Zinc in PDB 6cqs: Sediminispirochaeta Smaragdinae Sps-1 Metallo-Beta-Lactamase

All present enzymatic activity of Sediminispirochaeta Smaragdinae Sps-1 Metallo-Beta-Lactamase:
3.5.2.6;

The structure of Sediminispirochaeta Smaragdinae Sps-1 Metallo-Beta-Lactamase, PDB code: 6cqs was solved by R.C.Page, J.Vanpelt, Z.Cheng, M.W.Crowder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.86 / 1.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.601, 73.601, 108.784, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 19.4

The binding sites of Zinc atom in the Sediminispirochaeta Smaragdinae Sps-1 Metallo-Beta-Lactamase (pdb code 6cqs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Sediminispirochaeta Smaragdinae Sps-1 Metallo-Beta-Lactamase, PDB code: 6cqs:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Sediminispirochaeta Smaragdinae Sps-1 Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sediminispirochaeta Smaragdinae Sps-1 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:33.0 occ:1.00 ND1 A:HIS98 2.2 26.4 1.0 NE2 A:HIS188 2.3 21.1 1.0 CE1 A:HIS98 3.0 26.5 1.0 O A:HOH739 3.1 27.5 1.0 CE1 A:HIS188 3.2 25.6 1.0 CG A:HIS98 3.2 22.9 1.0 CD2 A:HIS188 3.2 22.9 1.0 O A:HOH699 3.3 29.0 1.0 ZN A:ZN502 3.5 27.7 1.0 CB A:HIS98 3.7 20.0 1.0 OD1 A:ASP100 3.8 25.6 1.0 O A:HOH730 4.1 29.8 1.0 NE2 A:HIS98 4.1 27.0 1.0 CD2 A:HIS98 4.3 28.6 1.0 ND1 A:HIS188 4.3 18.6 1.0 CG A:HIS188 4.4 18.3 1.0 SG A:CYS207 4.5 24.8 1.0 CB A:CYS207 4.5 20.3 1.0 CG A:ASP100 4.6 23.2 1.0 OD2 A:ASP100 4.7 24.1 1.0 OD1 A:ASN101 4.9 19.5 1.0

Zinc binding site 2 out of 3 in the Sediminispirochaeta Smaragdinae Sps-1 Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sediminispirochaeta Smaragdinae Sps-1 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:27.7 occ:1.00 NE2 A:HIS245 2.2 19.6 1.0 OD2 A:ASP100 2.2 24.1 1.0 SG A:CYS207 2.5 24.8 1.0 O A:HOH730 2.7 29.8 1.0 CG A:ASP100 3.1 23.2 1.0 CD2 A:HIS245 3.1 18.1 1.0 CE1 A:HIS245 3.1 17.6 1.0 OD1 A:ASP100 3.3 25.6 1.0 O A:HOH739 3.3 27.5 1.0 CB A:CYS207 3.4 20.3 1.0 ZN A:ZN501 3.5 33.0 1.0 O A:HOH611 4.1 17.7 1.0 ND1 A:HIS245 4.2 16.9 1.0 CG A:HIS245 4.3 19.1 1.0 NE2 A:HIS188 4.3 21.1 1.0 CB A:ASP100 4.4 16.4 1.0 O A:HOH616 4.4 25.3 1.0 CA A:CYS207 4.6 17.3 1.0 O A:HOH711 4.6 40.8 1.0 CE1 A:HIS188 4.8 25.6 1.0 CD2 A:HIS188 4.9 22.9 1.0 O A:HOH699 5.0 29.0 1.0

Zinc binding site 3 out of 3 in the Sediminispirochaeta Smaragdinae Sps-1 Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sediminispirochaeta Smaragdinae Sps-1 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:12.7 occ:0.50 OD2 A:ASP106 1.9 21.2 1.0 NE2 A:HIS110 2.4 18.0 1.0 OD1 A:ASP106 2.5 16.1 1.0 CG A:ASP106 2.5 15.7 1.0 CD2 A:HIS110 3.3 19.8 1.0 CE1 A:HIS110 3.4 21.5 1.0 CB A:ASP106 4.0 15.9 1.0 CG A:HIS110 4.5 17.2 1.0 ND1 A:HIS110 4.5 19.9 1.0 CD2 A:LEU109 4.6 41.5 1.0 O A:HOH733 4.8 31.8 1.0 CA A:ASP106 5.0 13.5 1.0

Z.Cheng, J.Vanpelt, A.Bergstrom, C.Bethel, A.Katko, C.Miller, K.Mason, E.Cumming, H.Zhang, R.L.Kimble, S.Fullington, S.L.Bretz, J.C.Nix, R.A.Bonomo, D.L.Tierney, R.C.Page, M.W.Crowder. A Noncanonical Metal Center Drives the Activity of the Sediminispirochaeta Smaragdinae Metallo-Beta-Lactamase Sps-1. Biochemistry V. 57 5218 2018.
ISSN: ISSN 1520-4995
PubMed: 30106565
DOI: 10.1021/ACS.BIOCHEM.8B00728