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Calcium in PDB 7v1w: Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Arabinofuranose

Protein crystallography data

The structure of Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Arabinofuranose, PDB code: 7v1w was solved by T.Kashima, T.Arakawa, C.Yamada, K.Fujita, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.77 / 1.86
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.451, 156.707, 100.849, 90, 110.66, 90
R / Rfree (%) 17.2 / 21.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Arabinofuranose (pdb code 7v1w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Arabinofuranose, PDB code: 7v1w:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7v1w

Go back to Calcium Binding Sites List in 7v1w
Calcium binding site 1 out of 6 in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Arabinofuranose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Arabinofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:17.3
occ:0.00
 OD2 C:ASP33 2.2 26.3 1.0
OD1 A:ASN272 2.4 23.6 1.0
O A:GLU270 2.4 24.1 1.0
OD1 C:ASN31 2.5 20.8 1.0
O A:HOH750 2.6 25.5 1.0
O A:HOH828 2.6 20.0 1.0
O A:THR288 2.7 20.5 1.0
CG C:ASP33 3.2 25.1 1.0
CG A:ASN272 3.5 23.1 1.0
C A:THR288 3.5 23.5 1.0
C A:GLU270 3.7 24.5 1.0
CG C:ASN31 3.7 24.9 1.0
ND2 A:ASN272 4.0 25.6 1.0
O C:HOH702 4.0 16.1 1.0
CB C:ASP33 4.1 24.4 1.0
OD1 C:ASP33 4.1 24.8 1.0
O C:HOH848 4.1 30.4 1.0
CA A:GLY289 4.2 24.9 1.0
N A:GLY289 4.2 25.9 1.0
N A:ASN272 4.4 21.1 1.0
CA A:GLU270 4.4 22.1 1.0
ND2 C:ASN31 4.5 23.6 1.0
OE1 A:GLU343 4.5 23.2 1.0
CA A:THR288 4.5 25.2 1.0
OE1 A:GLU270 4.5 24.0 1.0
C A:GLY271 4.6 25.3 1.0
N A:GLY271 4.6 21.8 1.0
CA C:ASN31 4.6 24.8 1.0
CB A:GLU270 4.7 24.6 1.0
ND1 A:HIS346 4.7 23.5 1.0
CB A:ASN272 4.7 22.7 1.0
CA A:GLY271 4.7 23.0 1.0
CB C:ASN31 4.7 23.6 1.0
CA A:ASN272 4.8 22.8 1.0
O3 A:BXX602 4.9 24.9 1.0
O C:ASN31 4.9 23.7 1.0

Calcium binding site 2 out of 6 in 7v1w

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Calcium binding site 2 out of 6 in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Arabinofuranose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Arabinofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:12.3
occ:0.00
 OD2 A:ASP33 2.4 19.0 1.0
OD1 B:ASN272 2.4 24.3 1.0
OD1 A:ASN31 2.4 21.6 1.0
O B:GLU270 2.5 18.5 1.0
O B:HOH842 2.5 17.3 1.0
O B:THR288 2.6 18.7 1.0
O B:HOH754 2.6 20.0 1.0
CG A:ASP33 3.2 22.4 1.0
CG B:ASN272 3.5 22.5 1.0
C B:THR288 3.5 23.1 1.0
CG A:ASN31 3.6 22.1 1.0
C B:GLU270 3.7 22.4 1.0
ND2 B:ASN272 4.0 24.2 1.0
O A:HOH848 4.0 22.4 1.0
OD1 A:ASP33 4.0 23.7 1.0
CB A:ASP33 4.1 21.9 1.0
O A:HOH704 4.1 18.9 1.0
N B:GLY289 4.2 21.2 1.0
CA B:GLY289 4.3 21.0 1.0
ND2 A:ASN31 4.4 22.1 1.0
N B:ASN272 4.4 21.6 1.0
CA B:THR288 4.5 21.3 1.0
OE1 B:GLU270 4.5 23.5 1.0
CA B:GLU270 4.5 20.6 1.0
C B:GLY271 4.5 21.6 1.0
OE1 B:GLU343 4.6 20.7 1.0
CA A:ASN31 4.6 23.2 1.0
N B:GLY271 4.6 19.0 1.0
CB A:ASN31 4.7 22.9 1.0
ND1 B:HIS346 4.7 20.0 1.0
CB B:ASN272 4.7 22.1 1.0
CA B:GLY271 4.7 19.5 1.0
CB B:GLU270 4.8 22.7 1.0
O3 B:BXX602 4.8 22.1 1.0
CA B:ASN272 4.9 21.3 1.0
O A:ASN31 5.0 22.8 1.0

Calcium binding site 3 out of 6 in 7v1w

Go back to Calcium Binding Sites List in 7v1w
Calcium binding site 3 out of 6 in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Arabinofuranose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Arabinofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:14.6
occ:0.00
 O C:GLU270 2.4 22.8 1.0
OD2 B:ASP33 2.5 23.1 1.0
OD1 B:ASN31 2.5 23.3 1.0
O C:HOH726 2.5 20.1 1.0
OD1 C:ASN272 2.5 22.2 1.0
O C:HOH805 2.6 23.9 1.0
O C:THR288 2.6 22.6 1.0
CG B:ASP33 3.4 24.2 1.0
C C:THR288 3.5 25.4 1.0
CG C:ASN272 3.5 19.9 1.0
C C:GLU270 3.7 22.8 1.0
CG B:ASN31 3.7 23.5 1.0
ND2 C:ASN272 4.0 23.9 1.0
O B:HOH709 4.0 15.8 1.0
N C:GLY289 4.1 23.5 1.0
CB B:ASP33 4.1 24.6 1.0
O B:HOH852 4.1 28.4 1.0
CA C:GLY289 4.2 26.1 1.0
OD1 B:ASP33 4.2 22.6 1.0
N C:ASN272 4.4 21.7 1.0
OE1 C:GLU270 4.5 24.1 1.0
CA C:GLU270 4.5 20.8 1.0
OE1 C:GLU343 4.5 24.4 1.0
CA C:THR288 4.5 24.0 1.0
ND2 B:ASN31 4.5 23.7 1.0
C C:GLY271 4.5 21.7 1.0
N C:GLY271 4.6 21.4 1.0
CA B:ASN31 4.6 23.1 1.0
CB B:ASN31 4.7 22.2 1.0
CB C:GLU270 4.7 21.9 1.0
ND1 C:HIS346 4.7 20.9 1.0
CB C:ASN272 4.8 19.6 1.0
CA C:GLY271 4.8 22.3 1.0
O3 C:BXX602 4.8 22.6 1.0
CA C:ASN272 4.8 19.9 1.0

Calcium binding site 4 out of 6 in 7v1w

Go back to Calcium Binding Sites List in 7v1w
Calcium binding site 4 out of 6 in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Arabinofuranose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Arabinofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:13.4
occ:0.00
 OD2 E:ASP33 2.4 20.5 1.0
OD1 E:ASN31 2.4 23.6 1.0
OD1 D:ASN272 2.4 23.0 1.0
O D:GLU270 2.4 18.8 1.0
O D:THR288 2.5 18.7 1.0
O D:HOH767 2.6 20.0 1.0
O D:HOH747 2.6 21.1 1.0
CG E:ASP33 3.2 22.7 1.0
CG D:ASN272 3.5 24.4 1.0
C D:THR288 3.5 21.1 1.0
CG E:ASN31 3.6 24.8 1.0
C D:GLU270 3.7 20.8 1.0
ND2 D:ASN272 4.0 24.6 1.0
O E:HOH702 4.0 16.9 1.0
CB E:ASP33 4.0 22.1 1.0
OD1 E:ASP33 4.1 25.4 1.0
N D:GLY289 4.1 22.5 1.0
CA D:GLY289 4.2 21.5 1.0
O E:HOH775 4.3 24.1 1.0
N D:ASN272 4.4 21.1 1.0
ND2 E:ASN31 4.4 23.3 1.0
CA D:THR288 4.4 21.7 1.0
CA D:GLU270 4.5 19.5 1.0
OE1 D:GLU270 4.5 23.2 1.0
OE1 D:GLU343 4.5 22.2 1.0
C D:GLY271 4.5 23.2 1.0
CA E:ASN31 4.6 26.5 1.0
N D:GLY271 4.6 21.1 1.0
CB E:ASN31 4.7 23.9 1.0
CB D:ASN272 4.7 23.9 1.0
CA D:GLY271 4.7 20.5 1.0
CB D:GLU270 4.7 22.6 1.0
ND1 D:HIS346 4.8 23.9 1.0
CA D:ASN272 4.8 21.6 1.0
O E:ASN31 4.9 24.3 1.0
O3 D:BXX602 4.9 23.0 1.0

Calcium binding site 5 out of 6 in 7v1w

Go back to Calcium Binding Sites List in 7v1w
Calcium binding site 5 out of 6 in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Arabinofuranose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Arabinofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca603

b:14.5
occ:0.00
 OD1 D:ASN31 2.4 23.7 1.0
O F:GLU270 2.4 19.9 1.0
OD2 D:ASP33 2.5 22.5 1.0
OD1 F:ASN272 2.5 21.1 1.0
O F:HOH714 2.5 17.9 1.0
O F:HOH635 2.6 21.6 1.0
O F:THR288 2.6 21.0 1.0
CG D:ASP33 3.3 27.8 1.0
CG F:ASN272 3.5 22.2 1.0
C F:THR288 3.6 24.9 1.0
CG D:ASN31 3.6 25.0 1.0
C F:GLU270 3.6 24.0 1.0
O D:HOH701 4.0 20.8 1.0
ND2 F:ASN272 4.1 24.6 1.0
OD1 D:ASP33 4.1 28.4 1.0
O D:HOH864 4.1 28.8 1.0
CB D:ASP33 4.1 25.7 1.0
CA F:GLY289 4.2 23.1 1.0
N F:GLY289 4.3 23.6 1.0
ND2 D:ASN31 4.3 25.1 1.0
N F:ASN272 4.4 24.4 1.0
CA F:GLU270 4.4 22.5 1.0
OE1 F:GLU270 4.5 21.9 1.0
OE1 F:GLU343 4.5 23.2 1.0
CA F:THR288 4.5 23.7 1.0
C F:GLY271 4.5 24.1 1.0
N F:GLY271 4.6 20.2 1.0
CA D:ASN31 4.6 25.2 1.0
CB F:GLU270 4.6 22.1 1.0
CB D:ASN31 4.7 23.0 1.0
ND1 F:HIS346 4.7 23.6 1.0
CA F:GLY271 4.7 22.1 1.0
CB F:ASN272 4.7 22.0 1.0
O3 F:BXX501 4.8 24.4 1.0
CA F:ASN272 4.9 23.9 1.0
O D:ASN31 4.9 22.6 1.0

Calcium binding site 6 out of 6 in 7v1w

Go back to Calcium Binding Sites List in 7v1w
Calcium binding site 6 out of 6 in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Arabinofuranose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Arabinofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca601

b:14.7
occ:0.00
 OD2 F:ASP33 2.3 24.0 1.0
OD1 F:ASN31 2.4 18.9 1.0
O E:GLU270 2.4 24.0 1.0
OD1 E:ASN272 2.4 23.1 1.0
O E:HOH751 2.5 25.6 1.0
O E:THR288 2.6 22.1 1.0
O E:HOH753 2.6 19.6 1.0
CG F:ASP33 3.3 27.8 1.0
CG E:ASN272 3.5 21.8 1.0
C E:THR288 3.5 24.3 1.0
CG F:ASN31 3.6 24.6 1.0
C E:GLU270 3.7 21.4 1.0
ND2 E:ASN272 3.9 23.3 1.0
O F:HOH602 4.0 16.5 1.0
CB F:ASP33 4.0 26.1 1.0
O F:HOH676 4.1 28.3 1.0
OD1 F:ASP33 4.1 27.1 1.0
CA E:GLY289 4.2 23.3 1.0
N E:GLY289 4.2 23.6 1.0
OE1 E:GLU270 4.4 22.9 1.0
ND2 F:ASN31 4.4 25.4 1.0
N E:ASN272 4.5 22.7 1.0
CA E:GLU270 4.5 21.7 1.0
CA E:THR288 4.5 24.8 1.0
C E:GLY271 4.6 23.1 1.0
CA F:ASN31 4.6 24.0 1.0
N E:GLY271 4.6 22.3 1.0
ND1 E:HIS346 4.6 19.1 1.0
CB F:ASN31 4.7 21.4 1.0
OE1 E:GLU343 4.7 24.1 1.0
O3 E:BXX602 4.7 24.5 1.0
CB E:GLU270 4.7 23.7 1.0
CB E:ASN272 4.7 21.7 1.0
CA E:GLY271 4.8 20.8 1.0
O F:ASN31 4.9 22.7 1.0
CA E:ASN272 4.9 21.9 1.0

Reference:

T.Kashima, K.Okumura, A.Ishiwata, M.Kaieda, T.Terada, T.Arakawa, C.Yamada, K.Shimizu, K.Tanaka, M.Kitaoka, Y.Ito, K.Fujita, S.Fushinobu. Identification of A Difructose Dianhydride I Synthase/Hydrolase From Oral Bacterium Establishes A Novel Glycoside Hydrolase Family. J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X
DOI: 10.1016/J.JBC.2021.101324
Page generated: Thu Jul 10 01:54:50 2025

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