Calcium in PDB 6q6j: Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid

All present enzymatic activity of Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid:
3.1.3.3;

The structure of Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid, PDB code: 6q6j was solved by J.Wouters, M.Haufroid, M.Mirgaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.94 / 1.99
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	49.230, 130.490, 157.760, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.7

The structure of Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid (pdb code 6q6j). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid, PDB code: 6q6j:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:31.9 occ:1.00 OD2 A:ASP20 2.2 36.9 1.0 OD2 A:ASP179 2.2 35.1 1.0 O A:ASP22 2.3 29.8 1.0 O A:HOH483 2.3 37.5 1.0 O A:HOH473 2.3 43.5 1.0 O A:HOH409 2.4 39.1 1.0 CG A:ASP20 3.1 36.1 1.0 CG A:ASP179 3.2 38.8 1.0 OD1 A:ASP20 3.3 35.6 1.0 C A:ASP22 3.4 34.8 1.0 OD1 A:ASP179 3.5 46.0 1.0 CB A:ASP22 4.1 35.9 1.0 OD2 A:ASP183 4.1 41.0 1.0 CA A:ASP22 4.2 32.5 1.0 CB A:SER23 4.3 39.4 1.0 N A:ASP22 4.4 33.6 1.0 OG1 A:THR24 4.4 31.6 1.0 CB A:ASP20 4.4 33.2 1.0 N A:SER23 4.5 31.8 1.0 CB A:ASP179 4.5 27.3 1.0 O A:HOH439 4.6 35.7 1.0 N A:ASP179 4.7 29.8 1.0 NZ A:LYS158 4.7 40.6 1.0 CE A:MET52 4.8 49.7 1.0 O A:HOH464 4.8 35.2 1.0 O A:HOH452 4.8 50.3 1.0 CA A:SER23 4.8 31.3 1.0 OG A:SER23 4.8 42.1 1.0 N A:GLY180 4.8 31.7 1.0 O A:HOH494 4.9 54.7 1.0 OE1 A:GLU29 4.9 58.2 1.0 O A:HOH470 4.9 43.7 1.0 N A:THR24 5.0 29.0 1.0

Calcium binding site 2 out of 3 in the Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:58.5 occ:1.00 O A:HOH458 2.3 45.4 1.0 O A:GLU185 2.5 40.7 1.0 O A:PRO188 2.5 32.5 1.0 C A:PRO188 3.7 31.9 1.0 C A:GLU185 3.7 44.1 1.0 CD A:PRO189 4.1 30.0 1.0 N A:PRO189 4.4 30.6 1.0 CA A:ALA186 4.4 37.2 1.0 N A:PRO188 4.5 34.8 1.0 N A:ALA186 4.5 35.8 1.0 C A:ALA186 4.5 30.4 1.0 CG A:PRO188 4.5 34.8 1.0 CD A:PRO188 4.6 32.5 1.0 CA A:GLU185 4.6 40.2 1.0 CA A:PRO188 4.7 29.0 1.0 N A:CYS187 4.7 31.6 1.0 C A:CYS187 4.8 36.2 1.0 O A:ALA186 5.0 30.1 1.0 CB A:GLU185 5.0 44.0 1.0

Calcium binding site 3 out of 3 in the Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Phosphoserine Phosphatase with Substrate Analogue Homo-Cysteic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:34.2 occ:1.00 O B:HOH438 2.3 36.9 1.0 OD1 B:ASP179 2.3 35.6 1.0 O B:ASP22 2.3 32.7 1.0 OD2 B:ASP20 2.4 38.4 1.0 O B:HOH463 2.5 44.4 1.0 O B:HOH414 2.6 39.9 1.0 CG B:ASP20 3.1 38.3 1.0 OD1 B:ASP20 3.2 42.9 1.0 CG B:ASP179 3.3 35.1 1.0 C B:ASP22 3.5 33.7 1.0 OD2 B:ASP179 3.5 41.9 1.0 CB B:ASP22 4.1 37.2 1.0 O1S B:HJT302 4.1 32.0 0.4 CA B:ASP22 4.2 32.1 1.0 CB B:SER23 4.2 34.6 1.0 OD2 B:ASP183 4.3 37.7 1.0 OG B:SER23 4.4 37.5 1.0 N B:ASP22 4.4 29.2 1.0 N B:SER23 4.5 31.9 1.0 CB B:ASP20 4.5 31.6 1.0 OG1 B:THR24 4.5 34.0 1.0 CG B:HJT302 4.6 40.6 0.4 CB B:ASP179 4.6 32.1 1.0 S B:HJT302 4.7 51.4 0.4 O2S B:HJT302 4.7 43.0 0.4 CA B:SER23 4.8 32.4 1.0 N B:ASP179 4.8 35.3 1.0 O B:HOH410 4.9 48.9 1.0 N B:GLY180 4.9 31.3 1.0 OXT B:HJT302 5.0 51.4 0.4 NH2 B:ARG202 5.0 43.1 1.0

M.Haufroid, M.Mirgaux, L.Leherte, J.Wouters. Crystal Structures and Snapshots Along the Reaction Pathway of Human Phosphoserine Phosphatase. Acta Crystallogr D Struct V. 75 592 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 31205021
DOI: 10.1107/S2059798319006867