Calcium in PDB 2pjp: Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna

The structure of Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna, PDB code: 2pjp was solved by N.Soler, D.Fourmy, S.Yoshizawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.50 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.498, 56.515, 48.414, 90.00, 95.60, 90.00
R / Rfree (%)	20 / 25.1

The structure of Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna also contains other interesting chemical elements:

Magnesium	(Mg)	17 atoms
Chlorine	(Cl)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna (pdb code 2pjp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna, PDB code: 2pjp:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:66.9 occ:1.00 OD1 A:ASP561 3.1 34.6 1.0 N A:LEU605 3.3 36.8 1.0 OD2 A:ASP561 3.5 33.7 1.0 CG A:ASP561 3.7 37.1 1.0 O A:GLY565 3.8 37.3 1.0 CB A:LEU605 4.0 38.6 1.0 CA A:LEU604 4.0 32.2 1.0 CB A:LEU604 4.0 31.7 1.0 C A:LEU604 4.1 33.2 1.0 CA A:LEU605 4.1 38.6 1.0 O A:LEU605 4.2 40.5 1.0 CD2 A:LEU604 4.5 35.5 1.0 C A:LEU605 4.7 40.6 1.0 CG A:LEU605 4.8 37.6 1.0 CG A:LEU604 4.8 34.4 1.0 C A:GLY565 4.9 37.2 1.0 O A:HOH42 4.9 25.2 1.0

Calcium binding site 2 out of 4 in the Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca141 b:82.7 occ:1.00 O A:HOH116 3.0 37.0 1.0 NH1 A:ARG558 3.6 44.6 1.0 NH2 A:ARG558 4.0 43.3 1.0 O A:HOH148 4.2 58.0 1.0 CZ A:ARG558 4.2 44.8 1.0 O A:HOH134 4.3 36.6 1.0 CE1 A:PHE595 4.6 35.3 1.0 CB A:ALA554 4.7 28.1 1.0 O A:HOH110 5.0 53.7 1.0

Calcium binding site 3 out of 4 in the Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca161 b:62.3 occ:1.00 O A:HOH46 3.7 30.2 1.0 OD2 A:ASP571 3.8 32.5 1.0 O A:HOH39 3.9 36.0 1.0 CB A:CYS564 3.9 41.8 1.0 OG A:SER566 4.2 33.2 1.0 O A:SER566 4.2 33.7 1.0 OD1 A:ASP602 4.2 37.2 1.0 O A:CYS564 4.3 42.4 1.0 SG A:CYS568 4.6 26.4 1.0 SG A:CYS564 4.8 46.0 1.0 C A:CYS564 4.8 41.3 1.0 C A:SER566 4.8 34.0 1.0 CA A:CYS564 4.9 42.1 1.0 CG A:ASP571 4.9 27.3 1.0

Calcium binding site 4 out of 4 in the Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca49 b:15.4 occ:1.00 OD2 A:ASP559 1.7 12.4 1.0 O A:HOH44 2.2 12.6 1.0 O A:HOH43 2.2 10.5 1.0 CG A:ASP559 2.8 28.0 1.0 CB A:ASP559 3.2 32.2 1.0 OD1 A:ASP559 3.9 28.7 1.0 NH2 A:ARG575 4.2 26.9 1.0 NE A:ARG575 4.5 30.0 1.0 CA A:MET556 4.6 27.6 1.0 CA A:ASP559 4.8 31.9 1.0 CZ A:ARG575 4.9 28.7 1.0 CG A:MET556 4.9 25.1 1.0 O A:ASN555 5.0 29.7 1.0

N.Soler, D.Fourmy, S.Yoshizawa. Structural Insight Into A Molecular Switch in Tandem Winged-Helix Motifs From Elongation Factor Selb. J.Mol.Biol. V. 370 728 2007.
ISSN: ISSN 0022-2836
PubMed: 17537456
DOI: 10.1016/J.JMB.2007.05.001