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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 4zyb:

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

Zinc (Zn) 4 atoms
Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 5 binding sites of Calcium where determined in the High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue, PDB code: 4zyb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4zyb

Go back to Calcium Binding Sites List in 4zyb
Calcium binding site 1 out of 5 in the High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca402

b:17.7
occ:1.00
 O A:GLY285 2.4 12.5 1.0
O A:HOH547 2.5 18.5 1.0
C A:GLY285 3.5 10.6 1.0
CA A:GLY285 4.2 9.4 1.0
N A:GLY285 4.2 9.8 1.0
N A:ASN286 4.5 11.2 1.0
O A:SER287 4.5 16.8 1.0
O A:HOH651 4.6 42.6 1.0
O A:HOH650 4.6 39.9 1.0
N A:SER287 4.6 10.9 1.0
CA A:ASN286 4.7 11.8 1.0
O A:SER283 4.8 12.4 1.0
C A:THR284 5.0 10.9 1.0

Calcium binding site 2 out of 5 in 4zyb

Go back to Calcium Binding Sites List in 4zyb
Calcium binding site 2 out of 5 in the High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca402

b:15.2
occ:0.52
 CA B:CA402 0.0 15.2 0.5
CA B:CA402 0.3 15.6 0.5
O B:HOH530 2.4 16.5 1.0
O B:GLY285 2.5 10.1 1.0
O B:HOH653 2.7 19.0 0.9
C B:GLY285 3.6 11.2 1.0
N B:GLY285 4.2 8.3 1.0
CA B:GLY285 4.3 9.9 1.0
O B:HOH684 4.3 18.6 0.5
O B:HOH651 4.5 39.1 1.0
O B:SER287 4.6 16.6 1.0
O B:SER283 4.6 12.0 1.0
N B:ASN286 4.6 8.3 1.0
N B:SER287 4.7 9.7 1.0
CA B:ASN286 4.8 10.9 1.0
C B:THR284 5.0 9.2 1.0

Calcium binding site 3 out of 5 in 4zyb

Go back to Calcium Binding Sites List in 4zyb
Calcium binding site 3 out of 5 in the High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
B:Ca402

b:15.6
occ:0.48
 CA B:CA402 0.0 15.6 0.5
CA B:CA402 0.3 15.2 0.5
O B:GLY285 2.3 10.1 1.0
O B:HOH530 2.5 16.5 1.0
O B:HOH653 3.0 19.0 0.9
C B:GLY285 3.4 11.2 1.0
CA B:GLY285 4.2 9.9 1.0
N B:GLY285 4.2 8.3 1.0
N B:ASN286 4.4 8.3 1.0
N B:SER287 4.5 9.7 1.0
O B:SER287 4.6 16.6 1.0
CA B:ASN286 4.6 10.9 1.0
O B:HOH684 4.6 18.6 0.5
O B:HOH651 4.6 39.1 1.0
O B:SER283 4.7 12.0 1.0
C B:THR284 5.0 9.2 1.0

Calcium binding site 4 out of 5 in 4zyb

Go back to Calcium Binding Sites List in 4zyb
Calcium binding site 4 out of 5 in the High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
C:Ca402

b:18.7
occ:1.00
 O C:HOH663 2.4 12.4 0.4
O C:GLY285 2.4 11.7 1.0
O C:HOH533 2.5 19.1 1.0
O C:HOH711 2.5 42.3 1.0
O C:HOH663 3.0 17.6 0.6
C C:GLY285 3.5 10.2 1.0
N C:GLY285 4.2 8.2 1.0
CA C:GLY285 4.2 8.8 1.0
O C:HOH658 4.5 37.2 1.0
N C:ASN286 4.5 10.2 1.0
O C:SER287 4.5 15.2 1.0
N C:SER287 4.6 11.7 1.0
O C:SER283 4.7 12.2 1.0
CA C:ASN286 4.8 12.1 1.0
O C:HOH654 4.8 35.7 1.0
C C:THR284 5.0 9.3 1.0

Calcium binding site 5 out of 5 in 4zyb

Go back to Calcium Binding Sites List in 4zyb
Calcium binding site 5 out of 5 in the High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of High Resolution Structure of M23 Peptidase Lytm with Substrate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:13.5
occ:1.00
 O D:GLY285 2.4 11.6 1.0
O D:HOH537 2.4 15.0 1.0
C D:GLY285 3.5 9.9 1.0
O D:HOH649 3.6 30.0 1.0
CA D:GLY285 4.2 7.0 1.0
N D:GLY285 4.2 8.1 1.0
O D:HOH668 4.4 31.8 1.0
N D:ASN286 4.4 8.7 1.0
O D:SER287 4.5 15.8 1.0
N D:SER287 4.5 9.9 1.0
CA D:ASN286 4.7 9.9 1.0
O D:SER283 4.7 11.8 1.0
C D:THR284 5.0 8.3 1.0

Reference:

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
Page generated: Wed Jul 9 03:58:45 2025

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