Zinc in PDB 4q6p: Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase

The structure of Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase, PDB code: 4q6p 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 / 2.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.023, 66.555, 144.055, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 25.2

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

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase (pdb code 4q6p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase, PDB code: 4q6p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:71.1 occ:1.00 ND1 A:HIS128 2.4 43.0 1.0 OE2 A:GLU49 2.5 34.4 1.0 OE1 A:GLU49 2.5 35.4 1.0 NE2 A:GLN46 2.5 63.2 1.0 O A:HOH673 2.7 40.9 1.0 CD A:GLU49 2.9 34.7 1.0 CD A:GLN46 3.2 59.5 1.0 CE1 A:HIS128 3.2 43.1 1.0 CG A:HIS128 3.4 41.5 1.0 OE1 A:GLN46 3.6 58.7 1.0 CB A:HIS128 3.7 39.6 1.0 N2 A:API510 3.8 51.1 1.0 C2 A:API510 4.0 54.2 1.0 O A:ASP129 4.1 34.7 1.0 O A:HOH638 4.1 26.4 1.0 CG A:GLN46 4.3 56.6 1.0 NE2 A:HIS128 4.3 43.8 1.0 CG A:GLU49 4.4 34.3 1.0 CD2 A:HIS128 4.4 43.6 1.0 CA A:HIS128 4.5 37.9 1.0 N A:ASP129 4.7 36.3 1.0 C1 A:API510 4.7 55.4 1.0 CB A:GLN46 4.8 53.0 1.0 OE2 A:GLU222 4.8 40.0 1.0 O A:HOH678 4.9 54.9 1.0 O A:HOH605 5.0 36.2 1.0

Zinc binding site 2 out of 8 in the Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:61.8 occ:1.00 O A:HOH662 2.2 53.4 1.0 OD2 A:ASP254 2.4 44.0 1.0 ND1 A:HIS62 2.4 44.6 1.0 OD1 A:ASP254 2.7 48.5 1.0 CG A:ASP254 2.9 45.6 1.0 O A:HOH703 3.0 45.3 1.0 CE1 A:HIS62 3.0 43.2 1.0 CG A:HIS62 3.4 43.2 1.0 CB A:HIS62 4.0 40.7 1.0 NE2 A:HIS62 4.1 43.2 1.0 CD2 A:HIS62 4.3 43.3 1.0 CB A:ASP254 4.3 43.3 1.0 CA A:HIS62 4.4 39.1 1.0

Zinc binding site 3 out of 8 in the Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:77.1 occ:1.00 O A:HOH712 2.2 31.9 1.0 O A:HOH713 2.4 28.9 1.0 O A:HOH611 2.4 23.8 1.0 ND1 A:HIS263 2.5 43.8 1.0 CE1 A:HIS263 3.0 44.8 1.0 CG A:HIS263 3.7 44.1 1.0 ND2 A:ASN267 3.7 48.8 1.0 NE2 A:HIS263 4.2 46.1 1.0 CB A:HIS263 4.3 42.1 1.0 CB A:ALA230 4.3 32.1 1.0 CA A:HIS263 4.4 40.5 1.0 N A:ALA230 4.4 32.2 1.0 CD2 A:HIS263 4.6 44.1 1.0 CB A:LEU229 4.7 32.5 1.0 CG A:ASN267 4.7 47.4 1.0 CA A:ALA230 4.8 32.1 1.0 OD1 A:ASN267 4.9 49.8 1.0 O A:HIS263 4.9 38.8 1.0 CD2 A:LEU229 5.0 33.4 1.0

Zinc binding site 4 out of 8 in the Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:79.8 occ:1.00 NE2 A:GLN320 2.3 48.6 1.0 OE2 A:GLU321 2.5 50.9 1.0 OE1 A:GLN320 2.6 41.9 1.0 CD A:GLN320 2.8 47.5 1.0 CD A:GLU321 3.1 46.1 1.0 CG A:GLU321 3.2 43.8 1.0 OE1 A:GLU321 4.2 46.6 1.0 CG A:GLN320 4.3 49.3 1.0 CB A:GLU321 4.6 43.8 1.0 NZ A:LYS289 4.9 46.6 1.0 N A:GLU321 4.9 45.9 1.0 NH1 A:ARG333 5.0 65.3 1.0

Zinc binding site 5 out of 8 in the Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:99.1 occ:1.00 OD2 A:ASP100 2.3 57.8 1.0 OD1 A:ASP100 2.7 57.4 1.0 CG A:ASP100 2.9 59.1 1.0 CB A:ASP100 4.4 60.9 1.0 CB A:ASN102 4.4 67.5 1.0 CG A:ASN102 4.6 68.7 1.0 OD1 A:ASN102 4.7 67.5 1.0 N A:ASN102 4.8 63.5 1.0

Zinc binding site 6 out of 8 in the Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:72.3 occ:1.00 O A:HOH714 2.2 25.3 1.0 NE2 A:HIS190 2.6 37.1 1.0 OE2 A:GLU188 2.8 58.4 1.0 CE1 A:HIS190 3.6 36.6 1.0 CD2 A:HIS190 3.6 35.9 1.0 CD A:GLU188 4.0 57.0 1.0 ND1 A:HIS190 4.7 36.8 1.0 CG A:HIS190 4.8 36.5 1.0 CG A:GLU188 4.8 47.9 1.0 OE1 A:GLU188 4.9 60.9 1.0 NE A:ARG135 4.9 37.8 1.0 CD A:ARG135 5.0 37.6 1.0

Zinc binding site 7 out of 8 in the Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:68.2 occ:1.00 O A:HOH649 2.5 20.9 1.0 ND1 A:HIS374 2.6 42.3 1.0 O A:HOH676 2.6 31.2 1.0 O A:HOH631 2.7 33.4 1.0 CG A:HIS374 3.4 42.0 1.0 CB A:HIS374 3.6 39.9 1.0 CE1 A:HIS374 3.6 40.4 1.0 CA A:HIS374 4.3 40.4 1.0 NZ A:LYS349 4.5 52.9 1.0 CD2 A:HIS374 4.6 41.3 1.0 NE2 A:HIS374 4.7 40.6 1.0 N A:ALA375 4.7 43.5 1.0 C A:HIS374 5.0 42.0 1.0 OH A:TYR372 5.0 39.1 1.0

Zinc binding site 8 out of 8 in the Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structural Analysis of the Zn-Form I of Helicobacter Pylori CSD4, A D, L-Carboxypeptidase within 5.0Å range:

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