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Calcium in PDB 8xxa: Rhodothermus Marinus Alpha-Amylase RMGH13_47A CBM48-A-B-C Domains in Complex with Branched Pentasaccharide

Enzymatic activity of Rhodothermus Marinus Alpha-Amylase RMGH13_47A CBM48-A-B-C Domains in Complex with Branched Pentasaccharide

All present enzymatic activity of Rhodothermus Marinus Alpha-Amylase RMGH13_47A CBM48-A-B-C Domains in Complex with Branched Pentasaccharide:
3.2.1.1;

Protein crystallography data

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

Resolution Low / High (Å) 47.94 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.508, 61.051, 99.808, 90, 106.11, 90
R / Rfree (%) 17.4 / 18.9

Other elements in 8xxa:

The structure of Rhodothermus Marinus Alpha-Amylase RMGH13_47A CBM48-A-B-C Domains in Complex with Branched Pentasaccharide 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 in Complex with Branched Pentasaccharide (pdb code 8xxa). 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 in Complex with Branched Pentasaccharide, PDB code: 8xxa:

Calcium binding site 1 out of 1 in 8xxa

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


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 in Complex with Branched Pentasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:12.1
occ:1.00
 O A:PHE451 2.2 11.4 1.0
O A:GLY453 2.3 12.7 1.0
OE2 A:GLU450 2.3 11.3 1.0
O A:HOH1363 2.3 13.2 1.0
OD2 A:ASP468 2.3 12.1 1.0
O A:HOH1145 2.4 12.0 1.0
CG A:ASP468 3.4 12.2 1.0
CD A:GLU450 3.4 12.2 1.0
C A:PHE451 3.4 12.0 1.0
C A:GLY453 3.5 11.7 1.0
OD1 A:ASP468 3.7 12.4 1.0
O A:HOH1161 3.8 12.1 1.0
N A:PHE451 3.8 11.6 1.0
N A:GLY453 3.9 11.9 1.0
CD1 A:PHE451 3.9 12.0 1.0
OE1 A:GLU450 4.0 12.8 1.0
O A:HOH1481 4.0 15.2 1.0
C A:ASP452 4.1 12.2 1.0
CA A:GLY453 4.2 12.0 1.0
CE1 A:PHE451 4.2 12.1 1.0
CA A:PHE451 4.3 11.9 1.0
O A:HOH1247 4.3 13.5 1.0
CG A:GLU450 4.4 12.0 1.0
N A:ASP452 4.4 12.3 1.0
OD1 A:ASN454 4.5 13.0 1.0
O A:ASP452 4.5 12.3 1.0
N A:ASN454 4.5 12.1 1.0
CA A:ASP452 4.5 11.8 1.0
CG A:PHE451 4.6 11.7 1.0
CB A:ASP468 4.7 12.9 1.0
C A:GLU450 4.7 12.3 1.0
CA A:ASN454 4.7 12.3 1.0
OD2 A:ASP357 4.8 13.4 1.0
CA A:GLU450 4.8 11.8 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 08:30:02 2025

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