Magnesium in PDB 5fjj: Three-Dimensional Structures of Two Heavily N-Glycosylated Aspergillus Sp. Family GH3 Beta-D-Glucosidases

Enzymatic activity of Three-Dimensional Structures of Two Heavily N-Glycosylated Aspergillus Sp. Family GH3 Beta-D-Glucosidases

All present enzymatic activity of Three-Dimensional Structures of Two Heavily N-Glycosylated Aspergillus Sp. Family GH3 Beta-D-Glucosidases:
3.2.1.21;

Protein crystallography data

The structure of Three-Dimensional Structures of Two Heavily N-Glycosylated Aspergillus Sp. Family GH3 Beta-D-Glucosidases, PDB code: 5fjj was solved by J.Agirre, A.Ariza, W.A.Offen, J.P.Turkenburg, S.M.Roberts, S.Mcnicholas, P.V.Harris, B.Mcbrayer, J.Dohnalek, K.D.Cowtan, G.J.Davies, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 114.43 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 139.020, 141.463, 193.339, 90.00, 90.00, 90.00
R / Rfree (%) 21.565 / 25.486

Other elements in 5fjj:

The structure of Three-Dimensional Structures of Two Heavily N-Glycosylated Aspergillus Sp. Family GH3 Beta-D-Glucosidases also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Three-Dimensional Structures of Two Heavily N-Glycosylated Aspergillus Sp. Family GH3 Beta-D-Glucosidases (pdb code 5fjj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Three-Dimensional Structures of Two Heavily N-Glycosylated Aspergillus Sp. Family GH3 Beta-D-Glucosidases, PDB code: 5fjj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5fjj

Go back to Magnesium Binding Sites List in 5fjj
Magnesium binding site 1 out of 4 in the Three-Dimensional Structures of Two Heavily N-Glycosylated Aspergillus Sp. Family GH3 Beta-D-Glucosidases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Three-Dimensional Structures of Two Heavily N-Glycosylated Aspergillus Sp. Family GH3 Beta-D-Glucosidases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:46.8
occ:1.00
 O A:HOH2532 2.1 13.8 0.5
O A:HOH2445 2.3 37.0 1.0
O A:HOH2515 2.7 41.9 1.0
OD2 A:ASP722 4.2 58.1 1.0
O A:ASP722 4.5 42.3 1.0
O7 A:NAG1202 4.5 32.6 1.0
OD1 A:ASP722 4.6 54.3 1.0
CG A:ASP722 4.7 45.8 1.0
O3 A:NAG1202 4.9 36.4 1.0

Magnesium binding site 2 out of 4 in 5fjj

Go back to Magnesium Binding Sites List in 5fjj
Magnesium binding site 2 out of 4 in the Three-Dimensional Structures of Two Heavily N-Glycosylated Aspergillus Sp. Family GH3 Beta-D-Glucosidases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Three-Dimensional Structures of Two Heavily N-Glycosylated Aspergillus Sp. Family GH3 Beta-D-Glucosidases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4001

b:31.9
occ:1.00
 O A:HOH2359 1.9 33.6 1.0
O A:HOH2533 1.9 25.7 1.0
O A:HOH2534 2.1 36.0 1.0
O A:HOH2353 2.1 30.7 1.0
O A:HOH2354 2.2 38.4 1.0
O A:HOH2355 2.3 23.2 1.0
OD2 A:ASP562 3.9 28.4 1.0
O A:HOH2357 3.9 33.3 1.0
OD1 A:ASP562 4.2 25.7 1.0
O A:ASP558 4.4 38.2 1.0
OD2 A:ASP558 4.4 37.2 1.0
CG A:ASP562 4.5 25.0 1.0
OD1 A:ASP558 4.7 40.5 1.0
O A:HOH2151 4.8 30.2 1.0
CG A:ASP558 4.8 39.0 1.0

Magnesium binding site 3 out of 4 in 5fjj

Go back to Magnesium Binding Sites List in 5fjj
Magnesium binding site 3 out of 4 in the Three-Dimensional Structures of Two Heavily N-Glycosylated Aspergillus Sp. Family GH3 Beta-D-Glucosidases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Three-Dimensional Structures of Two Heavily N-Glycosylated Aspergillus Sp. Family GH3 Beta-D-Glucosidases within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:43.0
occ:1.00
 O C:HOH2517 2.3 38.1 1.0
O3 C:NAG1202 4.6 27.7 1.0
OD2 C:ASP722 4.7 37.6 1.0
O7 C:NAG1202 4.7 30.9 1.0
C2 C:NAG1202 4.9 28.3 1.0
O C:ASP722 4.9 31.6 1.0

Magnesium binding site 4 out of 4 in 5fjj

Go back to Magnesium Binding Sites List in 5fjj
Magnesium binding site 4 out of 4 in the Three-Dimensional Structures of Two Heavily N-Glycosylated Aspergillus Sp. Family GH3 Beta-D-Glucosidases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Three-Dimensional Structures of Two Heavily N-Glycosylated Aspergillus Sp. Family GH3 Beta-D-Glucosidases within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg4001

b:27.9
occ:1.00
 O D:HOH2325 1.9 26.3 1.0
O D:HOH2462 2.0 37.6 1.0
O D:HOH2323 2.1 31.2 1.0
O D:HOH2326 2.1 30.7 1.0
O D:HOH2461 2.2 33.1 1.0
O D:HOH2322 2.3 19.5 1.0
OD2 D:ASP562 4.0 31.9 1.0
OD2 D:ASP558 4.1 34.3 1.0
OD1 D:ASP558 4.2 30.7 1.0
O D:ASP558 4.3 34.7 1.0
OD1 D:ASP562 4.3 25.6 1.0
CG D:ASP558 4.5 29.6 1.0
O D:HOH2143 4.6 39.2 1.0
CG D:ASP562 4.6 23.9 1.0

Reference:

J.Agirre, A.Ariza, W.A.Offen, J.P.Turkenburg, S.M.Roberts, S.Mcnicholas, P.V.Harris, B.Mcbrayer, J.Dohnalek, K.D.Cowtan, G.J.Davies, K.S.Wilson. Three-Dimensional Structures of Two Heavily N-Glycosylated Aspergillus Sp. Family GH3 Beta-D-Glucosidases Acta Crystallogr.,Sect.D V. 72 254 2016.
ISSN: ISSN 0907-4449
PubMed: 26894673
DOI: 10.1107/S2059798315024237
Page generated: Mon Dec 14 20:18:51 2020

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