Calcium in PDB 5d2u: Crystal Structure of Tppha Variant - H39A

The structure of Crystal Structure of Tppha Variant - H39A, PDB code: 5d2u was solved by J.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.23 / 1.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	38.042, 153.872, 82.761, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 26

The binding sites of Calcium atom in the Crystal Structure of Tppha Variant - H39A (pdb code 5d2u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Tppha Variant - H39A, PDB code: 5d2u:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Tppha Variant - H39A


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 Tppha Variant - H39A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:32.3 occ:1.00 O A:HOH411 2.2 25.6 1.0 O A:HOH429 2.4 34.5 1.0 O A:HOH441 2.4 24.0 1.0 OD2 A:ASP231 2.4 37.1 1.0 OD2 A:ASP34 2.5 29.6 1.0 OD1 A:ASP193 2.5 26.5 1.0 O A:HOH480 2.8 41.2 1.0 OD1 A:ASP34 3.0 21.1 1.0 CG A:ASP34 3.1 23.9 1.0 CG A:ASP231 3.4 37.7 1.0 O A:HOH476 3.5 35.7 1.0 CG A:ASP193 3.5 33.5 1.0 CA A:CA302 3.5 28.7 1.0 OD1 A:ASP231 3.8 28.8 1.0 OD2 A:ASP193 3.8 34.1 1.0 O A:HOH491 4.1 42.0 1.0 O A:HOH444 4.3 24.6 1.0 O A:HOH457 4.3 36.8 1.0 O A:HOH420 4.4 30.1 1.0 N A:GLY194 4.4 25.2 1.0 CB A:ASP34 4.5 22.3 1.0 O A:HOH413 4.5 21.2 1.0 OD1 A:ASP18 4.6 26.9 1.0 O A:ASN232 4.6 22.9 1.0 O A:HOH430 4.7 50.5 1.0 CB A:ASP231 4.7 27.9 1.0 N A:ASP193 4.8 24.3 1.0 CB A:ASP193 4.8 23.1 1.0 O A:HOH499 4.9 49.0 1.0 C A:ASP193 4.9 28.2 1.0 O A:HOH484 5.0 40.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Tppha Variant - H39A


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 Tppha Variant - H39A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:28.7 occ:1.00 O A:HOH444 2.3 24.6 1.0 O A:HOH476 2.3 35.7 1.0 O A:GLY35 2.3 29.0 1.0 O A:HOH429 2.3 34.5 1.0 OD1 A:ASP34 2.4 21.1 1.0 O A:HOH408 2.4 32.5 1.0 O A:HOH484 2.5 40.3 1.0 O A:HOH430 3.2 50.5 1.0 CA A:CA301 3.5 32.3 1.0 C A:GLY35 3.6 30.7 1.0 CG A:ASP34 3.6 23.9 1.0 O A:HOH491 4.0 42.0 1.0 OD2 A:ASP34 4.1 29.6 1.0 O A:HOH403 4.1 44.3 1.0 N A:GLY35 4.1 27.3 1.0 O A:HOH411 4.2 25.6 1.0 C A:ASP34 4.3 19.3 1.0 OE1 A:GLN17 4.4 37.5 1.0 O A:HOH441 4.4 24.0 1.0 CA A:GLY35 4.4 25.1 1.0 CB A:GLN17 4.4 32.1 1.0 OD1 A:ASP18 4.5 26.9 1.0 O A:HOH427 4.5 25.2 1.0 N A:MET36 4.5 28.3 1.0 O A:HOH502 4.5 46.4 1.0 OD1 A:ASN232 4.5 27.1 1.0 O A:ASP34 4.6 20.6 1.0 CA A:MET36 4.6 38.9 1.0 OD1 A:ASP231 4.7 28.8 1.0 CB A:MET36 4.7 34.1 1.0 CB A:ASP34 4.8 22.3 1.0 O A:HOH480 4.8 41.2 1.0 CA A:ASP34 4.9 21.2 1.0 OD2 A:ASP231 4.9 37.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Tppha Variant - H39A


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 Tppha Variant - H39A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:42.9 occ:1.00 O A:HOH475 2.2 42.8 1.0 O A:HOH454 2.4 41.5 1.0 OD2 A:ASP193 2.4 34.1 1.0 OD2 A:ASP119 2.5 30.6 1.0 CG A:ASP193 3.6 33.5 1.0 CG A:ASP119 3.7 31.9 1.0 CB A:ASP193 4.1 23.1 1.0 CA A:HIS161 4.1 61.6 1.0 O A:ARG160 4.2 54.8 1.0 O A:HOH480 4.2 41.2 1.0 O A:HOH411 4.3 25.6 1.0 O A:HOH420 4.3 30.1 1.0 OE1 A:GLU197 4.3 48.0 1.0 OD1 A:ASP119 4.5 25.3 1.0 C A:ARG160 4.6 60.1 1.0 CB A:ASP119 4.6 25.9 1.0 O A:HIS161 4.6 56.8 1.0 OD1 A:ASP193 4.6 26.5 1.0 N A:HIS161 4.6 62.9 1.0 C A:HIS161 4.7 59.0 1.0 O A:HOH424 4.7 28.7 1.0 CD A:GLU197 5.0 47.4 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Tppha Variant - H39A


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 Tppha Variant - H39A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:51.1 occ:1.00 O A:HIS227 2.3 42.4 1.0 OE1 A:GLU198 2.5 39.4 1.0 O A:HOH443 2.6 47.2 1.0 O A:HOH461 2.7 49.1 1.0 O A:HOH453 2.7 49.1 1.0 O A:HOH501 2.7 56.3 1.0 O A:HOH449 3.0 56.5 1.0 O A:HOH500 3.2 65.9 1.0 C A:HIS227 3.4 40.7 1.0 CD A:GLU198 3.6 42.2 1.0 OE2 A:GLU198 4.0 42.8 1.0 CA A:GLY228 4.1 34.7 1.0 N A:GLY228 4.2 39.4 1.0 CB A:HIS227 4.3 41.3 1.0 CA A:HIS227 4.4 39.5 1.0 CA A:GLU198 4.8 32.1 1.0 O A:HOH495 4.8 54.0 1.0 CG A:GLU198 4.9 34.0 1.0 O A:GLU198 4.9 37.1 1.0 CB A:GLU198 5.0 32.2 1.0

Y.Si, Y.Yuan, Y.Wang, J.Gao, Y.Hu, S.Feng, J.Su. Structural and Biochemical Characterization of A Cyanobacterial PP2C Phosphatase Reveals Insights Into Catalytic Mechanism and Substrate Recognition Catalysts 2016.
ISSN: ESSN 2073-4344
DOI: 10.3390/CATAL6050060