Calcium in PDB 4q6n: Structural Analysis of the Tripeptide-Bound Form of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase

The structure of Structural Analysis of the Tripeptide-Bound Form of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase, PDB code: 4q6n 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)	20.00 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.127, 66.383, 143.785, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 22.7

The binding sites of Calcium atom in the Structural Analysis of the Tripeptide-Bound Form of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase (pdb code 4q6n). 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 Tripeptide-Bound Form of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase, PDB code: 4q6n:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structural Analysis of the Tripeptide-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 Tripeptide-Bound Form of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:11.6 occ:0.50 OE1 A:GLN46 2.4 20.3 1.0 OE2 A:GLU49 2.6 10.2 1.0 O A:HOH601 2.7 15.8 1.0 OE1 A:GLU49 2.7 10.1 1.0 ND1 A:HIS128 2.7 11.5 1.0 O A:HOH784 2.9 24.8 1.0 CD A:GLU49 3.0 10.1 1.0 CD A:GLN46 3.3 18.5 1.0 O4 A:MHI501 3.4 30.1 1.0 CG A:HIS128 3.6 10.3 1.0 CE1 A:HIS128 3.7 11.8 1.0 NH2 A:ARG86 3.7 25.8 1.0 CB A:HIS128 3.8 9.5 1.0 C8 A:MHI501 3.9 29.6 1.0 C9 A:MHI501 4.1 23.4 1.0 CG A:GLN46 4.1 16.6 1.0 NE2 A:GLN46 4.2 18.4 1.0 O A:ASP129 4.2 9.8 1.0 N3 A:MHI501 4.2 25.9 1.0 O A:HOH610 4.3 9.0 1.0 CB A:GLN46 4.4 12.1 1.0 O A:HOH1023 4.4 33.2 1.0 CG A:GLU49 4.5 9.7 1.0 CA A:HIS128 4.6 8.6 1.0 OE2 A:GLU222 4.6 13.9 1.0 CZ A:ARG86 4.7 23.1 1.0 O5 A:MHI501 4.7 23.5 1.0 NE2 A:HIS128 4.8 11.8 1.0 C10 A:MHI501 4.8 24.2 1.0 CD2 A:HIS128 4.8 11.5 1.0 N A:ASP129 4.8 8.7 1.0 C7 A:MHI501 4.9 31.3 1.0 O A:HOH795 4.9 31.4 1.0

Calcium binding site 2 out of 3 in the Structural Analysis of the Tripeptide-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 Tripeptide-Bound Form of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:18.9 occ:1.00 O A:PHE386 2.2 19.6 1.0 O A:HOH752 2.3 24.3 1.0 OD1 A:ASN382 2.4 20.7 1.0 O A:HOH660 2.4 20.7 1.0 O A:VAL383 2.4 16.9 1.0 OE1 A:GLU396 2.5 17.7 1.0 OE2 A:GLU396 2.5 19.4 1.0 CD A:GLU396 2.8 19.0 1.0 C A:PHE386 3.4 19.8 1.0 C A:VAL383 3.5 16.5 1.0 CG A:ASN382 3.5 18.8 1.0 N A:VAL383 3.8 15.7 1.0 N A:PHE386 4.2 18.7 1.0 CA A:VAL383 4.2 15.8 1.0 ND2 A:ASN382 4.2 20.1 1.0 CA A:PHE386 4.3 19.8 1.0 CG A:GLU396 4.3 18.4 1.0 CG A:PRO394 4.3 33.1 1.0 N A:SER387 4.4 21.8 1.0 CA A:SER387 4.4 24.0 1.0 N A:ILE384 4.4 16.6 1.0 C A:ASN382 4.4 17.2 1.0 CB A:SER387 4.5 25.2 1.0 O A:HOH960 4.5 36.5 1.0 CA A:ILE384 4.5 16.7 1.0 N A:GLY385 4.6 17.8 1.0 CA A:ASN382 4.6 17.1 1.0 CB A:ASN382 4.7 18.2 1.0 CB A:VAL383 4.7 16.1 1.0 CB A:PHE386 4.7 18.1 1.0 O A:HOH716 4.7 22.9 1.0 O A:HOH936 4.8 31.4 1.0

Calcium binding site 3 out of 3 in the Structural Analysis of the Tripeptide-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 Tripeptide-Bound Form of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:22.0 occ:1.00 OD2 A:ASP254 1.8 16.4 1.0 ND1 A:HIS62 1.9 14.9 1.0 O A:HOH1031 2.1 32.4 1.0 CG A:ASP254 2.6 15.8 1.0 CE1 A:HIS62 2.6 15.7 1.0 OD1 A:ASP254 2.8 15.7 1.0 CG A:HIS62 3.1 14.2 1.0 O A:HOH852 3.3 25.9 1.0 CB A:HIS62 3.7 13.3 1.0 NE2 A:HIS62 3.9 15.7 1.0 CA A:HIS62 4.0 12.7 1.0 CB A:ASP254 4.0 14.9 1.0 CD2 A:HIS62 4.1 14.5 1.0 O A:MET61 4.2 13.3 1.0 O A:HOH962 4.5 44.1 1.0 O A:HOH980 4.7 49.7 1.0 O A:HOH951 4.8 30.0 1.0 C A:MET61 4.8 11.9 1.0 N A:HIS62 4.8 12.5 1.0 O A:HIS62 4.9 13.6 1.0 C A:HIS62 4.9 12.6 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