duan, M.A.Elsliger, J.Feuerhelm, S.K.Grzechnik, J.Hale, E.Hampton, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, A.Kumar, D.Marciano, A.T.Morse, E.Nigoghossian, L.Okach, S.Oommachen, R.Reyes, C.L.Rife, P.Schimmel, H.Van Den Bedem, D.Weekes, A.White, Q.Xu, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson. Crystal Structures of Two Novel Dye-Decolorizing Peroxidases Reveal A Beta-Barrel Fold with A Conserved Heme-Binding Motif. Proteins V. 69 223 2007.
ISSN: ISSN 0887-3585
PubMed: 17654545
DOI: 10.1002/PROT.21550