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Calcium in PDB 1ulv: Crystal Structure of Glucodextranase Complexed with Acarbose

Enzymatic activity of Crystal Structure of Glucodextranase Complexed with Acarbose

All present enzymatic activity of Crystal Structure of Glucodextranase Complexed with Acarbose:
3.2.1.70;

Protein crystallography data

The structure of Crystal Structure of Glucodextranase Complexed with Acarbose, PDB code: 1ulv was solved by M.Mizuno, T.Tonozuka, S.Suzuki, R.Uotsu-Tomita, 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) 49.59 / 2.42
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 198.795, 88.247, 80.994, 90.00, 112.55, 90.00
R / Rfree (%) 19.6 / 23.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Glucodextranase Complexed with Acarbose (pdb code 1ulv). 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 Complexed with Acarbose, PDB code: 1ulv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1ulv

Go back to Calcium Binding Sites List in 1ulv
Calcium binding site 1 out of 6 in the Crystal Structure of Glucodextranase Complexed with Acarbose


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 Complexed with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:36.5
occ:1.00
 O A:LEU139 2.4 19.4 1.0
O A:GLY144 2.4 24.9 1.0
OG1 A:THR142 2.5 24.2 1.0
OD2 A:ASP159 2.5 23.0 1.0
OD1 A:ASP146 2.5 30.6 1.0
O A:THR142 2.5 24.6 1.0
C A:THR142 3.4 23.7 1.0
C A:LEU139 3.4 19.1 1.0
CG A:ASP146 3.5 30.8 1.0
CG A:ASP159 3.5 26.3 1.0
CB A:THR142 3.6 22.7 1.0
C A:GLY144 3.6 26.2 1.0
N A:LEU139 3.8 17.8 1.0
CA A:THR142 3.9 22.4 1.0
OD2 A:ASP146 3.9 31.1 1.0
CB A:ASP159 3.9 26.6 1.0
CA A:LEU139 3.9 18.2 1.0
N A:THR142 4.0 20.9 1.0
C A:GLY145 4.1 26.9 1.0
CB A:LEU139 4.1 16.1 1.0
C A:SER138 4.2 19.5 1.0
N A:ASP146 4.2 27.4 1.0
CA A:GLY145 4.3 24.2 1.0
N A:GLY144 4.3 25.8 1.0
O A:GLY145 4.3 27.2 1.0
N A:GLY145 4.4 25.9 1.0
N A:SER143 4.4 25.1 1.0
C A:SER143 4.4 26.1 1.0
O A:SER138 4.6 22.4 1.0
OD1 A:ASP159 4.6 25.1 1.0
CA A:GLY144 4.6 25.8 1.0
N A:ALA140 4.6 20.5 1.0
CB A:ASP146 4.7 28.5 1.0
CA A:ASP146 4.7 27.3 1.0
CA A:SER138 4.7 20.1 1.0
O A:SER143 4.8 25.8 1.0
CB A:ALA140 4.8 20.9 1.0
CA A:SER143 4.8 25.9 1.0
CG2 A:THR142 4.9 19.5 1.0

Calcium binding site 2 out of 6 in 1ulv

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Calcium binding site 2 out of 6 in the Crystal Structure of Glucodextranase Complexed with Acarbose


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 Complexed with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2002

b:34.9
occ:1.00
 OE2 A:GLU409 2.3 27.8 1.0
O A:PHE358 2.3 19.8 1.0
O A:HOH3146 2.4 18.3 1.0
OE1 A:GLN362 2.5 15.4 1.0
O A:HOH3308 2.6 34.1 1.0
O A:HOH3190 2.7 28.7 1.0
CD A:GLN362 3.5 14.9 1.0
C A:PHE358 3.5 17.2 1.0
CD A:GLU409 3.5 24.6 1.0
CB A:GLN362 3.8 15.2 1.0
CG A:GLN362 3.8 14.4 1.0
CA A:PHE358 4.2 15.9 1.0
CG A:GLU409 4.3 25.6 1.0
CB A:PHE358 4.4 13.1 1.0
OE1 A:GLU409 4.5 24.6 1.0
O A:ASN408 4.5 20.0 1.0
N A:THR359 4.5 18.3 1.0
O A:GLN362 4.6 20.0 1.0
NE2 A:GLN362 4.6 15.2 1.0
CA A:THR359 4.7 19.2 1.0
CA A:GLN362 4.9 17.7 1.0
C A:GLN362 5.0 20.4 1.0
O A:THR359 5.0 20.3 1.0

Calcium binding site 3 out of 6 in 1ulv

Go back to Calcium Binding Sites List in 1ulv
Calcium binding site 3 out of 6 in the Crystal Structure of Glucodextranase Complexed with Acarbose


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 Complexed with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:27.6
occ:1.00
 OD1 A:ASN211 2.2 24.7 1.0
OD2 A:ASP136 2.3 18.9 1.0
O A:HOH3037 2.4 18.3 1.0
O A:HOH3041 2.4 22.0 1.0
O A:ILE212 2.4 28.2 1.0
O A:PRO137 2.5 19.5 1.0
CG A:ASN211 3.4 25.1 1.0
CG A:ASP136 3.5 16.6 1.0
N A:ILE212 3.5 26.0 1.0
C A:ILE212 3.5 28.3 1.0
C A:PRO137 3.6 18.8 1.0
O A:SER143 3.8 25.8 1.0
C A:ASN211 4.0 27.0 1.0
N A:PRO137 4.0 19.3 1.0
OD1 A:ASP136 4.0 16.4 1.0
O A:HOH3035 4.1 14.0 1.0
CA A:ASN211 4.1 27.5 1.0
CA A:ILE212 4.1 26.6 1.0
CG2 A:VAL185 4.2 25.6 1.0
CD A:PRO137 4.2 19.9 1.0
C A:ASP136 4.3 19.4 1.0
ND2 A:ASN211 4.4 20.1 1.0
CB A:ASN211 4.4 25.4 1.0
OD2 A:ASP146 4.4 31.1 1.0
CA A:PRO137 4.4 18.7 1.0
OG A:SER138 4.5 20.6 1.0
CG A:PRO137 4.5 20.3 1.0
CA A:ASP136 4.6 18.7 1.0
CB A:ASP136 4.7 17.4 1.0
N A:SER138 4.7 19.2 1.0
N A:SER213 4.7 28.8 1.0
C A:SER143 4.8 26.1 1.0
O A:ASN211 4.8 26.5 1.0
O A:ASP136 4.8 20.2 1.0
CA A:SER143 4.9 25.9 1.0
CA A:SER138 4.9 20.1 1.0

Calcium binding site 4 out of 6 in 1ulv

Go back to Calcium Binding Sites List in 1ulv
Calcium binding site 4 out of 6 in the Crystal Structure of Glucodextranase Complexed with Acarbose


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 Complexed with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2004

b:42.1
occ:1.00
 O A:ALA969 2.3 55.0 1.0
OD2 A:ASP985 2.3 46.8 1.0
OD2 A:ASP980 2.3 51.8 1.0
OD1 A:ASP985 2.4 46.2 1.0
O A:VAL946 2.5 47.7 1.0
O A:ASP982 2.5 46.4 1.0
CG A:ASP985 2.7 45.2 1.0
CG A:ASP980 3.1 51.9 1.0
OD1 A:ASP980 3.2 52.2 1.0
C A:ALA969 3.5 55.0 1.0
C A:VAL946 3.6 47.5 1.0
C A:ASP982 3.7 47.3 1.0
N A:ALA969 4.0 53.3 1.0
CB A:ASP985 4.2 44.6 1.0
CA A:ALA969 4.3 54.0 1.0
CA A:TYR947 4.4 49.4 1.0
N A:TYR947 4.5 48.6 1.0
CB A:ASP980 4.5 51.6 1.0
N A:GLY970 4.5 55.5 1.0
CB A:ASP982 4.5 49.2 1.0
O A:ASP985 4.6 44.2 1.0
N A:VAL946 4.6 46.2 1.0
CA A:VAL946 4.6 46.6 1.0
CA A:ASP982 4.6 48.4 1.0
N A:THR983 4.6 45.8 1.0
CA A:THR983 4.6 44.7 1.0
CA A:GLY970 4.7 55.1 1.0
O A:HOH3294 4.7 24.6 1.0
CB A:ALA969 4.7 54.2 1.0
CB A:VAL946 4.8 46.6 1.0
N A:ASP985 4.8 44.0 1.0
ND2 A:ASN987 4.8 34.6 1.0
N A:ASP982 4.9 49.1 1.0
CA A:ASP985 5.0 43.6 1.0

Calcium binding site 5 out of 6 in 1ulv

Go back to Calcium Binding Sites List in 1ulv
Calcium binding site 5 out of 6 in the Crystal Structure of Glucodextranase Complexed with Acarbose


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 Complexed with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2005

b:26.9
occ:1.00
 O A:LEU808 2.3 25.0 1.0
OD1 A:ASP782 2.3 26.0 1.0
O A:PRO783 2.3 34.5 1.0
OD2 A:ASP807 2.4 33.8 1.0
OD2 A:ASP990 2.9 41.1 1.0
CB A:ASP786 3.1 43.3 1.0
C A:LEU808 3.4 26.1 1.0
CG A:ASP782 3.5 29.5 1.0
C A:PRO783 3.6 35.1 1.0
CG A:ASP807 3.7 31.3 1.0
OD2 A:ASP786 3.7 43.0 1.0
N A:LEU808 3.7 29.0 1.0
CG A:ASP786 3.9 44.1 1.0
CB A:ASP782 4.0 29.7 1.0
C A:ASP807 4.1 29.7 1.0
CA A:CA2006 4.1 36.0 1.0
CA A:LEU808 4.1 27.3 1.0
CG A:ASP990 4.1 41.8 1.0
CA A:ASP786 4.2 43.0 1.0
C A:ASP782 4.3 31.5 1.0
N A:PRO783 4.3 33.0 1.0
N A:ASP786 4.3 42.9 1.0
O A:ASP782 4.4 31.6 1.0
OD1 A:ASP807 4.4 32.8 1.0
CA A:ASP807 4.4 29.6 1.0
N A:ALA784 4.4 37.1 1.0
CA A:ALA784 4.4 38.1 1.0
CA A:PRO783 4.5 34.2 1.0
N A:THR809 4.5 24.5 1.0
OD2 A:ASP782 4.5 30.6 1.0
CB A:LEU808 4.6 27.4 1.0
C A:ASP786 4.6 42.0 1.0
O A:ASP807 4.6 30.0 1.0
CB A:ASP807 4.7 30.1 1.0
CD A:PRO783 4.7 32.9 1.0
CA A:THR809 4.8 25.7 1.0
CB A:ASP990 4.8 39.9 1.0
CA A:ASP782 4.8 30.8 1.0
CG A:PRO783 4.8 34.6 1.0
N A:ASP787 4.9 41.0 1.0
C A:ALA784 4.9 38.1 1.0

Calcium binding site 6 out of 6 in 1ulv

Go back to Calcium Binding Sites List in 1ulv
Calcium binding site 6 out of 6 in the Crystal Structure of Glucodextranase Complexed with Acarbose


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 Complexed with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2006

b:36.0
occ:1.00
 OD2 A:ASP786 2.0 43.0 1.0
OE1 A:GLN999 2.3 32.2 1.0
O A:VAL991 2.3 27.3 1.0
OD1 A:ASP782 2.6 26.0 1.0
OD2 A:ASP782 2.7 30.6 1.0
CG A:ASP782 3.0 29.5 1.0
CG A:ASP786 3.2 44.1 1.0
CD A:GLN999 3.4 32.0 1.0
C A:VAL991 3.5 29.5 1.0
OD2 A:ASP990 3.7 41.1 1.0
N A:VAL991 3.8 32.2 1.0
CA A:CA2005 4.1 26.9 1.0
OD1 A:ASP786 4.1 47.1 1.0
CB A:ASP786 4.1 43.3 1.0
O A:HOH3245 4.1 24.4 1.0
CB A:ASP990 4.2 39.9 1.0
NE2 A:GLN999 4.3 33.0 1.0
CG A:ASP990 4.3 41.8 1.0
CA A:VAL991 4.3 30.6 1.0
CB A:GLN999 4.4 32.9 1.0
CG A:GLN999 4.4 31.5 1.0
N A:LEU992 4.5 27.1 1.0
CB A:ASP782 4.5 29.7 1.0
CD A:PRO783 4.6 32.9 1.0
CA A:LEU992 4.6 26.4 1.0
C A:ASP990 4.6 34.7 1.0
CG A:PRO783 4.7 34.6 1.0
CA A:ASP990 4.8 37.0 1.0
CD1 A:LEU992 4.9 26.1 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: Sat Dec 12 03:23:06 2020

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