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Calcium in PDB 7v1v: Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium, Ligand-Free Form

Protein crystallography data

The structure of Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium, Ligand-Free Form, PDB code: 7v1v 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) 49.69 / 1.96
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.552, 156.97, 100.909, 90, 109.93, 90
R / Rfree (%) 15.3 / 19.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium, Ligand-Free Form (pdb code 7v1v). 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, Ligand-Free Form, PDB code: 7v1v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7v1v

Go back to Calcium Binding Sites List in 7v1v
Calcium binding site 1 out of 6 in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium, Ligand-Free Form


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, Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:16.7
occ:1.00
 OD2 F:ASP33 2.3 14.7 1.0
OD1 A:ASN272 2.4 16.1 1.0
O A:GLU270 2.4 16.3 1.0
OD1 F:ASN31 2.5 14.7 1.0
O A:HOH789 2.5 12.8 1.0
O A:HOH725 2.5 13.7 1.0
O A:THR288 2.6 18.2 1.0
CG F:ASP33 3.3 14.9 1.0
CG A:ASN272 3.4 16.8 1.0
C A:THR288 3.5 17.4 1.0
C A:GLU270 3.7 16.3 1.0
CG F:ASN31 3.7 18.6 1.0
ND2 A:ASN272 3.9 18.9 1.0
O F:HOH706 3.9 7.8 1.0
CB F:ASP33 4.0 15.0 1.0
OD1 F:ASP33 4.1 17.2 1.0
N A:GLY289 4.2 16.6 1.0
CA A:GLY289 4.2 16.4 1.0
O F:HOH805 4.2 17.4 1.0
N A:ASN272 4.3 13.8 1.0
CA A:THR288 4.5 16.8 1.0
ND2 F:ASN31 4.5 18.4 1.0
OE1 A:GLU343 4.5 14.1 1.0
CA A:GLU270 4.5 16.8 1.0
C A:GLY271 4.6 15.3 1.0
OE1 A:GLU270 4.6 14.8 1.0
CA F:ASN31 4.6 17.4 1.0
N A:GLY271 4.6 15.2 1.0
CB A:ASN272 4.7 16.4 1.0
CA A:GLY271 4.7 15.8 1.0
CB F:ASN31 4.8 17.7 1.0
ND1 A:HIS346 4.8 14.2 1.0
CA A:ASN272 4.8 14.2 1.0
CB A:GLU270 4.8 17.4 1.0
O A:HOH668 4.8 32.7 1.0
O F:ASN31 4.9 16.6 1.0

Calcium binding site 2 out of 6 in 7v1v

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Calcium binding site 2 out of 6 in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium, Ligand-Free Form


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, Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:14.7
occ:1.00
 O B:GLU270 2.3 13.9 1.0
OD2 E:ASP33 2.4 14.1 1.0
OD1 B:ASN272 2.4 15.6 1.0
OD1 E:ASN31 2.4 12.5 1.0
O B:HOH756 2.5 15.3 1.0
O B:HOH666 2.5 12.7 1.0
O B:THR288 2.7 17.0 1.0
CG E:ASP33 3.4 14.2 1.0
CG B:ASN272 3.5 15.1 1.0
C B:GLU270 3.6 14.2 1.0
C B:THR288 3.6 13.8 1.0
CG E:ASN31 3.6 12.7 1.0
O E:HOH706 4.0 7.0 1.0
ND2 B:ASN272 4.1 15.3 1.0
O E:HOH863 4.1 12.2 1.0
CB E:ASP33 4.2 14.6 1.0
OD1 E:ASP33 4.2 14.5 1.0
CA B:GLY289 4.2 13.6 1.0
N B:GLY289 4.2 14.0 1.0
N B:ASN272 4.4 12.6 1.0
CA B:GLU270 4.4 13.6 1.0
ND2 E:ASN31 4.4 12.2 1.0
OE1 B:GLU270 4.5 13.2 1.0
OE1 B:GLU343 4.5 13.7 1.0
C B:GLY271 4.5 13.8 1.0
N B:GLY271 4.6 13.2 1.0
CA E:ASN31 4.6 14.9 1.0
CB B:GLU270 4.6 13.7 1.0
CA B:THR288 4.6 14.3 1.0
CB E:ASN31 4.7 15.1 1.0
CB B:ASN272 4.7 14.1 1.0
O B:HOH773 4.7 21.7 1.0
CA B:GLY271 4.7 14.2 1.0
ND1 B:HIS346 4.8 15.7 1.0
CA B:ASN272 4.8 13.8 1.0
O E:ASN31 4.8 15.7 1.0
C E:ASN31 5.0 16.5 1.0

Calcium binding site 3 out of 6 in 7v1v

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Calcium binding site 3 out of 6 in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium, Ligand-Free Form


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, Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:12.5
occ:1.00
 OD2 A:ASP33 2.3 13.4 1.0
O C:GLU270 2.3 9.0 1.0
OD1 A:ASN31 2.4 12.9 1.0
OD1 C:ASN272 2.4 12.0 1.0
O C:HOH701 2.4 11.9 1.0
O C:THR288 2.7 11.6 1.0
CG A:ASP33 3.3 15.6 1.0
CG C:ASN272 3.5 12.8 1.0
C C:GLU270 3.5 11.5 1.0
CG A:ASN31 3.6 15.2 1.0
C C:THR288 3.6 11.6 1.0
O A:HOH603 4.0 6.6 1.0
ND2 C:ASN272 4.1 12.6 1.0
CB A:ASP33 4.1 13.9 1.0
OD1 A:ASP33 4.2 16.2 1.0
CA C:GLY289 4.2 12.2 1.0
O A:HOH648 4.2 15.8 1.0
N C:GLY289 4.3 11.6 1.0
ND2 A:ASN31 4.3 15.3 1.0
N C:ASN272 4.3 13.7 1.0
CA C:GLU270 4.4 11.3 1.0
OE1 C:GLU270 4.4 13.0 1.0
OE1 C:GLU343 4.5 14.1 1.0
C C:GLY271 4.5 13.6 1.0
N C:GLY271 4.5 12.3 1.0
CA A:ASN31 4.6 15.5 1.0
CA C:THR288 4.6 12.1 1.0
ND1 C:HIS346 4.6 13.5 1.0
CB A:ASN31 4.6 14.7 1.0
CA C:GLY271 4.7 13.4 1.0
CB C:ASN272 4.7 13.6 1.0
CB C:GLU270 4.7 11.7 1.0
CA C:ASN272 4.8 12.8 1.0
O A:ASN31 4.8 14.8 1.0
O C:HOH750 4.8 17.8 1.0

Calcium binding site 4 out of 6 in 7v1v

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Calcium binding site 4 out of 6 in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium, Ligand-Free Form


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, Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:13.6
occ:1.00
 OD2 C:ASP33 2.4 13.5 1.0
O F:GLU270 2.4 15.7 1.0
OD1 C:ASN31 2.4 12.7 1.0
OD1 F:ASN272 2.4 16.2 1.0
O F:HOH819 2.4 17.6 1.0
O F:HOH830 2.5 14.0 1.0
O F:THR288 2.6 15.3 1.0
CG C:ASP33 3.4 15.1 1.0
CG F:ASN272 3.5 14.5 1.0
C F:THR288 3.5 12.8 1.0
CG C:ASN31 3.6 13.2 1.0
C F:GLU270 3.6 15.2 1.0
O C:HOH710 4.0 13.0 1.0
ND2 F:ASN272 4.1 13.8 1.0
O C:HOH604 4.1 8.8 1.0
CB C:ASP33 4.1 14.0 1.0
CA F:GLY289 4.1 13.5 1.0
N F:GLY289 4.2 13.3 1.0
OD1 C:ASP33 4.3 13.9 1.0
N F:ASN272 4.3 15.0 1.0
ND2 C:ASN31 4.4 13.0 1.0
C F:GLY271 4.4 16.6 1.0
CA F:GLU270 4.5 14.4 1.0
OE1 F:GLU270 4.5 13.0 1.0
CA F:THR288 4.5 13.2 1.0
OE1 F:GLU343 4.5 17.4 1.0
N F:GLY271 4.6 17.3 1.0
CA C:ASN31 4.6 13.7 1.0
O F:HOH862 4.6 16.4 1.0
CA F:GLY271 4.6 16.3 1.0
ND1 F:HIS346 4.7 12.4 1.0
CB C:ASN31 4.7 13.5 1.0
CB F:ASN272 4.7 15.6 1.0
CB F:GLU270 4.7 14.3 1.0
CA F:ASN272 4.8 15.0 1.0
O C:ASN31 4.9 14.2 1.0

Calcium binding site 5 out of 6 in 7v1v

Go back to Calcium Binding Sites List in 7v1v
Calcium binding site 5 out of 6 in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium, Ligand-Free Form


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, Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca801

b:11.7
occ:1.00
 OD1 B:ASN31 2.3 14.1 1.0
OD2 B:ASP33 2.3 13.2 1.0
O D:GLU270 2.4 12.1 1.0
OD1 D:ASN272 2.4 14.3 1.0
O D:HOH1013 2.5 16.4 1.0
O D:HOH1023 2.5 10.7 1.0
O D:THR288 2.7 13.5 1.0
CG B:ASP33 3.3 13.1 1.0
CG D:ASN272 3.5 11.6 1.0
CG B:ASN31 3.5 14.3 1.0
C D:GLU270 3.6 11.9 1.0
C D:THR288 3.6 11.9 1.0
O B:HOH798 4.0 16.4 1.0
ND2 D:ASN272 4.0 14.1 1.0
O B:HOH603 4.1 5.4 1.0
OD1 B:ASP33 4.1 13.3 1.0
CB B:ASP33 4.1 12.5 1.0
CA D:GLY289 4.3 11.4 1.0
N D:GLY289 4.3 11.8 1.0
ND2 B:ASN31 4.3 13.8 1.0
CA D:GLU270 4.4 11.4 1.0
OE1 D:GLU343 4.4 14.7 1.0
OE1 D:GLU270 4.4 15.2 1.0
N D:ASN272 4.5 12.5 1.0
C D:GLY271 4.5 12.4 1.0
CA B:ASN31 4.5 13.4 1.0
N D:GLY271 4.5 11.9 1.0
CB B:ASN31 4.6 13.2 1.0
CA D:THR288 4.6 11.3 1.0
CB D:GLU270 4.6 12.9 1.0
CA D:GLY271 4.7 12.3 1.0
ND1 D:HIS346 4.7 11.6 1.0
CB D:ASN272 4.7 12.8 1.0
O D:HOH1006 4.8 16.8 1.0
O B:ASN31 4.9 12.2 1.0
CA D:ASN272 4.9 12.4 1.0
O D:GLY271 5.0 10.3 1.0

Calcium binding site 6 out of 6 in 7v1v

Go back to Calcium Binding Sites List in 7v1v
Calcium binding site 6 out of 6 in the Difructose Dianhydride I Synthase/Hydrolase (ALPHAFFASE1) From Bifidobacterium Dentium, Ligand-Free Form


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, Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca602

b:12.3
occ:1.00
 OD2 D:ASP33 2.2 19.4 1.0
OD1 E:ASN272 2.4 11.6 1.0
O E:GLU270 2.4 15.4 1.0
OD1 D:ASN31 2.4 13.5 1.0
O E:HOH798 2.4 14.1 1.0
O E:HOH904 2.5 15.9 1.0
O E:THR288 2.7 14.5 1.0
CG D:ASP33 3.3 16.9 1.0
CG E:ASN272 3.4 11.1 1.0
C E:THR288 3.6 14.6 1.0
CG D:ASN31 3.6 14.2 1.0
C E:GLU270 3.7 13.5 1.0
O D:HOH1128 3.9 14.6 1.0
O D:HOH910 4.0 5.7 1.0
ND2 E:ASN272 4.0 10.6 1.0
CB D:ASP33 4.1 15.7 1.0
CA E:GLY289 4.1 13.9 1.0
OD1 D:ASP33 4.1 17.5 1.0
N E:GLY289 4.2 13.8 1.0
N E:ASN272 4.4 12.1 1.0
ND2 D:ASN31 4.4 13.1 1.0
OE1 E:GLU270 4.5 11.3 1.0
CA E:GLU270 4.5 13.2 1.0
C E:GLY271 4.5 12.3 1.0
CA E:THR288 4.6 14.4 1.0
OE2 E:GLU343 4.6 13.7 1.0
CA D:ASN31 4.6 14.5 1.0
N E:GLY271 4.6 13.7 1.0
CB D:ASN31 4.7 14.5 1.0
CB E:GLU270 4.7 13.3 1.0
CB E:ASN272 4.7 11.6 1.0
CA E:GLY271 4.7 13.4 1.0
ND1 E:HIS346 4.7 12.2 1.0
O E:HOH931 4.7 18.4 1.0
CA E:ASN272 4.8 11.8 1.0
O D:ASN31 4.9 13.6 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 01:54:48 2025

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