Zinc in PDB 3hmb: Mutant Endolysin From Bacillus Subtilis

All present enzymatic activity of Mutant Endolysin From Bacillus Subtilis:
3.5.1.28;

The structure of Mutant Endolysin From Bacillus Subtilis, PDB code: 3hmb was solved by L.Y.Low, R.Liddington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.70
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	62.670, 152.760, 188.880, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 24.9

The binding sites of Zinc atom in the Mutant Endolysin From Bacillus Subtilis (pdb code 3hmb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Mutant Endolysin From Bacillus Subtilis, PDB code: 3hmb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Mutant Endolysin From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mutant Endolysin From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn155 b:25.5 occ:1.00 ND1 A:HIS29 2.1 18.7 1.0 ND1 A:HIS130 2.3 26.1 1.0 SG A:CYS138 2.4 28.6 1.0 CE1 A:HIS29 3.0 20.2 1.0 CG A:HIS130 3.2 26.7 1.0 CG A:HIS29 3.2 20.1 1.0 CE1 A:HIS130 3.3 26.7 1.0 O A:HOH188 3.3 24.4 1.0 CB A:HIS130 3.4 24.6 1.0 CB A:CYS138 3.4 29.5 1.0 O A:HOH209 3.5 39.0 1.0 CB A:HIS29 3.6 19.3 1.0 NE2 A:HIS29 4.1 21.8 1.0 CA A:HIS29 4.2 20.9 1.0 CD2 A:HIS29 4.3 21.2 1.0 CD2 A:HIS130 4.3 26.6 1.0 NE2 A:HIS130 4.4 27.1 1.0 O A:HIS77 4.4 26.1 1.0 O A:HOH183 4.4 22.9 1.0 N A:ASN30 4.7 25.8 1.0 CA A:CYS138 4.9 31.3 1.0 OE1 A:GLU93 4.9 30.7 1.0 CA A:HIS130 4.9 25.5 1.0

Zinc binding site 2 out of 3 in the Mutant Endolysin From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mutant Endolysin From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn155 b:28.4 occ:1.00 ND1 B:HIS29 2.1 20.0 1.0 ND1 B:HIS130 2.2 25.3 1.0 SG B:CYS138 2.4 29.2 1.0 CE1 B:HIS29 3.0 17.8 1.0 CG B:HIS130 3.0 25.5 1.0 CE1 B:HIS130 3.2 24.7 1.0 CG B:HIS29 3.2 20.5 1.0 CB B:HIS130 3.3 25.5 1.0 CB B:CYS138 3.4 30.0 1.0 CB B:HIS29 3.6 20.9 1.0 O B:HOH206 3.7 26.1 1.0 CA B:HIS29 4.1 22.4 1.0 CD2 B:HIS130 4.1 25.0 1.0 NE2 B:HIS130 4.2 26.6 1.0 NE2 B:HIS29 4.2 19.4 1.0 CD2 B:HIS29 4.3 19.5 1.0 O B:HOH159 4.4 18.5 1.0 N B:ASN30 4.7 27.0 1.0 O B:HIS77 4.7 21.9 1.0 CA B:HIS130 4.7 24.2 1.0 CA B:CYS138 4.8 31.4 1.0 NZ B:LYS136 4.9 32.1 1.0 CE B:LYS136 4.9 29.4 1.0 O B:VAL28 4.9 20.7 1.0 CD B:LYS136 4.9 27.5 1.0

Zinc binding site 3 out of 3 in the Mutant Endolysin From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mutant Endolysin From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn155 b:46.2 occ:1.00 ND1 C:HIS29 2.2 37.1 1.0 ND1 C:HIS130 2.5 44.8 1.0 SG C:CYS138 2.5 50.1 1.0 CE1 C:HIS29 2.9 35.8 1.0 O C:HOH164 3.1 39.9 1.0 CG C:HIS29 3.2 35.5 1.0 CG C:HIS130 3.3 46.7 1.0 CE1 C:HIS130 3.4 45.2 1.0 CB C:CYS138 3.4 56.7 1.0 O C:HOH176 3.5 43.9 1.0 CB C:HIS130 3.5 48.8 1.0 CB C:HIS29 3.6 36.6 1.0 NE2 C:HIS29 3.9 36.2 1.0 CD2 C:HIS29 4.1 36.2 1.0 CA C:HIS29 4.1 36.7 1.0 CD2 C:HIS130 4.4 46.9 1.0 NE2 C:HIS130 4.4 45.9 1.0 O C:HIS77 4.5 43.1 1.0 N C:ASN30 4.6 39.2 1.0 OE2 C:GLU93 4.8 45.0 1.0 CA C:CYS138 4.8 59.3 1.0 O C:VAL28 4.9 36.4 1.0 CD C:LYS136 4.9 66.0 1.0 C C:HIS29 5.0 37.8 1.0

L.Y.Low, C.Yang, M.Perego, A.Osterman, R.Liddington. Role of Net Charge on Catalytic Domain and Influence of Cell Wall Binding Domain on Bactericidal Activity, Specificity, and Host Range of Phage Lysins. J.Biol.Chem. V. 286 34391 2011.
ISSN: ISSN 0021-9258
PubMed: 21816821
DOI: 10.1074/JBC.M111.244160