Sodium in PDB 4pvk: Engineered Oxidase Reveals Steric Control of Oxygen Reduction

The structure of Engineered Oxidase Reveals Steric Control of Oxygen Reduction, PDB code: 4pvk was solved by D.Zafred, A.Teufelberger, W.Keller, P.Macheroux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.27 / 1.30
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	117.370, 117.370, 201.000, 90.00, 90.00, 120.00
R / Rfree (%)	14.1 / 16

The structure of Engineered Oxidase Reveals Steric Control of Oxygen Reduction also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Engineered Oxidase Reveals Steric Control of Oxygen Reduction (pdb code 4pvk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Engineered Oxidase Reveals Steric Control of Oxygen Reduction, PDB code: 4pvk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Engineered Oxidase Reveals Steric Control of Oxygen Reduction


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Engineered Oxidase Reveals Steric Control of Oxygen Reduction within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:17.9 occ:1.00 OE2 A:GLU89 2.3 16.1 1.0 OE1 A:GLU338 2.3 18.0 1.0 O A:HOH816 2.3 24.5 1.0 O A:HOH713 2.4 15.4 1.0 O A:HOH745 2.5 18.9 1.0 O A:HOH726 2.5 17.9 1.0 CD A:GLU89 3.1 14.9 1.0 HH12 A:ARG44 3.2 26.3 1.0 CD A:GLU338 3.3 18.1 1.0 OE1 A:GLU89 3.4 17.2 1.0 OE2 A:GLU338 3.6 20.9 1.0 HA A:ASP441 3.6 16.2 1.0 H A:TYR339 3.7 16.9 1.0 H A:ILE442 3.8 17.1 1.0 HG23 A:ILE442 3.9 20.1 1.0 NH1 A:ARG44 4.0 21.9 1.0 HA A:GLU338 4.0 18.8 1.0 O A:HOH1204 4.1 38.8 1.0 HZ2 A:TRP45 4.2 21.0 1.0 OD1 A:ASP441 4.3 15.6 1.0 O A:TYR339 4.3 15.2 1.0 HH11 A:ARG44 4.3 26.3 1.0 HG2 A:GLU89 4.3 16.8 1.0 HH22 A:ARG44 4.4 28.0 1.0 CG A:GLU89 4.4 14.0 1.0 N A:ILE442 4.5 14.3 1.0 N A:TYR339 4.6 14.1 1.0 O A:ARG440 4.6 13.9 1.0 CA A:ASP441 4.6 13.5 1.0 O A:HOH1074 4.7 40.1 1.0 O A:HOH1086 4.7 43.1 1.0 CG A:GLU338 4.7 16.5 1.0 H A:ASP443 4.8 17.7 1.0 OD2 A:ASP443 4.8 28.2 1.0 CG2 A:ILE442 4.8 16.7 1.0 HD2 A:TYR339 4.8 18.9 1.0 CA A:GLU338 4.9 15.7 1.0 HG3 A:GLU89 4.9 16.8 1.0 HB3 A:TYR88 4.9 14.9 1.0 HB2 A:GLU338 4.9 19.7 1.0 O A:TYR88 4.9 14.5 1.0 HA A:GLU89 4.9 16.5 1.0 CZ A:ARG44 5.0 20.9 1.0 NH2 A:ARG44 5.0 23.4 1.0 CG A:ASP441 5.0 13.7 1.0

Sodium binding site 2 out of 2 in the Engineered Oxidase Reveals Steric Control of Oxygen Reduction


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Engineered Oxidase Reveals Steric Control of Oxygen Reduction within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:27.9 occ:1.00 O A:LYS430 2.2 22.5 1.0 O A:HOH1288 2.3 35.2 1.0 O A:HOH985 2.4 38.6 1.0 O A:HOH773 2.4 19.4 1.0 O A:HOH1047 2.4 38.8 1.0 O A:HOH1135 2.4 27.8 1.0 HZ1 A:LYS468 3.0 23.3 0.3 H A:LYS430 3.2 23.4 1.0 HZ3 A:LYS468 3.2 23.3 0.3 C A:LYS430 3.4 21.7 1.0 NZ A:LYS468 3.5 19.4 0.3 O A:ASN431 3.7 23.8 1.0 HB2 A:ASN431 3.8 29.4 1.0 C A:ASN431 3.9 21.5 1.0 N A:LYS430 3.9 19.5 1.0 HZ2 A:LYS468 4.0 23.3 0.3 HD2 A:PRO432 4.1 23.7 1.0 HB2 A:SER429 4.2 19.4 1.0 HG3 A:LYS430 4.2 35.0 1.0 CA A:LYS430 4.3 21.4 1.0 O A:PRO432 4.3 17.0 1.0 N A:ASN431 4.3 21.6 1.0 HE3 A:LYS468 4.4 28.9 0.7 N A:PRO432 4.4 19.2 1.0 CA A:ASN431 4.5 21.8 1.0 HG2 A:LYS430 4.6 35.0 1.0 CB A:ASN431 4.6 24.5 1.0 HE3 A:LYS468 4.6 23.9 0.3 CE A:LYS468 4.7 19.9 0.3 CD A:PRO432 4.7 19.7 1.0 OE1 A:GLN434 4.7 17.8 1.0 CG A:LYS430 4.8 29.2 1.0 HA A:SER429 4.8 20.6 1.0 HA A:LYS430 5.0 25.7 1.0 HB3 A:ASN431 5.0 29.4 1.0 C A:SER429 5.0 17.2 1.0

D.Zafred, A.Teufelberger, W.Keller, P.Macheroux. Engineered Oxidase Reveals Steric Control of Oxygen Reduction To Be Published.