Sodium in PDB 7vj2: Class II Photolyase Mmcpdii Oxidized to Semiquinone Tr-Sfx Studies (125 Us Time-Point)

All present enzymatic activity of Class II Photolyase Mmcpdii Oxidized to Semiquinone Tr-Sfx Studies (125 Us Time-Point):
4.1.99.3;

The structure of Class II Photolyase Mmcpdii Oxidized to Semiquinone Tr-Sfx Studies (125 Us Time-Point), PDB code: 7vj2 was solved by M.Maestre-Reyna, C.-H.Yang, W.-C.Huang, E.Nango, E.P.G.Ngura Putu, S.Franz-Badur, W.-J.Wu, H.-Y.Wu, P.-H.Wang, Y.Hosokawa, M.Saft, H.-J.Emmerich, J.-H.Liao, C.-C.Lee, K.-F.Huang, Y.-K.Chang, J.-H.Weng, A.Royant, W.Gad, A.H.Pang, C.-W.Chang, M.Sugahara, S.Owada, Y.Joti, A.Yamashita, R.Tanaka, T.Tanaka, F.J.Luo, K.Tono, S.Kiontke, J.Yamamoto, S.Iwata, L.-O.Essen, Y.Bessho, M.-D.Tsai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.62 / 3.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	70.85, 70.85, 247.21, 90, 90, 90
R / Rfree (%)	26.6 / 29.5

The binding sites of Sodium atom in the Class II Photolyase Mmcpdii Oxidized to Semiquinone Tr-Sfx Studies (125 Us Time-Point) (pdb code 7vj2). 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 Class II Photolyase Mmcpdii Oxidized to Semiquinone Tr-Sfx Studies (125 Us Time-Point), PDB code: 7vj2:

Sodium binding site 1 out of 1 in the Class II Photolyase Mmcpdii Oxidized to Semiquinone Tr-Sfx Studies (125 Us Time-Point)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Class II Photolyase Mmcpdii Oxidized to Semiquinone Tr-Sfx Studies (125 Us Time-Point) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1505 b:62.1 occ:1.00 CG A:GLU397 2.7 58.7 1.0 CD A:GLU397 2.9 61.9 1.0 OE2 A:GLU397 3.0 67.3 1.0 OE1 A:GLU397 3.7 60.6 1.0 CB A:GLU397 4.2 54.8 1.0 CA A:GLU397 4.9 54.9 1.0 O A:GLU397 4.9 51.6 1.0

M.Maestre-Reyna, C.H.Yang, E.Nango, W.C.Huang, E.P.G.Ngurah Putu, W.J.Wu, P.H.Wang, S.Franz-Badur, M.Saft, H.J.Emmerich, H.Y.Wu, C.C.Lee, K.F.Huang, Y.K.Chang, J.H.Liao, J.H.Weng, W.Gad, C.W.Chang, A.H.Pang, M.Sugahara, S.Owada, Y.Hosokawa, Y.Joti, A.Yamashita, R.Tanaka, T.Tanaka, F.Luo, K.Tono, K.C.Hsu, S.Kiontke, I.Schapiro, R.Spadaccini, A.Royant, J.Yamamoto, S.Iwata, L.O.Essen, Y.Bessho, M.D.Tsai. Serial Crystallography Captures Dynamic Control of Sequential Electron and Proton Transfer Events in A Flavoenzyme. Nat.Chem. V. 14 677 2022.
ISSN: ESSN 1755-4349
PubMed: 35393554
DOI: 10.1038/S41557-022-00922-3