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Calcium in PDB 5a2a: Crystal Structure of Anoxybacillus Alpha-Amylase Provides Insights Into A New Glycosyl Hydrolase Subclass

Enzymatic activity of Crystal Structure of Anoxybacillus Alpha-Amylase Provides Insights Into A New Glycosyl Hydrolase Subclass

All present enzymatic activity of Crystal Structure of Anoxybacillus Alpha-Amylase Provides Insights Into A New Glycosyl Hydrolase Subclass:
3.2.1.1;

Protein crystallography data

The structure of Crystal Structure of Anoxybacillus Alpha-Amylase Provides Insights Into A New Glycosyl Hydrolase Subclass, PDB code: 5a2a was solved by C.L.Ng, K.P.Chai, N.F.Othman, A.H.Teh, K.L.Ho, K.G.Chan, K.M.Goh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.429, 63.443, 122.758, 90.00, 90.00, 90.00
R / Rfree (%) 17.689 / 23.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Anoxybacillus Alpha-Amylase Provides Insights Into A New Glycosyl Hydrolase Subclass (pdb code 5a2a). 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 Anoxybacillus Alpha-Amylase Provides Insights Into A New Glycosyl Hydrolase Subclass, PDB code: 5a2a:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5a2a

Go back to Calcium Binding Sites List in 5a2a
Calcium binding site 1 out of 4 in the Crystal Structure of Anoxybacillus Alpha-Amylase Provides Insights Into A New Glycosyl Hydrolase Subclass


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 Anoxybacillus Alpha-Amylase Provides Insights Into A New Glycosyl Hydrolase Subclass within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1480

b:23.2
occ:1.00
 OD1 A:ASN139 2.4 15.3 1.0
O A:HIS217 2.4 16.1 1.0
O A:GLU173 2.5 22.6 1.0
O A:HOH2186 2.5 17.6 1.0
O A:HOH2155 2.6 20.0 1.0
OD2 A:ASP182 2.6 17.2 1.0
O A:HOH2154 2.6 17.4 1.0
OD1 A:ASP182 2.7 17.3 1.0
CG A:ASP182 3.0 17.2 1.0
C A:GLU173 3.5 23.0 1.0
CG A:ASN139 3.5 16.3 1.0
C A:HIS217 3.6 17.1 1.0
CA A:GLU173 4.1 23.6 1.0
ND2 A:ASN139 4.1 16.3 1.0
CB A:HIS217 4.2 19.2 1.0
O A:ASN139 4.4 18.8 1.0
CA A:HIS217 4.4 17.8 1.0
N A:VAL218 4.5 16.2 1.0
N A:ASN174 4.5 23.3 1.0
CB A:ASP182 4.5 17.5 1.0
O A:LEU183 4.5 21.0 1.0
CA A:VAL218 4.6 15.8 1.0
O A:GLY175 4.6 19.3 1.0
ND1 A:HIS158 4.6 22.4 1.0
CE1 A:HIS158 4.6 24.0 1.0
OE1 A:GLN185 4.6 14.9 1.0
CG2 A:VAL218 4.6 15.7 1.0
O A:VAL172 4.7 24.1 1.0
CB A:ASN139 4.7 15.5 1.0
CA A:ASN174 4.8 23.5 1.0
CA A:ASN139 4.9 16.5 1.0
O A:HOH2185 4.9 20.8 1.0
NE2 A:GLN185 4.9 14.2 1.0
CB A:GLU173 4.9 24.4 1.0

Calcium binding site 2 out of 4 in 5a2a

Go back to Calcium Binding Sites List in 5a2a
Calcium binding site 2 out of 4 in the Crystal Structure of Anoxybacillus Alpha-Amylase Provides Insights Into A New Glycosyl Hydrolase Subclass


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 Anoxybacillus Alpha-Amylase Provides Insights Into A New Glycosyl Hydrolase Subclass within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1481

b:26.5
occ:1.00
 OD1 A:ASP50 2.2 23.8 1.0
OD2 A:ASP65 2.2 14.6 1.0
OD1 A:ASN49 2.4 20.4 1.0
O A:HOH2042 2.5 25.2 1.0
O A:GLY63 2.6 18.9 1.0
O A:ASN46 2.6 24.3 1.0
OD1 A:ASN44 2.6 21.9 1.0
CG A:ASP50 3.3 24.9 1.0
CG A:ASN44 3.3 20.2 1.0
CG A:ASP65 3.4 14.8 1.0
CG A:ASN49 3.6 20.7 1.0
C A:GLY63 3.6 17.5 1.0
C A:ASN46 3.6 24.8 1.0
ND2 A:ASN44 3.8 20.7 1.0
CB A:ASP65 3.9 14.6 1.0
OD2 A:ASP50 3.9 25.3 1.0
CA A:GLY63 4.1 17.2 1.0
N A:ASN46 4.1 22.4 1.0
CA A:ASN46 4.2 23.7 1.0
C A:ASN49 4.3 23.4 1.0
ND2 A:ASN49 4.3 19.2 1.0
O A:HIS111 4.3 19.2 1.0
N A:ASP50 4.3 22.6 1.0
CB A:ASN46 4.3 23.6 1.0
CB A:ASN44 4.4 19.1 1.0
O A:ASN49 4.4 23.8 1.0
OD1 A:ASP65 4.4 14.7 1.0
CA A:ASN44 4.5 17.8 1.0
CA A:PRO47 4.5 27.7 1.0
CB A:ASP50 4.5 24.9 1.0
CA A:ASP50 4.6 24.6 1.0
N A:ASN49 4.6 22.1 1.0
N A:PRO47 4.6 26.7 1.0
C A:GLY64 4.7 15.1 1.0
CA A:ASN49 4.7 22.6 1.0
CB A:ASN49 4.7 21.0 1.0
C A:ASN44 4.8 18.4 1.0
N A:GLY45 4.8 18.7 1.0
N A:GLY64 4.8 16.9 1.0
C A:PRO47 4.8 27.2 1.0
O A:HOH2025 4.9 17.2 1.0
N A:ASP65 4.9 14.4 1.0
CA A:GLY64 5.0 15.5 1.0

Calcium binding site 3 out of 4 in 5a2a

Go back to Calcium Binding Sites List in 5a2a
Calcium binding site 3 out of 4 in the Crystal Structure of Anoxybacillus Alpha-Amylase Provides Insights Into A New Glycosyl Hydrolase Subclass


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 Anoxybacillus Alpha-Amylase Provides Insights Into A New Glycosyl Hydrolase Subclass within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1482

b:31.5
occ:1.00
 O A:HOH2092 2.3 44.5 1.0
O A:ASN92 2.4 16.5 1.0
OE1 A:GLU109 2.4 14.6 1.0
O A:HOH2091 2.5 32.5 1.0
OE1 A:GLU110 2.6 30.8 1.0
OE2 A:GLU110 2.8 31.0 1.0
O A:HOH2060 2.8 32.1 1.0
OE2 A:GLU109 2.9 16.4 1.0
CD A:GLU109 3.0 15.7 1.0
CD A:GLU110 3.1 30.6 1.0
C A:ASN92 3.5 17.1 1.0
N A:ASN92 3.9 15.0 1.0
CA A:ASN92 4.3 15.5 1.0
OH A:TYR61 4.3 16.6 1.0
O A:HOH2118 4.3 34.0 1.0
OE2 A:GLU103 4.5 32.6 1.0
O A:HOH2115 4.5 43.6 1.0
CG A:GLU109 4.5 15.6 1.0
N A:GLU93 4.6 17.4 1.0
O A:HOH2119 4.6 41.3 1.0
CG A:GLU110 4.6 28.8 1.0
CB A:ASN92 4.7 15.2 1.0
O A:GLU93 4.7 20.3 1.0
O A:HOH2105 4.8 32.5 1.0
C A:ALA91 4.8 14.3 1.0
C A:GLU93 4.8 21.1 1.0
ND1 A:HIS111 4.8 24.2 1.0
CA A:GLU93 4.8 20.3 1.0
N A:GLU110 4.9 20.8 1.0
CA A:ALA91 4.9 14.3 1.0

Calcium binding site 4 out of 4 in 5a2a

Go back to Calcium Binding Sites List in 5a2a
Calcium binding site 4 out of 4 in the Crystal Structure of Anoxybacillus Alpha-Amylase Provides Insights Into A New Glycosyl Hydrolase Subclass


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 Anoxybacillus Alpha-Amylase Provides Insights Into A New Glycosyl Hydrolase Subclass within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1483

b:23.6
occ:1.00
 O A:GLU400 2.3 14.2 1.0
O A:HOH2362 2.3 35.9 1.0
O A:HOH2361 2.5 23.6 1.0
O A:HOH2261 2.5 21.6 1.0
O A:HOH2360 2.5 22.3 1.0
C A:GLU400 3.5 14.7 1.0
O A:HOH2359 4.0 27.5 1.0
OE1 A:GLU283 4.1 23.3 1.0
CA A:GLU400 4.4 13.9 1.0
CA A:LYS401 4.5 17.0 1.0
CB A:GLU400 4.5 13.4 1.0
N A:LYS401 4.5 15.6 1.0
CD A:LYS401 4.5 21.6 1.0
OE1 A:GLU400 4.5 14.7 1.0
O A:HOH2262 4.6 31.7 1.0
N A:GLU400 4.7 13.9 1.0
CB A:LYS401 4.9 18.2 1.0

Reference:

K.P.Chai, N.F.B.Othman, A.Teh, K.L.Ho, K.Chan, M.S.Shamsir, K.M.Goh, C.L.Ng. Crystal Structure of Anoxybacillus Alpha-Amylase Provides Insights Into Maltose Binding of A New Glycosyl Hydrolase Subclass. Sci.Rep. V. 6 23126 2016.
ISSN: ISSN 2045-2322
PubMed: 26975884
DOI: 10.1038/SREP23126
Page generated: Sun Jul 14 16:12:34 2024

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