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Calcium in PDB 8xx9: Rhodothermus Marinus Alpha-Amylase RMGH13_47A CBM48-A-B-C Domains

Enzymatic activity of Rhodothermus Marinus Alpha-Amylase RMGH13_47A CBM48-A-B-C Domains

All present enzymatic activity of Rhodothermus Marinus Alpha-Amylase RMGH13_47A CBM48-A-B-C Domains:
3.2.1.1;

Protein crystallography data

The structure of Rhodothermus Marinus Alpha-Amylase RMGH13_47A CBM48-A-B-C Domains, PDB code: 8xx9 was solved by T.Tonozuka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.50 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.77, 102.389, 63.397, 90, 96.42, 90
R / Rfree (%) 14.8 / 17.5

Other elements in 8xx9:

The structure of Rhodothermus Marinus Alpha-Amylase RMGH13_47A CBM48-A-B-C Domains also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Rhodothermus Marinus Alpha-Amylase RMGH13_47A CBM48-A-B-C Domains (pdb code 8xx9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Rhodothermus Marinus Alpha-Amylase RMGH13_47A CBM48-A-B-C Domains, PDB code: 8xx9:

Calcium binding site 1 out of 1 in 8xx9

Go back to Calcium Binding Sites List in 8xx9
Calcium binding site 1 out of 1 in the Rhodothermus Marinus Alpha-Amylase RMGH13_47A CBM48-A-B-C Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rhodothermus Marinus Alpha-Amylase RMGH13_47A CBM48-A-B-C Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:14.9
occ:1.00
 O A:PHE451 2.3 13.9 1.0
O A:GLY453 2.3 13.9 1.0
OD2 A:ASP468 2.3 14.7 1.0
OE2 A:GLU450 2.3 15.0 1.0
O A:HOH1338 2.4 14.1 1.0
O A:HOH1149 2.4 14.6 1.0
CG A:ASP468 3.4 14.5 1.0
CD A:GLU450 3.4 13.5 1.0
C A:GLY453 3.4 14.2 1.0
C A:PHE451 3.5 13.7 1.0
OD1 A:ASP468 3.7 15.2 1.0
O A:HOH1207 3.8 13.9 1.0
N A:PHE451 3.8 13.3 1.0
N A:GLY453 3.9 15.6 1.0
CD1 A:PHE451 3.9 14.4 1.0
OE1 A:GLU450 4.0 14.2 1.0
O A:HOH1352 4.1 17.9 1.0
C A:ASP452 4.1 15.5 1.0
CE1 A:PHE451 4.2 14.8 1.0
CA A:GLY453 4.2 15.1 1.0
CA A:PHE451 4.2 12.9 1.0
O A:HOH1278 4.4 16.5 1.0
N A:ASN454 4.4 13.8 1.0
CG A:GLU450 4.4 13.4 1.0
N A:ASP452 4.5 14.9 1.0
OD1 A:ASN454 4.5 16.9 1.0
CA A:ASP452 4.5 15.5 1.0
CG A:PHE451 4.6 13.8 1.0
O A:ASP452 4.6 15.3 1.0
CA A:ASN454 4.6 14.7 1.0
CB A:ASP468 4.7 15.1 1.0
C A:GLU450 4.7 12.8 1.0
OD2 A:ASP357 4.7 17.9 1.0
CA A:GLU450 4.9 13.3 1.0
CZ A:PHE451 5.0 16.1 1.0

Reference:

Y.Miyasaka, K.Yokoyama, T.Kozono, Y.Kitano, T.Miyazaki, M.Sakaguchi, A.Nishikawa, T.Tonozuka. Structural Basis For the Recognition of Alpha-1,6-Branched Alpha-Glucan By GH13_47 Alpha-Amylase From Rhodothermus Marinus To Be Published.
Page generated: Thu Jul 10 08:29:48 2025

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