Calcium in PDB 5hjr: Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate
Enzymatic activity of Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate
All present enzymatic activity of Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate:
3.2.1.84;
Protein crystallography data
The structure of Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate, PDB code: 5hjr
was solved by
A.T.Caputo,
P.Roversi,
D.S.Alonzi,
J.L.Kiappes,
N.Zitzmann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
103.48 /
2.40
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
103.512,
174.664,
63.714,
90.00,
91.31,
90.00
|
R / Rfree (%)
|
17.7 /
20.2
|
Other elements in 5hjr:
The structure of Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate
(pdb code 5hjr). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate, PDB code: 5hjr:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 5hjr
Go back to
Calcium Binding Sites List in 5hjr
Calcium binding site 1 out
of 4 in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca202
b:56.5
occ:1.00
|
O
|
B:GLN50
|
2.2
|
61.7
|
1.0
|
OD1
|
B:ASP53
|
2.3
|
59.1
|
1.0
|
O
|
B:TYR55
|
2.3
|
54.0
|
1.0
|
OD2
|
B:ASP57
|
2.3
|
56.6
|
1.0
|
OD2
|
B:ASP63
|
2.3
|
60.3
|
1.0
|
OE2
|
B:GLU64
|
2.3
|
55.4
|
1.0
|
H
|
B:ASP53
|
3.3
|
53.0
|
1.0
|
H
|
B:TYR55
|
3.4
|
46.2
|
1.0
|
H
|
B:ASP57
|
3.4
|
56.6
|
1.0
|
HG2
|
B:GLU64
|
3.4
|
61.1
|
1.0
|
C
|
B:GLN50
|
3.4
|
64.8
|
1.0
|
CD
|
B:GLU64
|
3.4
|
57.6
|
1.0
|
HB3
|
B:GLN50
|
3.4
|
65.4
|
1.0
|
CG
|
B:ASP57
|
3.5
|
57.3
|
1.0
|
CG
|
B:ASP53
|
3.5
|
61.0
|
1.0
|
C
|
B:TYR55
|
3.5
|
54.8
|
1.0
|
CG
|
B:ASP63
|
3.5
|
60.2
|
1.0
|
HB2
|
B:ASP57
|
3.5
|
58.4
|
1.0
|
HB2
|
B:ASP63
|
3.6
|
56.4
|
1.0
|
HB3
|
B:TYR55
|
3.9
|
46.0
|
1.0
|
CG
|
B:GLU64
|
3.9
|
60.9
|
1.0
|
HA
|
B:CYS56
|
4.0
|
55.4
|
1.0
|
HA
|
B:GLN50
|
4.0
|
63.9
|
1.0
|
N
|
B:ASP57
|
4.0
|
57.1
|
1.0
|
HH12
|
A:ARG951
|
4.0
|
52.6
|
1.0
|
CB
|
B:ASP57
|
4.0
|
57.7
|
1.0
|
HA
|
B:VAL51
|
4.0
|
60.8
|
1.0
|
HG3
|
B:GLU64
|
4.1
|
61.9
|
1.0
|
CA
|
B:GLN50
|
4.1
|
64.1
|
1.0
|
CB
|
B:ASP63
|
4.2
|
56.4
|
1.0
|
HD12
|
B:ILE46
|
4.2
|
91.6
|
1.0
|
HD1
|
B:TYR55
|
4.2
|
43.9
|
1.0
|
OD2
|
B:ASP53
|
4.2
|
59.4
|
1.0
|
HH11
|
A:ARG951
|
4.2
|
52.0
|
1.0
|
N
|
B:TYR55
|
4.2
|
46.0
|
1.0
|
CB
|
B:GLN50
|
4.3
|
65.2
|
1.0
|
N
|
B:ASP53
|
4.3
|
53.0
|
1.0
|
CA
|
B:TYR55
|
4.3
|
46.6
|
1.0
|
H
|
B:ASN52
|
4.4
|
59.3
|
1.0
|
N
|
B:VAL51
|
4.4
|
61.3
|
1.0
|
CB
|
B:ASP53
|
4.4
|
53.4
|
1.0
|
HB3
|
B:ASP53
|
4.4
|
53.3
|
1.0
|
OD1
|
B:ASP57
|
4.5
|
59.8
|
1.0
|
N
|
B:CYS56
|
4.5
|
54.5
|
1.0
|
OE1
|
B:GLU64
|
4.5
|
55.8
|
1.0
|
OD1
|
B:ASP63
|
4.5
|
58.9
|
1.0
|
O
|
B:ASP63
|
4.5
|
53.7
|
1.0
|
NH1
|
A:ARG951
|
4.5
|
52.3
|
1.0
|
CA
|
B:CYS56
|
4.6
|
55.4
|
1.0
|
CB
|
B:TYR55
|
4.6
|
46.6
|
1.0
|
C
|
B:CYS56
|
4.6
|
56.2
|
1.0
|
CA
|
B:VAL51
|
4.7
|
61.0
|
1.0
|
CA
|
B:ASP57
|
4.7
|
57.9
|
1.0
|
N
|
B:ASN52
|
4.7
|
58.9
|
1.0
|
HD11
|
B:ILE46
|
4.8
|
91.9
|
1.0
|
CA
|
B:ASP53
|
4.8
|
51.7
|
1.0
|
H
|
B:ASP54
|
4.8
|
46.0
|
1.0
|
CD1
|
B:ILE46
|
4.9
|
92.0
|
1.0
|
C
|
B:ASP63
|
4.9
|
56.5
|
1.0
|
HB3
|
B:ASP63
|
4.9
|
57.0
|
1.0
|
HB2
|
B:GLN50
|
4.9
|
65.0
|
1.0
|
C
|
B:VAL51
|
5.0
|
63.5
|
1.0
|
HB3
|
B:ASP57
|
5.0
|
57.4
|
1.0
|
C
|
B:ASP53
|
5.0
|
52.8
|
1.0
|
N
|
B:ASP54
|
5.0
|
46.8
|
1.0
|
HG2
|
B:GLN50
|
5.0
|
74.6
|
1.0
|
|
Calcium binding site 2 out
of 4 in 5hjr
Go back to
Calcium Binding Sites List in 5hjr
Calcium binding site 2 out
of 4 in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca203
b:47.5
occ:1.00
|
O
|
B:VAL96
|
2.2
|
48.2
|
1.0
|
OE2
|
B:GLU105
|
2.3
|
49.0
|
1.0
|
O
|
B:ARG91
|
2.3
|
51.6
|
1.0
|
OD2
|
B:ASP98
|
2.3
|
53.8
|
1.0
|
OD2
|
B:ASP104
|
2.3
|
54.8
|
1.0
|
OD1
|
B:ASP94
|
2.4
|
42.7
|
1.0
|
H
|
B:ASP98
|
3.2
|
62.4
|
1.0
|
H
|
B:ASP94
|
3.2
|
48.7
|
1.0
|
H
|
B:VAL96
|
3.3
|
43.8
|
1.0
|
CD
|
B:GLU105
|
3.3
|
54.1
|
1.0
|
HG2
|
B:GLU105
|
3.4
|
55.0
|
1.0
|
CG
|
B:ASP94
|
3.4
|
46.5
|
1.0
|
C
|
B:VAL96
|
3.4
|
52.2
|
1.0
|
HB3
|
B:ARG91
|
3.4
|
41.6
|
1.0
|
HB2
|
B:ASP104
|
3.4
|
54.3
|
1.0
|
CG
|
B:ASP98
|
3.5
|
55.1
|
1.0
|
CG
|
B:ASP104
|
3.5
|
56.4
|
1.0
|
C
|
B:ARG91
|
3.5
|
52.0
|
1.0
|
HB2
|
B:ASP98
|
3.5
|
59.0
|
1.0
|
HB
|
B:VAL96
|
3.6
|
46.1
|
1.0
|
OD2
|
B:ASP94
|
3.8
|
51.1
|
1.0
|
CG
|
B:GLU105
|
3.8
|
54.4
|
1.0
|
N
|
B:ASP98
|
4.0
|
61.6
|
1.0
|
CB
|
B:ASP98
|
4.0
|
60.0
|
1.0
|
HA
|
B:VAL92
|
4.0
|
50.5
|
1.0
|
H
|
B:ASN93
|
4.0
|
48.0
|
1.0
|
N
|
B:VAL96
|
4.0
|
43.6
|
1.0
|
HH12
|
A:ARG840
|
4.0
|
66.0
|
1.0
|
CB
|
B:ASP104
|
4.0
|
54.1
|
1.0
|
HA
|
B:ARG91
|
4.1
|
43.0
|
1.0
|
CA
|
B:VAL96
|
4.1
|
43.3
|
1.0
|
HA
|
B:CYS97
|
4.2
|
59.6
|
1.0
|
HG3
|
B:GLU105
|
4.2
|
54.2
|
1.0
|
CA
|
B:ARG91
|
4.2
|
43.6
|
1.0
|
N
|
B:ASP94
|
4.2
|
47.5
|
1.0
|
CB
|
B:ARG91
|
4.3
|
42.4
|
1.0
|
OE1
|
B:GLU105
|
4.3
|
40.4
|
1.0
|
CB
|
B:VAL96
|
4.4
|
45.9
|
1.0
|
HD12
|
B:ILE87
|
4.4
|
48.4
|
1.0
|
N
|
B:CYS97
|
4.5
|
56.1
|
1.0
|
N
|
B:ASN93
|
4.5
|
48.8
|
1.0
|
OD1
|
B:ASP104
|
4.5
|
56.4
|
1.0
|
OD1
|
B:ASP98
|
4.5
|
51.9
|
1.0
|
N
|
B:VAL92
|
4.5
|
50.7
|
1.0
|
H
|
B:GLY95
|
4.5
|
41.6
|
1.0
|
HH22
|
A:ARG840
|
4.5
|
60.1
|
1.0
|
HG12
|
B:VAL96
|
4.5
|
44.4
|
1.0
|
CB
|
B:ASP94
|
4.5
|
47.1
|
1.0
|
CA
|
B:ASP98
|
4.6
|
60.7
|
1.0
|
O
|
B:ASP104
|
4.6
|
49.6
|
1.0
|
CA
|
B:CYS97
|
4.7
|
59.9
|
1.0
|
CA
|
B:VAL92
|
4.7
|
50.6
|
1.0
|
C
|
B:CYS97
|
4.7
|
64.3
|
1.0
|
HB3
|
B:ASP104
|
4.8
|
54.2
|
1.0
|
C
|
B:ASP104
|
4.8
|
51.8
|
1.0
|
CA
|
B:ASP94
|
4.8
|
46.0
|
1.0
|
N
|
B:GLY95
|
4.8
|
42.9
|
1.0
|
HB3
|
B:ASP94
|
4.8
|
47.1
|
1.0
|
HD11
|
B:ILE87
|
4.9
|
49.3
|
1.0
|
C
|
B:VAL92
|
4.9
|
51.8
|
1.0
|
HB2
|
B:ARG91
|
4.9
|
42.1
|
1.0
|
HB3
|
B:ASP98
|
4.9
|
60.1
|
1.0
|
HA
|
B:ASN93
|
5.0
|
51.2
|
1.0
|
|
Calcium binding site 3 out
of 4 in 5hjr
Go back to
Calcium Binding Sites List in 5hjr
Calcium binding site 3 out
of 4 in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca202
b:51.8
occ:1.00
|
OD2
|
D:ASP57
|
2.1
|
51.0
|
1.0
|
OD1
|
D:ASP53
|
2.1
|
52.8
|
1.0
|
OD2
|
D:ASP63
|
2.2
|
50.8
|
1.0
|
O
|
D:GLN50
|
2.3
|
52.6
|
1.0
|
O
|
D:TYR55
|
2.3
|
51.1
|
1.0
|
OE2
|
D:GLU64
|
2.5
|
59.4
|
1.0
|
CG
|
D:ASP57
|
3.2
|
52.2
|
1.0
|
HG2
|
D:GLU64
|
3.3
|
57.1
|
1.0
|
CG
|
D:ASP53
|
3.3
|
53.0
|
1.0
|
HB3
|
D:GLN50
|
3.3
|
53.6
|
1.0
|
H
|
D:ASP53
|
3.4
|
44.8
|
1.0
|
C
|
D:GLN50
|
3.4
|
53.4
|
1.0
|
CD
|
D:GLU64
|
3.4
|
65.6
|
1.0
|
H
|
D:TYR55
|
3.4
|
42.6
|
1.0
|
H
|
D:ASP57
|
3.4
|
53.4
|
1.0
|
CG
|
D:ASP63
|
3.4
|
51.8
|
1.0
|
C
|
D:TYR55
|
3.5
|
50.4
|
1.0
|
HB2
|
D:ASP57
|
3.6
|
56.5
|
1.0
|
CG
|
D:GLU64
|
3.8
|
57.0
|
1.0
|
HB2
|
D:ASP63
|
3.8
|
53.0
|
1.0
|
OD2
|
D:ASP53
|
3.8
|
50.2
|
1.0
|
HB3
|
D:TYR55
|
3.8
|
41.5
|
1.0
|
HA
|
D:GLN50
|
3.9
|
54.3
|
1.0
|
HH12
|
C:ARG951
|
3.9
|
49.3
|
1.0
|
CB
|
D:ASP57
|
4.0
|
56.4
|
1.0
|
HA
|
D:CYS56
|
4.0
|
49.9
|
1.0
|
N
|
D:ASP57
|
4.0
|
54.5
|
1.0
|
HG3
|
D:GLU64
|
4.0
|
57.3
|
1.0
|
CA
|
D:GLN50
|
4.1
|
53.0
|
1.0
|
HD1
|
D:TYR55
|
4.1
|
40.5
|
1.0
|
CB
|
D:GLN50
|
4.2
|
53.2
|
1.0
|
OD1
|
D:ASP57
|
4.2
|
49.2
|
1.0
|
HH11
|
C:ARG951
|
4.2
|
49.4
|
1.0
|
HA
|
D:VAL51
|
4.3
|
46.9
|
1.0
|
CB
|
D:ASP63
|
4.3
|
52.2
|
1.0
|
N
|
D:TYR55
|
4.3
|
42.3
|
1.0
|
HD12
|
D:ILE46
|
4.3
|
75.5
|
1.0
|
OD1
|
D:ASP63
|
4.3
|
51.9
|
1.0
|
N
|
D:ASP53
|
4.3
|
46.6
|
1.0
|
H
|
D:ASN52
|
4.4
|
47.9
|
1.0
|
CA
|
D:TYR55
|
4.4
|
42.2
|
1.0
|
CB
|
D:ASP53
|
4.4
|
47.9
|
1.0
|
N
|
D:CYS56
|
4.5
|
49.3
|
1.0
|
N
|
D:VAL51
|
4.5
|
46.8
|
1.0
|
NH1
|
C:ARG951
|
4.5
|
49.3
|
1.0
|
OE1
|
D:GLU64
|
4.5
|
51.7
|
1.0
|
CA
|
D:CYS56
|
4.5
|
51.1
|
1.0
|
HB3
|
D:ASP53
|
4.5
|
47.2
|
1.0
|
C
|
D:CYS56
|
4.6
|
56.6
|
1.0
|
CB
|
D:TYR55
|
4.6
|
42.4
|
1.0
|
O
|
D:ASP63
|
4.6
|
53.2
|
1.0
|
CA
|
D:ASP57
|
4.6
|
55.5
|
1.0
|
N
|
D:ASN52
|
4.7
|
48.4
|
1.0
|
HD11
|
D:ILE46
|
4.8
|
75.2
|
1.0
|
CA
|
D:VAL51
|
4.8
|
46.1
|
1.0
|
CA
|
D:ASP53
|
4.8
|
47.0
|
1.0
|
HB2
|
D:GLN50
|
4.9
|
52.3
|
1.0
|
HG2
|
D:GLN50
|
4.9
|
43.2
|
1.0
|
C
|
D:ASP63
|
4.9
|
54.1
|
1.0
|
HB3
|
D:ASP57
|
4.9
|
56.1
|
1.0
|
CD1
|
D:ILE46
|
4.9
|
75.6
|
1.0
|
H
|
D:ASP54
|
4.9
|
48.1
|
1.0
|
HB3
|
D:ASP63
|
5.0
|
53.4
|
1.0
|
|
Calcium binding site 4 out
of 4 in 5hjr
Go back to
Calcium Binding Sites List in 5hjr
Calcium binding site 4 out
of 4 in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca203
b:44.7
occ:1.00
|
O
|
D:VAL96
|
2.2
|
45.3
|
1.0
|
OE2
|
D:GLU105
|
2.2
|
40.9
|
1.0
|
O
|
D:ARG91
|
2.3
|
41.7
|
1.0
|
OD2
|
D:ASP98
|
2.3
|
51.8
|
1.0
|
OD2
|
D:ASP104
|
2.3
|
48.6
|
1.0
|
OD1
|
D:ASP94
|
2.4
|
45.7
|
1.0
|
H
|
D:ASP94
|
3.2
|
44.4
|
1.0
|
H
|
D:ASP98
|
3.2
|
54.5
|
1.0
|
H
|
D:VAL96
|
3.3
|
39.1
|
1.0
|
CD
|
D:GLU105
|
3.3
|
48.7
|
1.0
|
CG
|
D:ASP94
|
3.4
|
47.2
|
1.0
|
HG2
|
D:GLU105
|
3.4
|
47.0
|
1.0
|
C
|
D:VAL96
|
3.4
|
48.6
|
1.0
|
HB3
|
D:ARG91
|
3.4
|
41.9
|
1.0
|
HB2
|
D:ASP104
|
3.5
|
51.5
|
1.0
|
CG
|
D:ASP98
|
3.5
|
54.3
|
1.0
|
CG
|
D:ASP104
|
3.5
|
47.5
|
1.0
|
C
|
D:ARG91
|
3.5
|
43.5
|
1.0
|
HB2
|
D:ASP98
|
3.5
|
54.5
|
1.0
|
HB
|
D:VAL96
|
3.6
|
43.4
|
1.0
|
OD2
|
D:ASP94
|
3.8
|
43.3
|
1.0
|
CG
|
D:GLU105
|
3.8
|
47.0
|
1.0
|
N
|
D:ASP98
|
4.0
|
53.4
|
1.0
|
HA
|
D:VAL92
|
4.0
|
43.5
|
1.0
|
H
|
D:ASN93
|
4.0
|
47.0
|
1.0
|
CB
|
D:ASP98
|
4.0
|
54.1
|
1.0
|
N
|
D:VAL96
|
4.0
|
39.0
|
1.0
|
CB
|
D:ASP104
|
4.1
|
51.1
|
1.0
|
HA
|
D:ARG91
|
4.1
|
36.7
|
1.0
|
CA
|
D:VAL96
|
4.2
|
40.8
|
1.0
|
HA
|
D:CYS97
|
4.2
|
55.1
|
1.0
|
HG3
|
D:GLU105
|
4.2
|
47.3
|
1.0
|
N
|
D:ASP94
|
4.2
|
43.9
|
1.0
|
CA
|
D:ARG91
|
4.2
|
37.2
|
1.0
|
CB
|
D:ARG91
|
4.3
|
41.5
|
1.0
|
OE1
|
D:GLU105
|
4.3
|
50.3
|
1.0
|
CB
|
D:VAL96
|
4.4
|
43.3
|
1.0
|
HH12
|
C:ARG840
|
4.4
|
35.1
|
1.0
|
HD12
|
D:ILE87
|
4.4
|
49.3
|
1.0
|
N
|
D:CYS97
|
4.4
|
52.3
|
1.0
|
N
|
D:ASN93
|
4.5
|
46.6
|
1.0
|
OD1
|
D:ASP104
|
4.5
|
44.6
|
1.0
|
N
|
D:VAL92
|
4.5
|
45.0
|
1.0
|
OD1
|
D:ASP98
|
4.5
|
48.4
|
1.0
|
H
|
D:GLY95
|
4.5
|
43.5
|
1.0
|
CB
|
D:ASP94
|
4.5
|
43.2
|
1.0
|
HG12
|
D:VAL96
|
4.5
|
42.5
|
1.0
|
O
|
D:ASP104
|
4.6
|
50.5
|
1.0
|
CA
|
D:ASP98
|
4.6
|
53.0
|
1.0
|
CA
|
D:VAL92
|
4.7
|
44.3
|
1.0
|
CA
|
D:CYS97
|
4.7
|
56.2
|
1.0
|
C
|
D:CYS97
|
4.7
|
58.1
|
1.0
|
HH11
|
C:ARG840
|
4.7
|
36.6
|
1.0
|
C
|
D:ASP104
|
4.7
|
51.5
|
1.0
|
HB3
|
D:ASP104
|
4.8
|
50.6
|
1.0
|
CA
|
D:ASP94
|
4.8
|
41.3
|
1.0
|
N
|
D:GLY95
|
4.8
|
43.4
|
1.0
|
HB3
|
D:ASP94
|
4.8
|
43.2
|
1.0
|
HD11
|
D:ILE87
|
4.9
|
48.8
|
1.0
|
C
|
D:VAL92
|
4.9
|
47.0
|
1.0
|
HB2
|
D:ARG91
|
4.9
|
42.0
|
1.0
|
HB3
|
D:ASP98
|
4.9
|
54.4
|
1.0
|
HA
|
D:ASN93
|
5.0
|
48.1
|
1.0
|
NH1
|
C:ARG840
|
5.0
|
35.2
|
1.0
|
|
Reference:
A.T.Caputo,
D.S.Alonzi,
L.Marti,
I.B.Reca,
J.L.Kiappes,
W.B.Struwe,
A.Cross,
S.Basu,
E.D.Lowe,
B.Darlot,
A.Santino,
P.Roversi,
N.Zitzmann.
Structures of Mammalian Er Alpha-Glucosidase II Capture the Binding Modes of Broad-Spectrum Iminosugar Antivirals. Proc.Natl.Acad.Sci.Usa V. 113 E4630 2016.
ISSN: ESSN 1091-6490
PubMed: 27462106
DOI: 10.1073/PNAS.1604463113
Page generated: Sun Jul 14 20:02:26 2024
|