Calcium in PDB 6ya1: Zinc Metalloprotease Proa
Protein crystallography data
The structure of Zinc Metalloprotease Proa, PDB code: 6ya1
was solved by
S.Schmelz,
W.Blankenfeldt,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.39 /
1.48
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.262,
108.213,
47.39,
90,
90,
90
|
R / Rfree (%)
|
16.8 /
18.7
|
Other elements in 6ya1:
The structure of Zinc Metalloprotease Proa also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Zinc Metalloprotease Proa
(pdb code 6ya1). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Zinc Metalloprotease Proa, PDB code: 6ya1:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6ya1
Go back to
Calcium Binding Sites List in 6ya1
Calcium binding site 1 out
of 4 in the Zinc Metalloprotease Proa
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Zinc Metalloprotease Proa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca408
b:27.5
occ:1.00
|
OD1
|
A:ASP156
|
2.2
|
27.8
|
1.0
|
O
|
A:HOH618
|
2.2
|
26.8
|
1.0
|
CG
|
A:ASP156
|
3.1
|
24.6
|
1.0
|
OD2
|
A:ASP156
|
3.4
|
30.5
|
1.0
|
HG22
|
A:THR157
|
3.5
|
24.1
|
1.0
|
HG23
|
A:THR157
|
3.9
|
24.1
|
1.0
|
O
|
A:HOH801
|
4.1
|
37.3
|
1.0
|
CG2
|
A:THR157
|
4.2
|
20.0
|
1.0
|
HA
|
A:ASP156
|
4.3
|
18.6
|
1.0
|
CB
|
A:ASP156
|
4.5
|
19.7
|
1.0
|
HG21
|
A:THR157
|
4.6
|
24.1
|
1.0
|
CA
|
A:ASP156
|
4.8
|
15.5
|
1.0
|
C
|
A:ASP156
|
4.8
|
16.1
|
1.0
|
N
|
A:THR157
|
4.9
|
18.4
|
1.0
|
H
|
A:THR157
|
4.9
|
22.1
|
1.0
|
HB3
|
A:ASP156
|
5.0
|
23.7
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6ya1
Go back to
Calcium Binding Sites List in 6ya1
Calcium binding site 2 out
of 4 in the Zinc Metalloprotease Proa
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Zinc Metalloprotease Proa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca409
b:12.6
occ:1.00
|
O
|
A:HOH806
|
2.1
|
28.5
|
1.0
|
OD2
|
A:ASP224
|
2.1
|
21.0
|
1.0
|
O
|
A:HOH522
|
2.2
|
20.8
|
1.0
|
O
|
A:HOH747
|
2.2
|
24.3
|
1.0
|
CG
|
A:ASP224
|
3.0
|
33.0
|
1.0
|
OD1
|
A:ASP224
|
3.3
|
24.5
|
1.0
|
O
|
A:HOH690
|
4.1
|
31.0
|
1.0
|
O
|
A:HOH714
|
4.3
|
41.2
|
1.0
|
CB
|
A:ASP224
|
4.3
|
23.6
|
1.0
|
HB2
|
A:ASP224
|
4.3
|
28.3
|
1.0
|
O
|
A:THR157
|
4.3
|
20.4
|
1.0
|
HB
|
A:THR157
|
4.3
|
23.4
|
1.0
|
HB3
|
A:ASP224
|
4.8
|
28.3
|
1.0
|
HD3
|
A:LYS222
|
4.8
|
24.7
|
1.0
|
HA
|
A:THR157
|
4.8
|
25.8
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6ya1
Go back to
Calcium Binding Sites List in 6ya1
Calcium binding site 3 out
of 4 in the Zinc Metalloprotease Proa
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Zinc Metalloprotease Proa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca410
b:17.7
occ:1.00
|
OE2
|
A:GLU42
|
2.1
|
19.7
|
1.0
|
O
|
A:HOH658
|
2.1
|
36.5
|
1.0
|
O
|
A:HOH820
|
2.1
|
40.6
|
1.0
|
O
|
A:HOH577
|
2.2
|
25.8
|
1.0
|
O
|
A:HOH539
|
2.2
|
24.0
|
1.0
|
O
|
A:HOH726
|
2.2
|
47.0
|
1.0
|
CD
|
A:GLU42
|
3.0
|
16.8
|
1.0
|
OE1
|
A:GLU42
|
3.3
|
21.2
|
1.0
|
HE22
|
A:GLN129
|
3.4
|
19.3
|
1.0
|
HZ3
|
A:LYS47
|
3.5
|
27.7
|
1.0
|
HD3
|
A:LYS47
|
3.7
|
20.2
|
1.0
|
O
|
A:HOH778
|
3.8
|
44.4
|
1.0
|
O
|
A:HOH777
|
4.0
|
42.2
|
1.0
|
OE1
|
A:GLN129
|
4.2
|
14.5
|
1.0
|
NE2
|
A:GLN129
|
4.2
|
16.1
|
1.0
|
NZ
|
A:LYS47
|
4.3
|
23.1
|
1.0
|
CG
|
A:GLU42
|
4.4
|
15.8
|
1.0
|
HG2
|
A:GLU42
|
4.6
|
18.9
|
1.0
|
CD
|
A:LYS47
|
4.6
|
16.8
|
1.0
|
CD
|
A:GLN129
|
4.6
|
15.6
|
1.0
|
HG3
|
A:GLU42
|
4.6
|
18.9
|
1.0
|
HE2
|
A:LYS47
|
4.6
|
22.4
|
1.0
|
HZ2
|
A:LYS47
|
4.7
|
27.7
|
1.0
|
CE
|
A:LYS47
|
4.8
|
18.7
|
1.0
|
HB2
|
A:LYS47
|
4.8
|
15.1
|
1.0
|
O
|
A:HOH798
|
4.8
|
36.8
|
1.0
|
HZ1
|
A:LYS47
|
4.8
|
27.7
|
1.0
|
HE21
|
A:GLN129
|
4.8
|
19.3
|
1.0
|
HD3
|
A:PRO61
|
5.0
|
23.8
|
1.0
|
O
|
A:HOH774
|
5.0
|
36.0
|
1.0
|
HD2
|
A:LYS47
|
5.0
|
20.2
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6ya1
Go back to
Calcium Binding Sites List in 6ya1
Calcium binding site 4 out
of 4 in the Zinc Metalloprotease Proa
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Zinc Metalloprotease Proa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca411
b:26.9
occ:0.74
|
O
|
A:HOH687
|
2.2
|
28.3
|
1.0
|
O
|
A:HOH503
|
2.3
|
44.9
|
1.0
|
HZ1
|
A:LYS148
|
2.7
|
55.4
|
1.0
|
NZ
|
A:LYS148
|
3.4
|
46.2
|
1.0
|
HZ2
|
A:LYS148
|
3.5
|
55.4
|
1.0
|
HZ3
|
A:LYS148
|
3.7
|
55.4
|
1.0
|
O
|
A:ASP146
|
3.9
|
17.3
|
1.0
|
HD3
|
A:LYS148
|
4.4
|
27.5
|
1.0
|
O
|
A:HOH660
|
4.4
|
36.4
|
1.0
|
HG2
|
A:LYS148
|
4.4
|
24.3
|
1.0
|
OD2
|
A:ASP146
|
4.6
|
18.2
|
1.0
|
HB2
|
A:ASP146
|
4.6
|
16.1
|
1.0
|
CE
|
A:LYS148
|
4.7
|
31.4
|
1.0
|
CG
|
A:ASP146
|
4.8
|
16.1
|
1.0
|
CD
|
A:LYS148
|
4.9
|
22.9
|
1.0
|
HE3
|
A:LYS148
|
5.0
|
37.7
|
1.0
|
C
|
A:ASP146
|
5.0
|
17.6
|
1.0
|
|
Reference:
L.Scheithauer,
S.Thiem,
S.Schmelz,
A.Dellmann,
K.Bussow,
R.M.H.J.Brouwer,
C.M.Unal,
W.Blankenfeldt,
M.Steinert.
Zinc Metalloprotease Proa of Legionella Pneumophila Increases Alveolar Septal Thickness in Human Lung Tissue Explants By Collagen IV Degradation. Cell.Microbiol. 13313 2021.
ISSN: ESSN 1462-5822
PubMed: 33491325
DOI: 10.1111/CMI.13313
Page generated: Thu Jul 18 21:49:49 2024
|