Calcium in PDB 6ojd: A High-Resolution Crystal Structure of Covalent Complex of Nocb Thioesterase Domain with Fluorophosphonate Nocardicin G Analog

The structure of A High-Resolution Crystal Structure of Covalent Complex of Nocb Thioesterase Domain with Fluorophosphonate Nocardicin G Analog, PDB code: 6ojd was solved by K.D.Patel, A.M.Gulick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.55 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.680, 78.560, 146.890, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.5

The binding sites of Calcium atom in the A High-Resolution Crystal Structure of Covalent Complex of Nocb Thioesterase Domain with Fluorophosphonate Nocardicin G Analog (pdb code 6ojd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the A High-Resolution Crystal Structure of Covalent Complex of Nocb Thioesterase Domain with Fluorophosphonate Nocardicin G Analog, PDB code: 6ojd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the A High-Resolution Crystal Structure of Covalent Complex of Nocb Thioesterase Domain with Fluorophosphonate Nocardicin G Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of A High-Resolution Crystal Structure of Covalent Complex of Nocb Thioesterase Domain with Fluorophosphonate Nocardicin G Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2103 b:66.7 occ:1.00 O A:HOH2302 2.3 46.3 1.0 O A:HOH2312 2.5 69.0 1.0 O A:HOH2207 2.5 36.4 1.0 O A:HOH2295 2.6 38.8 1.0 O A:HOH2224 2.9 58.2 1.0 HA A:ASP1912 4.0 40.2 1.0 HG A:SER1911 4.0 39.2 1.0 OD2 A:ASP1915 4.3 32.7 1.0 HB3 A:SER1911 4.4 29.4 1.0 N A:ASP1912 4.6 26.1 1.0 CA A:ASP1912 4.6 33.5 1.0 H A:ASP1912 4.6 31.3 1.0 OG A:SER1911 4.6 32.7 1.0 CB A:ASP1912 4.7 37.5 1.0 O A:HOH2251 4.8 33.0 1.0 CB A:SER1911 5.0 24.5 1.0

Calcium binding site 2 out of 4 in the A High-Resolution Crystal Structure of Covalent Complex of Nocb Thioesterase Domain with Fluorophosphonate Nocardicin G Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of A High-Resolution Crystal Structure of Covalent Complex of Nocb Thioesterase Domain with Fluorophosphonate Nocardicin G Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2104 b:49.1 occ:1.00 OD1 A:ASP1818 2.6 53.2 1.0 O A:HOH2309 2.7 60.1 1.0 O A:HOH2300 2.8 56.7 1.0 OD2 A:ASP1818 3.0 53.0 1.0 CG A:ASP1818 3.2 50.7 1.0 HB3 A:ARG1820 3.3 39.7 1.0 HD2 A:ARG1820 3.9 53.0 1.0 HB2 A:ARG1820 4.0 39.7 1.0 HD2 A:PRO1819 4.1 52.2 1.0 CB A:ARG1820 4.1 33.0 1.0 H A:ARG1820 4.1 36.3 1.0 HE A:ARG1820 4.3 51.9 1.0 H A:GLU1821 4.5 42.9 1.0 CB A:ASP1818 4.6 43.6 1.0 CD A:ARG1820 4.7 44.2 1.0 N A:ARG1820 4.8 30.3 1.0 HB2 A:ASP1818 4.9 52.4 1.0 NE A:ARG1820 4.9 43.2 1.0 CG A:ARG1820 5.0 34.7 1.0 CD A:PRO1819 5.0 43.5 1.0

Calcium binding site 3 out of 4 in the A High-Resolution Crystal Structure of Covalent Complex of Nocb Thioesterase Domain with Fluorophosphonate Nocardicin G Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of A High-Resolution Crystal Structure of Covalent Complex of Nocb Thioesterase Domain with Fluorophosphonate Nocardicin G Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2103 b:25.9 occ:1.00 OD1 B:ASP1818 2.3 22.8 1.0 O2 B:GOL2105 2.4 30.3 1.0 O C:HOH2217 2.4 22.8 1.0 O1 B:GOL2105 2.4 30.0 1.0 OD2 C:ASP1732 2.4 21.6 1.0 O3 B:GOL2105 2.5 26.0 1.0 OD1 C:ASP1732 2.6 22.0 1.0 OD2 B:ASP1818 2.7 25.0 1.0 CG B:ASP1818 2.8 25.4 1.0 CG C:ASP1732 2.9 21.8 1.0 C2 B:GOL2105 3.1 32.4 1.0 HB3 B:ARG1820 3.1 28.8 1.0 C1 B:GOL2105 3.3 27.9 1.0 C3 B:GOL2105 3.3 33.1 1.0 H31 B:GOL2105 3.8 39.8 1.0 H C:THR1706 3.8 32.2 1.0 H12 B:GOL2105 3.8 33.5 1.0 H B:ARG1820 3.9 25.6 1.0 CB B:ARG1820 3.9 24.0 1.0 HB2 B:ARG1820 4.0 28.8 1.0 HD2 B:ARG1820 4.0 36.5 1.0 H2 B:GOL2105 4.0 38.9 1.0 HG2 B:GLU1821 4.1 39.9 1.0 HG1 C:THR1706 4.1 33.1 1.0 H11 B:GOL2105 4.1 33.5 1.0 O C:ASP1732 4.1 24.5 1.0 H32 B:GOL2105 4.2 39.8 1.0 HE B:ARG1820 4.2 36.9 1.0 OG1 C:THR1706 4.2 27.6 1.0 HD2 B:PRO1819 4.2 36.8 1.0 CB B:ASP1818 4.3 24.1 1.0 CB C:ASP1732 4.3 23.2 1.0 O C:THR1706 4.4 27.5 1.0 H B:GLU1821 4.4 30.2 1.0 HB1 C:ALA1705 4.4 28.5 1.0 N C:THR1706 4.5 26.8 1.0 HO2 C:GOL2105 4.5 84.2 1.0 HB2 B:ASP1818 4.5 28.9 1.0 HA C:ALA1705 4.6 27.5 1.0 N B:ARG1820 4.6 21.3 1.0 HB3 C:ASP1732 4.6 27.8 1.0 CD B:ARG1820 4.7 30.4 1.0 HB3 B:ASP1818 4.7 28.9 1.0 O3 C:GOL2105 4.7 67.3 1.0 NE B:ARG1820 4.8 30.8 1.0 HO3 C:GOL2105 4.8 80.7 1.0 HA C:ASP1732 4.8 31.1 1.0 CA B:ARG1820 4.9 23.3 1.0 CG B:ARG1820 4.9 31.7 1.0 HB2 C:ASP1732 4.9 27.8 1.0 C C:THR1706 4.9 23.8 1.0 C C:ASP1732 5.0 25.3 1.0

Calcium binding site 4 out of 4 in the A High-Resolution Crystal Structure of Covalent Complex of Nocb Thioesterase Domain with Fluorophosphonate Nocardicin G Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of A High-Resolution Crystal Structure of Covalent Complex of Nocb Thioesterase Domain with Fluorophosphonate Nocardicin G Analog within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2103 b:28.0 occ:1.00 HO1 C:GOL2104 2.2 32.0 1.0 O C:HOH2263 2.3 24.6 1.0 O2 C:GOL2104 2.4 35.6 1.0 O3 C:GOL2104 2.4 32.0 1.0 OD1 C:ASP1818 2.5 28.9 1.0 O1 C:GOL2104 2.6 26.6 1.0 OD2 C:ASP1818 2.7 27.1 1.0 CG C:ASP1818 2.9 29.0 1.0 C2 C:GOL2104 3.1 32.8 1.0 HB3 C:ARG1820 3.1 35.2 1.0 C3 C:GOL2104 3.2 35.4 1.0 C1 C:GOL2104 3.4 29.0 1.0 H31 C:GOL2104 3.6 42.5 1.0 HB2 C:ARG1820 3.8 35.2 1.0 H C:ARG1820 3.8 35.9 1.0 CB C:ARG1820 3.9 29.4 1.0 H12 C:GOL2104 4.0 34.8 1.0 H2 C:GOL2104 4.0 39.3 1.0 HD2 C:ARG1820 4.0 43.9 1.0 HD2 C:PRO1819 4.0 32.3 1.0 H32 C:GOL2104 4.1 42.5 1.0 H11 C:GOL2104 4.2 34.8 1.0 HE C:ARG1820 4.2 41.9 1.0 H C:GLU1821 4.4 32.0 1.0 CB C:ASP1818 4.4 28.8 1.0 N C:ARG1820 4.6 29.9 1.0 CD C:ARG1820 4.7 36.6 1.0 HB2 C:ASP1818 4.7 34.6 1.0 NE C:ARG1820 4.8 34.9 1.0 HB3 C:ASP1818 4.8 34.6 1.0 CG C:ARG1820 4.8 31.6 1.0 CA C:ARG1820 4.8 31.6 1.0 CD C:PRO1819 5.0 26.9 1.0

K.D.Patel, F.B.D'andrea, N.M.Gaudelli, A.R.Buller, C.A.Townsend, A.M.Gulick. Structure of A Bound Peptide Phosphonate Reveals the Mechanism of Nocardicin Bifunctional Thioesterase Epimerase-Hydrolase Half-Reactions. Nat Commun V. 10 3868 2019.
ISSN: ESSN 2041-1723
PubMed: 31455765
DOI: 10.1038/S41467-019-11740-6