Calcium in PDB 6tzy: Crystal Structure of A Lipin/Pah Phosphatidic Acid Phosphatase

The structure of Crystal Structure of A Lipin/Pah Phosphatidic Acid Phosphatase, PDB code: 6tzy was solved by V.I.Khayyo, M.V.Airola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.05 / 3.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.017, 135.126, 90.974, 90.00, 116.19, 90.00
R / Rfree (%)	23.7 / 26.8

The binding sites of Calcium atom in the Crystal Structure of A Lipin/Pah Phosphatidic Acid Phosphatase (pdb code 6tzy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of A Lipin/Pah Phosphatidic Acid Phosphatase, PDB code: 6tzy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of A Lipin/Pah Phosphatidic Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Lipin/Pah Phosphatidic Acid Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:0.9 occ:1.00 NZ A:LYS244 2.2 99.5 1.0 OD2 A:ASP272 2.3 74.1 1.0 OD2 A:ASP146 2.4 88.9 1.0 OD1 A:ASP272 2.5 74.0 1.0 O A:HOH515 2.5 59.4 1.0 OD1 A:ASN268 2.5 89.4 1.0 CG A:ASP272 2.7 75.3 1.0 CG A:ASP146 3.5 84.1 1.0 CG A:ASN268 3.7 89.4 1.0 CE A:LYS244 3.7 0.5 1.0 OD1 A:ASP146 4.2 87.1 1.0 CB A:ASP272 4.2 77.6 1.0 ND2 A:ASN268 4.4 89.4 1.0 CB A:ASP146 4.4 73.9 1.0 CD A:LYS244 4.4 0.6 1.0 N A:ASN268 4.5 78.2 1.0 O A:ASP148 4.6 75.4 1.0 N A:ARG269 4.7 91.2 1.0 CB A:ASN268 4.9 83.9 1.0 CB A:ARG269 5.0 94.8 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of A Lipin/Pah Phosphatidic Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Lipin/Pah Phosphatidic Acid Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca400 b:96.3 occ:1.00 OE2 B:GLU69 2.3 0.1 1.0 OE1 B:GLU69 2.6 0.6 1.0 CD B:GLU69 2.8 0.5 1.0 O B:LYS67 2.9 95.3 1.0 C B:LYS67 4.1 97.3 1.0 CG B:GLU69 4.3 0.2 1.0 N B:LYS67 4.8 0.4 1.0 N B:GLU69 5.0 97.5 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of A Lipin/Pah Phosphatidic Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Lipin/Pah Phosphatidic Acid Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:0.4 occ:1.00 NZ B:LYS244 2.3 98.2 1.0 OD2 B:ASP272 2.3 64.4 1.0 O B:HOH501 2.4 0.7 1.0 OD2 B:ASP146 2.4 89.5 1.0 OD1 B:ASP272 2.5 67.6 1.0 OD1 B:ASN268 2.5 76.0 1.0 CG B:ASP272 2.7 67.0 1.0 CG B:ASP146 3.1 84.8 1.0 OD1 B:ASP146 3.6 88.7 1.0 CE B:LYS244 3.7 97.1 1.0 CG B:ASN268 3.7 72.8 1.0 CB B:ASP146 4.0 74.3 1.0 CB B:ASP272 4.1 69.4 1.0 ND2 B:ASN268 4.4 71.5 1.0 N B:ASN268 4.4 73.5 1.0 O B:ASP148 4.5 82.0 1.0 CD B:LYS244 4.5 95.3 1.0 N B:ARG269 4.8 93.9 1.0 CB B:ASN268 4.8 73.0 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of A Lipin/Pah Phosphatidic Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Lipin/Pah Phosphatidic Acid Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:94.7 occ:1.00 OD2 C:ASP272 2.3 87.0 1.0 OD2 C:ASP146 2.4 0.8 1.0 OD1 C:ASP272 2.4 88.0 1.0 OD1 C:ASN268 2.5 1.0 1.0 CG C:ASP272 2.6 87.0 1.0 CG C:ASP146 3.4 0.0 1.0 NZ C:LYS244 3.4 79.3 1.0 CG C:ASN268 3.7 0.6 1.0 CB C:ASP272 4.1 86.2 1.0 OD1 C:ASP146 4.2 0.9 1.0 CB C:ASP146 4.2 0.9 1.0 N C:ASN268 4.2 0.4 1.0 ND2 C:ASN268 4.4 0.2 1.0 N C:ARG269 4.5 0.8 1.0 CE C:LYS244 4.7 76.4 1.0 CB C:ASN268 4.8 0.9 1.0 O C:ASP148 4.8 91.1 1.0 CD C:LYS244 4.8 72.6 1.0 CA C:ASN268 4.9 0.2 1.0 CA C:GLY267 4.9 0.1 1.0 CB C:ARG269 4.9 0.3 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of A Lipin/Pah Phosphatidic Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A Lipin/Pah Phosphatidic Acid Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:0.8 occ:1.00 OD1 D:ASN268 2.4 0.8 1.0 OD2 D:ASP272 2.4 0.2 1.0 OD2 D:ASP146 2.4 1.0 1.0 O D:HOH502 2.5 89.3 1.0 OD1 D:ASP272 3.1 0.2 1.0 CG D:ASP272 3.1 0.9 1.0 CG D:ASP146 3.4 0.5 1.0 CG D:ASN268 3.6 0.8 1.0 O D:ASP148 3.9 0.5 1.0 CB D:ASP146 4.1 0.8 1.0 N D:ASN268 4.2 0.1 1.0 OD1 D:ASP146 4.2 0.3 1.0 NZ D:LYS244 4.3 0.7 1.0 ND2 D:ASN268 4.3 0.8 1.0 N D:ARG269 4.3 0.0 1.0 CB D:ASP272 4.6 0.7 1.0 CB D:ASN268 4.6 0.7 1.0 OG1 D:THR150 4.7 0.0 1.0 CA D:ASN268 4.8 0.2 1.0 CE D:LYS244 4.9 0.2 1.0 C D:ASN268 5.0 0.3 1.0

V.I.Khayyo, R.M.Hoffmann, H.Wang, J.A.Bell, J.E.Burke, K.Reue, M.V.Airola. Crystal Structure of A Lipin/Pah Phosphatidic Acid Phosphatase Nat Commun V. 11 1309 2020.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-020-15124-Z