Sodium in PDB 8ell: Apo Human Biliverdin Reductase Beta (Cryogenic)

All present enzymatic activity of Apo Human Biliverdin Reductase Beta (Cryogenic):
1.3.1.24; 1.5.1.30;

The structure of Apo Human Biliverdin Reductase Beta (Cryogenic), PDB code: 8ell was solved by M.J.Mcleod, E.Z.Eisenmesser, E.Lee, R.E.Thorne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.10 / 1.52
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.187, 45.668, 104.213, 90, 90, 90
R / Rfree (%)	16 / 18.8

The binding sites of Sodium atom in the Apo Human Biliverdin Reductase Beta (Cryogenic) (pdb code 8ell). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Apo Human Biliverdin Reductase Beta (Cryogenic), PDB code: 8ell:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Apo Human Biliverdin Reductase Beta (Cryogenic)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apo Human Biliverdin Reductase Beta (Cryogenic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:12.3 occ:1.00 OG1 A:THR12 3.1 18.9 1.0 N A:ARG35 3.2 8.9 1.0 O A:HOH668 3.3 37.0 1.0 NH1 A:ARG39 3.3 12.7 1.0 O A:HOH557 3.5 23.5 1.0 CG2 A:THR12 3.8 15.9 1.0 CD A:ARG39 3.8 17.0 1.0 CA A:VAL34 3.9 8.7 1.0 CB A:ARG35 3.9 11.5 1.0 CB A:VAL34 4.0 10.7 1.0 CB A:THR12 4.0 15.1 1.0 C A:VAL34 4.0 9.4 1.0 CG A:ARG35 4.0 15.1 1.0 CA A:ARG35 4.1 9.1 1.0 CZ A:ARG39 4.3 12.4 1.0 O A:HOH505 4.4 21.9 1.0 NE A:ARG39 4.5 14.6 1.0 CG1 A:VAL34 4.5 11.9 1.0 O A:HOH564 4.6 34.4 1.0 N A:ASP36 4.7 10.2 1.0 O A:HOH584 4.7 41.4 1.0 C A:ARG35 5.0 10.0 1.0 O A:HOH679 5.0 22.8 1.0 O A:HOH579 5.0 32.1 1.0

Sodium binding site 2 out of 2 in the Apo Human Biliverdin Reductase Beta (Cryogenic)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Apo Human Biliverdin Reductase Beta (Cryogenic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:19.5 occ:1.00 OG1 A:THR166 2.8 14.0 1.0 OG A:SER202 2.8 14.7 1.0 O A:TYR200 2.8 10.8 1.0 O A:THR164 3.1 15.9 1.0 N A:SER202 3.5 12.9 1.0 C A:THR164 3.6 15.3 1.0 CD1 A:TYR200 3.6 11.9 1.0 CG2 A:THR164 3.6 19.4 1.0 CB A:THR164 3.6 17.0 1.0 CB A:SER202 3.7 14.8 1.0 CB A:THR166 3.7 11.1 1.0 N A:THR166 3.7 11.0 1.0 CA A:GLY171 3.8 12.8 1.0 CD A:PRO172 3.8 13.6 1.0 C A:TYR200 3.9 10.2 1.0 C A:PRO201 4.0 12.0 1.0 CA A:SER202 4.1 14.2 1.0 N A:VAL165 4.1 14.2 1.0 CE1 A:TYR200 4.1 13.0 1.0 CA A:THR164 4.2 17.5 1.0 C A:VAL165 4.2 13.3 1.0 CA A:THR166 4.3 10.6 1.0 O A:SER202 4.3 15.9 1.0 CA A:PRO201 4.3 11.3 1.0 CA A:VAL165 4.3 12.8 1.0 N A:PRO172 4.4 14.3 1.0 O A:HOH568 4.5 18.7 1.0 C A:GLY171 4.5 13.3 1.0 C A:SER202 4.5 15.3 1.0 N A:PRO201 4.6 10.9 1.0 CG A:TYR200 4.7 11.1 1.0 N A:GLY171 4.7 11.6 1.0 OG1 A:THR164 4.8 21.9 1.0 CG A:PRO172 4.8 16.3 1.0 CB A:TYR200 4.8 10.2 1.0 O A:PRO201 4.9 12.2 1.0 N A:THR164 4.9 15.6 1.0 CG2 A:THR166 5.0 14.9 1.0

E.Lee, M.J.Mcleod, J.S.Redzic, B.Marcolin, R.E.Thorne, P.Agarwal, E.Z.Eisenmesser. Identifying Structural and Dynamic Changes During the Biliverdin Reductase B Catalytic Cycle Front Mol Biosci V. 10 2023.
ISSN: ESSN 2296-889X
DOI: 10.3389/FMOLB.2023.1244587