Atomistry » Calcium » PDB 4zmp-5a3o » 5a2c
Atomistry »
  Calcium »
    PDB 4zmp-5a3o »
      5a2c »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy