Zinc in PDB 9flm: Crystal Structure of the C-Terminal Domain of Vlde From Streptococcus Pneumoniae in A Catalytically Competent Conformation

The structure of Crystal Structure of the C-Terminal Domain of Vlde From Streptococcus Pneumoniae in A Catalytically Competent Conformation, PDB code: 9flm 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)	28.56 / 1.50
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	57.111, 57.111, 32.674, 90, 90, 120
R / Rfree (%)	16.6 / 19.9

The binding sites of Zinc atom in the Crystal Structure of the C-Terminal Domain of Vlde From Streptococcus Pneumoniae in A Catalytically Competent Conformation (pdb code 9flm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the C-Terminal Domain of Vlde From Streptococcus Pneumoniae in A Catalytically Competent Conformation, PDB code: 9flm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the C-Terminal Domain of Vlde From Streptococcus Pneumoniae in A Catalytically Competent Conformation


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 From Streptococcus Pneumoniae in A Catalytically Competent Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:27.3 occ:1.00 O A:HOH524 2.0 32.7 1.0 OD1 A:ASP308 2.1 28.7 1.0 ND1 A:HIS375 2.2 22.4 1.0 NE2 A:HIS301 2.4 26.8 1.0 CG A:ASP308 2.8 27.9 1.0 OD2 A:ASP308 2.9 29.5 1.0 CE1 A:HIS375 3.1 23.6 1.0 CG A:HIS375 3.2 23.3 1.0 CD2 A:HIS301 3.3 27.3 1.0 CE1 A:HIS301 3.3 28.2 1.0 CB A:HIS375 3.6 23.4 1.0 NH2 A:ARG294 3.8 38.1 1.0 NE2 A:HIS375 4.2 23.8 1.0 NE2 A:HIS373 4.2 32.4 1.0 CB A:ASP308 4.3 26.4 1.0 CD2 A:HIS375 4.3 22.9 1.0 ND1 A:HIS301 4.4 27.4 1.0 CG A:HIS301 4.4 27.3 1.0 CA A:HIS375 4.5 22.5 1.0 CZ A:ARG294 4.5 36.9 1.0 NE2 A:HIS370 4.6 44.5 1.0 NH1 A:ARG294 4.6 36.4 1.0 CD2 A:HIS373 4.7 30.6 1.0 CD2 A:HIS370 4.8 43.7 1.0 CA A:ASP308 4.9 24.9 1.0 CB A:ALA306 5.0 26.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the C-Terminal Domain of Vlde From Streptococcus Pneumoniae in A Catalytically Competent Conformation


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 From Streptococcus Pneumoniae in A Catalytically Competent Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:23.0 occ:0.33 O A:HOH590 2.0 33.4 0.3 OXT A:GLY380 2.4 27.1 1.0 O A:GLY380 2.5 28.3 1.0 C A:GLY380 2.8 25.2 1.0 O A:HOH540 3.6 39.9 1.0 O A:HOH511 3.8 7.5 0.3 CA A:GLY380 4.3 25.5 1.0 O A:HOH537 4.5 33.4 1.0 O A:HOH623 4.6 34.4 1.0 N A:GLY380 5.0 24.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the C-Terminal Domain of Vlde From Streptococcus Pneumoniae in A Catalytically Competent Conformation


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 From Streptococcus Pneumoniae in A Catalytically Competent Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:24.6 occ:1.00 OE1 A:GLU279 2.3 29.6 1.0 OE2 A:GLU279 2.4 28.2 1.0 CD A:GLU279 2.7 27.8 1.0 CG A:GLU279 4.2 26.6 1.0 O A:HOH505 4.3 41.6 1.0 OD1 A:ASN283 4.5 40.0 1.0 O A:HOH582 4.8 33.8 1.0 O A:HOH567 4.9 31.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the C-Terminal Domain of Vlde From Streptococcus Pneumoniae in A Catalytically Competent Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the C-Terminal Domain of Vlde From Streptococcus Pneumoniae in A Catalytically Competent Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:33.7 occ:0.50 OD1 A:ASP372 2.0 40.1 1.0 ND1 A:HIS373 2.2 31.5 1.0 O A:VAL366 2.5 71.8 1.0 CE1 A:HIS373 2.7 32.4 1.0 CG A:ASP372 2.8 38.4 1.0 OD2 A:ASP372 3.1 39.9 1.0 CG A:HIS373 3.5 29.5 1.0 C A:VAL366 3.6 72.3 1.0 CA A:THR367 3.9 71.6 1.0 NE2 A:HIS373 4.0 32.4 1.0 O A:ASN369 4.0 53.6 1.0 N A:THR367 4.2 72.1 1.0 CB A:HIS373 4.2 28.4 1.0 CB A:ASP372 4.2 35.3 1.0 CD2 A:HIS373 4.3 30.6 1.0 N A:HIS373 4.4 27.6 1.0 CE A:MET310 4.4 37.2 1.0 C A:ASP372 4.5 31.6 1.0 O A:THR367 4.5 71.3 1.0 C A:THR367 4.6 70.5 1.0 N A:ASP372 4.6 35.5 1.0 CA A:ASP372 4.7 34.8 1.0 CG1 A:VAL366 4.7 72.3 1.0 CA A:VAL366 4.9 72.6 1.0 CA A:HIS373 4.9 27.6 1.0 CB A:VAL366 5.0 72.6 1.0 CB A:THR367 5.0 72.3 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