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Calcium in PDB 6wni: Crystal Structure of Clda, the First Cyclomaltodextrin Glucanotransferase with A Three-Domain Abc Distribution

Enzymatic activity of Crystal Structure of Clda, the First Cyclomaltodextrin Glucanotransferase with A Three-Domain Abc Distribution

All present enzymatic activity of Crystal Structure of Clda, the First Cyclomaltodextrin Glucanotransferase with A Three-Domain Abc Distribution:
2.4.1.19;

Protein crystallography data

The structure of Crystal Structure of Clda, the First Cyclomaltodextrin Glucanotransferase with A Three-Domain Abc Distribution, PDB code: 6wni was solved by E.Magana-Cuevas, S.Centeno-Leija, H.Serrano-Posada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.50 / 1.66
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 66.44, 66.44, 209.5, 90, 90, 120
R / Rfree (%) 18.8 / 21.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Clda, the First Cyclomaltodextrin Glucanotransferase with A Three-Domain Abc Distribution (pdb code 6wni). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Clda, the First Cyclomaltodextrin Glucanotransferase with A Three-Domain Abc Distribution, PDB code: 6wni:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6wni

Go back to Calcium Binding Sites List in 6wni
Calcium binding site 1 out of 6 in the Crystal Structure of Clda, the First Cyclomaltodextrin Glucanotransferase with A Three-Domain Abc Distribution


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 Clda, the First Cyclomaltodextrin Glucanotransferase with A Three-Domain Abc Distribution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:22.9
occ:1.00
 O A:HIS254 2.4 22.7 1.0
O A:HOH840 2.4 28.8 1.0
OD2 A:ASP220 2.4 25.6 1.0
O A:HOH793 2.4 26.8 1.0
OD1 A:ASN159 2.5 22.1 1.0
O A:HOH737 2.5 20.9 1.0
O A:GLN211 2.5 25.1 1.0
OD1 A:ASP220 2.7 24.4 1.0
CG A:ASP220 2.9 27.1 1.0
C A:GLN211 3.6 32.6 1.0
CG A:ASN159 3.6 20.6 1.0
C A:HIS254 3.6 19.7 1.0
CA A:GLN211 4.1 30.0 1.0
ND2 A:ASN159 4.2 17.2 1.0
O A:LEU221 4.2 25.0 1.0
O A:ASN159 4.3 18.8 1.0
CB A:HIS254 4.3 22.4 1.0
CG A:MET255 4.4 29.9 1.0
CB A:ASP220 4.4 26.2 1.0
CA A:MET255 4.4 28.1 1.0
N A:MET255 4.4 19.9 1.0
O A:LEU210 4.5 31.6 1.0
CA A:HIS254 4.5 25.6 1.0
O A:LYS213 4.6 24.8 1.0
OE1 A:GLN223 4.7 25.3 1.0
ND1 A:HIS196 4.7 29.8 1.0
N A:ASP212 4.7 31.8 1.0
O A:HOH930 4.7 33.1 1.0
CB A:ASN159 4.7 18.0 1.0
CE1 A:HIS196 4.8 29.2 1.0
NE2 A:GLN223 4.9 21.5 1.0
CA A:ASN159 5.0 18.9 1.0
CB A:GLN211 5.0 33.0 1.0

Calcium binding site 2 out of 6 in 6wni

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Calcium binding site 2 out of 6 in the Crystal Structure of Clda, the First Cyclomaltodextrin Glucanotransferase with A Three-Domain Abc Distribution


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 Clda, the First Cyclomaltodextrin Glucanotransferase with A Three-Domain Abc Distribution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:17.8
occ:1.00
 OD1 A:ASP52 2.3 17.6 1.0
OD2 A:ASP75 2.3 14.8 1.0
O A:ASP48 2.4 19.8 1.0
OD1 A:ASN51 2.4 20.2 1.0
OD1 A:ASN46 2.4 17.1 1.0
O A:HOH820 2.5 14.2 1.0
O A:GLY73 2.5 16.9 1.0
CG A:ASN46 3.2 18.9 1.0
CG A:ASP75 3.4 15.9 1.0
C A:ASP48 3.5 18.0 1.0
CG A:ASP52 3.5 24.0 1.0
C A:GLY73 3.6 17.0 1.0
CG A:ASN51 3.6 19.4 1.0
ND2 A:ASN46 3.7 19.1 1.0
CB A:ASP75 3.9 15.5 1.0
N A:ASP52 4.0 19.0 1.0
CA A:GLY73 4.0 14.3 1.0
N A:ASP48 4.1 20.7 1.0
ND2 A:ASN51 4.2 16.2 1.0
CA A:ASP52 4.2 20.6 1.0
CA A:ASP48 4.2 19.4 1.0
C A:ASN51 4.3 23.3 1.0
OD2 A:ASP52 4.3 23.5 1.0
CB A:ASN46 4.3 16.6 1.0
N A:PRO49 4.4 20.2 1.0
O A:HIS131 4.4 16.2 1.0
OD1 A:ASP75 4.4 15.0 1.0
CA A:PRO49 4.5 23.0 1.0
CB A:ASP52 4.5 19.9 1.0
CA A:ASN46 4.5 17.2 1.0
CB A:ASP48 4.6 21.4 1.0
N A:GLY74 4.7 14.7 1.0
C A:GLY74 4.7 13.7 1.0
N A:ASN51 4.7 21.6 1.0
O A:ASN51 4.8 18.4 1.0
CB A:ASN51 4.8 16.6 1.0
O A:HOH742 4.8 15.3 1.0
CA A:ASN51 4.8 17.8 1.0
O A:GLY74 4.8 16.5 1.0
N A:GLY47 4.8 17.1 1.0
C A:PRO49 4.9 19.2 1.0
C A:ASN46 4.9 17.9 1.0
N A:ASP75 4.9 14.7 1.0

Calcium binding site 3 out of 6 in 6wni

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Calcium binding site 3 out of 6 in the Crystal Structure of Clda, the First Cyclomaltodextrin Glucanotransferase with A Three-Domain Abc Distribution


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 Clda, the First Cyclomaltodextrin Glucanotransferase with A Three-Domain Abc Distribution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:15.0
occ:1.00
 OD1 A:ASN104 2.3 16.3 1.0
OD1 A:ASP101 2.4 16.8 1.0
O A:HOH906 2.4 15.2 1.0
OE2 A:GLU130 2.5 15.6 1.0
O A:ASN102 2.5 16.4 1.0
OE1 A:GLU129 2.5 15.2 1.0
OE1 A:GLU130 2.6 16.6 1.0
CD A:GLU130 2.9 16.5 1.0
OE2 A:GLU129 2.9 15.3 1.0
CD A:GLU129 3.0 13.4 1.0
CG A:ASN104 3.5 16.8 1.0
C A:ASN102 3.6 15.6 1.0
CG A:ASP101 3.6 17.8 1.0
N A:ASN102 3.7 12.1 1.0
O A:HOH824 4.0 18.4 1.0
O A:ILE103 4.2 16.3 1.0
CA A:ASN102 4.2 12.9 1.0
ND2 A:ASN104 4.2 17.8 1.0
C A:ILE103 4.3 19.2 1.0
OD2 A:ASP101 4.3 17.7 1.0
CG A:GLU130 4.4 14.3 1.0
C A:ASP101 4.5 18.8 1.0
CD A:ARG123 4.5 20.4 1.0
CG A:GLU129 4.5 14.5 1.0
N A:GLU130 4.5 13.9 1.0
CA A:ASN104 4.5 16.6 1.0
N A:ASN104 4.5 15.2 1.0
ND1 A:HIS131 4.6 16.6 1.0
CA A:ASP101 4.6 11.8 1.0
CB A:ASN104 4.6 14.7 1.0
OG A:SER57 4.6 17.4 1.0
CB A:SER57 4.6 14.3 1.0
N A:ILE103 4.7 14.8 1.0
CB A:ASP101 4.7 14.1 1.0
OH A:TYR71 4.8 15.6 1.0
CA A:GLU129 4.8 13.4 1.0
CB A:ASN102 4.8 12.3 1.0
CE1 A:HIS131 4.9 13.4 1.0
CA A:ILE103 5.0 19.3 1.0

Calcium binding site 4 out of 6 in 6wni

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Calcium binding site 4 out of 6 in the Crystal Structure of Clda, the First Cyclomaltodextrin Glucanotransferase with A Three-Domain Abc Distribution


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 Clda, the First Cyclomaltodextrin Glucanotransferase with A Three-Domain Abc Distribution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:18.2
occ:1.00
 OD2 B:ASP220 2.4 21.8 1.0
O B:HOH865 2.4 18.6 1.0
O B:HOH744 2.5 18.2 1.0
OD1 B:ASN159 2.5 17.1 1.0
O B:GLN211 2.5 17.0 1.0
O B:HOH919 2.5 18.9 1.0
O B:HIS254 2.5 15.8 1.0
OD1 B:ASP220 2.5 18.9 1.0
CG B:ASP220 2.8 22.4 1.0
CG B:ASN159 3.5 17.2 1.0
C B:GLN211 3.5 23.3 1.0
C B:HIS254 3.7 15.4 1.0
ND2 B:ASN159 4.1 14.9 1.0
CA B:GLN211 4.1 20.5 1.0
O B:ASN159 4.2 17.5 1.0
CB B:ASP220 4.3 20.4 1.0
O B:LEU221 4.3 19.7 1.0
CB B:HIS254 4.4 18.7 1.0
O B:LEU210 4.5 21.5 1.0
O B:LYS213 4.5 21.5 1.0
CG B:MET255 4.5 18.9 1.0
ND1 B:HIS196 4.5 23.4 1.0
N B:MET255 4.6 15.9 1.0
CA B:HIS254 4.6 16.9 1.0
CA B:MET255 4.6 17.2 1.0
O B:HOH767 4.6 23.8 1.0
N B:ASP212 4.6 22.0 1.0
CE1 B:HIS196 4.6 21.6 1.0
CB B:ASN159 4.7 14.1 1.0
OE1 B:GLN223 4.8 24.0 1.0
CA B:ASN159 5.0 13.3 1.0
NE2 B:GLN223 5.0 16.3 1.0
CA B:ASP212 5.0 25.7 1.0

Calcium binding site 5 out of 6 in 6wni

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Calcium binding site 5 out of 6 in the Crystal Structure of Clda, the First Cyclomaltodextrin Glucanotransferase with A Three-Domain Abc Distribution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Clda, the First Cyclomaltodextrin Glucanotransferase with A Three-Domain Abc Distribution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:18.7
occ:1.00
 OD2 B:ASP75 2.2 18.8 1.0
O B:GLY73 2.3 16.0 1.0
OD1 B:ASN46 2.4 17.2 1.0
OD1 B:ASN51 2.4 16.5 1.0
O B:HOH808 2.4 17.9 1.0
OD1 B:ASP52 2.4 21.9 1.0
O B:ASP48 2.5 18.3 1.0
CG B:ASP75 3.2 15.5 1.0
CG B:ASN46 3.2 20.5 1.0
C B:GLY73 3.5 15.8 1.0
C B:ASP48 3.5 22.1 1.0
CG B:ASN51 3.6 18.4 1.0
CG B:ASP52 3.6 24.4 1.0
CB B:ASP75 3.7 17.5 1.0
ND2 B:ASN46 3.8 20.2 1.0
CA B:GLY73 4.0 14.7 1.0
N B:ASP48 4.0 19.0 1.0
ND2 B:ASN51 4.1 18.6 1.0
N B:ASP52 4.2 21.7 1.0
CA B:ASP48 4.2 19.8 1.0
OD1 B:ASP75 4.3 16.6 1.0
CB B:ASN46 4.3 19.4 1.0
O B:HIS131 4.3 19.0 1.0
OD2 B:ASP52 4.4 23.1 1.0
CA B:ASP52 4.4 22.2 1.0
CA B:ASN46 4.4 19.7 1.0
N B:PRO49 4.4 18.5 1.0
C B:ASN51 4.4 19.9 1.0
CA B:PRO49 4.5 16.7 1.0
C B:GLY74 4.6 16.3 1.0
CB B:ASP48 4.6 19.9 1.0
N B:GLY74 4.6 14.4 1.0
CB B:ASP52 4.6 20.9 1.0
N B:GLY47 4.7 16.1 1.0
N B:ASP75 4.7 18.0 1.0
O B:GLY74 4.8 17.9 1.0
O B:HOH786 4.8 18.7 1.0
C B:ASN46 4.8 23.5 1.0
CB B:ASN51 4.8 21.1 1.0
O B:ASN51 4.8 16.8 1.0
CA B:ASP75 4.9 14.7 1.0
N B:ASN51 4.9 21.3 1.0
CA B:GLY74 4.9 14.9 1.0
CA B:ASN51 4.9 17.7 1.0
C B:PRO49 5.0 15.6 1.0

Calcium binding site 6 out of 6 in 6wni

Go back to Calcium Binding Sites List in 6wni
Calcium binding site 6 out of 6 in the Crystal Structure of Clda, the First Cyclomaltodextrin Glucanotransferase with A Three-Domain Abc Distribution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Clda, the First Cyclomaltodextrin Glucanotransferase with A Three-Domain Abc Distribution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:19.1
occ:1.00
 OE1 B:GLU129 2.4 19.5 1.0
OD1 B:ASN104 2.4 22.3 1.0
OD1 B:ASP101 2.4 19.7 1.0
O B:ASN102 2.4 20.9 1.0
O B:HOH887 2.5 19.9 1.0
OE2 B:GLU130 2.5 20.1 1.0
OE1 B:GLU130 2.7 17.1 1.0
OE2 B:GLU129 2.9 21.6 1.0
CD B:GLU130 2.9 16.8 1.0
CD B:GLU129 3.0 22.5 1.0
C B:ASN102 3.5 19.8 1.0
CG B:ASN104 3.6 15.2 1.0
CG B:ASP101 3.7 23.0 1.0
N B:ASN102 3.8 18.2 1.0
O B:HOH754 4.1 21.2 1.0
O B:ILE103 4.1 18.9 1.0
CA B:ASN102 4.2 14.1 1.0
C B:ILE103 4.3 26.7 1.0
OD2 B:ASP101 4.3 20.5 1.0
CG B:GLU130 4.4 19.0 1.0
ND2 B:ASN104 4.4 19.9 1.0
CG B:GLU129 4.4 14.3 1.0
N B:GLU130 4.5 18.7 1.0
C B:ASP101 4.5 22.4 1.0
N B:ASN104 4.6 18.5 1.0
CD B:ARG123 4.6 20.0 1.0
OH B:TYR71 4.6 17.2 1.0
N B:ILE103 4.6 14.8 1.0
CA B:ASN104 4.6 17.5 1.0
OG B:SER57 4.6 19.5 1.0
CB B:SER57 4.6 16.6 1.0
CA B:ASP101 4.7 17.2 1.0
ND1 B:HIS131 4.7 18.1 1.0
CB B:ASN104 4.7 15.8 1.0
CB B:ASP101 4.8 17.5 1.0
CB B:ASN102 4.8 17.4 1.0
CA B:GLU129 4.8 13.8 1.0
CA B:ILE103 4.9 15.6 1.0
CB B:GLU129 5.0 15.3 1.0

Reference:

S.Centeno-Leija, A.Lopez-Munguia, Y.Cardenas-Conejo, N.A.Mancilla-Margalli, B.Velazquez-Cruz, E.Magana-Cuevas, Y.Guerra-Borrego, R.Zatarain-Palacios, Y.Marin-Tovar, S.Gomez-Manzo, J.Marcial-Quino, B.Hernandez-Ochoa, J.A.Osuna-Castro, E.Rudino-Pinera, H.Serrano-Posada. Discovery of A Novel Group of Three-Domain Thermophilic Cyclomaltodextrin Glucanotransferases: Structural and Functional Implications. To Be Published.
Page generated: Tue Jul 16 17:30:18 2024

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