Calcium in PDB 6q3r: Aspergillus Aculeatus Galactanase

Enzymatic activity of Aspergillus Aculeatus Galactanase

All present enzymatic activity of Aspergillus Aculeatus Galactanase:
3.2.1.89;

Protein crystallography data

The structure of Aspergillus Aculeatus Galactanase, PDB code: 6q3r was solved by S.J.Muderspach, S.Torpenholt, L.Lo Leggio, J.C.N.Poulsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.17 / 2.69
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 200.200, 200.200, 106.830, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 21.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Aspergillus Aculeatus Galactanase (pdb code 6q3r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Aspergillus Aculeatus Galactanase, PDB code: 6q3r:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 6q3r

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Calcium binding site 1 out of 7 in the Aspergillus Aculeatus Galactanase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Aspergillus Aculeatus Galactanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca508

b:51.8
occ:1.00
 O A:ASP38 2.2 42.9 1.0
O A:HOH661 2.3 31.7 1.0
OD1 A:ASP38 2.5 54.6 1.0
O A:HOH685 2.6 30.9 1.0
O A:HOH696 2.7 30.6 1.0
C A:ASP38 3.2 40.2 1.0
CA A:ASP38 3.6 41.6 1.0
CG A:ASP38 3.7 50.1 1.0
CB A:ASP38 4.2 45.6 1.0
N A:ALA39 4.4 39.2 1.0
O A:HOH703 4.6 31.4 1.0
OD2 A:ASP38 4.7 48.0 1.0
O A:ALA37 4.8 32.6 1.0
CA A:ALA39 4.8 36.1 1.0
N A:ASP38 4.9 38.7 1.0
N A:GLY40 4.9 32.3 1.0

Calcium binding site 2 out of 7 in 6q3r

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Calcium binding site 2 out of 7 in the Aspergillus Aculeatus Galactanase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Aspergillus Aculeatus Galactanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca509

b:77.5
occ:1.00
 O A:HOH602 2.1 31.8 1.0
OE2 A:GLU64 2.8 39.0 1.0
OE1 A:GLU64 3.5 42.4 1.0
CD A:GLU64 3.5 42.5 1.0
OE2 B:GLU286 3.7 88.7 1.0
OD1 A:ASP17 3.8 58.2 1.0
O A:HOH692 3.9 26.0 1.0
N B:ALA1 4.0 57.5 1.0
O B:HOH508 4.3 32.2 1.0
OXT B:LEU334 4.4 51.2 1.0
O B:GLU333 4.5 53.6 1.0
OD2 A:ASP17 4.5 64.0 1.0
CG A:ASP17 4.6 55.8 1.0
CD B:GLU286 4.6 83.1 1.0
CA B:ALA1 4.6 53.2 1.0
O A:HOH684 4.7 30.1 1.0
OE1 B:GLU286 4.8 86.5 1.0
C B:LEU334 4.8 53.2 1.0

Calcium binding site 3 out of 7 in 6q3r

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Calcium binding site 3 out of 7 in the Aspergillus Aculeatus Galactanase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Aspergillus Aculeatus Galactanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca510

b:80.5
occ:0.50
 OE2 A:GLU329 3.1 66.8 1.0
CD A:GLU329 3.9 59.8 1.0
OE1 A:GLU329 4.1 59.5 1.0
CD2 A:LEU25 5.0 40.5 1.0

Calcium binding site 4 out of 7 in 6q3r

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Calcium binding site 4 out of 7 in the Aspergillus Aculeatus Galactanase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Aspergillus Aculeatus Galactanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca511

b:72.3
occ:1.00
 O A:HOH709 2.7 49.0 1.0
OE1 A:GLU147 3.1 38.0 1.0
CD A:GLU147 3.9 36.3 1.0
OE2 A:GLU147 4.0 38.4 1.0
O A:HOH632 4.2 29.8 1.0

Calcium binding site 5 out of 7 in 6q3r

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Calcium binding site 5 out of 7 in the Aspergillus Aculeatus Galactanase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Aspergillus Aculeatus Galactanase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca408

b:70.8
occ:1.00
 O B:HOH504 1.9 46.8 1.0
OD1 B:ASP17 2.9 54.3 1.0
O B:HOH570 2.9 43.6 1.0
O B:HOH565 3.1 45.1 1.0
OD2 B:ASP17 3.3 64.1 1.0
CG B:ASP17 3.5 53.2 1.0
OE2 B:GLU64 3.8 33.1 1.0
OE1 B:GLU64 4.1 43.1 1.0
CD B:GLU64 4.4 39.0 1.0
O B:LEU13 4.7 40.3 1.0
CB B:ASP17 5.0 51.0 1.0

Calcium binding site 6 out of 7 in 6q3r

Go back to Calcium Binding Sites List in 6q3r
Calcium binding site 6 out of 7 in the Aspergillus Aculeatus Galactanase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Aspergillus Aculeatus Galactanase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca409

b:64.7
occ:0.70
 OD2 B:ASP102 2.4 60.5 1.0
O B:HOH562 2.4 44.4 1.0
O B:HOH554 2.5 31.1 1.0
CG B:ASP102 3.2 48.6 1.0
OD1 B:ASP102 3.2 51.6 1.0
CB B:ASP102 4.7 44.7 1.0
OG1 B:THR105 4.8 41.4 1.0

Calcium binding site 7 out of 7 in 6q3r

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Calcium binding site 7 out of 7 in the Aspergillus Aculeatus Galactanase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Aspergillus Aculeatus Galactanase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca410

b:36.9
occ:0.50
 O B:HOH523 2.8 19.5 1.0
O3 B:GAL402 2.9 41.7 1.0
OE2 B:GLU246 2.9 39.1 1.0
OD2 B:ASP79 3.1 34.9 1.0
NE2 B:HIS81 3.1 35.6 1.0
OD1 B:ASN135 3.2 31.9 1.0
ND2 B:ASN135 3.4 33.4 1.0
O2 B:GAL402 3.4 37.6 1.0
CG B:ASN135 3.5 32.4 1.0
NH1 B:ARG45 3.6 33.1 1.0
CE1 B:HIS81 3.6 34.7 1.0
NH2 B:ARG45 3.8 39.0 1.0
C3 B:GAL402 3.8 44.8 1.0
NE1 B:TRP297 3.9 29.9 1.0
CD B:GLU246 4.0 38.5 1.0
CZ B:ARG45 4.1 36.1 1.0
O B:HOH512 4.2 45.5 1.0
CG B:ASP79 4.3 34.2 1.0
C2 B:GAL402 4.3 43.0 1.0
CD2 B:HIS81 4.4 35.4 1.0
OE1 B:GLU246 4.6 37.2 1.0
CD1 B:TRP297 4.6 29.7 1.0
CE2 B:TRP297 4.6 30.5 1.0
CB B:ASN135 4.7 33.8 1.0
OD1 B:ASP79 4.7 34.8 1.0
OD2 B:ASP8 4.8 31.9 1.0
CB B:ARG47 4.8 30.4 1.0
CZ2 B:TRP297 4.9 30.7 1.0
ND1 B:HIS81 4.9 34.1 1.0
CG B:GLU246 5.0 38.9 1.0

Reference:

S.Torpenholt, J.C.N.Poulsen, S.J.Muderspach, L.De Maria, L.Lo Leggio. Structure of Aspergillus Aculeatus Beta-1,4-Galactanase in Complex with Galactobiose. Acta Crystallogr.,Sect.F V. 75 399 2019.
ISSN: ESSN 2053-230X
PubMed: 31204685
DOI: 10.1107/S2053230X19005612
Page generated: Sat Dec 12 07:26:54 2020

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