Zinc in PDB 9fln: Crystal Structure of the C-Terminal Domain of Vlde H373A From Streptococcus Pneumoniae

The structure of Crystal Structure of the C-Terminal Domain of Vlde H373A From Streptococcus Pneumoniae, PDB code: 9fln was solved by V.Miguel-Ruano, I.Acebron, U.P.De Jose, D.Straume, L.S.Havarstein, J.A.Hermoso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.57 / 1.14
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	59.139, 59.139, 32.481, 90, 90, 120
R / Rfree (%)	10.7 / 12.8

The binding sites of Zinc atom in the Crystal Structure of the C-Terminal Domain of Vlde H373A From Streptococcus Pneumoniae (pdb code 9fln). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the C-Terminal Domain of Vlde H373A From Streptococcus Pneumoniae, PDB code: 9fln:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the C-Terminal Domain of Vlde H373A From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the C-Terminal Domain of Vlde H373A From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:17.0 occ:0.33 O A:HOH549 1.4 23.9 0.3 O A:HOH502 1.6 20.6 0.3 O A:GLY380 2.5 21.6 1.0 OXT A:GLY380 2.7 21.0 1.0 C A:GLY380 2.9 19.7 1.0 O A:HOH606 3.4 36.2 1.0 CA A:GLY380 4.4 19.3 1.0 O A:HOH509 4.6 27.9 1.0 HE22 A:GLN273 4.7 18.2 1.0 HA3 A:GLY380 4.8 19.2 1.0 HA2 A:GLY380 4.9 19.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the C-Terminal Domain of Vlde H373A From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the C-Terminal Domain of Vlde H373A From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:19.4 occ:1.00 OE2 A:GLU313 2.2 29.2 1.0 OE1 A:GLU313 2.8 30.3 1.0 CD A:GLU313 2.9 29.4 1.0 CG A:GLU313 4.3 28.7 1.0 HB3 A:GLU313 4.6 27.7 1.0 HG2 A:GLU313 4.7 28.6 1.0 HG3 A:GLU313 4.9 28.6 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the C-Terminal Domain of Vlde H373A From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the C-Terminal Domain of Vlde H373A From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:13.7 occ:1.00 HD1 A:HIS375 1.4 14.5 0.0 HE2 A:HIS301 1.4 15.7 0.0 HE2 A:HIS370 1.5 15.7 0.0 O A:HOH575 2.2 21.8 1.0 OD1 A:ASP308 2.3 16.2 1.0 ND1 A:HIS375 2.3 14.5 1.0 NE2 A:HIS370 2.3 15.8 1.0 NE2 A:HIS301 2.3 15.6 1.0 OD2 A:ASP308 2.5 17.1 1.0 CG A:ASP308 2.7 16.8 1.0 HB2 A:HIS375 3.0 14.3 1.0 CE1 A:HIS370 3.1 16.8 1.0 CE1 A:HIS301 3.2 16.8 1.0 CE1 A:HIS375 3.2 14.5 1.0 HE1 A:HIS370 3.2 16.8 1.0 HE1 A:HIS301 3.3 16.6 1.0 HE1 A:HIS375 3.3 14.6 1.0 CG A:HIS375 3.3 13.9 1.0 CD2 A:HIS370 3.4 16.2 1.0 CD2 A:HIS301 3.4 15.9 1.0 HD2 A:HIS301 3.6 16.0 1.0 HD2 A:HIS370 3.6 16.2 1.0 CB A:HIS375 3.6 14.3 1.0 HH21 A:ARG294 3.7 26.3 1.0 NH2 A:ARG294 4.1 26.5 1.0 HA A:HIS375 4.2 14.7 1.0 O A:HOH566 4.2 26.5 1.0 CB A:ASP308 4.2 16.5 1.0 ND1 A:HIS370 4.3 17.2 1.0 HB3 A:HIS375 4.3 14.3 1.0 ND1 A:HIS301 4.3 16.8 1.0 NE2 A:HIS375 4.3 14.8 1.0 HH22 A:ARG294 4.4 26.3 1.0 HH11 A:ARG294 4.4 25.1 1.0 HB3 A:ALA306 4.4 16.1 1.0 O A:HOH580 4.4 29.2 1.0 CD2 A:HIS375 4.4 14.1 1.0 CG A:HIS370 4.4 16.6 1.0 CG A:HIS301 4.5 16.5 1.0 CA A:HIS375 4.5 14.8 1.0 HB3 A:ASP308 4.6 16.5 1.0 O A:HOH525 4.6 20.5 1.0 HB2 A:ASP308 4.6 16.4 1.0 CZ A:ARG294 4.7 25.7 1.0 NH1 A:ARG294 4.8 24.9 1.0 HA A:ASP308 4.9 15.9 1.0 O A:HOH513 5.0 28.4 1.0

V.Miguel-Ruano, I.Acebron, M.Lee, A.J.Martin-Galiano, C.Freton, U.P.De Jose, B.Ramachandran, F.Gago, M.Kjos, D.Hesek, C.Grangeasse, L.S.Havarstein, D.Straume, S.Mobashery, J.A.Hermoso. Characterization of Vlde (SPR1875), A Pneumococcal Two-State L,D-Endopeptidase with A Four-Zinc Cluster in the Active Site. Acs Catalysis V. 14 18786 2024.
ISSN: ESSN 2155-5435
PubMed: 39722888
DOI: 10.1021/ACSCATAL.4C05090