Atomistry » Calcium » PDB 7uww-7vmj » 7v1x
Atomistry »
  Calcium »
    PDB 7uww-7vmj »
      7v1x »

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

Go back to Calcium Binding Sites List in 7v1x
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

Go back to Calcium Binding Sites List in 7v1x
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

Go back to Calcium Binding Sites List in 7v1x
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy