Calcium in PDB 7yix: The Cryo-Em Structure of Human Tissue Nonspecific Alkaline Phosphatase and Single-Chain Fragment Variable (Scfv) Complex.

All present enzymatic activity of The Cryo-Em Structure of Human Tissue Nonspecific Alkaline Phosphatase and Single-Chain Fragment Variable (Scfv) Complex.:
3.1.3.1; 3.9.1.1;

The structure of The Cryo-Em Structure of Human Tissue Nonspecific Alkaline Phosphatase and Single-Chain Fragment Variable (Scfv) Complex. also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	4 atoms

The binding sites of Calcium atom in the The Cryo-Em Structure of Human Tissue Nonspecific Alkaline Phosphatase and Single-Chain Fragment Variable (Scfv) Complex. (pdb code 7yix). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the The Cryo-Em Structure of Human Tissue Nonspecific Alkaline Phosphatase and Single-Chain Fragment Variable (Scfv) Complex., PDB code: 7yix:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the The Cryo-Em Structure of Human Tissue Nonspecific Alkaline Phosphatase and Single-Chain Fragment Variable (Scfv) Complex.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Cryo-Em Structure of Human Tissue Nonspecific Alkaline Phosphatase and Single-Chain Fragment Variable (Scfv) Complex. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:59.2 occ:1.00 OD1 A:ASP306 2.4 61.6 1.0 OE1 A:GLU235 2.4 68.3 1.0 OE2 A:GLU235 2.5 68.3 1.0 O A:PHE290 2.5 55.2 1.0 OE1 A:GLU291 2.7 60.7 1.0 CD A:GLU235 2.8 68.3 1.0 CG A:ASP306 3.2 61.6 1.0 OD2 A:ASP306 3.3 61.6 1.0 CD A:GLU291 3.6 60.7 1.0 C A:PHE290 3.7 55.2 1.0 OE2 A:GLU291 4.0 60.7 1.0 CG A:GLU235 4.3 68.3 1.0 O A:THR305 4.3 62.8 1.0 NH2 A:ARG223 4.4 59.5 1.0 OH A:TYR236 4.4 71.2 1.0 CA A:GLU291 4.4 60.7 1.0 N A:GLU291 4.5 60.7 1.0 CA A:PHE290 4.7 55.2 1.0 CB A:ASP306 4.7 61.6 1.0 CB A:PHE290 4.8 55.2 1.0 CG A:GLU291 4.8 60.7 1.0 OG1 A:THR305 4.8 62.8 1.0 CB A:GLU291 4.8 60.7 1.0 C A:THR305 4.9 62.8 1.0

Calcium binding site 2 out of 2 in the The Cryo-Em Structure of Human Tissue Nonspecific Alkaline Phosphatase and Single-Chain Fragment Variable (Scfv) Complex.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Cryo-Em Structure of Human Tissue Nonspecific Alkaline Phosphatase and Single-Chain Fragment Variable (Scfv) Complex. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca605 b:60.2 occ:1.00 OE2 B:GLU235 2.4 66.5 1.0 OE1 B:GLU235 2.5 66.5 1.0 O B:PHE290 2.5 53.5 1.0 OE2 B:GLU291 2.6 59.4 1.0 OD1 B:ASP306 2.8 61.0 1.0 CD B:GLU235 2.8 66.5 1.0 OD2 B:ASP306 3.2 61.0 1.0 CG B:ASP306 3.3 61.0 1.0 O B:THR305 3.4 63.4 1.0 CD B:GLU291 3.7 59.4 1.0 C B:PHE290 3.7 53.5 1.0 CG B:GLU291 4.0 59.4 1.0 CG B:GLU235 4.3 66.5 1.0 OH B:TYR236 4.5 70.1 1.0 CA B:GLU291 4.5 59.4 1.0 C B:THR305 4.5 63.4 1.0 N B:GLU291 4.5 59.4 1.0 CA B:PHE290 4.6 53.5 1.0 CB B:ASP306 4.7 61.0 1.0 CB B:PHE290 4.7 53.5 1.0 OE1 B:GLU291 4.8 59.4 1.0 CB B:GLU291 4.8 59.4 1.0 CB B:THR305 5.0 63.4 1.0 NH1 B:ARG223 5.0 59.5 1.0

Y.Yu, K.Rong, D.Yao, Q.Zhang, X.Cao, B.Rao, Y.Xia, Y.Lu, Y.Shen, Y.Yao, H.Xu, P.Ma, Y.Cao, A.Qin. The Structural Pathology For Hypophosphatasia Caused By Malfunctional Tissue Non-Specific Alkaline Phosphatase. Nat Commun V. 14 4048 2023.
ISSN: ESSN 2041-1723
PubMed: 37422472
DOI: 10.1038/S41467-023-39833-3