Zinc in PDB 6gpz: Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1

The structure of Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1, PDB code: 6gpz was solved by R.M.Cleverley, R.J.Lewis, Z.J.Rutter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.29 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	26.577, 31.415, 81.032, 90.00, 92.41, 90.00
R / Rfree (%)	17.3 / 20.4

The binding sites of Zinc atom in the Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1 (pdb code 6gpz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1, PDB code: 6gpz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:30.2 occ:1.00 N B:GLY-2 2.0 46.0 1.0 OE2 A:GLU50 2.1 39.2 1.0 O B:GLY-2 2.1 40.9 1.0 OE1 A:GLU50 2.5 38.9 1.0 CD A:GLU50 2.6 31.9 1.0 C B:GLY-2 2.8 39.7 1.0 CA B:GLY-2 2.8 43.3 1.0 CE B:MET0 3.7 63.6 1.0 CG A:GLU50 4.1 32.7 1.0 N B:HIS-1 4.1 34.5 1.0 ZN A:ZN102 4.4 31.3 1.0 CG B:MET0 4.8 48.7 1.0 CB A:GLU50 4.8 24.6 1.0 CA B:HIS-1 4.9 32.0 1.0 OE1 A:GLU54 5.0 50.7 1.0

Zinc binding site 2 out of 8 in the Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:27.5 occ:1.00 OE1 A:GLU47 1.9 37.9 1.0 OE1 B:GLN52 2.0 31.8 1.0 N1 B:IMD106 2.0 27.6 1.0 ND1 B:HIS-1 2.0 34.2 1.0 CD A:GLU47 2.6 35.0 1.0 OE2 A:GLU47 2.8 33.0 1.0 C5 B:IMD106 2.8 30.8 1.0 CE1 B:HIS-1 3.0 31.6 1.0 CG B:HIS-1 3.0 29.4 1.0 CD B:GLN52 3.2 30.5 1.0 C2 B:IMD106 3.2 33.3 1.0 CB B:HIS-1 3.4 31.6 1.0 CA B:HIS-1 3.7 32.0 1.0 CG B:GLN52 3.8 26.0 1.0 CG A:GLU47 4.0 29.6 1.0 C4 B:IMD106 4.0 28.1 1.0 NE2 B:HIS-1 4.1 33.2 1.0 CD1 A:LEU51 4.1 31.3 1.0 CD2 B:HIS-1 4.2 27.9 1.0 N3 B:IMD106 4.2 34.8 1.0 NE2 B:GLN52 4.2 29.8 1.0 N B:MET0 4.4 28.8 1.0 CG2 B:ILE48 4.4 20.1 1.0 C B:HIS-1 4.6 30.2 1.0 N B:HIS-1 4.7 34.5 1.0 CG A:LEU51 4.8 23.3 1.0 CD2 A:LEU51 4.8 30.6 1.0 O B:MET0 5.0 30.8 1.0

Zinc binding site 3 out of 8 in the Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn103 b:61.4 occ:1.00 O A:GLY-2 2.1 88.6 1.0 OE1 B:GLU47 2.1 71.5 1.0 OE1 B:GLU50 2.4 66.5 1.0 CD B:GLU47 2.8 57.8 1.0 OE2 B:GLU47 2.8 58.6 1.0 N A:GLY-2 2.9 71.2 1.0 OE2 B:GLU50 2.9 69.8 1.0 CD B:GLU50 2.9 65.8 1.0 C A:GLY-2 3.1 74.9 1.0 CA A:GLY-2 3.5 72.3 1.0 CG B:GLU47 4.3 47.0 1.0 N A:HIS-1 4.3 63.4 1.0 CG B:GLU50 4.4 47.6 1.0 O A:HOH232 4.6 62.5 1.0 CA A:HIS-1 4.8 57.9 1.0 CB B:GLU50 4.8 29.5 1.0 O A:HIS-1 4.9 66.7 1.0 CB B:GLU47 4.9 26.2 1.0

Zinc binding site 4 out of 8 in the Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn104 b:17.4 occ:1.00 OE2 B:GLU32 2.0 16.6 1.0 OE1 B:GLU32 2.4 15.7 1.0 CD B:GLU32 2.5 18.2 1.0 O B:HOH201 4.0 49.6 1.0 CG B:GLU32 4.0 13.9 1.0 O B:HOH237 4.1 26.4 1.0 O B:HOH244 4.2 51.0 1.0 CD B:GLU28 4.2 33.8 1.0 OE2 B:GLU28 4.4 38.9 1.0 OE1 B:GLU28 4.4 20.9 1.0 O B:HOH207 4.5 23.6 1.0 CG B:GLU28 4.6 23.5 1.0 CB B:GLU32 5.0 12.3 1.0

Zinc binding site 5 out of 8 in the Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn105 b:42.9 occ:1.00 NE2 B:HIS45 2.0 37.8 1.0 OE1 B:GLU49 2.4 68.7 1.0 CD B:GLU49 2.6 61.1 1.0 OE2 B:GLU49 2.8 63.4 1.0 CE1 B:HIS45 2.9 37.6 1.0 CD2 B:HIS45 3.1 40.9 1.0 CG B:GLU49 3.5 44.8 1.0 ND1 B:HIS45 4.0 33.5 1.0 CG B:HIS45 4.1 30.4 1.0 CB B:GLU49 5.0 24.9 1.0

Zinc binding site 6 out of 8 in the Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:20.2 occ:1.00 O A:HOH208 1.9 24.3 1.0 OE2 A:GLU17 2.2 30.1 1.0 OE1 A:GLU17 2.2 29.1 1.0 CD A:GLU17 2.5 20.9 1.0 CG A:GLU17 4.0 13.3 1.0 O A:HOH213 4.1 36.5 1.0 O A:HOH216 4.2 32.9 1.0 O A:HOH229 4.3 16.1 1.0 CB A:GLU17 4.9 15.2 1.0 O A:HOH207 5.0 33.4 1.0

Zinc binding site 7 out of 8 in the Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:31.3 occ:1.00 N3 B:IMD106 2.0 34.8 1.0 OE1 A:GLU50 2.1 38.9 1.0 OE2 A:GLU54 2.2 48.1 1.0 OE1 A:GLU54 2.6 50.7 1.0 CD A:GLU54 2.7 47.4 1.0 C2 B:IMD106 2.8 33.3 1.0 CD A:GLU50 3.1 31.9 1.0 C4 B:IMD106 3.2 28.1 1.0 CG A:GLU50 3.5 32.7 1.0 N B:GLY-2 4.0 46.0 1.0 N1 B:IMD106 4.1 27.6 1.0 CG A:GLU54 4.2 43.7 1.0 CA B:GLY-2 4.2 43.3 1.0 OE2 A:GLU50 4.3 39.2 1.0 C5 B:IMD106 4.3 30.8 1.0 C B:GLY-2 4.3 39.7 1.0 ZN B:ZN101 4.4 30.2 1.0 O B:HOH217 4.4 45.0 1.0 O B:GLY-2 4.4 40.9 1.0 CD2 A:LEU51 4.6 30.6 1.0 N B:HIS-1 4.8 34.5 1.0 CB A:GLU50 4.9 24.6 1.0 CB A:GLU54 5.0 36.8 1.0

Zinc binding site 8 out of 8 in the Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cell Division Regulator Gpsb in Complex with Peptide Fragment of L. Monocytogenes Penicillin Binding Protein PBPA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:60.7 occ:1.00 NE2 A:HIS45 2.4 49.3 1.0 CE1 A:HIS45 3.0 49.1 1.0 CD2 A:HIS45 3.3 53.6 1.0 ND1 A:HIS45 4.0 52.3 1.0 CG A:HIS45 4.2 42.1 1.0 CB A:GLU49 4.8 27.4 1.0 O A:HIS45 4.9 24.0 1.0

R.M.Cleverley, Z.J.Rutter, J.Rismondo, F.Corona, H.T.Tsui, F.A.Alatawi, R.A.Daniel, S.Halbedel, O.Massidda, M.E.Winkler, R.J.Lewis. The Cell Cycle Regulator Gpsb Functions As Cytosolic Adaptor For Multiple Cell Wall Enzymes. Nat Commun V. 10 261 2019.
ISSN: ESSN 2041-1723
PubMed: 30651563
DOI: 10.1038/S41467-018-08056-2