Sodium in PDB 7ykb: Neutron Structure of Pcya D105N Mutant Complexed with Biliverdin at Room Temperature

All present enzymatic activity of Neutron Structure of Pcya D105N Mutant Complexed with Biliverdin at Room Temperature:
1.3.7.5;

The structure of Neutron Structure of Pcya D105N Mutant Complexed with Biliverdin at Room Temperature, PDB code: 7ykb was solved by M.Unno, R.Nanasawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.38
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.174, 97.523, 43.277, 90, 90, 90
R / Rfree (%)	16.6 / 18.1

The binding sites of Sodium atom in the Neutron Structure of Pcya D105N Mutant Complexed with Biliverdin at Room Temperature (pdb code 7ykb). 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 Neutron Structure of Pcya D105N Mutant Complexed with Biliverdin at Room Temperature, PDB code: 7ykb:

Sodium binding site 1 out of 1 in the Neutron Structure of Pcya D105N Mutant Complexed with Biliverdin at Room Temperature


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Neutron Structure of Pcya D105N Mutant Complexed with Biliverdin at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:51.9 occ:1.00 OE1 A:GLU146 2.4 55.7 1.0 D2 A:HOH511 2.8 72.9 1.0 HG A:SER168 3.0 28.9 0.7 HB3 A:GLU146 3.0 20.0 1.0 HG3 A:GLN147 3.3 23.9 0.5 HB2 A:SER168 3.5 22.1 0.3 CD A:GLU146 3.6 76.5 1.0 OG A:SER168 3.6 24.0 0.7 HB3 A:SER168 3.6 21.7 0.7 HG2 A:GLN147 3.7 23.9 0.5 O A:HOH511 3.8 60.8 1.0 HB2 A:GLU146 3.8 20.0 1.0 HB3 A:SER168 3.8 22.1 0.3 CG A:GLN147 3.8 19.9 0.5 CB A:GLU146 3.8 16.6 1.0 CD A:GLN147 3.8 22.3 0.5 OE1 A:GLN147 3.9 31.7 0.5 CB A:SER168 4.1 18.4 0.3 CB A:SER168 4.1 18.1 0.7 D2 A:HOH574 4.1 56.1 1.0 D1 A:HOH511 4.2 72.9 1.0 O A:HOH574 4.2 46.8 1.0 CG A:GLU146 4.2 46.3 1.0 HB2 A:GLN147 4.3 15.4 0.5 D1 A:HOH574 4.4 56.1 1.0 NE2 A:GLN147 4.5 16.9 0.5 OE2 A:GLU146 4.6 71.1 1.0 HG2 A:GLU146 4.7 55.5 1.0 OG A:SER168 4.7 21.9 0.3 HB2 A:SER168 4.7 21.7 0.7 DE22 A:GLN147 4.8 20.3 0.5 DE21 A:GLN147 4.9 20.3 0.5

T.Joutsuka, R.Nanasawa, K.Igarashi, K.Horie, M.Sugishima, Y.Hagiwara, K.Wada, K.Fukuyama, N.Yano, S.Mori, A.Ostermann, K.Kusaka, M.Unno. Neutron Crystallography and Quantum Chemical Analysis of Bilin Reductase Pcya Mutants Reveal Substrate and Catalytic Residue Protonation States. J.Biol.Chem. V. 299 02763 2022.
ISSN: ESSN 1083-351X
PubMed: 36463961
DOI: 10.1016/J.JBC.2022.102763