Calcium in PDB 5wmm: Crystal Structure of An Adenylation Domain Interrupted By A Methylation Domain (AMA4) From Nonribosomal Peptide Synthetase Tios

The structure of Crystal Structure of An Adenylation Domain Interrupted By A Methylation Domain (AMA4) From Nonribosomal Peptide Synthetase Tios, PDB code: 5wmm was solved by A.H.Pang, S.Mori, S.Garneau-Tsodikova, O.V.Tsodikov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.712, 136.712, 228.234, 90.00, 90.00, 120.00
R / Rfree (%)	23.6 / 25.3

The structure of Crystal Structure of An Adenylation Domain Interrupted By A Methylation Domain (AMA4) From Nonribosomal Peptide Synthetase Tios also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Calcium atom in the Crystal Structure of An Adenylation Domain Interrupted By A Methylation Domain (AMA4) From Nonribosomal Peptide Synthetase Tios (pdb code 5wmm). 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 An Adenylation Domain Interrupted By A Methylation Domain (AMA4) From Nonribosomal Peptide Synthetase Tios, PDB code: 5wmm:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of An Adenylation Domain Interrupted By A Methylation Domain (AMA4) From Nonribosomal Peptide Synthetase Tios


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 An Adenylation Domain Interrupted By A Methylation Domain (AMA4) From Nonribosomal Peptide Synthetase Tios within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:78.6 occ:1.00 OD2 A:ASP200 2.4 71.2 1.0 OD2 A:ASP198 2.5 74.9 1.0 OE1 A:GLU277 2.8 81.0 1.0 CG A:ASP198 3.4 75.1 1.0 CD A:GLU277 3.5 78.8 1.0 CG A:ASP200 3.6 71.4 1.0 NH2 A:ARG319 3.6 80.2 1.0 OD1 A:ASP198 3.7 77.6 1.0 O A:CYS195 3.7 66.8 1.0 OE2 A:GLU277 4.1 79.7 1.0 CB A:ASP200 4.2 70.4 1.0 CG A:GLU277 4.3 77.1 1.0 CZ A:ARG319 4.5 80.0 1.0 OD1 A:ASP200 4.6 70.8 1.0 NH1 A:ARG319 4.7 81.1 1.0 CB A:ASP198 4.8 73.3 1.0 C A:CYS195 4.9 65.5 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of An Adenylation Domain Interrupted By A Methylation Domain (AMA4) From Nonribosomal Peptide Synthetase Tios


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 An Adenylation Domain Interrupted By A Methylation Domain (AMA4) From Nonribosomal Peptide Synthetase Tios within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1007 b:0.8 occ:1.00 O A:SER525 3.3 80.4 1.0 OE2 A:GLU529 3.3 0.4 1.0 OE1 A:GLU528 3.4 0.4 1.0 C A:SER525 4.2 81.9 1.0 CD A:GLU528 4.2 98.6 1.0 CG A:PRO710 4.3 72.9 1.0 CA A:SER525 4.3 83.1 1.0 CB A:SER525 4.3 83.1 1.0 CB A:GLU529 4.4 94.6 1.0 CD A:GLU529 4.5 0.5 1.0 CG A:GLU528 4.5 95.3 1.0 CB A:GLU528 4.5 92.2 1.0 N A:GLU529 4.6 90.7 1.0 OG A:SER525 4.6 84.7 1.0 CA A:GLU529 4.8 91.4 1.0 CB A:PRO710 4.9 73.2 1.0 CG A:GLU529 5.0 97.2 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of An Adenylation Domain Interrupted By A Methylation Domain (AMA4) From Nonribosomal Peptide Synthetase Tios


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 An Adenylation Domain Interrupted By A Methylation Domain (AMA4) From Nonribosomal Peptide Synthetase Tios within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1008 b:84.3 occ:1.00 CD2 A:PHE212 4.0 68.3 1.0 C A:GLY422 4.0 77.6 1.0 CA A:GLY422 4.1 78.8 1.0 CE2 A:PHE212 4.1 68.5 1.0 O A:GLY422 4.1 77.3 1.0 CG A:PHE212 4.4 68.3 1.0 CG A:PRO257 4.4 64.1 1.0 CE1 A:PHE423 4.5 79.3 1.0 O A:ARG421 4.5 81.0 1.0 CZ A:PHE212 4.5 68.5 1.0 CZ A:PHE423 4.5 79.9 1.0 N A:PHE423 4.6 76.7 1.0 CD1 A:PHE423 4.6 78.2 1.0 CD1 A:PHE212 4.7 69.1 1.0 CE2 A:PHE423 4.7 78.8 1.0 CD A:PRO209 4.8 69.3 1.0 CE1 A:PHE212 4.8 69.4 1.0 CG A:PHE423 4.8 78.0 1.0 CG A:PRO209 4.9 69.1 1.0 CD2 A:PHE423 4.9 78.2 1.0

S.Mori, A.H.Pang, T.A.Lundy, A.Garzan, O.V.Tsodikov, S.Garneau-Tsodikova. Structural Basis For Backbone N-Methylation By An Interrupted Adenylation Domain. Nat. Chem. Biol. V. 14 428 2018.
ISSN: ESSN 1552-4469
PubMed: 29556104
DOI: 10.1038/S41589-018-0014-7