Atomistry » Calcium » PDB 7uww-7vmj » 7v1v
Atomistry »
  Calcium »
    PDB 7uww-7vmj »
      7v1v »

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

Go back to Calcium Binding Sites List in 7v1v
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

Go back to Calcium Binding Sites List in 7v1v
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

Go back to Calcium Binding Sites List in 7v1v
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: Fri Jul 19 05:14:51 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy