Calcium in PDB 4q6o: Structural Analysis of the Mdap-Bound Form of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase

The structure of Structural Analysis of the Mdap-Bound Form of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase, PDB code: 4q6o 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)	50.00 / 1.41
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.931, 66.668, 143.997, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 21.2

The binding sites of Calcium atom in the Structural Analysis of the Mdap-Bound Form of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase (pdb code 4q6o). 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 Mdap-Bound Form of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase, PDB code: 4q6o:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structural Analysis of the Mdap-Bound 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 Mdap-Bound Form of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:24.0 occ:1.00 OE1 A:GLN46 2.3 22.9 1.0 O A:HOH885 2.3 32.6 1.0 O A:HOH601 2.3 22.6 1.0 OE1 A:GLU49 2.7 11.6 1.0 OE2 A:GLU49 2.7 12.3 1.0 ND1 A:HIS128 2.9 14.9 1.0 CD A:GLU49 3.0 11.9 1.0 CD A:GLN46 3.3 21.3 1.0 O A:HOH851 3.6 39.8 1.0 CG A:HIS128 3.7 13.3 1.0 CB A:HIS128 3.8 12.4 1.0 CE1 A:HIS128 3.9 15.3 1.0 O A:HOH1184 3.9 53.0 1.0 N2 A:API504 4.0 21.0 1.0 C2 A:API504 4.1 20.6 1.0 CG A:GLN46 4.1 18.1 1.0 NE2 A:GLN46 4.2 22.6 1.0 O A:ASP129 4.2 12.1 1.0 O A:HOH1218 4.2 53.1 1.0 O A:HOH608 4.3 11.7 1.0 OE2 A:GLU222 4.3 15.9 0.5 OE2 A:GLU222 4.3 13.7 0.5 CB A:GLN46 4.4 15.6 1.0 O A:HOH832 4.5 33.1 1.0 CG A:GLU49 4.5 11.7 1.0 C1 A:API504 4.5 21.7 1.0 O A:HOH892 4.6 41.6 1.0 O2 A:API504 4.6 21.7 1.0 CA A:HIS128 4.7 11.7 1.0 N A:ASP129 4.8 11.1 1.0 CD2 A:HIS128 4.9 14.6 1.0 CD A:GLU222 4.9 13.2 0.5 NE2 A:HIS128 4.9 15.2 1.0 OE1 A:GLU222 5.0 13.1 0.5

Calcium binding site 2 out of 3 in the Structural Analysis of the Mdap-Bound 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 Mdap-Bound Form of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:18.6 occ:1.00 O A:PHE386 2.3 20.0 1.0 OD1 A:ASN382 2.3 19.8 1.0 O A:HOH751 2.4 22.8 1.0 O A:VAL383 2.5 17.7 1.0 OE1 A:GLU396 2.5 18.3 1.0 O A:HOH669 2.5 21.6 1.0 OE2 A:GLU396 2.5 20.3 1.0 CD A:GLU396 2.8 19.4 1.0 C A:VAL383 3.5 16.9 1.0 C A:PHE386 3.5 20.4 1.0 CG A:ASN382 3.5 20.4 1.0 N A:VAL383 3.9 16.4 1.0 N A:PHE386 4.2 18.6 1.0 CA A:VAL383 4.2 16.6 1.0 ND2 A:ASN382 4.3 21.8 1.0 CG A:GLU396 4.3 19.2 1.0 CG A:PRO394 4.4 29.6 1.0 CA A:PHE386 4.4 19.1 1.0 CA A:SER387 4.4 23.7 1.0 N A:SER387 4.4 21.9 1.0 C A:ASN382 4.4 17.3 1.0 N A:ILE384 4.4 17.1 1.0 O A:HOH890 4.5 34.0 1.0 CA A:ILE384 4.5 18.0 1.0 O A:HOH1225 4.6 41.2 1.0 CB A:SER387 4.6 25.0 1.0 CA A:ASN382 4.6 17.8 1.0 N A:GLY385 4.6 19.0 1.0 CB A:ASN382 4.7 18.5 1.0 CB A:VAL383 4.7 16.6 1.0 CB A:PHE386 4.8 19.0 1.0 O A:HOH796 4.8 22.6 1.0 O A:HOH764 4.8 26.2 1.0 O A:HOH1046 4.9 39.9 1.0

Calcium binding site 3 out of 3 in the Structural Analysis of the Mdap-Bound 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 Mdap-Bound Form of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:24.4 occ:1.00 OD2 A:ASP254 1.8 20.1 1.0 ND1 A:HIS62 2.0 16.9 1.0 O A:HOH838 2.2 33.3 1.0 CG A:ASP254 2.6 19.2 1.0 CE1 A:HIS62 2.8 17.5 1.0 OD1 A:ASP254 2.8 19.1 1.0 O A:HOH985 3.1 51.2 1.0 O A:HOH1031 3.2 38.5 1.0 CG A:HIS62 3.2 15.5 1.0 O A:HOH1011 3.3 29.5 1.0 CB A:HIS62 3.7 14.5 1.0 NE2 A:HIS62 4.0 16.8 1.0 CA A:HIS62 4.0 13.7 1.0 CB A:ASP254 4.0 18.4 1.0 CD2 A:HIS62 4.2 16.2 1.0 O A:MET61 4.2 15.2 1.0 O A:HOH1266 4.3 50.2 1.0 O A:HOH1141 4.4 41.1 1.0 O A:HOH1003 4.7 44.4 1.0 C A:MET61 4.8 13.9 1.0 O A:HOH1256 4.8 53.7 1.0 O A:HOH1289 4.8 66.0 1.0 O A:HIS62 4.8 15.5 1.0 N A:HIS62 4.9 13.7 1.0 O A:HOH943 4.9 36.2 1.0 C A:HIS62 5.0 14.2 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