Calcium in PDB 7jmv: Crystal Structure of the Pea Pathogenicity Protein 2 From Madurella Mycetomatis Complexed with 4-Nitrocatechol

The structure of Crystal Structure of the Pea Pathogenicity Protein 2 From Madurella Mycetomatis Complexed with 4-Nitrocatechol, PDB code: 7jmv was solved by M.Zeug, N.Markovic, C.V.Iancu, J.Tripp, M.Oreb, J.Choe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.76 / 1.57
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.74, 98.74, 62.287, 90, 90, 120
R / Rfree (%)	17.7 / 19.1

The structure of Crystal Structure of the Pea Pathogenicity Protein 2 From Madurella Mycetomatis Complexed with 4-Nitrocatechol also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Calcium atom in the Crystal Structure of the Pea Pathogenicity Protein 2 From Madurella Mycetomatis Complexed with 4-Nitrocatechol (pdb code 7jmv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Pea Pathogenicity Protein 2 From Madurella Mycetomatis Complexed with 4-Nitrocatechol, PDB code: 7jmv:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Pea Pathogenicity Protein 2 From Madurella Mycetomatis Complexed with 4-Nitrocatechol


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 the Pea Pathogenicity Protein 2 From Madurella Mycetomatis Complexed with 4-Nitrocatechol within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:20.6 occ:1.00 O A:PHE240 2.3 22.3 1.0 O A:HIS243 2.3 23.0 1.0 O A:HOH539 2.4 25.6 1.0 O A:HOH483 2.4 21.5 1.0 OD1 A:ASP238 2.5 23.6 1.0 OD2 A:ASP238 2.6 24.2 1.0 CG A:ASP238 2.8 25.7 1.0 C A:HIS243 3.4 28.5 1.0 C A:PHE240 3.5 26.3 1.0 HB2 A:PHE240 3.6 26.9 1.0 HH22 A:ARG223 3.7 26.5 1.0 HA A:TRP241 3.9 30.9 1.0 HD1 A:TRP241 4.0 26.6 1.0 H A:HIS243 4.0 32.2 1.0 H A:PHE240 4.1 28.6 1.0 CB A:PHE240 4.3 22.4 1.0 CA A:PHE240 4.3 23.7 1.0 CB A:ASP238 4.4 25.2 1.0 HB3 A:PHE240 4.4 26.9 1.0 NH2 A:ARG223 4.4 22.1 1.0 N A:PHE240 4.5 23.9 1.0 N A:TRP241 4.5 23.8 1.0 HH21 A:ARG223 4.5 26.5 1.0 CA A:TRP241 4.6 25.8 1.0 CA A:HIS243 4.7 24.7 1.0 N A:HIS243 4.7 26.9 1.0 O A:HOH557 4.7 37.3 1.0 HB2 A:ASP238 4.7 30.3 1.0 HB3 A:ASP238 4.8 30.3 1.0 CD1 A:TRP241 4.9 22.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Pea Pathogenicity Protein 2 From Madurella Mycetomatis Complexed with 4-Nitrocatechol


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 the Pea Pathogenicity Protein 2 From Madurella Mycetomatis Complexed with 4-Nitrocatechol within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:42.5 occ:1.00 O A:HOH457 2.3 29.6 1.0 O A:HOH485 2.3 43.1 1.0 OD1 A:ASP24 2.4 24.4 1.0 O A:HOH404 2.5 37.6 1.0 O A:HOH536 2.5 29.9 1.0 HZ3 A:LYS151 3.1 53.9 1.0 HE3 A:LYS151 3.4 48.6 1.0 CG A:ASP24 3.5 27.1 1.0 NZ A:LYS151 3.8 44.9 1.0 HE1 A:TRP158 3.8 24.5 1.0 CE A:LYS151 3.9 40.5 1.0 HA A:ASP24 3.9 21.6 1.0 HZ1 A:LYS151 4.0 53.9 1.0 HE2 A:LYS151 4.0 48.6 1.0 OD2 A:ASP24 4.1 28.0 1.0 HG3 A:GLU20 4.2 45.1 1.0 HZ2 A:LYS151 4.5 53.9 1.0 CA A:ASP24 4.6 18.1 1.0 NE1 A:TRP158 4.6 20.4 1.0 N A:ASP24 4.6 18.5 1.0 O A:HOH562 4.6 38.4 1.0 HB3 A:LEU23 4.6 29.0 1.0 O A:GLY156 4.6 28.3 1.0 CB A:ASP24 4.6 18.6 1.0 O A:GLU20 4.7 24.0 1.0 H A:ASP24 4.7 22.2 1.0 HB2 A:LEU23 4.8 29.0 1.0 HD1 A:TRP158 4.8 22.7 1.0 C A:LEU23 4.9 17.6 1.0

M.Zeug, N.Markovic, C.V.Iancu, J.Tripp, M.Oreb, J.Y.Choe. Crystal Structures of Non-Oxidative Decarboxylases Reveal A New Mechanism of Action with A Catalytic Dyad and Structural Twists. Sci Rep V. 11 3056 2021.
ISSN: ESSN 2045-2322
PubMed: 33542397
DOI: 10.1038/S41598-021-82660-Z