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Calcium in PDB 7v1x: Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Fructofuranose

Protein crystallography data

The structure of Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Fructofuranose, PDB code: 7v1x 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) 48.69 / 1.76
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.439, 156.304, 100.744, 90, 110.09, 90
R / Rfree (%) 17.5 / 21

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-Fructofuranose (pdb code 7v1x). 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-Fructofuranose, PDB code: 7v1x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7v1x

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Calcium binding site 1 out of 6 in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Fructofuranose


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-Fructofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:10.1
occ:0.00
 OD2 D:ASP33 2.4 13.4 1.0
OD1 D:ASN31 2.5 16.5 1.0
O A:GLU270 2.5 16.4 1.0
O A:HOH900 2.5 14.7 1.0
O A:HOH926 2.5 14.2 1.0
OD1 A:ASN272 2.5 15.1 1.0
O A:THR288 2.6 15.2 1.0
CG D:ASP33 3.3 13.7 1.0
C A:THR288 3.5 16.6 1.0
CG A:ASN272 3.6 16.9 1.0
C A:GLU270 3.7 16.9 1.0
CG D:ASN31 3.7 17.2 1.0
O D:HOH702 4.0 9.8 1.0
CB D:ASP33 4.1 14.9 1.0
ND2 A:ASN272 4.1 17.2 1.0
OD1 D:ASP33 4.1 16.8 1.0
O D:HOH863 4.1 19.2 1.0
CA A:GLY289 4.2 14.9 1.0
N A:GLY289 4.2 15.3 1.0
N A:ASN272 4.4 15.3 1.0
CA A:GLU270 4.4 15.2 1.0
OE1 A:GLU270 4.4 16.2 1.0
ND2 D:ASN31 4.5 15.8 1.0
C A:GLY271 4.5 15.8 1.0
CA A:THR288 4.5 17.3 1.0
CA D:ASN31 4.6 17.1 1.0
OE1 A:GLU343 4.6 16.7 1.0
N A:GLY271 4.6 16.0 1.0
CB D:ASN31 4.7 16.7 1.0
CB A:GLU270 4.7 15.8 1.0
ND1 A:HIS346 4.7 16.8 1.0
CA A:GLY271 4.7 16.0 1.0
O4 A:FRU702 4.8 19.5 1.0
CB A:ASN272 4.8 17.5 1.0
O D:ASN31 4.8 17.5 1.0
CA A:ASN272 4.9 16.2 1.0
C D:ASN31 5.0 18.2 1.0

Calcium binding site 2 out of 6 in 7v1x

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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-Fructofuranose


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-Fructofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:8.7
occ:0.00
 OD2 A:ASP33 2.4 14.4 1.0
O B:GLU270 2.4 12.6 1.0
OD1 B:ASN272 2.5 15.4 1.0
OD1 A:ASN31 2.5 13.0 1.0
O B:HOH718 2.5 11.7 1.0
O B:HOH640 2.6 13.2 1.0
O B:THR288 2.7 13.2 1.0
CG A:ASP33 3.3 16.3 1.0
C B:THR288 3.6 14.2 1.0
CG B:ASN272 3.6 15.3 1.0
C B:GLU270 3.6 15.6 1.0
CG A:ASN31 3.7 15.6 1.0
O A:HOH802 4.1 8.3 1.0
O A:HOH958 4.1 18.6 1.0
ND2 B:ASN272 4.1 17.3 1.0
CB A:ASP33 4.1 16.1 1.0
OD1 A:ASP33 4.2 15.3 1.0
CA B:GLY289 4.2 13.6 1.0
N B:GLY289 4.3 15.0 1.0
CA B:GLU270 4.4 13.9 1.0
N B:ASN272 4.4 14.2 1.0
OE1 B:GLU270 4.4 16.1 1.0
ND2 A:ASN31 4.4 15.4 1.0
CA B:THR288 4.5 14.4 1.0
C B:GLY271 4.6 14.9 1.0
OE1 B:GLU343 4.6 16.2 1.0
CA A:ASN31 4.6 15.6 1.0
N B:GLY271 4.6 14.0 1.0
CA B:GLY271 4.7 15.2 1.0
CB A:ASN31 4.7 15.3 1.0
CB B:GLU270 4.7 13.3 1.0
CB B:ASN272 4.8 15.1 1.0
ND1 B:HIS346 4.8 15.1 1.0
O4 B:FRU501 4.8 18.6 1.0
O A:ASN31 4.8 14.1 1.0
CA B:ASN272 4.9 14.2 1.0
C A:ASN31 5.0 16.6 1.0
O B:GLY271 5.0 15.4 1.0

Calcium binding site 3 out of 6 in 7v1x

Go back to Calcium Binding Sites List in 7v1x
Calcium binding site 3 out of 6 in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Fructofuranose


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-Fructofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca701

b:11.2
occ:0.00
 OD2 F:ASP33 2.4 18.4 1.0
OD1 C:ASN272 2.4 16.1 1.0
O C:GLU270 2.4 15.3 1.0
OD1 F:ASN31 2.5 16.5 1.0
O C:HOH878 2.5 17.1 1.0
O C:THR288 2.6 16.3 1.0
CG F:ASP33 3.3 16.9 1.0
C C:THR288 3.5 17.5 1.0
CG C:ASN272 3.5 19.4 1.0
C C:GLU270 3.7 19.1 1.0
CG F:ASN31 3.7 17.9 1.0
ND2 C:ASN272 4.0 19.9 1.0
CB F:ASP33 4.0 17.9 1.0
O F:HOH805 4.0 11.2 1.0
OD1 F:ASP33 4.1 18.2 1.0
O F:HOH935 4.2 21.2 1.0
CA C:GLY289 4.2 16.5 1.0
N C:GLY289 4.2 18.2 1.0
N C:ASN272 4.3 14.5 1.0
CA C:THR288 4.4 17.4 1.0
CA C:GLU270 4.5 17.8 1.0
C C:GLY271 4.5 16.7 1.0
ND2 F:ASN31 4.5 18.2 1.0
OE1 C:GLU270 4.5 16.1 1.0
OE1 C:GLU343 4.5 16.2 1.0
CA F:ASN31 4.6 17.9 1.0
N C:GLY271 4.6 18.5 1.0
CB C:ASN272 4.7 17.3 1.0
CA C:GLY271 4.7 17.0 1.0
CB F:ASN31 4.7 17.1 1.0
CB C:GLU270 4.7 18.6 1.0
ND1 C:HIS346 4.7 17.4 1.0
CA C:ASN272 4.8 16.2 1.0
O F:ASN31 4.8 17.3 1.0
O4 C:FRU702 4.9 22.3 1.0
O C:GLY271 5.0 17.8 1.0

Calcium binding site 4 out of 6 in 7v1x

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Calcium binding site 4 out of 6 in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Fructofuranose


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-Fructofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:9.5
occ:0.00
 OD2 C:ASP33 2.4 13.3 1.0
O E:GLU270 2.4 11.8 1.0
OD1 E:ASN272 2.5 15.2 1.0
OD1 C:ASN31 2.5 13.4 1.0
O E:HOH727 2.5 13.1 1.0
O E:HOH735 2.5 11.8 1.0
O E:THR288 2.7 14.9 1.0
CG C:ASP33 3.4 15.8 1.0
C E:THR288 3.5 16.3 1.0
CG E:ASN272 3.6 17.2 1.0
C E:GLU270 3.7 15.1 1.0
CG C:ASN31 3.7 17.7 1.0
ND2 E:ASN272 4.1 18.5 1.0
CB C:ASP33 4.1 15.4 1.0
O C:HOH949 4.1 17.7 1.0
CA E:GLY289 4.2 14.9 1.0
OD1 C:ASP33 4.2 14.7 1.0
N E:GLY289 4.2 15.5 1.0
N E:ASN272 4.4 16.3 1.0
ND2 C:ASN31 4.5 17.6 1.0
CA E:GLU270 4.5 14.8 1.0
OE1 E:GLU270 4.5 14.4 1.0
C E:GLY271 4.5 16.1 1.0
CA E:THR288 4.5 16.4 1.0
OE1 E:GLU343 4.6 18.2 1.0
CA C:ASN31 4.6 18.6 1.0
N E:GLY271 4.6 13.7 1.0
CB C:ASN31 4.7 16.9 1.0
CA E:GLY271 4.7 15.3 1.0
CB E:GLU270 4.7 13.8 1.0
ND1 E:HIS346 4.7 15.9 1.0
CB E:ASN272 4.8 17.3 1.0
O4 E:FRU501 4.8 18.2 1.0
CA E:ASN272 4.8 16.6 1.0
O C:ASN31 4.9 18.1 1.0
C C:ASN31 5.0 18.7 1.0

Calcium binding site 5 out of 6 in 7v1x

Go back to Calcium Binding Sites List in 7v1x
Calcium binding site 5 out of 6 in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Fructofuranose


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-Fructofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:9.6
occ:0.00
 OD2 B:ASP33 2.4 15.6 1.0
O D:GLU270 2.5 16.2 1.0
OD1 D:ASN272 2.5 14.2 1.0
OD1 B:ASN31 2.5 13.9 1.0
O D:HOH749 2.5 15.3 1.0
O D:HOH828 2.5 13.4 1.0
O D:THR288 2.6 16.1 1.0
CG B:ASP33 3.4 18.0 1.0
C D:THR288 3.5 16.8 1.0
CG D:ASN272 3.5 14.1 1.0
C D:GLU270 3.7 16.4 1.0
CG B:ASN31 3.7 15.6 1.0
O B:HOH819 4.0 19.1 1.0
ND2 D:ASN272 4.0 17.2 1.0
O B:HOH601 4.1 12.6 1.0
CB B:ASP33 4.1 17.5 1.0
CA D:GLY289 4.2 15.4 1.0
N D:GLY289 4.2 17.1 1.0
OD1 B:ASP33 4.2 18.5 1.0
N D:ASN272 4.4 16.8 1.0
CA D:GLU270 4.4 15.5 1.0
ND2 B:ASN31 4.5 15.0 1.0
CA D:THR288 4.5 16.0 1.0
OE1 D:GLU270 4.5 15.6 1.0
OE1 D:GLU343 4.5 18.1 1.0
C D:GLY271 4.5 16.7 1.0
CA B:ASN31 4.6 16.7 1.0
N D:GLY271 4.6 16.2 1.0
CB B:ASN31 4.7 14.9 1.0
CB D:GLU270 4.7 14.8 1.0
ND1 D:HIS346 4.7 15.5 1.0
CB D:ASN272 4.7 15.7 1.0
CA D:GLY271 4.7 15.8 1.0
CA D:ASN272 4.8 15.6 1.0
O4 D:FRU602 4.9 18.2 1.0
O B:ASN31 4.9 16.3 1.0

Calcium binding site 6 out of 6 in 7v1x

Go back to Calcium Binding Sites List in 7v1x
Calcium binding site 6 out of 6 in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium in Complex with Beta-D-Fructofuranose


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-Fructofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca701

b:11.2
occ:0.00
 OD2 E:ASP33 2.4 15.3 1.0
O F:GLU270 2.5 17.3 1.0
OD1 E:ASN31 2.5 17.5 1.0
OD1 F:ASN272 2.5 16.1 1.0
O F:HOH921 2.5 19.9 1.0
O F:HOH875 2.6 14.6 1.0
O F:THR288 2.6 14.4 1.0
CG E:ASP33 3.4 16.8 1.0
C F:THR288 3.5 16.2 1.0
CG F:ASN272 3.6 16.0 1.0
C F:GLU270 3.7 18.4 1.0
CG E:ASN31 3.7 17.5 1.0
CB E:ASP33 4.1 16.8 1.0
O E:HOH785 4.1 18.1 1.0
ND2 F:ASN272 4.1 16.7 1.0
CA F:GLY289 4.1 14.7 1.0
N F:GLY289 4.2 16.3 1.0
OD1 E:ASP33 4.3 16.3 1.0
N F:ASN272 4.4 17.3 1.0
CA F:THR288 4.4 17.1 1.0
ND2 E:ASN31 4.5 16.7 1.0
CA F:GLU270 4.5 17.1 1.0
C F:GLY271 4.5 17.8 1.0
OE1 F:GLU270 4.5 17.6 1.0
OE1 F:GLU343 4.6 20.0 1.0
CA E:ASN31 4.6 18.2 1.0
N F:GLY271 4.6 19.2 1.0
CB E:ASN31 4.7 17.4 1.0
CB F:GLU270 4.7 16.4 1.0
CA F:GLY271 4.7 18.5 1.0
ND1 F:HIS346 4.7 16.7 1.0
CB F:ASN272 4.8 16.6 1.0
O4 F:FRU702 4.8 20.1 1.0
CA F:ASN272 4.9 16.7 1.0
O E:ASN31 4.9 19.5 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: Fri Jul 19 05:15:52 2024

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