Calcium in PDB 4q6m: Structural Analysis of the Apo-Form of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase

The structure of Structural Analysis of the Apo-Form of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase, PDB code: 4q6m was solved by H.S.Kim, J.Kim, H.N.Im, D.R.An, M.Lee, D.Hesek, S.Mobashery, J.Y.Kim, K.Cho, H.J.Yoon, B.W.Han, B.I.Lee, S.W.Suh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.81 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.141, 66.549, 144.053, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22

The binding sites of Calcium atom in the Structural Analysis of the Apo-Form of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase (pdb code 4q6m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structural Analysis of the Apo-Form of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase, PDB code: 4q6m:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structural Analysis of the Apo-Form of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Analysis of the Apo-Form of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:15.2 occ:1.00 NE2 A:GLN46 2.3 12.9 1.0 O A:HOH740 2.4 18.8 1.0 O A:HOH789 2.4 21.1 1.0 O A:HOH635 2.4 13.4 1.0 OE2 A:GLU49 2.5 11.7 1.0 OE1 A:GLU49 2.6 10.8 1.0 ND1 A:HIS128 2.7 11.9 1.0 CD A:GLU49 2.9 11.4 1.0 CD A:GLN46 3.3 14.6 1.0 CE1 A:HIS128 3.5 12.4 1.0 CG A:HIS128 3.7 11.0 1.0 O A:HOH683 3.9 19.2 1.0 CB A:HIS128 3.9 10.1 1.0 CG A:GLN46 4.1 13.7 1.0 OE1 A:GLN46 4.1 17.6 1.0 O A:ASP129 4.1 10.9 1.0 O A:HOH607 4.4 10.8 1.0 CB A:GLN46 4.4 11.8 1.0 CG A:GLU49 4.4 11.0 1.0 O3 A:GOL504 4.4 34.8 1.0 OE2 A:GLU222 4.6 19.3 1.0 CA A:HIS128 4.7 10.0 1.0 NE2 A:HIS128 4.7 12.2 1.0 CD2 A:HIS128 4.8 12.1 1.0 N A:ASP129 4.8 9.8 1.0 O A:HOH628 4.8 15.2 1.0

Calcium binding site 2 out of 3 in the Structural Analysis of the Apo-Form of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Analysis of the Apo-Form of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:18.0 occ:1.00 O A:PHE386 2.2 18.5 1.0 O A:HOH730 2.3 23.4 1.0 OD1 A:ASN382 2.4 18.8 1.0 O A:VAL383 2.4 16.6 1.0 O A:HOH692 2.4 22.0 1.0 OE1 A:GLU396 2.5 17.0 1.0 OE2 A:GLU396 2.5 19.1 1.0 CD A:GLU396 2.8 18.6 1.0 C A:PHE386 3.4 19.1 1.0 C A:VAL383 3.5 15.8 1.0 CG A:ASN382 3.6 19.2 1.0 N A:VAL383 3.9 15.5 1.0 N A:PHE386 4.2 18.4 1.0 CA A:VAL383 4.2 15.4 1.0 ND2 A:ASN382 4.3 20.4 1.0 CA A:PHE386 4.3 18.6 1.0 CG A:GLU396 4.3 18.5 1.0 CG A:PRO394 4.4 29.0 1.0 N A:SER387 4.4 20.7 1.0 N A:ILE384 4.4 16.0 1.0 CA A:SER387 4.4 22.7 1.0 C A:ASN382 4.4 17.1 1.0 CA A:ILE384 4.5 16.6 1.0 N A:GLY385 4.6 17.5 1.0 CB A:SER387 4.6 24.4 1.0 CA A:ASN382 4.6 17.4 1.0 CB A:ASN382 4.7 17.8 1.0 CB A:VAL383 4.7 15.8 1.0 CB A:PHE386 4.8 18.0 1.0 O A:HOH788 4.8 28.1 1.0 O A:HOH753 4.8 23.9 1.0

Calcium binding site 3 out of 3 in the Structural Analysis of the Apo-Form of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Analysis of the Apo-Form of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:15.6 occ:1.00 OD2 A:ASP254 1.9 18.2 1.0 ND1 A:HIS62 2.0 16.5 1.0 O A:HOH802 2.2 32.1 1.0 CG A:ASP254 2.6 17.3 1.0 CE1 A:HIS62 2.8 17.3 1.0 OD1 A:ASP254 2.8 16.8 1.0 O A:HOH850 3.1 27.9 1.0 CG A:HIS62 3.2 14.9 1.0 CB A:HIS62 3.7 13.8 1.0 NE2 A:HIS62 4.0 15.7 1.0 CA A:HIS62 4.0 12.4 1.0 O A:HOH1014 4.0 42.4 1.0 CB A:ASP254 4.0 16.6 1.0 CD2 A:HIS62 4.2 15.2 1.0 O A:MET61 4.2 13.0 1.0 O A:HIS62 4.8 13.6 1.0 C A:MET61 4.8 12.2 1.0 N A:HIS62 4.9 12.2 1.0 O A:HOH1025 4.9 50.2 1.0 C A:HIS62 4.9 12.5 1.0

H.S.Kim, J.Kim, H.N.Im, D.R.An, M.Lee, D.Hesek, S.Mobashery, J.Y.Kim, K.Cho, H.J.Yoon, B.W.Han, B.I.Lee, S.W.Suh. Structural Basis For the Recognition of Muramyltripeptide By Helicobacter Pylori CSD4, A D,L-Carboxypeptidase Controlling the Helical Cell Shape Acta Crystallogr.,Sect.D V. 70 2014.
ISSN: ESSN 1399-0047
DOI: 10.1107/S1399004714018732