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Calcium in PDB 9us4: Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase in Complex with Acarbose

Enzymatic activity of Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase in Complex with Acarbose

All present enzymatic activity of Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase in Complex with Acarbose:
3.2.1.98;

Protein crystallography data

The structure of Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase in Complex with Acarbose, PDB code: 9us4 was solved by Z.Fujimoto, N.Kishine, M.Momma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.68 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.913, 108.244, 82.284, 90, 96.77, 90
R / Rfree (%) 18.9 / 22.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase in Complex with Acarbose (pdb code 9us4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase in Complex with Acarbose, PDB code: 9us4:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 9us4

Go back to Calcium Binding Sites List in 9us4
Calcium binding site 1 out of 4 in the Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:11.3
occ:1.00
 OD2 A:ASP227 2.3 12.0 1.0
O A:GLY225 2.3 11.1 1.0
OD1 A:ASP207 2.4 13.6 1.0
OD1 A:ASN206 2.4 13.8 1.0
O A:ASN203 2.4 14.7 1.0
O A:HOH971 2.5 8.7 1.0
OD1 A:ASN201 2.5 12.1 1.0
CG A:ASN201 3.4 12.0 1.0
C A:ASN203 3.4 14.7 1.0
CG A:ASP227 3.4 12.0 1.0
C A:GLY225 3.4 11.2 1.0
CG A:ASN206 3.5 14.1 1.0
CG A:ASP207 3.6 13.7 1.0
ND2 A:ASN201 3.9 11.9 1.0
CA A:GLY225 3.9 11.3 1.0
CB A:ASP227 3.9 12.0 1.0
ND2 A:ASN206 4.1 14.2 1.0
N A:ASN203 4.1 14.2 1.0
N A:PRO204 4.2 15.0 1.0
N A:ASP207 4.2 13.8 1.0
CA A:PRO204 4.2 14.9 1.0
CA A:ASN203 4.3 14.5 1.0
OD2 A:ASP207 4.3 13.7 1.0
O A:ASN286 4.4 13.8 1.0
CA A:ASP207 4.4 13.8 1.0
OD1 A:ASP227 4.4 11.9 1.0
CB A:ASN201 4.4 12.0 1.0
C A:ASN206 4.5 13.9 1.0
CA A:ASN201 4.5 11.9 1.0
N A:GLY226 4.6 11.3 1.0
CB A:ASP207 4.6 13.8 1.0
C A:PRO204 4.6 14.9 1.0
C A:GLY226 4.7 11.4 1.0
N A:ASN206 4.7 14.1 1.0
CB A:ASN206 4.7 14.0 1.0
N A:ASP227 4.8 11.7 1.0
N A:GLY202 4.8 12.5 1.0
CB A:ASN203 4.8 14.7 1.0
O A:GLY226 4.8 11.3 1.0
CA A:ASN206 4.9 14.1 1.0
C A:ASN201 4.9 12.2 1.0
O A:HOH847 4.9 12.1 1.0
O A:PRO204 4.9 14.8 1.0
CA A:GLY226 5.0 11.3 1.0
CA A:ASP227 5.0 12.0 1.0

Calcium binding site 2 out of 4 in 9us4

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Calcium binding site 2 out of 4 in the Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:13.0
occ:1.00
 O A:HIS464 2.3 14.7 1.0
O A:LEU397 2.4 15.3 1.0
O A:HOH855 2.4 8.0 1.0
O A:HOH826 2.5 12.4 1.0
OD1 A:ASN314 2.5 12.6 1.0
OD1 A:ASP406 2.5 14.2 1.0
O A:HOH904 2.5 10.8 1.0
OD2 A:ASP406 2.7 13.8 1.0
CG A:ASP406 2.9 14.0 1.0
C A:LEU397 3.4 15.3 1.0
C A:HIS464 3.6 14.7 1.0
CG A:ASN314 3.6 12.9 1.0
O A:ASN314 4.2 12.3 1.0
CA A:LEU397 4.3 15.6 1.0
CB A:HIS464 4.3 14.5 1.0
N A:THR398 4.3 15.3 1.0
ND2 A:ASN314 4.4 12.9 1.0
CA A:HIS464 4.4 14.7 1.0
NH1 A:ARG383 4.4 14.2 1.0
CB A:ASP406 4.4 14.0 1.0
CG2 A:VAL465 4.4 14.5 1.0
O A:LEU407 4.5 13.9 1.0
O A:ASP396 4.5 16.0 1.0
O A:MET399 4.5 15.9 1.0
N A:VAL465 4.5 14.7 1.0
CA A:THR398 4.5 15.4 1.0
CB A:ASN314 4.6 12.7 1.0
CA A:ASN314 4.7 12.6 1.0
CA A:VAL465 4.7 14.9 1.0
C A:ASN314 4.9 12.5 1.0

Calcium binding site 3 out of 4 in 9us4

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Calcium binding site 3 out of 4 in the Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:15.7
occ:1.00
 OD1 B:ASP207 2.2 17.4 1.0
O B:GLY225 2.3 15.9 1.0
OD1 B:ASN206 2.3 15.1 1.0
OD2 B:ASP227 2.4 14.7 1.0
O B:HOH924 2.4 16.5 1.0
O B:ASN203 2.4 16.3 1.0
OD1 B:ASN201 2.5 16.2 1.0
C B:GLY225 3.4 15.6 1.0
C B:ASN203 3.5 16.7 1.0
CG B:ASN201 3.5 16.3 1.0
CG B:ASP227 3.5 14.7 1.0
CG B:ASP207 3.5 17.4 1.0
CG B:ASN206 3.5 15.6 1.0
CA B:GLY225 3.9 15.6 1.0
CB B:ASP227 4.0 14.9 1.0
ND2 B:ASN201 4.0 16.0 1.0
ND2 B:ASN206 4.1 15.5 1.0
N B:ASP207 4.2 17.0 1.0
N B:ASN203 4.2 16.8 1.0
OD2 B:ASP207 4.2 17.7 1.0
N B:PRO204 4.3 16.8 1.0
CA B:PRO204 4.3 16.9 1.0
CA B:ASP207 4.3 17.3 1.0
CA B:ASN203 4.3 16.7 1.0
O B:ASN286 4.4 18.1 1.0
C B:ASN206 4.4 16.2 1.0
OD1 B:ASP227 4.5 14.8 1.0
CB B:ASP207 4.5 17.4 1.0
CB B:ASN201 4.5 16.4 1.0
CA B:ASN201 4.6 16.6 1.0
N B:GLY226 4.6 15.4 1.0
C B:PRO204 4.6 16.7 1.0
C B:GLY226 4.7 15.2 1.0
N B:ASN206 4.7 15.8 1.0
CB B:ASN206 4.7 15.7 1.0
N B:ASP227 4.8 15.0 1.0
N B:GLY202 4.8 17.0 1.0
O B:GLY226 4.8 15.4 1.0
CA B:ASN206 4.8 16.0 1.0
CB B:ASN203 4.8 16.6 1.0
O B:PRO204 4.9 17.0 1.0
C B:ASN201 4.9 16.8 1.0
O B:ASN206 5.0 16.3 1.0
CA B:GLY226 5.0 15.2 1.0
O B:HOH836 5.0 19.4 1.0

Calcium binding site 4 out of 4 in 9us4

Go back to Calcium Binding Sites List in 9us4
Calcium binding site 4 out of 4 in the Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:15.1
occ:1.00
 O B:HIS464 2.2 18.1 1.0
O B:LEU397 2.4 18.6 1.0
OD1 B:ASN314 2.4 16.5 1.0
OD1 B:ASP406 2.4 17.9 1.0
O B:HOH970 2.5 16.5 1.0
O B:HOH829 2.5 14.2 1.0
O B:HOH938 2.6 12.1 1.0
OD2 B:ASP406 2.8 18.0 1.0
CG B:ASP406 2.9 18.2 1.0
C B:LEU397 3.4 19.0 1.0
C B:HIS464 3.4 18.2 1.0
CG B:ASN314 3.6 16.6 1.0
O B:ASN314 4.2 15.9 1.0
CB B:HIS464 4.2 17.9 1.0
CA B:LEU397 4.2 18.9 1.0
CA B:HIS464 4.3 18.3 1.0
ND2 B:ASN314 4.3 16.6 1.0
N B:THR398 4.3 19.1 1.0
N B:VAL465 4.4 18.5 1.0
O B:ASP396 4.4 18.9 1.0
CG2 B:VAL465 4.4 18.7 1.0
CB B:ASP406 4.4 17.9 1.0
O B:MET399 4.5 19.4 1.0
NH2 B:ARG383 4.5 18.4 1.0
CA B:THR398 4.5 19.3 1.0
O B:LEU407 4.6 17.7 1.0
CB B:ASN314 4.6 16.5 1.0
CA B:VAL465 4.6 18.7 1.0
CA B:ASN314 4.7 16.5 1.0
C B:ASN314 4.9 16.2 1.0
O B:HOH978 5.0 18.3 1.0
O B:HOH1045 5.0 17.2 1.0

Reference:

Z.Fujimoto, N.Kishine, M.Momma. Crystal Structure of Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase. J.Biochem. 2025.
ISSN: ISSN 0021-924X
PubMed: 40576559
DOI: 10.1093/JB/MVAF034
Page generated: Mon Aug 4 19:02:07 2025

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