Calcium in PDB 1omd: Structure of Oncomodulin Refined at 1.85 Angstroms Resolution. An Example of Extensive Molecular Aggregation Via CA2+

The structure of Structure of Oncomodulin Refined at 1.85 Angstroms Resolution. An Example of Extensive Molecular Aggregation Via CA2+, PDB code: 1omd was solved by F.R.Ahmed, M.Przybylska, D.R.Rose, G.I.Birnbaum, M.E.Pippy, J.P.Macmanus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.590, 64.280, 33.070, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Calcium atom in the Structure of Oncomodulin Refined at 1.85 Angstroms Resolution. An Example of Extensive Molecular Aggregation Via CA2+ (pdb code 1omd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of Oncomodulin Refined at 1.85 Angstroms Resolution. An Example of Extensive Molecular Aggregation Via CA2+, PDB code: 1omd:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of Oncomodulin Refined at 1.85 Angstroms Resolution. An Example of Extensive Molecular Aggregation Via CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Oncomodulin Refined at 1.85 Angstroms Resolution. An Example of Extensive Molecular Aggregation Via CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca109 b:5.8 occ:1.00 OD1 A:ASP90 2.2 10.2 1.0 OD1 A:ASP92 2.3 10.2 1.0 OD1 A:ASP94 2.3 9.0 1.0 O A:HOH111 2.5 14.2 1.0 OE1 A:GLU101 2.5 7.5 1.0 O A:LYS96 2.5 8.9 1.0 OE2 A:GLU101 2.5 9.2 1.0 CD A:GLU101 2.8 8.6 1.0 CG A:ASP94 3.2 9.1 1.0 CG A:ASP90 3.4 12.3 1.0 CG A:ASP92 3.4 11.2 1.0 OD2 A:ASP94 3.6 9.8 1.0 C A:LYS96 3.7 8.9 1.0 OD2 A:ASP92 3.9 12.2 1.0 OD2 A:ASP90 4.2 16.1 1.0 CA A:ASP90 4.2 9.2 1.0 N A:LYS96 4.3 8.9 1.0 N A:ASP92 4.3 9.1 1.0 N A:ASN91 4.3 9.2 1.0 CG A:GLU101 4.3 9.4 1.0 CB A:ASP90 4.4 11.3 1.0 N A:ASP94 4.4 8.9 1.0 CB A:ASP94 4.5 9.1 1.0 N A:ILE97 4.6 8.9 1.0 CA A:LYS96 4.6 8.9 1.0 CB A:ASP92 4.6 10.4 1.0 CA A:ILE97 4.7 8.9 1.0 O A:HOH144 4.7 34.0 1.0 N A:GLY98 4.7 8.9 1.0 CA A:ASP92 4.8 9.1 1.0 C A:ASP90 4.8 9.2 1.0 CA A:ASP94 4.8 8.8 1.0 N A:GLY95 4.8 8.8 1.0 CG A:LYS96 4.8 15.7 1.0 O A:HOH130 4.9 19.1 1.0 C A:ASP92 4.9 9.0 1.0 C A:ASP94 4.9 8.8 1.0 N A:GLY93 5.0 9.0 1.0

Calcium binding site 2 out of 3 in the Structure of Oncomodulin Refined at 1.85 Angstroms Resolution. An Example of Extensive Molecular Aggregation Via CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Oncomodulin Refined at 1.85 Angstroms Resolution. An Example of Extensive Molecular Aggregation Via CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca110 b:4.4 occ:1.00 OD1 A:ASP51 2.2 9.4 1.0 O A:HOH112 2.2 19.0 1.0 O A:TYR57 2.3 9.7 1.0 OD2 A:ASP53 2.3 9.8 1.0 OE2 A:GLU62 2.5 7.6 1.0 OE1 A:GLU62 2.5 6.2 1.0 OG A:SER55 2.5 5.5 1.0 CD A:GLU62 2.8 8.5 1.0 CG A:ASP53 3.4 10.1 1.0 CG A:ASP51 3.4 8.5 1.0 C A:TYR57 3.5 9.8 1.0 O A:HOH113 3.6 28.5 1.0 CB A:SER55 3.7 7.7 1.0 OD1 A:ASP53 3.8 11.2 1.0 N A:SER55 3.9 9.3 1.0 N A:ASP53 4.2 9.3 1.0 OD2 A:ASP51 4.2 8.8 1.0 N A:TYR57 4.3 9.6 1.0 CA A:ASP51 4.3 9.4 1.0 CA A:SER55 4.3 9.3 1.0 CG A:GLU62 4.3 6.4 1.0 CB A:ASP51 4.4 9.4 1.0 N A:LEU58 4.4 9.9 1.0 CA A:TYR57 4.4 9.7 1.0 CA A:LEU58 4.5 10.0 1.0 C A:ASP51 4.5 9.4 1.0 N A:GLN54 4.5 9.3 1.0 CB A:ASP53 4.6 8.3 1.0 O A:HOH136 4.7 23.4 1.0 N A:ASP59 4.7 10.3 1.0 CA A:ASP53 4.7 9.3 1.0 OD2 A:ASP59 4.7 23.7 1.0 N A:ASN52 4.7 9.3 1.0 N A:GLY56 4.8 9.4 1.0 C A:ASP53 4.8 9.3 1.0 C A:SER55 4.9 9.4 1.0 OD1 A:ASP59 4.9 23.5 1.0 O A:ASP51 5.0 9.3 1.0 C A:GLN54 5.0 9.3 1.0

Calcium binding site 3 out of 3 in the Structure of Oncomodulin Refined at 1.85 Angstroms Resolution. An Example of Extensive Molecular Aggregation Via CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Oncomodulin Refined at 1.85 Angstroms Resolution. An Example of Extensive Molecular Aggregation Via CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca135 b:4.9 occ:0.80 OE1 A:GLN71 2.3 9.2 1.0 OD1 A:ASP73 2.5 7.6 1.0 OD2 A:ASP73 2.5 9.8 1.0 O A:HOH169 2.5 12.0 1.0 CG A:ASP73 2.8 7.9 1.0 CD A:GLN71 3.4 11.0 1.0 O A:HOH118 3.8 15.8 1.0 CG A:GLN71 4.3 9.7 1.0 NE2 A:GLN71 4.3 9.7 1.0 CB A:ASP73 4.3 7.0 1.0 CB A:GLN71 4.5 7.6 1.0

F.R.Ahmed, M.Przybylska, D.R.Rose, G.I.Birnbaum, M.E.Pippy, J.P.Macmanus. Structure of Oncomodulin Refined at 1.85 A Resolution. An Example of Extensive Molecular Aggregation Via CA2+. J.Mol.Biol. V. 216 127 1990.
ISSN: ISSN 0022-2836
PubMed: 2231727
DOI: 10.1016/S0022-2836(05)80065-8