Calcium in PDB 4q6q: Structural Analysis of the Zn-Form II of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase

The structure of Structural Analysis of the Zn-Form II of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase, PDB code: 4q6q 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)	30.00 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.314, 66.928, 144.806, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.5

The structure of Structural Analysis of the Zn-Form II of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Structural Analysis of the Zn-Form II of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase (pdb code 4q6q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structural Analysis of the Zn-Form II of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase, PDB code: 4q6q:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structural Analysis of the Zn-Form II 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 Zn-Form II of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:43.2 occ:1.00 O A:HOH772 3.5 39.5 1.0 O A:HOH614 3.6 26.4 1.0 CD2 A:LEU229 4.0 23.0 1.0 CG A:LYS329 4.1 25.3 1.0 NZ A:LYS329 4.1 28.5 1.0 CG A:PRO50 4.3 23.1 1.0 CB A:ASN328 4.3 23.5 1.0 CB A:PRO50 4.4 23.3 1.0 CE A:LYS329 4.6 27.3 1.0 O A:HOH761 4.7 34.8 1.0 CD1 A:LEU229 4.8 22.6 1.0 C A:ASN328 4.8 23.9 1.0 CG A:LEU229 4.8 22.8 1.0 N A:LYS329 4.9 23.6 1.0 CD A:LYS329 5.0 27.6 1.0

Calcium binding site 2 out of 2 in the Structural Analysis of the Zn-Form II 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 Zn-Form II of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:38.2 occ:1.00 O A:HOH787 2.3 38.5 1.0 O A:HOH813 2.4 42.7 1.0 O A:HOH773 2.4 35.0 1.0 OE1 A:GLU176 2.6 39.2 1.0 OD1 A:ASN173 2.6 30.3 1.0 O A:HOH674 2.8 33.1 1.0 OE2 A:GLU176 2.9 36.2 1.0 CD A:GLU176 3.1 37.3 1.0 CG A:ASN173 3.5 30.3 1.0 ND2 A:ASN173 4.0 28.4 1.0 CB A:ASN173 4.4 29.0 1.0 O A:HOH697 4.6 27.8 1.0 CG A:GLU176 4.6 32.7 1.0 O A:HOH736 4.7 35.8 1.0 CA A:ASN173 4.8 28.3 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