Sodium in PDB 7w3e: Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K

All present enzymatic activity of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K:
1.9.3.1; 7.1.1.9;

The structure of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K, PDB code: 7w3e was solved by T.Tsukihara, A.Shimada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.76 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	181.666, 203.752, 177.683, 90, 90, 90
R / Rfree (%)	16.2 / 18.2

The structure of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iron	(Fe)	6 atoms
Copper	(Cu)	6 atoms
Zinc	(Zn)	2 atoms

The binding sites of Sodium atom in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K (pdb code 7w3e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K, PDB code: 7w3e:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:25.4 occ:1.00 O A:HOH871 2.2 24.9 1.0 O A:GLY45 2.3 30.5 1.0 OE1 A:GLU40 2.3 28.2 1.0 O A:SER441 2.3 26.1 1.0 O A:GLU40 2.4 25.6 1.0 CD A:GLU40 3.2 28.6 1.0 O A:HOH774 3.4 34.5 1.0 C A:GLU40 3.4 23.9 1.0 C A:GLY45 3.5 29.6 1.0 CG A:GLU40 3.5 25.2 1.0 C A:SER441 3.6 25.0 1.0 O A:HOH896 3.8 31.8 1.0 CB A:ASP442 3.9 27.0 1.0 CA A:ASP442 3.9 26.0 1.0 O A:GLN43 4.0 27.0 1.0 CA A:THR46 4.0 31.8 1.0 CG A:ASP442 4.1 25.5 1.0 OD1 A:ASP442 4.1 27.2 1.0 N A:THR46 4.2 31.3 1.0 N A:ASP442 4.2 25.1 1.0 CA A:GLU40 4.3 24.8 1.0 N A:LEU41 4.3 25.7 1.0 CA A:LEU41 4.4 23.9 1.0 N A:LEU47 4.4 30.9 1.0 OE2 A:GLU40 4.4 31.3 1.0 N A:GLY45 4.5 27.4 1.0 CB A:GLU40 4.5 24.7 1.0 CA A:GLY45 4.6 28.9 1.0 C A:THR46 4.6 32.8 1.0 CD2 A:LEU41 4.6 25.8 1.0 CA A:SER441 4.7 26.3 1.0 OD2 A:ASP442 4.8 27.6 1.0 O A:HOH843 4.9 34.3 1.0 CB A:SER441 5.0 27.0 1.0

Sodium binding site 2 out of 4 in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:38.2 occ:1.00 NE2 C:HIS148 2.2 38.5 1.0 NE2 C:HIS232 2.5 28.6 1.0 CE1 C:HIS148 3.2 49.7 1.0 CD2 C:HIS232 3.2 28.5 1.0 CD2 C:HIS148 3.2 39.8 1.0 CD C:GLU236 3.3 43.6 1.0 CG C:GLU236 3.4 39.1 1.0 OE1 C:GLU236 3.6 40.3 1.0 CE1 C:HIS232 3.6 27.3 1.0 OE2 C:GLU236 3.6 40.7 1.0 SD C:MET152 4.1 37.0 1.0 CG C:MET152 4.2 31.4 1.0 ND1 C:HIS148 4.3 44.0 1.0 CG C:HIS148 4.4 35.0 1.0 CG C:HIS232 4.5 24.9 1.0 ND1 C:HIS232 4.6 27.0 1.0 O C:HOH516 4.8 44.0 1.0 CE C:MET152 4.9 29.5 1.0 CB C:GLU236 4.9 26.8 1.0

Sodium binding site 3 out of 4 in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K within 5.0Å range: probe atom residue distance (Å) B Occ N:Na605 b:29.8 occ:1.00 O N:HOH860 2.2 29.0 1.0 O N:GLY45 2.3 33.6 1.0 OE1 N:GLU40 2.3 34.1 1.0 O N:SER441 2.3 30.1 1.0 O N:GLU40 2.4 31.6 1.0 CD N:GLU40 3.3 33.7 1.0 C N:GLU40 3.4 30.1 1.0 O N:HOH820 3.5 41.0 1.0 C N:GLY45 3.5 35.1 1.0 CG N:GLU40 3.5 29.2 1.0 C N:SER441 3.5 29.7 1.0 O N:HOH873 3.9 35.2 1.0 CB N:ASP442 3.9 32.2 1.0 CA N:ASP442 3.9 31.0 1.0 O N:GLN43 4.0 31.4 1.0 CG N:ASP442 4.1 30.3 1.0 OD1 N:ASP442 4.1 32.7 1.0 CA N:THR46 4.1 36.9 1.0 N N:ASP442 4.2 32.1 1.0 N N:LEU41 4.2 30.0 1.0 N N:THR46 4.2 37.7 1.0 CA N:GLU40 4.3 28.7 1.0 CA N:LEU41 4.3 29.9 1.0 N N:GLY45 4.4 32.7 1.0 CB N:GLU40 4.4 29.3 1.0 OE2 N:GLU40 4.5 36.6 1.0 N N:LEU47 4.5 37.7 1.0 CA N:GLY45 4.6 34.8 1.0 CD2 N:LEU41 4.6 29.8 1.0 CA N:SER441 4.7 30.3 1.0 C N:THR46 4.7 39.3 1.0 OD2 N:ASP442 4.8 32.4 1.0

Sodium binding site 4 out of 4 in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K within 5.0Å range: probe atom residue distance (Å) B Occ P:Na302 b:38.8 occ:1.00 NE2 P:HIS148 2.3 38.0 1.0 O P:HOH546 2.3 74.0 1.0 NE2 P:HIS232 2.5 26.3 1.0 CD2 P:HIS232 3.2 28.2 1.0 CE1 P:HIS148 3.3 48.3 1.0 CD2 P:HIS148 3.3 33.1 1.0 CD P:GLU236 3.3 55.8 1.0 CG P:GLU236 3.4 35.3 1.0 OE2 P:GLU236 3.6 42.1 1.0 CE1 P:HIS232 3.6 27.4 1.0 OE1 P:GLU236 3.6 46.6 1.0 SD P:MET152 4.0 36.7 1.0 CG P:MET152 4.2 30.8 1.0 ND1 P:HIS148 4.4 42.4 1.0 CG P:HIS148 4.4 31.5 1.0 CG P:HIS232 4.5 25.3 1.0 ND1 P:HIS232 4.6 24.4 1.0 O P:HOH490 4.6 48.5 1.0 O P:HOH533 4.7 61.1 1.0 CE P:MET152 4.9 29.4 1.0 CB P:GLU236 4.9 26.4 1.0

A.Shimada, J.Baba, K.Shinzawa-Itoh, T.Tsukihara, S.Yoshikawa. Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K. To Be Published.