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Calcium in PDB 5a2c: 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: 5a2c 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) 61.49 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.816, 63.532, 122.970, 90.00, 90.00, 90.00
R / Rfree (%) 15.585 / 20.914

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 5a2c). 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: 5a2c:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5a2c

Go back to Calcium Binding Sites List in 5a2c
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:Ca1477

b:18.9
occ:1.00
 OD1 A:ASN139 2.4 14.7 1.0
O A:HOH2200 2.5 14.8 1.0
O A:GLU173 2.5 19.8 1.0
OD2 A:ASP182 2.5 16.3 1.0
O A:HIS217 2.5 15.5 1.0
O A:HOH2249 2.5 16.2 1.0
O A:HOH2201 2.5 18.8 1.0
OD1 A:ASP182 2.5 16.0 1.0
CG A:ASP182 2.9 16.4 1.0
C A:GLU173 3.5 21.5 1.0
CG A:ASN139 3.5 15.5 1.0
C A:HIS217 3.6 16.8 1.0
ND2 A:ASN139 4.1 16.9 1.0
CB A:HIS217 4.1 19.2 1.0
CA A:GLU173 4.2 21.5 1.0
CB A:ASP182 4.4 17.7 1.0
O A:ASN139 4.4 16.6 1.0
CA A:HIS217 4.4 18.1 1.0
N A:ASN174 4.5 20.9 1.0
ND1 A:HIS158 4.6 19.0 1.0
O A:GLY175 4.6 18.8 1.0
O A:LEU183 4.6 19.6 1.0
N A:VAL218 4.6 16.3 1.0
CE1 A:HIS158 4.6 18.0 1.0
CG2 A:VAL218 4.6 16.7 1.0
CA A:VAL218 4.7 17.3 1.0
CA A:ASN174 4.7 22.9 1.0
OE1 A:GLN185 4.7 18.4 1.0
CB A:ASN139 4.7 14.7 1.0
O A:VAL172 4.8 21.7 1.0
NE2 A:GLN185 4.8 17.8 1.0
O A:HOH2248 4.9 19.6 1.0
CA A:ASN139 4.9 15.3 1.0
C A:ASN174 5.0 21.9 1.0

Calcium binding site 2 out of 4 in 5a2c

Go back to Calcium Binding Sites List in 5a2c
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:Ca1478

b:16.2
occ:1.00
 OD1 A:ASP50 2.3 18.3 1.0
OD2 A:ASP65 2.3 15.7 1.0
O A:HOH2059 2.4 20.7 1.0
OD1 A:ASN44 2.4 17.5 1.0
OD1 A:ASN49 2.4 18.5 1.0
O A:GLY63 2.5 15.9 1.0
O A:ASN46 2.5 19.6 1.0
CG A:ASN44 3.2 16.8 1.0
CG A:ASP65 3.4 16.2 1.0
CG A:ASP50 3.5 20.9 1.0
C A:ASN46 3.6 20.4 1.0
C A:GLY63 3.6 15.3 1.0
CG A:ASN49 3.6 18.6 1.0
ND2 A:ASN44 3.7 16.7 1.0
CB A:ASP65 4.0 15.3 1.0
CA A:GLY63 4.0 15.6 1.0
OD2 A:ASP50 4.1 20.2 1.0
N A:ASN46 4.1 19.3 1.0
ND2 A:ASN49 4.2 18.3 1.0
CB A:ASN44 4.3 16.9 1.0
CA A:ASN46 4.3 19.6 1.0
CA A:PRO47 4.3 26.7 1.0
C A:ASN49 4.4 19.0 1.0
O A:HIS111 4.4 15.9 1.0
CA A:ASN44 4.4 16.4 1.0
N A:ASP50 4.4 19.6 1.0
N A:PRO47 4.5 23.9 1.0
OD1 A:ASP65 4.5 16.1 1.0
O A:ASN49 4.6 18.1 1.0
CA A:ASP50 4.6 19.5 1.0
CB A:ASP50 4.6 19.9 1.0
N A:ASN49 4.7 19.1 1.0
CB A:ASN46 4.7 19.6 1.0
C A:PRO47 4.7 23.9 1.0
C A:ASN44 4.7 17.4 1.0
N A:GLY64 4.7 14.5 1.0
CB A:ASN49 4.8 18.2 1.0
O A:HOH2033 4.8 12.8 1.0
C A:GLY64 4.8 14.5 1.0
CA A:ASN49 4.8 19.7 1.0
N A:GLY45 4.8 17.3 1.0
N A:ASP65 4.9 14.4 1.0
O A:GLY64 5.0 15.5 1.0

Calcium binding site 3 out of 4 in 5a2c

Go back to Calcium Binding Sites List in 5a2c
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:Ca1479

b:18.7
occ:1.00
 O A:HOH2129 2.4 20.6 1.0
O A:ASN92 2.4 17.9 1.0
O A:HOH2128 2.4 22.4 1.0
OE1 A:GLU110 2.4 20.5 1.0
OE1 A:GLU109 2.5 12.5 1.0
OE2 A:GLU110 2.5 20.0 1.0
O A:HOH2089 2.5 23.9 1.0
CD A:GLU110 2.8 18.6 1.0
OE2 A:GLU109 3.0 13.9 1.0
CD A:GLU109 3.1 14.2 1.0
C A:ASN92 3.6 16.8 1.0
N A:ASN92 4.0 14.5 1.0
CG A:GLU110 4.3 18.9 1.0
CA A:ASN92 4.3 15.2 1.0
O A:HOH2157 4.3 30.6 1.0
O A:HOH2155 4.4 45.4 1.0
OH A:TYR61 4.4 15.0 1.0
O A:HOH2142 4.6 27.7 1.0
CG A:GLU109 4.6 13.3 1.0
O A:HOH2047 4.6 29.6 1.0
O A:HOH2068 4.6 24.9 1.0
N A:GLU93 4.6 18.0 1.0
ND1 A:HIS111 4.6 18.0 1.0
OE2 A:GLU103 4.6 26.5 1.0
O A:HOH2156 4.7 29.4 1.0
N A:GLU110 4.7 15.9 1.0
CB A:ASN92 4.8 14.4 1.0
C A:GLU93 4.8 19.4 1.0
O A:GLU93 4.9 17.9 1.0
CA A:GLU93 4.9 19.1 1.0
C A:ALA91 4.9 15.4 1.0
CB A:ALA91 5.0 16.8 1.0
CE1 A:HIS111 5.0 18.9 1.0

Calcium binding site 4 out of 4 in 5a2c

Go back to Calcium Binding Sites List in 5a2c
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:Ca1480

b:21.5
occ:1.00
 O A:HOH2451 1.6 23.9 1.0
O A:HOH2450 2.1 26.8 1.0
O A:GLU400 2.2 16.7 1.0
O A:HOH2334 2.3 29.3 1.0
O A:HOH2449 2.4 20.1 1.0
O A:HOH2333 2.5 18.0 1.0
O A:HOH2332 2.6 25.1 1.0
C A:GLU400 3.4 15.4 1.0
O A:HOH2448 3.5 21.4 1.0
OE1 A:GLU283 4.1 35.1 1.0
CD A:LYS401 4.3 20.7 0.5
CA A:GLU400 4.3 14.9 1.0
N A:LYS401 4.3 16.3 1.0
CA A:LYS401 4.3 17.2 0.5
CA A:LYS401 4.3 17.3 0.5
O A:HOH2233 4.4 29.0 1.0
CB A:GLU400 4.4 14.9 1.0
O A:HOH2330 4.4 23.2 1.0
N A:GLU400 4.4 13.7 1.0
OE1 A:GLU400 4.5 16.6 1.0
CD A:LYS401 4.5 21.2 0.5
CB A:LYS401 4.8 18.0 0.5
CB A:LYS401 4.8 18.3 0.5
O A:HOH2446 5.0 34.5 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 16:13:07 2024

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