Zinc in PDB 4zyb: High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue

All present enzymatic activity of High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue:
3.4.24.75;

The structure of High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue, PDB code: 4zyb was solved by M.Grabowska, E.Jagielska, H.Czapinska, M.Bochtler, I.Sabala, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.30 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	31.988, 101.563, 77.763, 90.00, 91.48, 90.00
R / Rfree (%)	15 / 18.5

The structure of High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue also contains other interesting chemical elements:

Calcium	(Ca)	5 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue (pdb code 4zyb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue, PDB code: 4zyb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:11.0 occ:1.00 OD1 A:ASP214 2.0 12.1 1.0 OP1 A:4SQ409 2.0 12.9 1.0 NE2 A:HIS210 2.0 11.8 1.0 ND1 A:HIS293 2.0 8.1 1.0 CG A:ASP214 2.7 11.1 1.0 OD2 A:ASP214 2.8 13.1 1.0 CE1 A:HIS293 2.9 6.3 1.0 P A:4SQ409 3.0 12.0 1.0 CE1 A:HIS210 3.0 10.4 1.0 OP2 A:4SQ409 3.0 9.2 1.0 CD2 A:HIS210 3.0 13.5 1.0 CG A:HIS293 3.1 9.6 1.0 CB A:HIS293 3.6 8.2 1.0 NE2 A:HIS293 4.1 9.4 1.0 ND1 A:HIS210 4.1 10.4 1.0 CB A:ASP214 4.1 11.0 1.0 CA3 A:4SQ409 4.1 12.8 1.0 CG A:HIS210 4.1 10.4 1.0 OH A:TYR204 4.2 18.9 1.0 CN3 A:4SQ409 4.2 16.0 1.0 CD2 A:HIS293 4.2 9.2 1.0 N2 A:4SQ409 4.3 16.5 0.5 CA2 A:4SQ409 4.3 15.3 1.0 CE1 A:TYR204 4.4 14.2 1.0 N A:ASP214 4.5 9.7 1.0 CA A:HIS293 4.5 8.0 1.0 C A:VAL213 4.5 11.3 0.4 NE2 A:HIS291 4.5 11.7 1.0 CA A:ASP214 4.6 11.5 1.0 O A:VAL213 4.6 7.8 0.4 C A:VAL213 4.6 7.6 0.6 O A:HOH632 4.6 11.0 1.0 N2 A:4SQ409 4.7 21.2 0.5 CZ A:TYR204 4.8 18.8 1.0 C A:GLY212 4.8 9.6 1.0 O A:VAL213 4.8 10.2 0.6 O A:GLY212 4.9 11.3 1.0 N A:VAL213 4.9 8.8 0.4 N A:VAL213 4.9 8.8 0.6

Zinc binding site 2 out of 4 in the High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:8.1 occ:1.00 OD1 B:ASP214 1.9 8.1 1.0 OP1 B:4SQ406 1.9 10.1 1.0 ND1 B:HIS293 2.0 8.1 1.0 NE2 B:HIS210 2.1 6.2 1.0 CG B:ASP214 2.6 8.1 1.0 OD2 B:ASP214 2.8 10.5 1.0 CE1 B:HIS293 2.9 6.8 1.0 P B:4SQ406 2.9 11.2 1.0 OP2 B:4SQ406 3.0 9.0 1.0 CE1 B:HIS210 3.0 6.0 1.0 CD2 B:HIS210 3.1 6.1 1.0 CG B:HIS293 3.1 6.6 1.0 CB B:HIS293 3.6 6.1 1.0 NE2 B:HIS293 4.1 7.9 1.0 CB B:ASP214 4.1 7.0 1.0 ND1 B:HIS210 4.1 6.7 1.0 OH B:TYR204 4.2 10.3 1.0 CG B:HIS210 4.2 7.8 1.0 CD2 B:HIS293 4.2 6.5 1.0 CN3 B:4SQ406 4.2 12.5 1.0 CA3 B:4SQ406 4.2 13.1 1.0 CA2 B:4SQ406 4.2 16.2 1.0 CE1 B:TYR204 4.4 8.7 1.0 CA B:HIS293 4.4 6.5 1.0 N B:ASP214 4.5 7.2 1.0 C B:VAL213 4.6 9.8 0.3 C B:VAL213 4.6 6.9 0.7 CA B:ASP214 4.6 6.3 1.0 NE2 B:HIS291 4.6 9.5 1.0 N2 B:4SQ406 4.7 36.6 0.4 O B:VAL213 4.7 7.2 0.3 O B:VAL213 4.7 7.3 0.7 CZ B:TYR204 4.7 7.2 1.0 O B:HOH627 4.7 8.3 1.0 C B:GLY212 4.8 6.0 1.0 N B:VAL213 4.9 6.0 0.7 N B:VAL213 4.9 6.7 0.3 N2 B:4SQ406 5.0 27.2 0.6

Zinc binding site 3 out of 4 in the High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:10.7 occ:1.00 OP2 C:4SQ404 1.8 12.7 1.0 OD1 C:ASP214 2.0 9.9 1.0 ND1 C:HIS293 2.0 7.9 1.0 NE2 C:HIS210 2.1 11.6 1.0 CG C:ASP214 2.7 11.7 1.0 OD2 C:ASP214 2.8 13.6 1.0 CE1 C:HIS293 2.9 7.3 1.0 P C:4SQ404 2.9 11.8 1.0 CD2 C:HIS210 3.0 10.2 1.0 CE1 C:HIS210 3.1 9.8 1.0 OP1 C:4SQ404 3.1 11.3 1.0 CG C:HIS293 3.1 8.2 1.0 CB C:HIS293 3.6 6.5 1.0 CA2 C:4SQ404 3.9 21.1 1.0 NE2 C:HIS293 4.0 9.1 1.0 CB C:ASP214 4.1 9.1 1.0 ND1 C:HIS210 4.2 10.3 1.0 CG C:HIS210 4.2 11.2 1.0 OH C:TYR204 4.2 16.8 1.0 CD2 C:HIS293 4.2 8.6 1.0 CN3 C:4SQ404 4.3 14.4 1.0 CA3 C:4SQ404 4.3 18.9 1.0 CE1 C:TYR204 4.4 17.4 1.0 N C:ASP214 4.5 9.3 1.0 CA C:HIS293 4.5 7.2 1.0 C C:VAL213 4.6 8.9 1.0 CA C:ASP214 4.6 8.3 1.0 NE2 C:HIS291 4.6 12.4 1.0 O C:VAL213 4.7 9.1 1.0 O C:HOH626 4.7 9.9 1.0 C C:GLY212 4.7 9.8 1.0 CZ C:TYR204 4.8 14.4 1.0 O C:GLY212 4.8 10.8 1.0 N C:VAL213 4.9 8.2 1.0

Zinc binding site 4 out of 4 in the High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:7.7 occ:1.00 OD1 D:ASP214 1.9 7.8 1.0 OP2 D:4SQ404 1.9 6.8 1.0 ND1 D:HIS293 2.0 6.6 1.0 NE2 D:HIS210 2.1 7.4 1.0 CG D:ASP214 2.6 7.7 1.0 OD2 D:ASP214 2.8 8.9 1.0 CE1 D:HIS293 2.9 6.1 1.0 P D:4SQ404 3.0 9.9 1.0 CE1 D:HIS210 3.0 8.2 1.0 OP1 D:4SQ404 3.1 11.1 1.0 CD2 D:HIS210 3.1 8.1 1.0 CG D:HIS293 3.2 5.9 1.0 CB D:HIS293 3.6 5.3 1.0 NE2 D:HIS293 4.1 7.6 1.0 CB D:ASP214 4.1 8.6 1.0 ND1 D:HIS210 4.1 5.9 1.0 OH D:TYR204 4.2 11.7 1.0 CA3 D:4SQ404 4.2 12.6 1.0 CG D:HIS210 4.2 6.0 1.0 CD2 D:HIS293 4.2 6.4 1.0 CN3 D:4SQ404 4.2 13.9 1.0 CA2 D:4SQ404 4.3 16.8 1.0 CE1 D:TYR204 4.3 7.7 1.0 N D:ASP214 4.4 8.0 1.0 CA D:HIS293 4.5 6.4 1.0 C D:VAL213 4.5 9.7 0.6 CA D:ASP214 4.6 6.2 1.0 NE2 D:HIS291 4.6 9.6 1.0 C D:VAL213 4.6 3.8 0.4 N2 D:4SQ404 4.6 26.9 0.5 O D:VAL213 4.6 5.7 0.6 N2 D:4SQ404 4.7 16.0 0.5 CZ D:TYR204 4.7 8.1 1.0 O D:HOH636 4.8 7.3 1.0 O D:VAL213 4.8 7.6 0.4 C D:GLY212 4.8 5.9 1.0 N D:VAL213 4.9 6.9 0.6 N D:VAL213 4.9 6.4 0.4 O D:GLY212 5.0 6.7 1.0

M.Grabowska, E.Jagielska, H.Czapinska, M.Bochtler, I.Sabala. High Resolution Structure of An M23 Peptidase with A Substrate Analogue. Sci Rep V. 5 14833 2015.
ISSN: ESSN 2045-2322
PubMed: 26437833
DOI: 10.1038/SREP14833