Sodium in PDB 8pe9: Complex Between DDR1 Ds-Like Domain and Prth-101 Fab

All present enzymatic activity of Complex Between DDR1 Ds-Like Domain and Prth-101 Fab:
2.7.10.1;

The structure of Complex Between DDR1 Ds-Like Domain and Prth-101 Fab, PDB code: 8pe9 was solved by J.Liu, H.Chiang, W.Xiong, V.Laurent, S.C.Griffiths, J.Duelfer, H.Deng, X.Sun, Y.W.Yin, W.Li, L.P.Audoly, Z.An, T.Schuerpf, R.Li, N.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.22 / 3.15
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	117.096, 144.45, 52.299, 90, 90, 90
R / Rfree (%)	27.8 / 30.9

The structure of Complex Between DDR1 Ds-Like Domain and Prth-101 Fab also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Zinc	(Zn)	3 atoms

The binding sites of Sodium atom in the Complex Between DDR1 Ds-Like Domain and Prth-101 Fab (pdb code 8pe9). 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 Complex Between DDR1 Ds-Like Domain and Prth-101 Fab, PDB code: 8pe9:

Sodium binding site 1 out of 1 in the Complex Between DDR1 Ds-Like Domain and Prth-101 Fab


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex Between DDR1 Ds-Like Domain and Prth-101 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Na5004 b:22.5 occ:1.00 CE1 A:PHE263 2.8 68.2 1.0 CD1 A:PHE263 3.1 67.5 1.0 O A:TYR267 3.5 62.8 1.0 N A:GLU269 3.8 62.1 1.0 CZ A:PHE263 4.0 68.0 1.0 OG A:SER265 4.2 67.7 1.0 CG A:PRO197 4.2 67.0 1.0 CB A:GLU269 4.4 64.3 1.0 CA A:VAL268 4.4 62.4 1.0 CG A:PHE263 4.5 66.6 1.0 C A:TYR267 4.6 62.7 1.0 C A:VAL268 4.6 62.4 1.0 CA A:GLU269 4.7 62.2 1.0 OH H:TYR55 5.0 57.0 1.0 N A:VAL268 5.0 62.2 1.0

J.Liu, H.C.Chiang, W.Xiong, V.Laurent, S.C.Griffiths, J.Dulfer, H.Deng, X.Sun, Y.W.Yin, W.Li, L.P.Audoly, Z.An, T.Schurpf, R.Li, N.Zhang. A Highly Selective Humanized DDR1 Mab Reverses Immune Exclusion By Disrupting Collagen Fiber Alignment in Breast Cancer. J Immunother Cancer V. 11 2023.
ISSN: ESSN 2051-1426
PubMed: 37328286
DOI: 10.1136/JITC-2023-006720