Zinc in PDB 2b0p: Truncated S. Aureus Lytm, P212121 Crystal Form

All present enzymatic activity of Truncated S. Aureus Lytm, P212121 Crystal Form:
3.4.24.75;

The structure of Truncated S. Aureus Lytm, P212121 Crystal Form, PDB code: 2b0p was solved by M.Firczuk, A.Mucha, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.84 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	32.093, 78.261, 102.049, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 22.2

The structure of Truncated S. Aureus Lytm, P212121 Crystal Form also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Zinc atom in the Truncated S. Aureus Lytm, P212121 Crystal Form (pdb code 2b0p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Truncated S. Aureus Lytm, P212121 Crystal Form, PDB code: 2b0p:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Truncated S. Aureus Lytm, P212121 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Truncated S. Aureus Lytm, P212121 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:23.1 occ:1.00 O2 A:CAC500 2.0 22.5 1.0 OD1 A:ASP214 2.0 9.4 1.0 NE2 A:HIS210 2.1 12.0 1.0 ND1 A:HIS293 2.1 8.1 1.0 CG A:ASP214 2.8 10.9 1.0 OD2 A:ASP214 2.9 11.6 1.0 O1 A:CAC500 3.0 23.1 1.0 CE1 A:HIS293 3.0 9.3 1.0 AS A:CAC500 3.0 21.2 1.0 CE1 A:HIS210 3.0 9.1 1.0 CD2 A:HIS210 3.1 10.4 1.0 CG A:HIS293 3.2 7.4 1.0 CB A:HIS293 3.6 6.7 1.0 OH A:TYR204 4.1 14.5 1.0 NE2 A:HIS293 4.1 7.1 1.0 ND1 A:HIS210 4.2 8.4 1.0 CG A:HIS210 4.2 9.2 1.0 CB A:ASP214 4.2 8.9 1.0 CD2 A:HIS293 4.3 7.3 1.0 CE1 A:TYR204 4.3 15.6 1.0 C1 A:CAC500 4.5 28.7 1.0 CA A:HIS293 4.5 6.2 1.0 C2 A:CAC500 4.5 28.8 1.0 NE2 A:HIS291 4.5 10.9 1.0 N A:ASP214 4.6 8.9 1.0 CA A:ASP214 4.7 9.6 1.0 CZ A:TYR204 4.7 17.1 1.0 C A:VAL213 4.7 7.6 1.0 O A:HOH712 4.8 20.9 1.0 O A:VAL213 4.9 7.8 1.0 C A:GLY212 4.9 7.2 1.0

Zinc binding site 2 out of 2 in the Truncated S. Aureus Lytm, P212121 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Truncated S. Aureus Lytm, P212121 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:18.1 occ:1.00 O2 B:CAC501 1.9 14.6 1.0 OD1 B:ASP214 2.0 6.5 1.0 ND1 B:HIS293 2.1 6.6 1.0 NE2 B:HIS210 2.1 6.8 1.0 CG B:ASP214 2.8 6.2 1.0 OD2 B:ASP214 2.8 7.1 1.0 CE1 B:HIS293 3.0 5.3 1.0 CE1 B:HIS210 3.1 6.6 1.0 O1 B:CAC501 3.1 23.1 1.0 CD2 B:HIS210 3.1 4.4 1.0 AS B:CAC501 3.1 15.5 1.0 CG B:HIS293 3.1 4.5 1.0 CB B:HIS293 3.5 4.2 1.0 NE2 B:HIS293 4.1 5.7 1.0 OH B:TYR204 4.1 7.8 1.0 ND1 B:HIS210 4.2 5.2 1.0 CB B:ASP214 4.2 6.6 1.0 CD2 B:HIS293 4.2 3.8 1.0 CG B:HIS210 4.2 7.0 1.0 CE1 B:TYR204 4.3 6.9 1.0 CA B:HIS293 4.4 5.5 1.0 C1 B:CAC501 4.5 24.0 1.0 C2 B:CAC501 4.5 22.9 1.0 N B:ASP214 4.6 7.0 1.0 CZ B:TYR204 4.6 5.0 1.0 CA B:ASP214 4.7 5.9 1.0 C B:VAL213 4.7 5.2 1.0 NE2 B:HIS291 4.7 7.6 1.0 O B:VAL213 4.8 5.5 1.0 O B:HOH713 4.8 19.0 1.0 C B:GLY212 4.9 5.4 1.0

M.Firczuk, A.Mucha, M.Bochtler. Crystal Structures of Active Lytm. J.Mol.Biol. V. 354 578 2005.
ISSN: ISSN 0022-2836
PubMed: 16269153
DOI: 10.1016/J.JMB.2005.09.082