Calcium in PDB 7aq1: Crystal Structure of Human Mature Meprin Beta in Complex with the Specific Inhibitor Mwt-S-270

Enzymatic activity of Crystal Structure of Human Mature Meprin Beta in Complex with the Specific Inhibitor Mwt-S-270

All present enzymatic activity of Crystal Structure of Human Mature Meprin Beta in Complex with the Specific Inhibitor Mwt-S-270:
3.4.24.63;

Protein crystallography data

The structure of Crystal Structure of Human Mature Meprin Beta in Complex with the Specific Inhibitor Mwt-S-270, PDB code: 7aq1 was solved by M.Linnert, C.Parthier, C.Fritz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.97 / 2.41
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.25, 72.44, 135.47, 90, 118.43, 90
R / Rfree (%) 19.9 / 23.6

Other elements in 7aq1:

The structure of Crystal Structure of Human Mature Meprin Beta in Complex with the Specific Inhibitor Mwt-S-270 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Mature Meprin Beta in Complex with the Specific Inhibitor Mwt-S-270 (pdb code 7aq1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human Mature Meprin Beta in Complex with the Specific Inhibitor Mwt-S-270, PDB code: 7aq1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7aq1

Go back to Calcium Binding Sites List in 7aq1
Calcium binding site 1 out of 4 in the Crystal Structure of Human Mature Meprin Beta in Complex with the Specific Inhibitor Mwt-S-270


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Mature Meprin Beta in Complex with the Specific Inhibitor Mwt-S-270 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca606

b:42.9
occ:1.00
OE2 A:GLU268 2.4 50.8 1.0
O A:PHE310 2.4 38.3 1.0
O A:SER266 2.5 36.6 1.0
OD2 A:ASP298 2.5 34.3 1.0
OG A:SER300 2.5 38.8 1.0
OD1 A:ASP418 2.6 37.5 1.0
OD2 A:ASP418 2.7 39.5 1.0
CG A:ASP418 3.0 37.6 1.0
HB2 A:SER300 3.1 45.1 1.0
HB3 A:SER266 3.3 42.2 1.0
HB2 A:ASP298 3.3 49.0 1.0
H A:SER300 3.3 44.4 1.0
H A:PHE310 3.3 53.4 1.0
CB A:SER300 3.4 35.6 1.0
CD A:GLU268 3.5 49.1 1.0
CG A:ASP298 3.5 38.4 1.0
C A:PHE310 3.6 36.8 1.0
C A:SER266 3.6 37.1 1.0
HG2 A:GLU268 3.7 48.6 1.0
N A:PHE310 3.8 42.5 1.0
CB A:ASP298 3.9 39.0 1.0
HB2 A:PHE267 4.0 45.8 1.0
HA A:SER266 4.0 44.5 1.0
N A:SER300 4.1 35.5 1.0
HB3 A:SER300 4.1 45.1 1.0
CB A:SER266 4.1 35.2 1.0
HA2 A:GLY309 4.1 63.3 1.0
CA A:SER266 4.2 37.3 1.0
CG A:GLU268 4.2 42.2 1.0
OD1 A:ASP419 4.2 35.5 1.0
HB3 A:PHE311 4.2 45.0 1.0
H A:HIS299 4.2 44.2 1.0
HB3 A:ASP298 4.3 49.0 1.0
HA A:PHE311 4.3 45.4 1.0
H A:ASP419 4.3 43.8 1.0
CA A:PHE310 4.3 43.3 1.0
CA A:SER300 4.4 40.6 1.0
HG A:SER266 4.4 57.8 1.0
HD2 A:PHE267 4.5 45.1 1.0
CB A:ASP418 4.5 37.6 1.0
OE1 A:GLU268 4.5 57.8 1.0
N A:PHE311 4.6 40.6 1.0
C A:GLY309 4.6 42.7 1.0
HG3 A:GLU268 4.7 48.6 1.0
OD1 A:ASP298 4.7 44.0 1.0
N A:PHE267 4.7 38.4 1.0
H A:ASN301 4.7 57.1 1.0
HB2 A:SER266 4.8 42.2 1.0
OG A:SER266 4.8 47.8 1.0
N A:HIS299 4.8 38.6 1.0
CA A:PHE311 4.8 37.6 1.0
HB2 A:ASP418 4.8 44.7 1.0
CA A:GLY309 4.8 50.1 1.0
HB2 A:PHE310 4.9 57.7 1.0
C A:PHE267 4.9 39.0 1.0
CB A:PHE267 4.9 37.6 1.0
HA A:SER300 4.9 51.0 1.0
N A:GLU268 4.9 47.5 1.0
HA A:ASP418 5.0 37.6 1.0
HB3 A:ASP418 5.0 44.7 1.0
CB A:PHE311 5.0 37.1 1.0

Calcium binding site 2 out of 4 in 7aq1

Go back to Calcium Binding Sites List in 7aq1
Calcium binding site 2 out of 4 in the Crystal Structure of Human Mature Meprin Beta in Complex with the Specific Inhibitor Mwt-S-270


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Mature Meprin Beta in Complex with the Specific Inhibitor Mwt-S-270 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca607

b:67.3
occ:1.00
OD1 A:ASP284 2.3 67.7 1.0
OD1 A:ASP281 2.4 77.3 1.0
O A:SER278 2.4 73.5 1.0
OD2 A:ASP281 2.4 72.0 1.0
O A:ALA283 2.6 64.0 1.0
CG A:ASP281 2.7 77.7 1.0
HA A:ASP284 3.3 73.0 1.0
C A:ALA283 3.5 56.5 1.0
CG A:ASP284 3.5 60.6 1.0
C A:SER278 3.5 72.5 1.0
H A:VAL326 3.9 62.3 1.0
H A:SER278 3.9 65.9 1.0
CA A:ASP284 4.0 63.2 1.0
HB3 A:SER278 4.0 72.1 1.0
N A:ASP284 4.0 61.3 1.0
H A:ALA283 4.1 79.2 1.0
HA A:SER279 4.1 95.7 1.0
N A:SER278 4.1 53.0 1.0
HB3 A:GLN277 4.2 68.1 1.0
CB A:ASP281 4.2 75.9 1.0
HA A:ALA325 4.3 64.7 1.0
CA A:SER278 4.3 61.9 1.0
CB A:ASP284 4.3 61.8 1.0
OD2 A:ASP284 4.4 60.2 1.0
N A:ALA283 4.5 68.5 1.0
CA A:ALA283 4.5 61.2 1.0
N A:SER279 4.5 95.1 1.0
HB2 A:ASP281 4.5 84.1 1.0
O A:VAL326 4.6 60.5 1.0
CB A:SER278 4.6 58.8 1.0
HB3 A:ASP281 4.7 84.1 1.0
H A:ASP281 4.7 92.2 1.0
CA A:SER279 4.7 92.5 1.0
N A:VAL326 4.7 53.6 1.0
HA A:ALA283 4.8 70.8 1.0
H A:ASP284 4.8 69.5 1.0
C A:GLN277 4.8 58.0 1.0
HB2 A:ASP284 4.8 70.8 1.0
HB1 A:ALA325 4.9 61.6 1.0
OE1 A:GLN277 4.9 59.3 1.0
CA A:ASP281 5.0 79.6 1.0

Calcium binding site 3 out of 4 in 7aq1

Go back to Calcium Binding Sites List in 7aq1
Calcium binding site 3 out of 4 in the Crystal Structure of Human Mature Meprin Beta in Complex with the Specific Inhibitor Mwt-S-270


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human Mature Meprin Beta in Complex with the Specific Inhibitor Mwt-S-270 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca605

b:39.0
occ:1.00
O B:PHE310 2.4 38.6 1.0
OG B:SER300 2.4 35.8 1.0
O B:SER266 2.5 40.0 1.0
OD2 B:ASP298 2.5 46.2 1.0
OD2 B:ASP418 2.5 34.1 1.0
OD1 B:ASP418 2.6 38.7 1.0
OE1 B:GLU268 2.6 43.7 1.0
CG B:ASP418 2.9 41.5 1.0
HB2 B:SER300 3.1 47.2 1.0
H B:PHE310 3.3 47.1 1.0
H B:SER300 3.3 52.0 1.0
HB2 B:ASP298 3.3 52.1 1.0
CB B:SER300 3.3 37.7 1.0
HB2 B:SER266 3.3 43.1 1.0
CG B:ASP298 3.5 43.1 1.0
C B:PHE310 3.6 41.1 1.0
C B:SER266 3.6 39.7 1.0
CD B:GLU268 3.8 50.1 1.0
HB2 B:PHE267 3.8 44.7 1.0
N B:PHE310 3.8 38.4 1.0
HG2 B:GLU268 3.9 46.6 1.0
CB B:ASP298 3.9 46.2 1.0
HB3 B:SER300 4.0 47.2 1.0
N B:SER300 4.0 43.0 1.0
HA B:SER266 4.0 43.1 1.0
HA2 B:GLY309 4.1 60.5 1.0
CB B:SER266 4.2 35.6 1.0
OD1 B:ASP419 4.2 47.3 1.0
CA B:SER266 4.2 36.0 1.0
HB3 B:PHE311 4.3 51.5 1.0
HD2 B:PHE267 4.3 43.1 1.0
H B:HIS299 4.3 51.8 1.0
HB3 B:ASP298 4.3 52.1 1.0
H B:ASP419 4.3 48.8 1.0
HA B:PHE311 4.3 49.3 1.0
CA B:SER300 4.3 42.3 1.0
CA B:PHE310 4.3 44.0 1.0
CG B:GLU268 4.4 40.3 1.0
CB B:ASP418 4.4 36.4 1.0
N B:PHE311 4.6 40.5 1.0
OD1 B:ASP298 4.7 49.8 1.0
C B:GLY309 4.7 46.2 1.0
N B:PHE267 4.7 39.5 1.0
HB2 B:ASP418 4.7 42.1 1.0
H B:ASN301 4.7 55.0 1.0
CB B:PHE267 4.7 38.7 1.0
HB2 B:PHE310 4.8 56.4 1.0
HB3 B:SER266 4.8 43.1 1.0
OE2 B:GLU268 4.8 61.5 1.0
CA B:PHE311 4.8 40.9 1.0
N B:HIS299 4.8 43.9 1.0
C B:PHE267 4.8 40.9 1.0
HB3 B:ASP418 4.8 42.1 1.0
CA B:GLY309 4.9 51.1 1.0
HA B:SER300 4.9 52.1 1.0
HG3 B:GLU268 4.9 46.6 1.0
HA B:ASP418 4.9 43.6 1.0
N B:GLU268 5.0 41.3 1.0
CA B:PHE267 5.0 47.4 1.0
OG B:SER266 5.0 48.6 1.0

Calcium binding site 4 out of 4 in 7aq1

Go back to Calcium Binding Sites List in 7aq1
Calcium binding site 4 out of 4 in the Crystal Structure of Human Mature Meprin Beta in Complex with the Specific Inhibitor Mwt-S-270


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human Mature Meprin Beta in Complex with the Specific Inhibitor Mwt-S-270 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca606

b:69.9
occ:1.00
OD1 B:ASP284 2.3 74.0 1.0
OD1 B:ASP281 2.4 84.3 1.0
O B:ALA283 2.4 68.3 1.0
O B:SER278 2.4 72.5 1.0
OD2 B:ASP281 2.4 76.9 1.0
CG B:ASP281 2.7 82.7 1.0
O B:HOH702 2.9 46.2 1.0
HA B:ASP284 3.1 76.9 1.0
C B:ALA283 3.3 70.9 1.0
CG B:ASP284 3.5 66.1 1.0
C B:SER278 3.6 77.9 1.0
CA B:ASP284 3.8 74.2 1.0
N B:ASP284 3.8 71.6 1.0
H B:ALA283 3.9 87.1 1.0
HA B:SER279 4.0 91.2 1.0
HB3 B:GLN277 4.0 55.9 1.0
H B:VAL326 4.1 62.2 1.0
H B:SER278 4.1 72.3 1.0
HB3 B:SER278 4.1 80.1 1.0
HA B:ALA325 4.2 71.3 1.0
CB B:ASP281 4.2 79.2 1.0
CB B:ASP284 4.2 67.0 1.0
N B:SER278 4.3 63.8 1.0
N B:ALA283 4.3 76.2 1.0
CA B:ALA283 4.3 65.5 1.0
CA B:SER278 4.4 67.2 1.0
OD2 B:ASP284 4.4 72.7 1.0
HB2 B:ASP281 4.5 81.5 1.0
N B:SER279 4.6 96.1 1.0
H B:ASP284 4.6 72.5 1.0
HA B:ALA283 4.6 74.8 1.0
HB1 B:ALA325 4.7 71.0 1.0
CA B:SER279 4.7 92.2 1.0
HB3 B:ASP281 4.7 81.5 1.0
H B:ASP281 4.7 89.7 1.0
HB2 B:ASP284 4.7 68.8 1.0
CB B:SER278 4.8 71.3 1.0
OE1 B:GLN277 4.8 50.1 1.0
O B:VAL326 4.8 51.6 1.0
N B:VAL326 4.9 53.5 1.0
C B:GLN277 4.9 54.6 1.0
C B:ASP281 5.0 88.3 1.0
CB B:GLN277 5.0 46.6 1.0
CA B:ASP281 5.0 81.5 1.0
HB3 B:ASP284 5.0 68.8 1.0

Reference:

M.Linnert, C.Fritz, C.Jager, D.Schlenzig, D.Ramsbeck, M.Kleinschmidt, M.Wermann, H.-U.Demuth, S.Schilling. Structure and Dynamics of Meprin Beta in Complex with A Hydroxamate-Based Inhibitor Preprints 2021.
DOI: 10.20944/PREPRINTS202102.0520.V1
Page generated: Sat Apr 17 14:05:52 2021

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