Zinc 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
Sodium	(Na)	1 atom

The binding sites of Zinc 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 Zinc atom.
In total 3 binding sites of Zinc where determined in the Complex Between DDR1 Ds-Like Domain and Prth-101 Fab, PDB code: 8pe9:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Complex Between DDR1 Ds-Like Domain and Prth-101 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn5003 b:83.0 occ:1.00 OD1 A:ASP367 2.1 76.8 1.0 CG A:ASP367 2.9 76.2 1.0 OD2 A:ASP367 3.2 78.3 1.0 CB A:ASP367 4.2 72.1 1.0 CA A:ASP367 4.9 70.6 1.0

Zinc binding site 2 out of 3 in the Complex Between DDR1 Ds-Like Domain and Prth-101 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex Between DDR1 Ds-Like Domain and Prth-101 Fab within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:91.1 occ:1.00 OD1 L:ASP75 2.2 61.3 1.0 OD2 H:ASP124 2.9 71.1 1.0 CB H:ASP124 2.9 63.9 1.0 CG L:ASP75 3.0 60.6 1.0 OD2 L:ASP75 3.0 63.0 1.0 CG H:ASP124 3.3 68.7 1.0 O L:LEU76 3.6 55.0 1.0 CA H:ASP124 4.1 62.0 1.0 N H:ASP124 4.1 61.8 1.0 CB L:ASP75 4.4 55.8 1.0 OD1 H:ASP124 4.6 69.4 1.0 N L:LEU76 4.6 54.1 1.0 C H:ASP124 4.7 61.8 1.0 C L:LEU76 4.8 54.9 1.0 CA L:ASP75 5.0 53.8 1.0

Zinc binding site 3 out of 3 in the Complex Between DDR1 Ds-Like Domain and Prth-101 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complex Between DDR1 Ds-Like Domain and Prth-101 Fab within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn301 b:121.0 occ:1.00 NE2 H:HIS194 2.3 66.4 1.0 ND2 L:ASN160 2.3 64.2 1.0 CE1 H:HIS194 2.8 66.5 1.0 OD1 L:ASN159 3.3 64.6 1.0 CG L:ASN160 3.4 63.6 1.0 CD2 H:HIS194 3.5 65.2 1.0 ND2 L:ASN159 3.6 63.8 1.0 OD1 L:ASN160 3.7 64.9 1.0 CG L:ASN159 3.8 63.4 1.0 OG1 L:THR194 4.0 66.3 1.0 ND1 H:HIS194 4.1 65.9 1.0 OD2 L:ASP192 4.2 73.2 1.0 OD2 L:ASP189 4.2 75.2 1.0 CG H:HIS194 4.4 63.9 1.0 OD1 L:ASP192 4.7 71.5 1.0 CB L:ASN160 4.7 60.2 1.0 OG L:SER196 4.7 65.0 1.0 CG L:ASP192 4.9 71.0 1.0 N L:ASN160 4.9 58.7 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