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Calcium in PDB 1ug9: Crystal Structure of Glucodextranase From Arthrobacter Globiformis I42

Enzymatic activity of Crystal Structure of Glucodextranase From Arthrobacter Globiformis I42

All present enzymatic activity of Crystal Structure of Glucodextranase From Arthrobacter Globiformis I42:
3.2.1.70;

Protein crystallography data

The structure of Crystal Structure of Glucodextranase From Arthrobacter Globiformis I42, PDB code: 1ug9 was solved by M.Mizuno, T.Tonozuka, S.Suzuki, R.Uotsu-Tomita, A.Ohtaki, S.Kamitori, A.Nishikawa, Y.Sakano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.89 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 199.860, 88.535, 80.781, 90.00, 113.08, 90.00
R / Rfree (%) 18.9 / 23.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Glucodextranase From Arthrobacter Globiformis I42 (pdb code 1ug9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Glucodextranase From Arthrobacter Globiformis I42, PDB code: 1ug9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1ug9

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Calcium binding site 1 out of 6 in the Crystal Structure of Glucodextranase From Arthrobacter Globiformis I42


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Glucodextranase From Arthrobacter Globiformis I42 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:28.2
occ:1.00
 OD2 A:ASP159 2.2 27.4 1.0
OD1 A:ASP146 2.3 20.4 1.0
O A:LEU139 2.3 21.5 1.0
O A:GLY144 2.4 22.8 1.0
O A:THR142 2.4 23.0 1.0
OG1 A:THR142 2.4 18.8 1.0
CG A:ASP159 3.3 28.4 1.0
C A:THR142 3.3 22.4 1.0
CG A:ASP146 3.4 20.5 1.0
C A:LEU139 3.5 19.7 1.0
CB A:THR142 3.6 20.9 1.0
C A:GLY144 3.6 23.7 1.0
CA A:THR142 3.9 21.2 1.0
OD2 A:ASP146 3.9 23.7 1.0
CB A:ASP159 3.9 27.0 1.0
N A:LEU139 4.0 18.1 1.0
CA A:LEU139 4.0 19.0 1.0
O A:HOH3198 4.0 26.6 1.0
N A:THR142 4.1 21.6 1.0
C A:GLY145 4.1 22.6 1.0
CB A:LEU139 4.2 18.3 1.0
N A:GLY144 4.2 25.4 1.0
C A:SER138 4.3 18.8 1.0
O A:GLY145 4.3 22.9 1.0
N A:ASP146 4.3 21.2 1.0
OD1 A:ASP159 4.3 31.0 1.0
N A:SER143 4.4 24.1 1.0
C A:SER143 4.4 25.1 1.0
CA A:GLY145 4.4 22.3 1.0
N A:GLY145 4.5 24.4 1.0
O A:SER138 4.6 19.6 1.0
CB A:ASP146 4.6 21.1 1.0
CA A:GLY144 4.6 23.9 1.0
N A:ALA140 4.6 21.1 1.0
CB A:ALA140 4.7 20.8 1.0
CA A:SER143 4.7 25.2 1.0
CA A:ASP146 4.7 21.5 1.0
CG2 A:THR142 4.8 15.8 1.0
O A:SER143 4.9 24.6 1.0
CA A:SER138 4.9 20.1 1.0
CA A:ALA140 5.0 22.2 1.0

Calcium binding site 2 out of 6 in 1ug9

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Calcium binding site 2 out of 6 in the Crystal Structure of Glucodextranase From Arthrobacter Globiformis I42


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Glucodextranase From Arthrobacter Globiformis I42 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2002

b:33.9
occ:1.00
 OE2 A:GLU409 2.3 33.0 1.0
O A:HOH3404 2.3 26.2 1.0
O A:PHE358 2.4 20.0 1.0
OE1 A:GLN362 2.5 19.2 1.0
O A:HOH3191 3.1 35.9 1.0
CD A:GLN362 3.4 18.4 1.0
CD A:GLU409 3.5 30.6 1.0
C A:PHE358 3.6 18.7 1.0
CB A:GLN362 3.7 19.1 1.0
CG A:GLN362 3.8 19.2 1.0
O A:HOH3468 4.1 34.6 1.0
OE1 A:GLU409 4.3 31.1 1.0
CA A:PHE358 4.4 18.5 1.0
CG A:GLU409 4.4 31.1 1.0
O A:GLN362 4.5 23.2 1.0
O A:ASN408 4.5 23.9 1.0
N A:THR359 4.5 19.1 1.0
NE2 A:GLN362 4.6 19.8 1.0
CA A:THR359 4.6 21.6 1.0
CB A:PHE358 4.7 15.7 1.0
O A:THR359 4.7 21.7 1.0
CA A:GLN362 4.9 20.9 1.0
C A:GLN362 4.9 23.0 1.0
C A:THR359 5.0 21.0 1.0

Calcium binding site 3 out of 6 in 1ug9

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Calcium binding site 3 out of 6 in the Crystal Structure of Glucodextranase From Arthrobacter Globiformis I42


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Glucodextranase From Arthrobacter Globiformis I42 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:30.2
occ:1.00
 OD2 A:ASP136 2.3 24.7 1.0
O A:ILE212 2.3 24.9 1.0
OD1 A:ASN211 2.4 25.3 1.0
O A:PRO137 2.5 20.6 1.0
O A:HOH3061 2.6 24.5 1.0
C A:ILE212 3.4 25.5 1.0
CG A:ASP136 3.5 21.9 1.0
N A:ILE212 3.6 25.4 1.0
CG A:ASN211 3.6 25.3 1.0
C A:PRO137 3.6 20.2 1.0
O A:HOH3120 3.8 22.6 1.0
N A:PRO137 3.9 21.1 1.0
C A:ASN211 4.0 25.9 1.0
O A:SER143 4.0 24.6 1.0
CG2 A:VAL185 4.1 26.4 1.0
CA A:ILE212 4.1 24.5 1.0
OD1 A:ASP136 4.1 21.6 1.0
CD A:PRO137 4.1 21.0 1.0
C A:ASP136 4.2 22.1 1.0
CA A:ASN211 4.2 27.3 1.0
CA A:PRO137 4.4 20.0 1.0
CG A:PRO137 4.5 19.9 1.0
CA A:ASP136 4.5 20.9 1.0
ND2 A:ASN211 4.5 23.1 1.0
N A:SER213 4.5 25.7 1.0
CB A:ASN211 4.5 27.2 1.0
CB A:ASP136 4.6 21.7 1.0
OG A:SER138 4.7 22.0 1.0
N A:SER138 4.7 19.1 1.0
O A:ASN211 4.7 25.4 1.0
O A:ASP136 4.8 22.8 1.0
CA A:SER213 4.8 26.8 1.0
OD2 A:ASP146 4.8 23.7 1.0
CA A:SER138 5.0 20.1 1.0
CD1 A:ILE212 5.0 24.4 1.0

Calcium binding site 4 out of 6 in 1ug9

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Calcium binding site 4 out of 6 in the Crystal Structure of Glucodextranase From Arthrobacter Globiformis I42


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Glucodextranase From Arthrobacter Globiformis I42 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2004

b:36.5
occ:1.00
 OD2 A:ASP980 2.2 36.2 1.0
O A:ALA969 2.2 37.3 1.0
O A:VAL946 2.4 38.2 1.0
O A:ASP982 2.4 42.9 1.0
OD1 A:ASP985 2.5 37.1 1.0
OD2 A:ASP985 2.7 37.5 1.0
CG A:ASP985 3.0 37.4 1.0
CG A:ASP980 3.0 38.3 1.0
OD1 A:ASP980 3.2 35.6 1.0
C A:ALA969 3.4 37.6 1.0
C A:VAL946 3.6 37.5 1.0
C A:ASP982 3.7 42.8 1.0
N A:ALA969 4.0 36.4 1.0
CA A:ALA969 4.2 36.8 1.0
O A:HOH3071 4.4 27.6 1.0
N A:GLY970 4.4 39.1 1.0
CA A:TYR947 4.4 38.3 1.0
CB A:ASP980 4.4 39.6 1.0
CA A:THR983 4.5 41.1 1.0
N A:TYR947 4.5 38.3 1.0
N A:THR983 4.5 41.5 1.0
CB A:ASP985 4.5 36.4 1.0
CA A:GLY970 4.5 39.5 1.0
CB A:ALA969 4.6 36.1 1.0
O A:ASP985 4.6 36.5 1.0
CB A:ASP982 4.6 42.5 1.0
CA A:VAL946 4.6 36.8 1.0
CA A:ASP982 4.6 43.4 1.0
N A:VAL946 4.7 36.2 1.0
ND2 A:ASN987 4.8 29.8 1.0
CB A:VAL946 4.8 37.1 1.0
N A:ASP982 5.0 44.0 1.0

Calcium binding site 5 out of 6 in 1ug9

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Calcium binding site 5 out of 6 in the Crystal Structure of Glucodextranase From Arthrobacter Globiformis I42


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Glucodextranase From Arthrobacter Globiformis I42 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2005

b:28.1
occ:1.00
 OD1 A:ASP782 2.3 29.5 1.0
O A:LEU808 2.3 25.5 1.0
O A:PRO783 2.3 31.6 1.0
OD2 A:ASP807 2.4 27.1 1.0
OD2 A:ASP990 2.8 34.6 1.0
CB A:ASP786 2.9 38.2 1.0
C A:LEU808 3.4 26.1 1.0
CG A:ASP782 3.5 29.7 1.0
CG A:ASP807 3.5 28.6 1.0
C A:PRO783 3.6 30.7 1.0
N A:LEU808 3.6 28.5 1.0
OD2 A:ASP786 3.7 39.6 1.0
CG A:ASP786 3.9 40.2 1.0
CA A:CA2006 3.9 32.6 1.0
CG A:ASP990 3.9 36.5 1.0
CA A:LEU808 4.0 25.5 1.0
CA A:ASP786 4.1 38.1 1.0
C A:ASP807 4.1 29.6 1.0
N A:ASP786 4.2 37.3 1.0
OD1 A:ASP807 4.2 27.9 1.0
CA A:ALA784 4.3 33.4 1.0
CB A:ASP782 4.3 28.3 1.0
OD2 A:ASP782 4.4 29.4 1.0
N A:ALA784 4.4 32.1 1.0
CA A:ASP807 4.4 29.3 1.0
CB A:LEU808 4.4 24.3 1.0
C A:ASP786 4.5 38.3 1.0
C A:ASP782 4.5 28.2 1.0
N A:PRO783 4.5 28.4 1.0
N A:THR809 4.5 24.6 1.0
O A:ASP782 4.5 28.2 1.0
CB A:ASP807 4.6 28.9 1.0
CA A:PRO783 4.6 29.3 1.0
N A:ASP787 4.6 38.1 1.0
CB A:ASP990 4.7 36.1 1.0
OD1 A:ASP990 4.7 39.1 1.0
C A:ALA784 4.7 33.4 1.0
CA A:THR809 4.8 26.1 1.0
O A:ASP807 4.8 30.9 1.0
N A:GLY785 4.9 34.3 1.0
CG A:PRO783 5.0 28.5 1.0

Calcium binding site 6 out of 6 in 1ug9

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Calcium binding site 6 out of 6 in the Crystal Structure of Glucodextranase From Arthrobacter Globiformis I42


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Glucodextranase From Arthrobacter Globiformis I42 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2006

b:32.6
occ:1.00
 OD2 A:ASP786 2.0 39.6 1.0
OE1 A:GLN999 2.2 29.4 1.0
O A:VAL991 2.3 27.4 1.0
OD2 A:ASP782 2.4 29.4 1.0
O A:HOH3199 2.5 23.5 1.0
OD1 A:ASP782 2.8 29.5 1.0
CG A:ASP782 2.9 29.7 1.0
CG A:ASP786 3.0 40.2 1.0
OD2 A:ASP990 3.1 34.6 1.0
CD A:GLN999 3.3 29.6 1.0
C A:VAL991 3.5 28.1 1.0
N A:VAL991 3.8 31.2 1.0
CB A:ASP786 3.8 38.2 1.0
CA A:CA2005 3.9 28.1 1.0
CG A:ASP990 3.9 36.5 1.0
OD1 A:ASP786 3.9 44.0 1.0
CB A:ASP990 3.9 36.1 1.0
NE2 A:GLN999 4.0 29.2 1.0
CA A:VAL991 4.3 29.1 1.0
CG A:GLN999 4.4 29.8 1.0
C A:ASP990 4.4 32.6 1.0
O A:HOH3092 4.4 15.5 1.0
CB A:ASP782 4.4 28.3 1.0
N A:LEU992 4.5 27.2 1.0
CB A:GLN999 4.5 30.8 1.0
CA A:ASP990 4.5 33.7 1.0
O A:HOH3430 4.6 30.4 1.0
CA A:LEU992 4.6 27.1 1.0
CD1 A:LEU992 4.8 23.3 1.0
O A:HOH3307 4.8 27.4 1.0
CD A:PRO783 4.9 27.3 1.0
CG A:PRO783 4.9 28.5 1.0
O A:ASP786 5.0 37.5 1.0

Reference:

M.Mizuno, T.Tonozuka, S.Suzuki, R.Uotsu-Tomita, S.Kamitori, A.Nishikawa, Y.Sakano. Structural Insights Into Substrate Specificity and Function of Glucodextranase J.Biol.Chem. V. 279 10575 2004.
ISSN: ISSN 0021-9258
PubMed: 14660574
DOI: 10.1074/JBC.M310771200
Page generated: Tue Jul 8 02:32:14 2025

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