Calcium in PDB 7jmr: Crystal Structure of the Pea Pathogenicity Protein 2 From Madurella Mycetomatis

The structure of Crystal Structure of the Pea Pathogenicity Protein 2 From Madurella Mycetomatis, PDB code: 7jmr 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)	38.74 / 1.67
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.853, 98.853, 62.38, 90, 90, 120
R / Rfree (%)	17.7 / 19.6

The structure of Crystal Structure of the Pea Pathogenicity Protein 2 From Madurella Mycetomatis 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 (pdb code 7jmr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Pea Pathogenicity Protein 2 From Madurella Mycetomatis, PDB code: 7jmr:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Pea Pathogenicity Protein 2 From Madurella Mycetomatis


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:56.1 occ:1.00 O A:HOH481 2.4 36.3 1.0 O A:HOH543 2.4 49.3 1.0 O A:HOH520 2.4 45.0 1.0 O A:HOH466 2.4 46.6 1.0 OD1 A:ASN230 2.6 35.1 1.0 CG A:ASN230 3.7 31.6 1.0 HD21 A:ASN230 4.1 42.1 1.0 O A:HOH422 4.2 47.6 1.0 HA A:ASN230 4.3 35.1 1.0 ND2 A:ASN230 4.4 35.1 1.0 HD21 A:ASN235 4.7 45.7 1.0 HD22 A:ASN235 4.8 45.7 1.0 O A:GLY226 4.8 30.0 1.0 H A:ASN230 4.8 34.5 1.0 HB2 A:GLU229 4.8 37.1 1.0 N A:ASN230 4.9 28.8 1.0 CA A:ASN230 4.9 29.3 1.0 CB A:ASN230 4.9 31.1 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Pea Pathogenicity Protein 2 From Madurella Mycetomatis


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:28.6 occ:1.00 O A:PHE240 2.3 31.0 1.0 O A:HIS243 2.3 29.9 1.0 O A:HOH523 2.4 31.5 1.0 O A:HOH483 2.5 28.1 1.0 OD1 A:ASP238 2.5 29.9 1.0 OD2 A:ASP238 2.5 30.6 1.0 CG A:ASP238 2.8 31.1 1.0 C A:HIS243 3.4 35.4 1.0 C A:PHE240 3.5 33.1 1.0 HB2 A:PHE240 3.6 37.8 1.0 HH22 A:ARG223 3.7 34.2 1.0 HA A:TRP241 3.8 40.8 1.0 HD1 A:TRP241 4.0 36.4 1.0 H A:PHE240 4.0 37.2 1.0 H A:HIS243 4.1 42.8 1.0 CB A:PHE240 4.3 31.5 1.0 CA A:PHE240 4.3 31.7 1.0 CB A:ASP238 4.4 30.3 1.0 HB3 A:PHE240 4.4 37.8 1.0 NH2 A:ARG223 4.4 28.5 1.0 N A:PHE240 4.5 31.0 1.0 HH21 A:ARG223 4.5 34.2 1.0 N A:TRP241 4.5 32.0 1.0 CA A:TRP241 4.6 34.0 1.0 CA A:HIS243 4.7 31.2 1.0 N A:HIS243 4.7 35.6 1.0 HB2 A:ASP238 4.7 36.4 1.0 HB3 A:ASP238 4.8 36.4 1.0 CD1 A:TRP241 4.9 30.3 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Pea Pathogenicity Protein 2 From Madurella Mycetomatis


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 the Pea Pathogenicity Protein 2 From Madurella Mycetomatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:41.6 occ:1.00 O A:HOH433 2.3 36.2 1.0 OD1 A:ASP24 2.4 29.1 1.0 O A:HOH403 2.4 42.5 1.0 O A:HOH511 2.5 34.7 1.0 CG A:ASP24 3.5 34.4 1.0 O A:HOH412 3.5 47.4 1.0 HE1 A:TRP158 3.8 31.1 1.0 HA A:ASP24 3.9 29.4 1.0 OD2 A:ASP24 4.1 31.5 1.0 HG3 A:GLU20 4.1 59.4 1.0 HD2 A:LYS151 4.2 45.2 1.0 CA A:ASP24 4.5 24.5 1.0 O A:HOH542 4.5 42.7 1.0 N A:ASP24 4.6 25.1 1.0 NE1 A:TRP158 4.6 26.0 1.0 CB A:ASP24 4.6 25.5 1.0 O A:GLU20 4.6 32.2 1.0 O A:GLY156 4.7 33.2 1.0 H A:ASP24 4.7 30.2 1.0 HB2 A:LEU23 4.7 34.4 1.0 HB3 A:LEU23 4.7 34.4 1.0 HD1 A:TRP158 4.8 32.4 1.0 HZ2 A:LYS151 4.9 61.8 1.0 HG2 A:GLU20 4.9 59.4 1.0 C A:LEU23 4.9 25.9 1.0 CG A:GLU20 4.9 49.5 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