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:
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: Thu Jul 18 23:04:03 2024
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