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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:

Fluorine (F) 2 atoms

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: Sat Dec 12 05:28:35 2020

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