Calcium in PDB 8wg0: Crystal Structure of GH97 Glucodextranase From Flavobacterium Johnsoniae in Complex with Glucose

Enzymatic activity of Crystal Structure of GH97 Glucodextranase From Flavobacterium Johnsoniae in Complex with Glucose

All present enzymatic activity of Crystal Structure of GH97 Glucodextranase From Flavobacterium Johnsoniae in Complex with Glucose:
3.2.1.70;

Protein crystallography data

The structure of Crystal Structure of GH97 Glucodextranase From Flavobacterium Johnsoniae in Complex with Glucose, PDB code: 8wg0 was solved by R.Kurata, S.Nakamura, T.Miyazaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.13 / 1.95
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 307.927, 103.691, 95.671, 90, 90, 90
R / Rfree (%) 18.9 / 22.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of GH97 Glucodextranase From Flavobacterium Johnsoniae in Complex with Glucose (pdb code 8wg0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of GH97 Glucodextranase From Flavobacterium Johnsoniae in Complex with Glucose, PDB code: 8wg0:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 8wg0

Go back to Calcium Binding Sites List in 8wg0
Calcium binding site 1 out of 4 in the Crystal Structure of GH97 Glucodextranase From Flavobacterium Johnsoniae in Complex with Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of GH97 Glucodextranase From Flavobacterium Johnsoniae in Complex with Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:26.1
occ:1.00
 OE1 A:GLU485 2.3 25.9 1.0
OE1 A:GLU503 2.3 22.4 1.0
O2 A:GLC802 2.3 25.8 1.0
OE1 A:GLU171 2.3 24.9 1.0
OE1 A:GLU509 2.4 25.2 1.0
O A:HOH1025 2.4 31.5 1.0
O1 A:GLC802 2.7 30.1 1.0
HO2 A:GLC802 2.8 27.0 1.0
H1 A:GLC802 2.9 33.3 1.0
C1 A:GLC802 3.2 37.5 1.0
CD A:GLU509 3.3 24.5 1.0
C2 A:GLC802 3.3 30.8 1.0
CD A:GLU503 3.3 25.1 1.0
CD A:GLU485 3.5 28.1 1.0
HO1 A:GLC802 3.5 32.4 1.0
CD A:GLU171 3.5 23.1 1.0
HD1 A:HIS484 3.5 30.0 0.0
OE2 A:GLU509 3.6 27.0 1.0
OE2 A:GLU503 3.7 24.6 1.0
HG3 A:GLU485 3.8 25.7 1.0
H2 A:GLC802 3.8 30.4 1.0
O A:HOH1051 3.8 21.3 1.0
O A:HOH929 3.9 22.7 1.0
HB3 A:HIS484 3.9 25.5 1.0
OE2 A:GLU171 3.9 26.5 1.0
CG A:GLU485 4.2 25.2 1.0
HE1 A:TYR510 4.3 24.6 1.0
H3 A:GLC802 4.3 28.4 1.0
ND1 A:HIS484 4.3 25.4 1.0
OE2 A:GLU485 4.4 27.1 1.0
HG23 A:VAL448 4.4 27.5 1.0
C3 A:GLC802 4.4 28.2 1.0
O A:HOH1005 4.4 38.7 1.0
O A:HOH921 4.4 23.4 1.0
HG2 A:GLU485 4.5 26.1 1.0
CG A:GLU503 4.6 22.4 1.0
CG A:GLU509 4.6 22.8 1.0
O5 A:GLC802 4.7 31.4 1.0
HG2 A:GLU503 4.7 23.5 1.0
HG2 A:GLU509 4.7 23.5 1.0
HG2 A:GLU171 4.7 23.2 1.0
HB3 A:GLU503 4.8 25.3 1.0
CG A:GLU171 4.8 22.4 1.0
CB A:HIS484 4.8 24.1 1.0
H A:GLU485 4.9 25.1 1.0
O A:HOH922 5.0 25.8 1.0
O3 A:GLC802 5.0 25.4 1.0

Calcium binding site 2 out of 4 in 8wg0

Go back to Calcium Binding Sites List in 8wg0
Calcium binding site 2 out of 4 in the Crystal Structure of GH97 Glucodextranase From Flavobacterium Johnsoniae in Complex with Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of GH97 Glucodextranase From Flavobacterium Johnsoniae in Complex with Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca801

b:39.5
occ:1.00
 OE1 B:GLU485 2.3 35.8 1.0
O B:HOH958 2.3 37.2 1.0
HO2 B:GLC802 2.3 34.8 1.0
OE1 B:GLU509 2.3 33.7 1.0
O2 B:GLC802 2.4 33.6 1.0
OE1 B:GLU503 2.4 36.3 1.0
OE1 B:GLU171 2.4 30.5 1.0
O1 B:GLC802 2.6 40.8 1.0
H1 B:GLC802 2.7 39.8 1.0
C1 B:GLC802 3.0 42.4 1.0
C2 B:GLC802 3.2 37.9 1.0
CD B:GLU509 3.3 38.1 1.0
CD B:GLU503 3.4 35.4 1.0
CD B:GLU171 3.4 31.3 1.0
HO1 B:GLC802 3.4 41.7 1.0
CD B:GLU485 3.5 39.8 1.0
OE2 B:GLU509 3.5 34.3 1.0
HD1 B:HIS484 3.6 30.0 0.0
H2 B:GLC802 3.8 38.5 1.0
OE2 B:GLU503 3.8 35.6 1.0
OE2 B:GLU171 3.8 29.6 1.0
HG3 B:GLU485 3.9 33.3 1.0
O B:HOH956 3.9 32.9 1.0
HB3 B:HIS484 3.9 32.8 1.0
O B:HOH960 4.1 28.2 1.0
O B:HOH964 4.1 50.4 1.0
CG B:GLU485 4.3 32.5 1.0
HE1 B:TYR510 4.3 33.6 1.0
OE2 B:GLU485 4.4 40.6 1.0
H3 B:GLC802 4.4 40.3 1.0
ND1 B:HIS484 4.4 34.7 1.0
HG23 B:VAL448 4.4 34.2 1.0
C3 B:GLC802 4.4 41.4 1.0
O5 B:GLC802 4.5 38.5 1.0
HG2 B:GLU485 4.6 33.6 1.0
CG B:GLU509 4.7 35.5 1.0
O B:HOH927 4.7 38.0 1.0
HG2 B:GLU509 4.7 35.8 1.0
HG2 B:GLU171 4.7 31.5 1.0
CG B:GLU503 4.7 32.8 1.0
CG B:GLU171 4.7 31.1 1.0
HG2 B:GLU503 4.8 32.9 1.0
CB B:HIS484 4.9 32.1 1.0
HB3 B:GLU503 4.9 34.1 1.0
H B:GLU485 5.0 32.3 1.0
O B:HOH916 5.0 40.8 1.0

Calcium binding site 3 out of 4 in 8wg0

Go back to Calcium Binding Sites List in 8wg0
Calcium binding site 3 out of 4 in the Crystal Structure of GH97 Glucodextranase From Flavobacterium Johnsoniae in Complex with Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of GH97 Glucodextranase From Flavobacterium Johnsoniae in Complex with Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca801

b:30.9
occ:1.00
 OE1 C:GLU503 2.3 23.3 1.0
O2 C:GLC802 2.3 27.6 1.0
OE1 C:GLU171 2.3 24.4 1.0
OE1 C:GLU509 2.3 26.7 1.0
OE1 C:GLU485 2.3 28.4 1.0
O C:HOH1007 2.4 29.1 1.0
HO2 C:GLC802 2.7 28.9 1.0
O1 C:GLC802 2.7 29.0 1.0
H1 C:GLC802 3.0 35.9 1.0
C1 C:GLC802 3.2 41.6 1.0
CD C:GLU509 3.3 27.8 1.0
CD C:GLU503 3.4 28.3 1.0
C2 C:GLC802 3.4 32.0 1.0
CD C:GLU171 3.4 22.7 1.0
HO1 C:GLC802 3.4 32.5 1.0
CD C:GLU485 3.5 28.3 1.0
HD1 C:HIS484 3.6 30.0 0.0
OE2 C:GLU509 3.6 29.7 1.0
O C:HOH1005 3.8 26.5 1.0
OE2 C:GLU503 3.8 28.5 1.0
HG3 C:GLU485 3.8 28.3 1.0
OE2 C:GLU171 3.8 27.7 1.0
H2 C:GLC802 4.0 32.2 1.0
O C:HOH1024 4.0 27.9 1.0
HB3 C:HIS484 4.0 29.1 1.0
HE1 C:TYR510 4.2 25.0 1.0
CG C:GLU485 4.2 28.7 1.0
O C:HOH928 4.3 38.8 1.0
H3 C:GLC802 4.3 31.3 1.0
HG23 C:VAL448 4.4 29.4 1.0
ND1 C:HIS484 4.4 27.2 1.0
C3 C:GLC802 4.5 30.8 1.0
OE2 C:GLU485 4.5 28.0 1.0
HG2 C:GLU485 4.5 28.5 1.0
O C:HOH960 4.6 28.7 1.0
CG C:GLU509 4.6 27.9 1.0
CG C:GLU503 4.7 26.8 1.0
HG2 C:GLU171 4.7 24.1 1.0
HG2 C:GLU509 4.7 27.6 1.0
CG C:GLU171 4.7 23.5 1.0
O5 C:GLC802 4.7 37.1 1.0
HB3 C:GLU503 4.8 26.8 1.0
HG2 C:GLU503 4.8 27.1 1.0
H C:GLU485 4.9 25.2 1.0
CB C:HIS484 4.9 30.6 1.0
O C:HOH916 5.0 30.4 1.0
HG3 C:GLU509 5.0 28.1 1.0
HH C:TYR510 5.0 30.0 0.0

Calcium binding site 4 out of 4 in 8wg0

Go back to Calcium Binding Sites List in 8wg0
Calcium binding site 4 out of 4 in the Crystal Structure of GH97 Glucodextranase From Flavobacterium Johnsoniae in Complex with Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of GH97 Glucodextranase From Flavobacterium Johnsoniae in Complex with Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca801

b:41.5
occ:1.00
 OE1 D:GLU485 2.2 37.5 1.0
OE1 D:GLU509 2.3 37.5 1.0
OE1 D:GLU503 2.4 39.8 1.0
O D:HOH911 2.4 32.7 1.0
O2 D:GLC802 2.4 37.3 1.0
OE1 D:GLU171 2.4 32.2 1.0
HO2 D:GLC802 2.5 39.4 1.0
O1 D:GLC802 2.6 47.3 1.0
H1 D:GLC802 2.8 45.2 1.0
C1 D:GLC802 3.1 47.4 1.0
C2 D:GLC802 3.3 43.1 1.0
CD D:GLU509 3.3 40.2 1.0
HO1 D:GLC802 3.3 48.0 1.0
CD D:GLU503 3.4 37.1 1.0
CD D:GLU485 3.4 39.2 1.0
CD D:GLU171 3.5 35.1 1.0
HD1 D:HIS484 3.6 30.0 0.0
OE2 D:GLU509 3.6 38.5 1.0
HG3 D:GLU485 3.8 38.7 1.0
OE2 D:GLU503 3.8 32.6 1.0
OE2 D:GLU171 3.8 35.8 1.0
O D:HOH964 3.9 40.6 1.0
H2 D:GLC802 3.9 40.7 1.0
HB3 D:HIS484 4.0 32.3 1.0
O D:HOH950 4.1 33.3 1.0
CG D:GLU485 4.2 39.1 1.0
HE1 D:TYR510 4.3 40.5 1.0
ND1 D:HIS484 4.4 33.3 1.0
OE2 D:GLU485 4.4 29.1 1.0
H3 D:GLC802 4.4 39.4 1.0
HG23 D:VAL448 4.4 34.5 1.0
C3 D:GLC802 4.5 37.1 1.0
HG2 D:GLU485 4.5 38.6 1.0
O5 D:GLC802 4.5 43.2 1.0
O D:HOH929 4.6 36.7 1.0
CG D:GLU509 4.7 38.1 1.0
CG D:GLU503 4.7 37.8 1.0
HG2 D:GLU509 4.7 38.4 1.0
CG D:GLU171 4.8 34.0 1.0
O D:HOH903 4.8 34.5 1.0
HG2 D:GLU171 4.8 35.1 1.0
HB3 D:GLU503 4.8 38.2 1.0
HG2 D:GLU503 4.8 38.1 1.0
CB D:HIS484 4.9 31.3 1.0
H D:GLU485 4.9 36.5 1.0

Reference:

S.Nakamura, R.Kurata, T.Miyazaki. Structural Insights Into Alpha-(1->6)-Linkage Preference of GH97 Glucodextranase From Flavobacterium Johnsoniae. Febs J. 2024.
ISSN: ISSN 1742-464X
PubMed: 38661728
DOI: 10.1111/FEBS.17139
Page generated: Fri Jul 19 12:38:46 2024

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