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Calcium in PDB 1h3g: Cyclomaltodextrinase From Flavobacterium Sp. No. 92: From Dna Sequence to Protein Structure

Enzymatic activity of Cyclomaltodextrinase From Flavobacterium Sp. No. 92: From Dna Sequence to Protein Structure

All present enzymatic activity of Cyclomaltodextrinase From Flavobacterium Sp. No. 92: From Dna Sequence to Protein Structure:
3.2.1.54;

Protein crystallography data

The structure of Cyclomaltodextrinase From Flavobacterium Sp. No. 92: From Dna Sequence to Protein Structure, PDB code: 1h3g was solved by H.B.Fritzsche, T.Schwede, S.Jelakovic, G.E.Schulz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.10 / 2.10
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.339, 181.339, 231.511, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 22.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Cyclomaltodextrinase From Flavobacterium Sp. No. 92: From Dna Sequence to Protein Structure (pdb code 1h3g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cyclomaltodextrinase From Flavobacterium Sp. No. 92: From Dna Sequence to Protein Structure, PDB code: 1h3g:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1h3g

Go back to Calcium Binding Sites List in 1h3g
Calcium binding site 1 out of 4 in the Cyclomaltodextrinase From Flavobacterium Sp. No. 92: From Dna Sequence to Protein Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cyclomaltodextrinase From Flavobacterium Sp. No. 92: From Dna Sequence to Protein Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca700

b:34.1
occ:1.00
 OD1 A:ASP125 2.2 26.9 1.0
OD1 A:ASN124 2.2 24.5 1.0
OD1 A:ASP146 2.3 23.6 1.0
OD1 A:ASN119 2.4 24.0 1.0
O A:GLY144 2.4 21.3 1.0
O A:HOH2093 2.4 34.0 1.0
O A:ASP121 2.5 28.1 1.0
CG A:ASN119 3.3 26.3 1.0
C A:ASP121 3.3 29.2 1.0
CG A:ASP146 3.3 21.9 1.0
CG A:ASN124 3.4 25.0 1.0
C A:GLY144 3.5 20.9 1.0
CG A:ASP125 3.5 26.5 1.0
CB A:ASP146 3.8 21.5 1.0
ND2 A:ASN119 3.8 27.4 1.0
N A:ASP125 3.8 26.2 1.0
CA A:GLY144 4.0 20.8 1.0
ND2 A:ASN124 4.0 24.5 1.0
N A:PRO122 4.0 29.2 1.0
CA A:PRO122 4.1 29.1 1.0
N A:ASP121 4.1 29.7 1.0
CA A:ASP125 4.2 26.9 1.0
CA A:ASP121 4.2 29.5 1.0
OD2 A:ASP125 4.2 28.8 1.0
C A:ASN124 4.3 26.2 1.0
OD2 A:ASP146 4.3 23.6 1.0
O A:ARG194 4.4 24.3 1.0
CB A:ASN119 4.4 25.5 1.0
CB A:ASP125 4.4 27.0 1.0
CA A:ASN119 4.4 25.7 1.0
C A:GLY145 4.5 20.9 1.0
C A:PRO122 4.5 28.7 1.0
N A:ASN124 4.5 26.7 1.0
CB A:ASP121 4.6 30.4 1.0
O A:GLY145 4.6 20.3 1.0
N A:GLY145 4.6 21.1 1.0
CB A:ASN124 4.6 26.7 1.0
N A:ASP146 4.7 20.7 1.0
CA A:ASN124 4.7 26.2 1.0
O A:PRO122 4.8 28.2 1.0
O A:ASN124 4.8 25.1 1.0
C A:ASN119 4.8 26.6 1.0
CA A:ASP146 4.9 21.6 1.0
N A:GLY120 4.9 27.5 1.0
CA A:GLY145 4.9 20.9 1.0

Calcium binding site 2 out of 4 in 1h3g

Go back to Calcium Binding Sites List in 1h3g
Calcium binding site 2 out of 4 in the Cyclomaltodextrinase From Flavobacterium Sp. No. 92: From Dna Sequence to Protein Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cyclomaltodextrinase From Flavobacterium Sp. No. 92: From Dna Sequence to Protein Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:35.3
occ:1.00
 O A:HOH2184 2.2 34.4 1.0
OD2 A:ASP280 2.2 27.2 1.0
O A:TYR315 2.3 20.4 1.0
O A:THR270 2.3 22.2 1.0
O A:HOH2209 2.4 27.4 1.0
OG A:SER222 2.6 30.4 1.0
CG A:ASP280 3.0 23.2 1.0
OD1 A:ASP280 3.0 26.6 1.0
O A:HOH2216 3.0 39.1 1.0
C A:THR270 3.1 23.1 1.0
C A:TYR315 3.4 22.2 1.0
CA A:THR270 3.8 22.5 1.0
CB A:SER222 3.9 25.3 1.0
O A:SER222 4.0 22.9 1.0
N A:LYS271 4.0 24.3 1.0
CB A:TYR315 4.2 22.1 1.0
CA A:TYR315 4.3 22.2 1.0
N A:SER316 4.3 22.1 1.0
CA A:LYS271 4.3 25.7 1.0
CA A:SER316 4.4 22.2 1.0
O A:GLY272 4.4 25.3 1.0
CB A:ASP280 4.4 22.4 1.0
CA A:SER222 4.4 24.4 1.0
O A:PHE269 4.4 22.6 1.0
C A:SER222 4.6 23.5 1.0
OE1 A:GLN283 4.6 34.2 1.0
CB A:THR270 4.6 23.1 1.0
C A:LYS271 4.7 25.4 1.0
O A:LEU281 4.8 20.6 1.0
N A:THR270 4.9 22.3 1.0

Calcium binding site 3 out of 4 in 1h3g

Go back to Calcium Binding Sites List in 1h3g
Calcium binding site 3 out of 4 in the Cyclomaltodextrinase From Flavobacterium Sp. No. 92: From Dna Sequence to Protein Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cyclomaltodextrinase From Flavobacterium Sp. No. 92: From Dna Sequence to Protein Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca700

b:42.0
occ:1.00
 O B:ASP121 2.2 33.3 1.0
OD1 B:ASN124 2.3 30.8 1.0
OD1 B:ASP146 2.3 29.7 1.0
OD1 B:ASP125 2.3 31.9 1.0
O B:GLY144 2.3 27.9 1.0
O B:HOH2125 2.5 41.4 1.0
OD1 B:ASN119 2.7 29.4 1.0
CG B:ASP146 3.3 29.2 1.0
C B:ASP121 3.3 33.2 1.0
CG B:ASN119 3.3 31.8 1.0
C B:GLY144 3.4 28.3 1.0
CG B:ASN124 3.5 32.7 1.0
CG B:ASP125 3.5 33.0 1.0
CB B:ASP146 3.7 28.9 1.0
ND2 B:ASN119 3.7 34.2 1.0
N B:ASP125 3.9 33.2 1.0
CA B:GLY144 4.0 28.3 1.0
N B:PRO122 4.1 33.1 1.0
ND2 B:ASN124 4.1 32.1 1.0
CA B:ASP125 4.1 33.4 1.0
CA B:PRO122 4.1 33.2 1.0
N B:ASP121 4.2 32.6 1.0
C B:ASN124 4.2 33.5 1.0
CA B:ASP121 4.2 33.3 1.0
O B:ARG194 4.3 29.6 1.0
OD2 B:ASP125 4.3 29.7 1.0
OD2 B:ASP146 4.3 29.2 1.0
C B:GLY145 4.4 28.7 1.0
CB B:ASN119 4.4 31.2 1.0
CB B:ASP125 4.5 33.5 1.0
O B:GLY145 4.5 29.6 1.0
CA B:ASN119 4.5 31.1 1.0
N B:GLY145 4.6 28.3 1.0
N B:ASP146 4.6 28.6 1.0
C B:PRO122 4.6 32.9 1.0
N B:ASN124 4.6 33.3 1.0
CB B:ASP121 4.6 33.6 1.0
CB B:ASN124 4.7 33.2 1.0
CA B:ASN124 4.7 33.4 1.0
O B:ASN124 4.7 33.1 1.0
CA B:ASP146 4.7 28.8 1.0
O B:PRO122 4.8 32.6 1.0
CA B:GLY145 4.9 28.7 1.0
C B:ASN119 4.9 31.4 1.0

Calcium binding site 4 out of 4 in 1h3g

Go back to Calcium Binding Sites List in 1h3g
Calcium binding site 4 out of 4 in the Cyclomaltodextrinase From Flavobacterium Sp. No. 92: From Dna Sequence to Protein Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cyclomaltodextrinase From Flavobacterium Sp. No. 92: From Dna Sequence to Protein Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:41.0
occ:1.00
 O B:HOH2163 2.2 39.9 1.0
O B:THR270 2.3 25.7 1.0
O B:TYR315 2.4 25.4 1.0
OG B:SER222 2.4 33.4 1.0
OD2 B:ASP280 2.5 30.8 1.0
O B:HOH2158 2.5 35.5 1.0
OD1 B:ASP280 2.7 28.8 1.0
CG B:ASP280 3.0 29.1 1.0
C B:THR270 3.2 26.4 1.0
C B:TYR315 3.5 26.4 1.0
CB B:SER222 3.7 29.1 1.0
CA B:THR270 3.9 26.2 1.0
O B:SER222 3.9 28.1 1.0
N B:LYS271 4.1 27.0 1.0
CB B:TYR315 4.3 25.7 1.0
CA B:SER222 4.3 28.9 1.0
N B:SER316 4.3 26.9 1.0
CA B:SER316 4.4 27.1 1.0
CA B:TYR315 4.4 25.8 1.0
CA B:LYS271 4.4 28.2 1.0
CB B:ASP280 4.5 28.2 1.0
C B:SER222 4.5 28.3 1.0
O B:GLY272 4.5 30.1 1.0
OE1 B:GLN283 4.5 32.2 1.0
O B:PHE269 4.6 25.0 1.0
O B:LEU281 4.6 26.7 1.0
CB B:THR270 4.7 26.1 1.0
C B:LYS271 4.8 28.9 1.0
O B:HOH2164 5.0 26.6 1.0

Reference:

H.B.Fritzsche, T.Schwede, G.E.Schulz. Covalent and Three-Dimensional Structure of the Cyclodextrinase From Flavobacterium Sp. No. 92. Eur.J.Biochem. V. 270 2332 2003.
ISSN: ISSN 0014-2956
PubMed: 12752453
DOI: 10.1046/J.1432-1033.2003.03603.X
Page generated: Thu Jul 11 09:50:00 2024

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