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Calcium in PDB 9us6: Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase, Terbium Derivative

Enzymatic activity of Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase, Terbium Derivative

All present enzymatic activity of Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase, Terbium Derivative:
3.2.1.98;

Protein crystallography data

The structure of Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase, Terbium Derivative, PDB code: 9us6 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) 46.90 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.884, 107.496, 82.083, 90, 96.6, 90
R / Rfree (%) 16.4 / 22

Other elements in 9us6:

The structure of Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase, Terbium Derivative also contains other interesting chemical elements:

Terbium (Tb) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase, Terbium Derivative (pdb code 9us6). 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, Terbium Derivative, PDB code: 9us6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 9us6

Go back to Calcium Binding Sites List in 9us6
Calcium binding site 1 out of 4 in the Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase, Terbium Derivative


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, Terbium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:19.2
occ:1.00
 O A:HOH1012 2.3 14.0 1.0
O A:GLY225 2.4 16.8 1.0
OD2 A:ASP227 2.4 16.3 1.0
OD1 A:ASP207 2.4 20.9 1.0
O A:ASN203 2.4 22.1 1.0
OD1 A:ASN206 2.5 22.5 1.0
OD1 A:ASN201 2.5 16.5 1.0
C A:ASN203 3.4 22.1 1.0
CG A:ASP227 3.4 16.5 1.0
C A:GLY225 3.5 16.6 1.0
CG A:ASN201 3.5 16.6 1.0
CG A:ASN206 3.6 22.8 1.0
CG A:ASP207 3.6 21.1 1.0
CB A:ASP227 3.9 16.8 1.0
CA A:GLY225 4.0 16.3 1.0
ND2 A:ASN201 4.1 16.6 1.0
N A:PRO204 4.1 21.9 1.0
N A:ASN203 4.1 21.0 1.0
CA A:PRO204 4.1 21.9 1.0
ND2 A:ASN206 4.2 23.3 1.0
N A:ASP207 4.2 22.1 1.0
CA A:ASN203 4.3 22.1 1.0
O A:ASN286 4.3 19.6 1.0
OD2 A:ASP207 4.4 20.9 1.0
C A:ASN206 4.4 22.4 1.0
OD1 A:ASP227 4.5 15.7 1.0
CA A:ASP207 4.5 21.7 1.0
C A:PRO204 4.5 21.8 1.0
CB A:ASN201 4.6 16.6 1.0
N A:GLY226 4.6 16.5 1.0
N A:ASN206 4.6 22.6 1.0
CB A:ASP207 4.6 21.2 1.0
CA A:ASN201 4.6 16.8 1.0
C A:GLY226 4.7 17.2 1.0
N A:ASP227 4.8 17.1 1.0
CB A:ASN206 4.8 22.2 1.0
CB A:ASN203 4.8 22.3 1.0
O A:PRO204 4.8 21.8 1.0
CA A:ASN206 4.8 22.5 1.0
O A:ASN206 4.9 22.0 1.0
N A:GLY202 4.9 17.5 1.0
O A:GLY226 4.9 17.6 1.0
CA A:GLY226 4.9 16.8 1.0
C A:ASN201 5.0 17.0 1.0
CA A:ASP227 5.0 17.1 1.0

Calcium binding site 2 out of 4 in 9us6

Go back to Calcium Binding Sites List in 9us6
Calcium binding site 2 out of 4 in the Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase, Terbium Derivative


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, Terbium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:20.4
occ:1.00
 O A:HOH1257 2.2 12.4 1.0
O A:LEU397 2.3 26.2 1.0
O A:HOH1256 2.4 14.7 1.0
O A:HIS464 2.4 22.4 1.0
OD1 A:ASP406 2.5 22.0 1.0
O A:HOH1258 2.5 20.7 1.0
OD2 A:ASP406 2.5 21.7 1.0
OD1 A:ASN314 2.6 17.6 1.0
CG A:ASP406 2.8 22.2 1.0
C A:LEU397 3.3 26.5 1.0
C A:HIS464 3.6 22.8 1.0
CG A:ASN314 3.7 17.6 1.0
CA A:LEU397 4.1 27.3 1.0
NH1 A:ARG383 4.2 21.6 1.0
N A:THR398 4.2 26.6 1.0
O A:MET399 4.3 26.4 1.0
CB A:HIS464 4.3 23.2 1.0
O A:ASP396 4.3 30.8 1.0
ND2 A:ASN314 4.3 17.4 1.0
CB A:ASP406 4.3 22.5 1.0
CA A:THR398 4.4 26.8 1.0
O A:ASN314 4.4 18.9 1.0
O A:LEU407 4.5 25.6 1.0
CA A:HIS464 4.5 23.4 1.0
N A:VAL465 4.6 22.5 1.0
CG2 A:VAL465 4.6 21.5 1.0
CA A:VAL465 4.8 22.0 1.0
C A:THR398 4.8 26.5 1.0
CB A:ASN314 4.8 17.9 1.0
CA A:ASN314 4.9 18.2 1.0
O A:HOH1044 4.9 20.9 1.0
O A:HOH1033 4.9 19.9 1.0
N A:MET399 5.0 26.8 1.0

Calcium binding site 3 out of 4 in 9us6

Go back to Calcium Binding Sites List in 9us6
Calcium binding site 3 out of 4 in the Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase, Terbium Derivative


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, Terbium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:21.6
occ:1.00
 OD1 B:ASP207 2.2 20.0 1.0
OD2 B:ASP227 2.3 21.2 1.0
O B:ASN203 2.4 22.5 1.0
OD1 B:ASN206 2.4 22.8 1.0
O B:GLY225 2.4 22.4 1.0
OD1 B:ASN201 2.5 19.5 1.0
O B:HOH1131 2.7 15.3 1.0
C B:ASN203 3.4 22.6 1.0
CG B:ASP207 3.4 21.3 1.0
CG B:ASP227 3.4 21.4 1.0
C B:GLY225 3.5 22.5 1.0
CG B:ASN201 3.5 19.9 1.0
CG B:ASN206 3.5 22.9 1.0
CB B:ASP227 3.9 21.3 1.0
CA B:GLY225 4.0 22.7 1.0
ND2 B:ASN201 4.0 19.7 1.0
OD2 B:ASP207 4.0 21.4 1.0
ND2 B:ASN206 4.0 22.8 1.0
N B:ASN203 4.1 22.6 1.0
N B:PRO204 4.2 22.6 1.0
CA B:PRO204 4.2 22.4 1.0
CA B:ASN203 4.2 22.9 1.0
N B:ASP207 4.3 22.8 1.0
OD1 B:ASP227 4.4 20.5 1.0
C B:ASN206 4.5 22.9 1.0
O B:ASN286 4.5 26.3 1.0
CA B:ASP207 4.5 22.5 1.0
CB B:ASP207 4.5 21.7 1.0
C B:PRO204 4.5 22.2 1.0
N B:ASN206 4.6 22.9 1.0
CB B:ASN201 4.6 20.2 1.0
N B:GLY226 4.6 22.1 1.0
CB B:ASN203 4.6 23.7 1.0
CA B:ASN201 4.7 20.7 1.0
O B:PRO204 4.7 21.6 1.0
C B:GLY226 4.7 22.1 1.0
CB B:ASN206 4.7 23.0 1.0
N B:ASP227 4.7 21.4 1.0
CA B:ASN206 4.8 22.8 1.0
N B:GLY202 4.9 20.7 1.0
C B:ASN201 4.9 21.0 1.0
CA B:ASP227 4.9 21.2 1.0
CA B:GLY226 4.9 22.0 1.0
O B:GLY226 5.0 22.4 1.0
O B:ASN206 5.0 22.9 1.0

Calcium binding site 4 out of 4 in 9us6

Go back to Calcium Binding Sites List in 9us6
Calcium binding site 4 out of 4 in the Klebsiella Pneumoniae Maltohexaose-Producing Alpha-Amylase, Terbium Derivative


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, Terbium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:26.2
occ:1.00
 O B:LEU397 2.3 28.8 1.0
OD1 B:ASP406 2.4 27.0 1.0
O B:HIS464 2.4 26.8 1.0
O B:HOH1112 2.4 19.8 1.0
OD1 B:ASN314 2.4 25.4 1.0
O B:HOH1111 2.4 12.2 1.0
OD2 B:ASP406 2.6 26.6 1.0
O B:HOH1110 2.6 18.6 1.0
CG B:ASP406 2.8 26.9 1.0
C B:LEU397 3.4 28.4 1.0
C B:HIS464 3.6 28.2 1.0
CG B:ASN314 3.6 24.8 1.0
NH1 B:ARG383 4.1 27.3 1.0
O B:ASN314 4.2 22.7 1.0
CA B:LEU397 4.2 28.5 1.0
ND2 B:ASN314 4.3 24.8 1.0
CB B:ASP406 4.3 27.7 1.0
CG2 B:VAL465 4.3 28.7 1.0
CB B:HIS464 4.4 28.5 1.0
N B:THR398 4.4 28.3 1.0
CA B:HIS464 4.5 28.8 1.0
O B:ASP396 4.5 29.5 1.0
O B:MET399 4.5 25.6 1.0
N B:VAL465 4.5 28.4 1.0
CA B:THR398 4.6 27.9 1.0
CA B:VAL465 4.6 28.6 1.0
O B:LEU407 4.6 30.1 1.0
CB B:ASN314 4.7 24.4 1.0
CA B:ASN314 4.8 23.9 1.0
C B:ASN314 4.9 23.5 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 19:03:33 2025

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