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Calcium in PDB 6m5a: Crystal Structure of GH121 Beta-L-Arabinobiosidase HYPBA2 From Bifidobacterium Longum

Protein crystallography data

The structure of Crystal Structure of GH121 Beta-L-Arabinobiosidase HYPBA2 From Bifidobacterium Longum, PDB code: 6m5a was solved by K.Saito, 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) 44.35 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.526, 88.616, 127.918, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of GH121 Beta-L-Arabinobiosidase HYPBA2 From Bifidobacterium Longum (pdb code 6m5a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of GH121 Beta-L-Arabinobiosidase HYPBA2 From Bifidobacterium Longum, PDB code: 6m5a:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6m5a

Go back to Calcium Binding Sites List in 6m5a
Calcium binding site 1 out of 3 in the Crystal Structure of GH121 Beta-L-Arabinobiosidase HYPBA2 From Bifidobacterium Longum


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 GH121 Beta-L-Arabinobiosidase HYPBA2 From Bifidobacterium Longum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1024

b:22.5
occ:1.00
 OD2 A:ASP505 2.3 19.8 1.0
O A:LEU503 2.3 19.9 1.0
OD1 A:ASP532 2.3 21.2 1.0
OD1 A:ASN499 2.4 23.0 1.0
OD1 A:ASN501 2.4 23.1 1.0
OD1 A:ASN497 2.4 21.4 1.0
C A:LEU503 3.4 23.7 1.0
CG A:ASP532 3.4 21.4 1.0
CG A:ASP505 3.4 20.2 1.0
CG A:ASN499 3.4 24.3 1.0
CG A:ASN501 3.4 22.9 1.0
CG A:ASN497 3.6 21.2 1.0
OD2 A:ASP532 3.8 23.4 1.0
ND2 A:ASN499 3.9 23.9 1.0
CB A:ASP505 3.9 21.3 1.0
ND2 A:ASN501 4.0 21.0 1.0
N A:ASP505 4.0 20.5 1.0
CA A:ASN497 4.1 21.6 1.0
CA A:LEU503 4.1 22.4 1.0
CB A:LEU503 4.1 22.7 1.0
N A:LEU503 4.1 23.0 1.0
C A:ILE504 4.2 23.6 1.0
N A:ASN501 4.2 25.4 1.0
CB A:ASN497 4.4 20.9 1.0
N A:ILE504 4.4 22.7 1.0
N A:ASN499 4.4 23.8 1.0
C A:ASN497 4.4 23.5 1.0
OD1 A:ASP505 4.5 22.2 1.0
CA A:ILE504 4.5 22.4 1.0
ND2 A:ASN497 4.5 20.4 1.0
CA A:ASP505 4.6 20.8 1.0
CB A:ASN501 4.6 22.9 1.0
N A:ASP500 4.6 26.7 1.0
O A:GLN496 4.7 21.9 1.0
CB A:ASN499 4.7 23.3 1.0
N A:ASN498 4.7 24.1 1.0
CB A:ASP532 4.7 21.2 1.0
O A:ILE504 4.7 19.0 1.0
CA A:ASN501 4.7 24.0 1.0
C A:ASN501 4.8 23.2 1.0
CA A:ASN499 4.8 25.3 1.0
C A:ASN499 4.8 24.4 1.0
O A:ASN501 4.9 24.0 1.0
O A:ASN497 5.0 21.6 1.0

Calcium binding site 2 out of 3 in 6m5a

Go back to Calcium Binding Sites List in 6m5a
Calcium binding site 2 out of 3 in the Crystal Structure of GH121 Beta-L-Arabinobiosidase HYPBA2 From Bifidobacterium Longum


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 GH121 Beta-L-Arabinobiosidase HYPBA2 From Bifidobacterium Longum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1025

b:49.3
occ:1.00
 O A:VAL730 2.2 51.5 1.0
OD1 A:ASN726 2.2 45.1 1.0
OD1 A:ASP728 2.4 50.5 1.0
O A:HOH1157 2.5 40.6 1.0
OD1 A:ASP724 2.5 62.9 1.0
OD2 A:ASP735 2.5 51.3 1.0
OD1 A:ASP735 2.6 40.3 1.0
CG A:ASP735 2.9 46.8 1.0
CG A:ASP728 3.2 57.5 1.0
CG A:ASN726 3.3 51.2 1.0
C A:VAL730 3.5 60.6 1.0
CG A:ASP724 3.5 61.6 1.0
OD2 A:ASP728 3.6 52.3 1.0
ND2 A:ASN726 3.9 53.3 1.0
CA A:ASP724 4.1 53.9 1.0
N A:VAL730 4.1 66.7 1.0
N A:ASP728 4.1 69.5 1.0
CB A:ASP724 4.2 55.4 1.0
N A:ASN726 4.2 53.7 1.0
CB A:ASP728 4.3 62.7 1.0
CA A:VAL730 4.3 62.7 1.0
OD2 A:ASP724 4.3 64.5 1.0
N A:GLY727 4.4 60.4 1.0
CB A:ASP735 4.4 43.5 1.0
C A:ASP724 4.4 55.2 1.0
N A:ILE731 4.4 61.0 1.0
CB A:ASN726 4.5 56.2 1.0
N A:VAL725 4.5 51.8 1.0
CA A:ASP728 4.6 60.9 1.0
N A:GLY729 4.6 56.2 1.0
OD1 A:ASN732 4.6 44.2 1.0
CA A:ILE731 4.7 67.7 1.0
CA A:ASN726 4.7 56.7 1.0
N A:ASN732 4.8 53.8 1.0
C A:ASN726 4.8 61.3 1.0
C A:ASP728 4.8 57.5 1.0
CB A:VAL730 4.9 66.9 1.0

Calcium binding site 3 out of 3 in 6m5a

Go back to Calcium Binding Sites List in 6m5a
Calcium binding site 3 out of 3 in the Crystal Structure of GH121 Beta-L-Arabinobiosidase HYPBA2 From Bifidobacterium Longum


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 GH121 Beta-L-Arabinobiosidase HYPBA2 From Bifidobacterium Longum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1026

b:24.8
occ:1.00
 OD1 A:ASP345 2.2 28.3 1.0
OD1 A:ASP349 2.2 23.7 1.0
O A:THR346 2.3 22.6 1.0
O A:HOH1502 2.3 31.3 1.0
OD2 A:ASP352 2.3 25.8 1.0
O A:HOH1294 2.3 27.3 1.0
CG A:ASP349 3.4 25.4 1.0
CG A:ASP345 3.4 27.6 1.0
C A:THR346 3.4 21.6 1.0
CG A:ASP352 3.5 22.7 1.0
N A:THR346 3.6 22.8 1.0
OD2 A:ASP349 4.0 28.8 1.0
O A:HOH1122 4.0 37.6 1.0
CA A:THR346 4.2 23.1 1.0
O A:HOH1168 4.2 41.0 1.0
OD2 A:ASP345 4.2 29.3 1.0
OD1 A:ASP352 4.3 24.3 1.0
C A:ASP345 4.3 23.1 1.0
CA A:ASP345 4.3 22.9 1.0
OH A:TYR792 4.4 24.8 1.0
CB A:ASP352 4.4 23.8 1.0
O A:HOH1580 4.4 46.4 1.0
CB A:ASP345 4.4 26.5 1.0
CA A:ASP349 4.4 24.8 1.0
O A:HOH1125 4.5 31.2 1.0
N A:PRO347 4.5 24.2 1.0
CB A:ASP349 4.5 23.0 1.0
N A:ASP349 4.7 24.5 1.0
CA A:PRO347 4.7 24.9 1.0
C A:PRO347 4.7 27.2 1.0
N A:GLU348 4.7 26.5 1.0
CE1 A:TYR792 4.8 26.9 1.0
OG1 A:THR346 4.8 23.2 1.0
C A:GLU348 4.9 26.2 1.0

Reference:

K.Saito, A.H.Viborg, S.Sakamoto, T.Arakawa, C.Yamada, K.Fujita, S.Fushinobu. Crystal Structure of Beta-L-Arabinobiosidase Belonging to Glycoside Hydrolase Family 121. Plos One 2020.
ISSN: ESSN 1932-6203
Page generated: Wed Jul 9 16:01:47 2025

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