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Calcium in PDB 6k0v: Catalytic Domain of GH87 Alpha-1,3-Glucanase D1069A in Complex with Tetrasaccharides

Protein crystallography data

The structure of Catalytic Domain of GH87 Alpha-1,3-Glucanase D1069A in Complex with Tetrasaccharides, PDB code: 6k0v was solved by T.Itoh, R.Intuy, W.Suyotha, J.Hayashi, S.Yano, K.Makabe, M.Wakayama, T.Hibi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.91 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.865, 132.617, 131.773, 90.00, 90.94, 90.00
R / Rfree (%) 17.9 / 22.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Catalytic Domain of GH87 Alpha-1,3-Glucanase D1069A in Complex with Tetrasaccharides (pdb code 6k0v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Catalytic Domain of GH87 Alpha-1,3-Glucanase D1069A in Complex with Tetrasaccharides, PDB code: 6k0v:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6k0v

Go back to Calcium Binding Sites List in 6k0v
Calcium binding site 1 out of 4 in the Catalytic Domain of GH87 Alpha-1,3-Glucanase D1069A in Complex with Tetrasaccharides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Catalytic Domain of GH87 Alpha-1,3-Glucanase D1069A in Complex with Tetrasaccharides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2007

b:21.9
occ:1.00
 O A:SER764 2.3 21.4 1.0
OD1 A:ASP882 2.3 21.8 1.0
O A:SER767 2.4 26.9 1.0
OE1 A:GLU737 2.4 24.6 1.0
OE2 A:GLU739 2.6 30.1 1.0
OE1 A:GLU739 2.6 26.4 1.0
O A:ASP882 2.8 25.9 1.0
CD A:GLU739 2.9 25.4 1.0
C A:SER764 3.4 23.8 1.0
CD A:GLU737 3.5 24.2 1.0
C A:SER767 3.5 24.6 1.0
CG A:ASP882 3.6 25.1 1.0
C A:ASP882 3.6 25.9 1.0
CA A:ASP882 4.0 24.3 1.0
N A:SER764 4.1 23.0 1.0
CA A:SER764 4.1 24.3 1.0
CB A:GLU737 4.2 20.8 1.0
CB A:SER764 4.2 22.0 1.0
OE2 A:GLU737 4.2 26.9 1.0
N A:SER768 4.3 23.6 1.0
N A:SER767 4.3 25.9 1.0
CA A:SER768 4.4 22.9 1.0
CG A:GLU737 4.4 18.4 1.0
CB A:ASP882 4.4 18.8 1.0
CG A:GLU739 4.4 23.8 1.0
N A:ALA738 4.5 22.4 1.0
OD2 A:ASP882 4.5 23.5 1.0
CA A:SER767 4.5 27.2 1.0
CB A:ALA763 4.5 25.7 1.0
N A:GLY765 4.5 25.5 1.0
CA A:GLU737 4.6 24.3 1.0
N A:LEU883 4.6 22.0 1.0
CA A:GLY765 4.7 24.2 1.0
CB A:SER768 4.7 26.1 1.0
C A:ALA763 4.8 23.5 1.0
OG A:SER764 4.9 30.1 1.0
C A:GLY765 4.9 25.7 1.0
N A:GLU739 4.9 23.9 1.0
C A:GLU737 5.0 24.0 1.0

Calcium binding site 2 out of 4 in 6k0v

Go back to Calcium Binding Sites List in 6k0v
Calcium binding site 2 out of 4 in the Catalytic Domain of GH87 Alpha-1,3-Glucanase D1069A in Complex with Tetrasaccharides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Catalytic Domain of GH87 Alpha-1,3-Glucanase D1069A in Complex with Tetrasaccharides within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2006

b:26.1
occ:1.00
 OD1 B:ASP882 2.2 27.0 1.0
O B:SER764 2.3 29.9 1.0
OE1 B:GLU737 2.3 31.4 1.0
O B:SER767 2.3 33.4 1.0
OE2 B:GLU739 2.5 35.1 1.0
OE1 B:GLU739 2.5 33.8 1.0
O B:ASP882 2.6 26.7 1.0
CD B:GLU739 2.9 32.8 1.0
CD B:GLU737 3.3 28.1 1.0
C B:SER764 3.4 31.1 1.0
CG B:ASP882 3.4 31.1 1.0
C B:ASP882 3.5 27.0 1.0
C B:SER767 3.5 30.7 1.0
CA B:ASP882 3.8 28.5 1.0
OE2 B:GLU737 4.0 27.4 1.0
CB B:SER764 4.0 25.2 1.0
CA B:SER764 4.1 22.2 1.0
N B:SER764 4.1 26.6 1.0
CB B:GLU737 4.2 26.5 1.0
CB B:ASP882 4.3 29.0 1.0
CG B:GLU737 4.3 31.2 1.0
N B:SER767 4.3 33.1 1.0
OD2 B:ASP882 4.3 26.5 1.0
OG B:SER764 4.3 31.4 1.0
CG B:GLU739 4.4 25.8 1.0
N B:SER768 4.4 32.4 1.0
CA B:SER768 4.4 33.4 1.0
CA B:SER767 4.4 35.9 1.0
CB B:ALA763 4.5 28.6 1.0
N B:GLY765 4.5 34.1 1.0
CA B:GLU737 4.5 31.7 1.0
N B:LEU883 4.6 27.2 1.0
N B:ALA738 4.6 31.3 1.0
CA B:GLY765 4.7 29.3 1.0
C B:ALA763 4.7 30.0 1.0
CB B:SER768 4.8 29.7 1.0
O B:HOH2135 4.9 32.2 1.0
CB B:LEU883 4.9 25.9 1.0
C B:GLY765 5.0 33.7 1.0

Calcium binding site 3 out of 4 in 6k0v

Go back to Calcium Binding Sites List in 6k0v
Calcium binding site 3 out of 4 in the Catalytic Domain of GH87 Alpha-1,3-Glucanase D1069A in Complex with Tetrasaccharides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Catalytic Domain of GH87 Alpha-1,3-Glucanase D1069A in Complex with Tetrasaccharides within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2007

b:27.6
occ:1.00
 OD1 C:ASP882 2.2 29.5 1.0
OE1 C:GLU739 2.3 33.9 1.0
O C:SER767 2.4 29.7 1.0
O C:SER764 2.5 23.4 1.0
OE1 C:GLU737 2.5 29.3 1.0
OE2 C:GLU739 2.6 32.1 1.0
CD C:GLU739 2.7 33.2 1.0
O C:ASP882 2.7 27.9 1.0
CG C:ASP882 3.4 28.2 1.0
C C:SER764 3.5 26.9 1.0
C C:ASP882 3.5 28.1 1.0
CD C:GLU737 3.5 27.4 1.0
C C:SER767 3.6 27.4 1.0
CA C:ASP882 3.9 26.3 1.0
CG C:GLU739 4.1 35.3 1.0
CB C:SER764 4.1 20.8 1.0
CA C:SER764 4.1 30.5 1.0
N C:SER764 4.2 32.7 1.0
CB C:GLU737 4.2 27.9 1.0
OD2 C:ASP882 4.3 24.3 1.0
CB C:ASP882 4.3 23.5 1.0
OE2 C:GLU737 4.3 28.9 1.0
CA C:SER768 4.3 29.2 1.0
N C:SER768 4.4 29.7 1.0
CG C:GLU737 4.4 24.6 1.0
N C:SER767 4.4 25.9 1.0
N C:ALA738 4.4 25.0 1.0
CB C:ALA763 4.4 28.7 1.0
CB C:SER768 4.5 27.3 1.0
CA C:GLU737 4.5 32.6 1.0
N C:GLY765 4.6 23.9 1.0
N C:LEU883 4.6 24.9 1.0
CA C:SER767 4.6 28.3 1.0
OG C:SER764 4.6 24.9 1.0
CB C:LEU883 4.8 26.8 1.0
CA C:GLY765 4.8 24.9 1.0
C C:ALA763 4.9 27.5 1.0
C C:GLU737 5.0 26.3 1.0
N C:GLU739 5.0 30.5 1.0

Calcium binding site 4 out of 4 in 6k0v

Go back to Calcium Binding Sites List in 6k0v
Calcium binding site 4 out of 4 in the Catalytic Domain of GH87 Alpha-1,3-Glucanase D1069A in Complex with Tetrasaccharides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Catalytic Domain of GH87 Alpha-1,3-Glucanase D1069A in Complex with Tetrasaccharides within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2007

b:32.0
occ:1.00
 OD1 D:ASP882 2.1 31.6 1.0
OE1 D:GLU737 2.3 37.7 1.0
O D:SER764 2.4 38.1 1.0
O D:SER767 2.5 29.9 1.0
O D:ASP882 2.6 34.8 1.0
OE2 D:GLU739 2.6 43.1 1.0
OE1 D:GLU739 2.7 39.8 1.0
CD D:GLU739 3.0 39.3 1.0
CG D:ASP882 3.2 32.3 1.0
C D:ASP882 3.3 36.1 1.0
CD D:GLU737 3.4 34.0 1.0
C D:SER764 3.5 30.6 1.0
C D:SER767 3.6 32.6 1.0
CA D:ASP882 3.7 32.2 1.0
N D:SER764 4.0 25.8 1.0
CB D:SER764 4.0 28.4 1.0
CA D:SER764 4.0 32.1 1.0
OE2 D:GLU737 4.1 36.5 1.0
CB D:ASP882 4.1 29.5 1.0
OD2 D:ASP882 4.1 33.2 1.0
CB D:GLU737 4.2 34.8 1.0
CG D:GLU737 4.3 33.3 1.0
N D:LEU883 4.4 32.4 1.0
CA D:SER768 4.4 29.4 1.0
N D:SER768 4.4 28.5 1.0
CB D:ALA763 4.4 27.9 1.0
CG D:GLU739 4.5 40.0 1.0
CA D:GLU737 4.5 35.0 1.0
N D:ALA738 4.5 31.7 1.0
N D:SER767 4.5 35.3 1.0
CB D:SER768 4.5 35.0 1.0
N D:GLY765 4.6 27.1 1.0
CA D:SER767 4.7 37.6 1.0
C D:ALA763 4.7 27.3 1.0
CB D:LEU883 4.8 32.8 1.0
CA D:LEU883 4.9 31.0 1.0
CA D:GLY765 4.9 26.7 1.0
C D:GLU737 5.0 35.2 1.0

Reference:

T.Itoh, R.Intuy, W.Suyotha, J.Hayashi, S.Yano, K.Makabe, M.Wakayama, T.Hibi. 28STRUCTURAL Insights Into Substrate Recognition and Catalysis By Glycoside Hydrolase Family 87 Alpha-1,3-Glucanase From Paenibacillus Glycanilyticus FH11. Febs J. 2019.
ISSN: ISSN 1742-464X
PubMed: 31788942
DOI: 10.1111/FEBS.15161
Page generated: Wed Jul 9 15:21:41 2025

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