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Calcium in PDB 5a2b: 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: 5a2b 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) 63.35 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.013, 65.296, 126.708, 90.00, 90.00, 90.00
R / Rfree (%) 15.463 / 19.273

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 5a2b). 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: 5a2b:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5a2b

Go back to Calcium Binding Sites List in 5a2b
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:Ca1479

b:24.6
occ:1.00
 O A:GLU173 2.4 22.0 1.0
OD1 A:ASN139 2.4 19.5 1.0
O A:HOH2146 2.4 18.9 1.0
O A:HOH2176 2.4 22.4 1.0
O A:HIS217 2.5 23.4 1.0
O A:HOH2145 2.5 21.9 1.0
OD2 A:ASP182 2.6 24.0 1.0
OD1 A:ASP182 2.6 22.7 1.0
CG A:ASP182 2.9 24.8 1.0
C A:GLU173 3.5 24.8 1.0
CG A:ASN139 3.5 19.8 1.0
C A:HIS217 3.6 20.8 1.0
ND2 A:ASN139 4.1 20.4 1.0
CB A:HIS217 4.1 21.2 1.0
CA A:GLU173 4.2 23.2 1.0
O A:ASN139 4.3 20.9 1.0
CB A:ASP182 4.4 25.1 1.0
CA A:HIS217 4.4 20.5 1.0
N A:ASN174 4.5 26.4 1.0
O A:GLY175 4.5 27.0 1.0
O A:LEU183 4.5 24.3 1.0
N A:VAL218 4.6 19.6 1.0
ND1 A:HIS158 4.6 24.4 1.0
CE1 A:HIS158 4.6 23.9 1.0
CG2 A:VAL218 4.6 22.6 1.0
OE1 A:GLN185 4.7 25.1 1.0
CA A:VAL218 4.7 21.3 1.0
O A:VAL172 4.7 24.9 1.0
CB A:ASN139 4.7 19.1 1.0
CA A:ASN174 4.7 28.2 1.0
O A:HOH2175 4.8 23.6 1.0
NE2 A:GLN185 4.9 25.3 1.0
CA A:ASN139 4.9 19.7 1.0
C A:ASN174 5.0 26.5 1.0

Calcium binding site 2 out of 4 in 5a2b

Go back to Calcium Binding Sites List in 5a2b
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:Ca1480

b:22.5
occ:1.00
 OD2 A:ASP65 2.2 21.1 1.0
OD1 A:ASP50 2.3 23.1 1.0
OD1 A:ASN49 2.3 20.0 1.0
O A:HOH2046 2.4 22.1 1.0
OD1 A:ASN44 2.4 18.9 1.0
O A:ASN46 2.5 24.6 1.0
O A:GLY63 2.6 19.8 1.0
CG A:ASN44 3.2 20.6 1.0
CG A:ASP65 3.3 20.9 1.0
C A:ASN46 3.5 25.8 1.0
CG A:ASP50 3.5 23.9 1.0
CG A:ASN49 3.5 21.9 1.0
C A:GLY63 3.6 19.2 1.0
ND2 A:ASN44 3.7 20.1 1.0
CB A:ASP65 3.9 19.1 1.0
CA A:GLY63 4.0 19.0 1.0
OD2 A:ASP50 4.2 23.0 1.0
N A:ASN46 4.2 24.3 1.0
ND2 A:ASN49 4.2 20.0 1.0
N A:ASP50 4.3 24.0 1.0
C A:ASN49 4.3 24.2 1.0
CA A:PRO47 4.3 28.5 1.0
CA A:ASN46 4.3 25.5 1.0
O A:HIS111 4.3 21.1 1.0
N A:PRO47 4.3 28.1 1.0
CB A:ASN44 4.3 20.2 1.0
OD1 A:ASP65 4.4 19.9 1.0
CA A:ASN44 4.5 20.2 1.0
CA A:ASP50 4.6 23.6 1.0
CB A:ASN46 4.6 24.8 1.0
N A:ASN49 4.6 26.7 1.0
CB A:ASP50 4.6 23.6 1.0
CB A:ASN49 4.7 23.5 1.0
C A:PRO47 4.7 28.4 1.0
O A:ASN49 4.7 25.1 1.0
CA A:ASN49 4.7 25.3 1.0
N A:GLY64 4.7 18.4 1.0
O A:HOH2025 4.8 18.3 1.0
C A:GLY64 4.8 17.7 1.0
C A:ASN44 4.9 20.6 1.0
N A:GLY45 4.9 20.1 1.0
N A:ASP65 5.0 17.7 1.0

Calcium binding site 3 out of 4 in 5a2b

Go back to Calcium Binding Sites List in 5a2b
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:Ca1481

b:24.7
occ:1.00
 O A:HOH2098 2.4 22.1 1.0
O A:HOH2099 2.4 24.2 1.0
O A:HOH2116 2.4 25.0 1.0
O A:HOH2075 2.5 21.6 1.0
O A:ASN92 2.5 20.7 1.0
OE1 A:GLU109 2.5 21.2 1.0
O A:HOH2053 2.7 42.6 1.0
OE2 A:GLU109 2.7 22.3 1.0
CD A:GLU109 3.0 19.1 1.0
C A:ASN92 3.7 19.8 1.0
OE1 A:GLU110 3.8 32.9 1.0
N A:ASN92 4.2 20.7 1.0
OH A:TYR61 4.3 19.6 1.0
CA A:ASN92 4.4 20.3 1.0
CG A:GLU109 4.5 18.6 1.0
O A:GLU93 4.5 21.1 1.0
ND1 A:HIS111 4.6 26.7 1.0
OE2 A:GLU103 4.6 31.4 1.0
C A:GLU93 4.7 23.1 1.0
N A:GLU93 4.7 20.0 1.0
O A:HOH2108 4.8 40.0 1.0
O A:HOH2054 4.8 33.0 1.0
CA A:GLU93 4.8 22.3 1.0
CB A:ASN92 4.9 21.5 1.0
CE1 A:HIS111 4.9 25.6 1.0

Calcium binding site 4 out of 4 in 5a2b

Go back to Calcium Binding Sites List in 5a2b
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:Ca1482

b:24.9
occ:1.00
 O A:GLU400 2.3 17.8 1.0
O A:HOH2410 2.3 30.0 1.0
O A:HOH2351 2.4 35.2 1.0
O A:HOH2353 2.4 35.4 1.0
O A:HOH2352 2.5 20.6 1.0
O A:HOH2248 2.5 21.4 1.0
O A:HOH2350 2.7 30.1 1.0
C A:GLU400 3.5 20.0 1.0
O A:HOH2411 3.6 48.1 1.0
O A:HOH2247 4.1 41.3 1.0
CA A:GLU400 4.2 20.4 1.0
N A:GLU400 4.2 18.6 1.0
CB A:GLU400 4.4 19.7 1.0
OE1 A:GLU283 4.4 30.5 1.0
N A:LYS401 4.5 18.5 1.0
O A:HOH2354 4.5 25.5 1.0
OE1 A:GLU400 4.5 20.0 1.0
O A:HOH2347 4.6 29.8 1.0
CA A:LYS401 4.6 20.4 1.0
CD A:LYS401 4.9 35.5 1.0
CB A:LYS401 5.0 24.6 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 16:12:40 2024

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