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Calcium in PDB 3bh4: High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase

Enzymatic activity of High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase

All present enzymatic activity of High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase:
3.2.1.1;

Protein crystallography data

The structure of High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase, PDB code: 3bh4 was solved by J.Alikhajeh, K.Khajeh, B.Ranjbar, H.Naderi-Manesh, Y.H.Lin, M.Y.Liu, C.J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 89.760, 148.676, 76.197, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 21.9

Other elements in 3bh4:

The structure of High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase (pdb code 3bh4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase, PDB code: 3bh4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3bh4

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Calcium binding site 1 out of 8 in the High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca485

b:10.7
occ:1.00
 OD2 A:ASP408 2.4 12.8 1.0
O A:TYR303 2.4 11.8 1.0
O A:GLY301 2.5 11.9 1.0
O A:PRO407 2.5 9.9 1.0
OD1 A:ASP431 2.6 11.3 1.0
OD2 A:ASP431 2.6 12.3 1.0
O A:HOH505 2.8 17.5 1.0
CG A:ASP431 2.9 12.4 1.0
C A:PRO407 3.4 9.7 1.0
C A:GLY301 3.5 11.2 1.0
CG A:ASP408 3.5 13.9 1.0
C A:TYR303 3.5 11.2 1.0
CA A:ASP408 3.8 10.2 1.0
N A:TYR303 3.9 10.6 1.0
N A:ASP408 4.0 9.4 1.0
C A:GLY302 4.0 10.6 1.0
CB A:ASP408 4.2 11.1 1.0
CA A:GLY301 4.2 12.3 1.0
CA A:TYR303 4.3 10.2 1.0
N A:GLY302 4.3 11.3 1.0
CG A:MET305 4.3 9.0 1.0
O A:HOH686 4.3 23.6 1.0
CA A:GLY302 4.4 10.8 1.0
CB A:ASP431 4.5 11.5 1.0
OD1 A:ASP408 4.5 16.6 1.0
O A:GLY302 4.5 11.9 1.0
N A:MET305 4.5 10.2 1.0
CA A:PRO407 4.5 10.2 1.0
N A:ASP304 4.5 10.3 1.0
CB A:PRO407 4.6 12.3 1.0
CA A:ASP304 4.7 10.7 1.0
O A:HOH494 4.8 10.8 1.0
CB A:TYR303 4.9 11.2 1.0

Calcium binding site 2 out of 8 in 3bh4

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Calcium binding site 2 out of 8 in the High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca486

b:11.3
occ:1.00
 OD1 A:ASN103 2.4 11.8 1.0
O A:HIS236 2.4 12.2 1.0
O A:ASP195 2.5 12.9 1.0
OD1 A:ASP201 2.5 13.8 1.0
OD1 A:ASP195 2.5 14.4 1.0
O A:HOH506 2.7 16.5 1.0
CG A:ASP201 3.2 13.9 1.0
OD2 A:ASP201 3.3 15.6 1.0
C A:ASP195 3.3 13.5 1.0
CG A:ASP195 3.5 14.7 1.0
CG A:ASN103 3.5 11.2 1.0
C A:HIS236 3.6 10.8 1.0
O A:HOH495 3.8 13.0 1.0
CA A:ASP195 3.8 13.3 1.0
NA A:NA489 4.0 12.6 1.0
O A:ASN103 4.0 11.9 1.0
CB A:HIS236 4.1 11.9 1.0
ND2 A:ASN103 4.2 12.7 1.0
CB A:ASP195 4.3 14.7 1.0
OD2 A:ASP195 4.4 13.9 1.0
CA A:HIS236 4.4 10.8 1.0
O A:HOH498 4.4 12.3 1.0
N A:TYR196 4.4 13.0 1.0
N A:ILE237 4.5 10.7 1.0
CA A:ILE237 4.6 10.7 1.0
CB A:ASN103 4.6 12.3 1.0
CB A:ASP201 4.7 13.3 1.0
O A:VAL202 4.7 13.0 1.0
CA A:ASN103 4.7 11.6 1.0
CA A:TYR196 4.8 12.5 1.0
C A:ASN103 4.8 12.1 1.0
CG1 A:ILE237 4.8 11.0 1.0

Calcium binding site 3 out of 8 in 3bh4

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Calcium binding site 3 out of 8 in the High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca487

b:11.3
occ:1.00
 OD1 A:ASN445 2.5 11.9 1.0
OE2 A:GLU448 2.5 14.8 1.0
OE1 A:GLN483 2.6 17.4 1.0
OE1 A:GLU448 2.7 14.1 1.0
O A:HOH539 2.7 15.7 1.0
O A:HOH500 2.7 15.7 1.0
O A:HOH525 2.9 16.2 1.0
CD A:GLU448 2.9 13.6 1.0
O A:HOH550 2.9 23.4 1.0
CG A:ASN445 3.5 12.4 1.0
CD A:GLN483 3.5 18.1 1.0
NE2 A:GLN483 4.1 19.8 1.0
CB A:ASN445 4.1 12.4 1.0
NZ A:LYS444 4.2 13.1 1.0
O A:ALA421 4.3 14.1 1.0
O A:SER423 4.3 11.3 1.0
CA A:ASN445 4.3 12.9 1.0
CG A:GLU448 4.4 14.3 1.0
O A:LYS444 4.5 13.2 1.0
ND2 A:ASN445 4.6 12.3 1.0
CG A:GLN483 4.6 17.8 1.0
CB A:GLN483 4.7 16.4 1.0
CA A:LYS422 4.8 11.2 1.0
O A:HOH588 4.8 22.7 1.0
NE1 A:TRP450 4.9 12.6 1.0
C A:LYS422 4.9 12.0 1.0
CZ2 A:TRP450 5.0 11.3 1.0

Calcium binding site 4 out of 8 in 3bh4

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Calcium binding site 4 out of 8 in the High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca488

b:13.6
occ:1.00
 O A:ALA182 2.5 16.9 1.0
OD1 A:ASP184 2.5 15.5 1.0
OD2 A:ASP160 2.6 15.3 1.0
OD2 A:ASP205 2.6 17.4 1.0
OD1 A:ASP203 2.6 15.7 1.0
OD1 A:ASP160 2.6 16.3 1.0
CG A:ASP160 2.9 14.6 1.0
O A:HOH566 3.0 26.2 1.0
CG A:ASP203 3.3 16.2 1.0
CG A:ASP205 3.4 16.8 1.0
CG A:ASP184 3.5 14.9 1.0
C A:ALA182 3.7 17.5 1.0
CB A:ASP205 3.7 15.7 1.0
OD2 A:ASP203 3.7 15.6 1.0
N A:ASP184 3.7 14.2 1.0
C A:TRP183 4.1 15.2 1.0
CA A:ASP184 4.1 14.9 1.0
OD2 A:ASP184 4.1 12.8 1.0
N A:ALA182 4.2 20.1 1.0
CB A:ASP203 4.2 13.3 1.0
N A:ASP205 4.3 16.4 1.0
CA A:ASP203 4.4 13.8 1.0
CB A:ASP184 4.4 14.0 1.0
CB A:ASP160 4.4 13.7 1.0
OD1 A:ASP205 4.4 18.2 1.0
CA A:TRP183 4.5 15.4 1.0
N A:TRP183 4.5 15.8 1.0
O A:TRP183 4.6 15.8 1.0
NA A:NA489 4.6 12.6 1.0
CA A:ALA182 4.6 18.1 1.0
CA A:ASP205 4.6 16.4 1.0
N A:TYR204 4.7 13.5 1.0
O A:HOH688 4.7 19.4 1.0
C A:ASP203 4.7 13.3 1.0
OD2 A:ASP195 4.9 13.9 1.0
O A:GLY180 5.0 24.5 1.0

Calcium binding site 5 out of 8 in 3bh4

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Calcium binding site 5 out of 8 in the High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1

b:10.4
occ:1.00
 OD1 B:ASN103 2.4 11.7 1.0
O B:HIS236 2.4 10.8 1.0
O B:ASP195 2.4 11.1 1.0
OD1 B:ASP201 2.4 12.1 1.0
OD1 B:ASP195 2.5 11.4 1.0
O B:HOH492 2.7 14.9 1.0
CG B:ASP201 3.2 11.8 1.0
OD2 B:ASP201 3.2 12.5 1.0
C B:ASP195 3.3 10.1 1.0
CG B:ASP195 3.5 12.2 1.0
CG B:ASN103 3.5 10.5 1.0
CD1 B:ILE237 3.6 17.7 1.0
C B:HIS236 3.6 9.5 1.0
O B:HOH493 3.8 11.2 1.0
CA B:ASP195 3.8 10.3 1.0
NA B:NA488 4.0 10.9 1.0
O B:ASN103 4.0 10.1 1.0
CB B:HIS236 4.1 10.4 1.0
ND2 B:ASN103 4.2 11.9 1.0
CB B:ASP195 4.3 10.9 1.0
CA B:HIS236 4.4 10.0 1.0
OD2 B:ASP195 4.4 11.5 1.0
O B:HOH518 4.4 11.8 1.0
N B:TYR196 4.4 10.7 1.0
N B:ILE237 4.5 9.1 1.0
CB B:ASN103 4.6 10.5 1.0
CB B:ASP201 4.6 12.2 1.0
CA B:ILE237 4.6 10.3 1.0
O B:VAL202 4.6 11.8 1.0
CA B:TYR196 4.7 10.2 1.0
CA B:ASN103 4.8 9.9 1.0
C B:ASN103 4.8 9.6 1.0
CG1 B:ILE237 4.8 11.8 1.0

Calcium binding site 6 out of 8 in 3bh4

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Calcium binding site 6 out of 8 in the High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca485

b:10.5
occ:1.00
 O B:TYR303 2.4 11.8 1.0
OD1 B:ASP408 2.4 12.1 1.0
O B:GLY301 2.5 13.0 1.0
O B:PRO407 2.5 11.0 1.0
OD1 B:ASP431 2.6 11.4 1.0
OD2 B:ASP431 2.6 11.4 1.0
O B:HOH516 2.8 17.9 1.0
CG B:ASP431 2.9 11.8 1.0
C B:PRO407 3.4 10.3 1.0
C B:GLY301 3.4 11.7 1.0
C B:TYR303 3.6 10.7 1.0
CG B:ASP408 3.6 12.9 1.0
CA B:ASP408 3.8 10.7 1.0
N B:TYR303 3.9 9.9 1.0
N B:ASP408 3.9 10.6 1.0
C B:GLY302 4.0 10.4 1.0
CB B:ASP408 4.2 12.5 1.0
CA B:GLY301 4.3 12.1 1.0
N B:GLY302 4.3 11.0 1.0
CG B:MET305 4.3 11.2 1.0
CA B:TYR303 4.3 10.7 1.0
CA B:GLY302 4.4 11.2 1.0
O B:GLY302 4.4 11.1 1.0
CB B:ASP431 4.4 11.9 1.0
N B:MET305 4.5 10.2 1.0
CA B:PRO407 4.5 11.2 1.0
N B:ASP304 4.5 11.2 1.0
CB B:PRO407 4.6 11.5 1.0
OD2 B:ASP408 4.6 15.9 1.0
CA B:ASP304 4.6 10.6 1.0
O B:HOH501 4.7 10.9 1.0
CB B:TYR303 4.9 10.6 1.0

Calcium binding site 7 out of 8 in 3bh4

Go back to Calcium Binding Sites List in 3bh4
Calcium binding site 7 out of 8 in the High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca486

b:11.2
occ:1.00
 O B:ALA182 2.4 13.7 1.0
OD1 B:ASP184 2.4 13.1 1.0
OD1 B:ASP203 2.5 12.3 1.0
OD2 B:ASP205 2.5 12.3 1.0
OD2 B:ASP160 2.6 12.0 1.0
OD1 B:ASP160 2.6 12.9 1.0
O B:HOH511 2.8 16.0 1.0
CG B:ASP160 2.9 12.3 1.0
CG B:ASP203 3.3 13.7 1.0
CG B:ASP205 3.4 11.3 1.0
CG B:ASP184 3.4 11.5 1.0
C B:ALA182 3.6 15.0 1.0
CB B:ASP205 3.7 12.5 1.0
OD2 B:ASP203 3.7 14.0 1.0
N B:ASP184 3.7 12.0 1.0
C B:TRP183 4.0 13.9 1.0
OD2 B:ASP184 4.1 11.5 1.0
CA B:ASP184 4.1 11.9 1.0
CB B:ASP203 4.2 12.5 1.0
N B:ALA182 4.2 16.8 1.0
N B:ASP205 4.3 12.0 1.0
CA B:ASP203 4.4 11.4 1.0
OD1 B:ASP205 4.4 13.9 1.0
CB B:ASP160 4.4 12.2 1.0
CB B:ASP184 4.4 11.5 1.0
CA B:TRP183 4.4 13.6 1.0
N B:TRP183 4.5 14.6 1.0
O B:TRP183 4.5 14.3 1.0
NA B:NA488 4.5 10.9 1.0
CA B:ALA182 4.6 16.0 1.0
O B:HOH719 4.6 23.0 1.0
O B:HOH593 4.6 16.5 1.0
N B:TYR204 4.6 10.2 1.0
CA B:ASP205 4.7 11.8 1.0
C B:ASP203 4.7 11.4 1.0
O B:HOH649 4.8 20.6 1.0
OD2 B:ASP195 4.8 11.5 1.0

Calcium binding site 8 out of 8 in 3bh4

Go back to Calcium Binding Sites List in 3bh4
Calcium binding site 8 out of 8 in the High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of High Resolution Crystal Structure of Bacillus Amyloliquefaciens Alpha- Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca487

b:12.5
occ:1.00
 OD1 B:ASN445 2.5 14.0 1.0
OE2 B:GLU448 2.6 15.9 1.0
NE2 B:GLN483 2.6 13.7 1.0
OE1 B:GLU448 2.7 14.3 1.0
O B:HOH523 2.8 18.8 1.0
O B:HOH546 2.8 18.7 1.0
O B:HOH558 2.9 20.1 1.0
CD B:GLU448 3.0 14.9 1.0
O B:HOH573 3.0 24.8 1.0
CG B:ASN445 3.6 13.6 1.0
CD B:GLN483 3.6 17.8 1.0
OE1 B:GLN483 4.1 19.9 1.0
CB B:ASN445 4.2 14.4 1.0
NZ B:LYS444 4.2 14.6 1.0
O B:SER423 4.3 12.9 1.0
CA B:ASN445 4.4 13.9 1.0
O B:LYS444 4.4 15.6 1.0
CG B:GLU448 4.5 15.0 1.0
CB B:GLN483 4.6 16.3 1.0
ND2 B:ASN445 4.6 13.6 1.0
CG B:GLN483 4.6 16.0 1.0
CA B:LYS422 4.6 17.6 1.0
C B:LYS422 4.8 14.7 1.0
O B:HOH658 4.8 25.7 1.0
NE1 B:TRP450 4.9 13.5 1.0

Reference:

J.Alikhajeh, K.Khajeh, B.Ranjbar, H.Naderi-Manesh, Y.H.Lin, E.Liu, H.H.Guan, Y.C.Hsieh, P.Chuankhayan, Y.C.Huang, J.Jeyaraman, M.Y.Liu, C.J.Chen. Structure of Bacillus Amyloliquefaciens Alpha-Amylase at High Resolution: Implications For Thermal Stability. Acta Crystallogr.,Sect.F V. 66 121 2010.
ISSN: ESSN 1744-3091
PubMed: 20124706
DOI: 10.1107/S1744309109051938
Page generated: Sat Jul 13 08:17:05 2024

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