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Calcium in PDB 2cdo: Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose

Protein crystallography data

The structure of Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose, PDB code: 2cdo was solved by J.Henshaw, A.Horne, A.L.Van Bueren, V.A.Money, D.N.Bolam, M.Czjzek, R.M.Weiner, S.W.Hutcheson, G.J.Davies, A.B.Boraston, H.J.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 98.53 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.036, 54.979, 196.820, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 24.1

Other elements in 2cdo:

The structure of Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose also contains other interesting chemical elements:

Chlorine (Cl) 10 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose (pdb code 2cdo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose, PDB code: 2cdo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2cdo

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Calcium binding site 1 out of 8 in the Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1139

b:14.3
occ:1.00
 OE1 A:GLU8 2.2 19.3 1.0
O A:THR36 2.2 15.0 1.0
OD1 A:ASP132 2.3 15.3 1.0
O A:ASP132 2.4 10.7 1.0
OE2 A:GLU10 2.5 15.3 1.0
O A:HOH2044 2.5 14.1 1.0
OE1 A:GLU10 2.6 16.2 1.0
CD A:GLU10 2.9 18.0 1.0
C A:ASP132 3.3 10.4 1.0
C A:THR36 3.4 15.2 1.0
CD A:GLU8 3.4 18.5 1.0
CG A:ASP132 3.5 15.1 1.0
CA A:ASP132 3.8 10.7 1.0
N A:THR36 4.1 16.1 1.0
CA A:THR36 4.1 15.5 1.0
O A:HOH2008 4.1 30.6 1.0
OE2 A:GLU8 4.2 23.7 1.0
CB A:ASP132 4.3 11.0 1.0
CB A:GLU8 4.3 14.2 1.0
CG A:GLU8 4.4 15.3 1.0
N A:LYS133 4.4 10.4 1.0
N A:ALA37 4.4 14.5 1.0
CG A:GLU10 4.4 13.6 1.0
CB A:THR36 4.4 16.0 1.0
N A:ALA9 4.5 11.3 1.0
O A:HOH2136 4.5 20.0 1.0
OD2 A:ASP132 4.5 16.0 1.0
CB A:LYS133 4.5 11.4 1.0
CA A:GLU8 4.5 12.1 1.0
CA A:ALA37 4.6 13.4 1.0
CA A:LYS133 4.8 11.9 1.0
O A:HOH2009 4.8 26.5 1.0
C A:GLU8 4.9 11.8 1.0
C A:ASN35 4.9 16.9 1.0
N A:GLU10 5.0 13.3 1.0

Calcium binding site 2 out of 8 in 2cdo

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Calcium binding site 2 out of 8 in the Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1140

b:15.0
occ:1.00
 OD2 A:ASP45 2.3 12.2 1.0
O A:PRO26 2.3 17.1 1.0
O A:HOH2021 2.3 15.8 1.0
O A:TYR40 2.3 12.3 1.0
OD1 A:ASN42 2.4 14.6 1.0
OD2 A:ASP21 2.4 25.7 1.0
CG A:ASP45 3.3 14.0 1.0
C A:PRO26 3.4 17.2 1.0
CG A:ASP21 3.4 27.2 1.0
CG A:ASN42 3.4 11.9 1.0
C A:TYR40 3.5 13.2 1.0
OD1 A:ASP45 3.7 15.1 1.0
N A:ASN42 3.8 11.3 1.0
CB A:ASN42 4.0 11.7 1.0
CB A:ASP21 4.0 25.6 1.0
O A:HOH2033 4.1 14.9 1.0
CA A:PRO26 4.2 19.0 1.0
CB A:TYR40 4.3 14.1 1.0
CA A:VAL41 4.3 11.0 1.0
OD1 A:ASP21 4.4 22.5 1.0
N A:VAL41 4.4 11.1 1.0
N A:VAL27 4.4 15.5 1.0
CA A:TYR40 4.5 12.3 1.0
C A:VAL41 4.5 10.9 1.0
CA A:ASN42 4.6 11.2 1.0
O A:PHE19 4.6 23.1 1.0
CB A:ASP45 4.6 11.0 1.0
ND2 A:ASN42 4.6 13.9 1.0
CA A:VAL27 4.6 15.2 1.0
CB A:PRO26 4.8 18.7 1.0
CG2 A:VAL27 4.9 12.1 1.0

Calcium binding site 3 out of 8 in 2cdo

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Calcium binding site 3 out of 8 in the Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1139

b:10.7
occ:1.00
 O B:THR36 2.3 10.4 1.0
OD1 B:ASP132 2.3 13.1 1.0
OE1 B:GLU8 2.4 10.4 1.0
OE1 B:GLU10 2.4 9.6 1.0
O B:ASP132 2.5 8.8 1.0
O B:HOH2046 2.6 11.3 1.0
OE2 B:GLU10 2.6 11.7 1.0
CD B:GLU10 2.9 12.7 1.0
C B:ASP132 3.4 8.2 1.0
C B:THR36 3.4 11.0 1.0
CD B:GLU8 3.5 13.8 1.0
CG B:ASP132 3.6 13.5 1.0
CA B:ASP132 3.9 8.1 1.0
CB B:GLU8 4.1 11.1 1.0
N B:THR36 4.2 13.8 1.0
CA B:THR36 4.2 12.5 1.0
CB B:ASP132 4.3 9.3 1.0
CG B:GLU8 4.4 9.5 1.0
N B:ALA9 4.4 8.6 1.0
OE2 B:GLU8 4.4 12.8 1.0
CG B:GLU10 4.4 9.3 1.0
N B:ALA37 4.4 10.7 1.0
O B:HOH2142 4.5 16.2 1.0
N B:LYS133 4.5 7.9 1.0
CB B:THR36 4.5 12.7 1.0
OD2 B:ASP132 4.5 16.8 1.0
CA B:GLU8 4.5 10.0 1.0
NZ B:LYS133 4.5 19.1 0.5
CB B:LYS133 4.5 8.9 0.5
CB B:LYS133 4.5 8.4 0.5
CA B:ALA37 4.6 10.1 1.0
O B:HOH2017 4.7 24.8 1.0
C B:GLU8 4.8 10.3 1.0
CA B:LYS133 4.8 8.3 0.5
CA B:LYS133 4.8 8.0 0.5
O B:HOH2013 4.9 19.8 1.0
CE B:LYS133 4.9 18.2 0.5
N B:GLU10 5.0 7.6 1.0

Calcium binding site 4 out of 8 in 2cdo

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Calcium binding site 4 out of 8 in the Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1140

b:10.2
occ:1.00
 O B:TYR40 2.2 7.9 1.0
OD2 B:ASP45 2.3 9.2 1.0
O B:PRO26 2.3 12.1 1.0
OD2 B:ASP21 2.3 13.1 1.0
ND2 B:ASN42 2.4 6.0 1.0
O B:HOH2021 2.5 14.5 1.0
CG B:ASP45 3.3 10.9 1.0
CG B:ASP21 3.3 20.1 1.0
C B:TYR40 3.4 9.0 1.0
C B:PRO26 3.4 13.6 1.0
CG B:ASN42 3.5 9.4 1.0
OD1 B:ASP45 3.7 10.5 1.0
N B:ASN42 3.9 8.6 1.0
CB B:ASN42 3.9 9.5 1.0
CB B:ASP21 4.0 21.2 1.0
O B:HOH2035 4.0 12.8 1.0
CB B:TYR40 4.1 10.1 1.0
CA B:PRO26 4.2 14.6 1.0
OD1 B:ASP21 4.3 15.6 1.0
CA B:TYR40 4.3 8.8 1.0
N B:VAL41 4.3 8.4 1.0
N B:VAL27 4.4 12.0 1.0
CA B:VAL41 4.4 8.0 1.0
CA B:VAL27 4.5 10.2 1.0
C B:VAL41 4.5 7.8 1.0
CB B:ASP45 4.6 6.7 1.0
CA B:ASN42 4.6 8.2 1.0
OD1 B:ASN42 4.6 13.7 1.0
O B:PHE19 4.7 19.1 1.0
CG2 B:VAL27 4.8 8.3 1.0
CB B:PRO26 4.9 16.6 1.0

Calcium binding site 5 out of 8 in 2cdo

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Calcium binding site 5 out of 8 in the Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1139

b:14.7
occ:1.00
 OE1 C:GLU8 2.1 13.1 1.0
O C:THR36 2.2 17.9 1.0
OD1 C:ASP132 2.2 17.8 1.0
OE1 C:GLU10 2.4 19.9 1.0
O C:HOH2117 2.5 21.0 1.0
O C:ASP132 2.5 12.2 1.0
OE2 C:GLU10 2.6 19.1 1.0
CD C:GLU10 2.9 18.7 1.0
CD C:GLU8 3.4 15.4 1.0
C C:ASP132 3.4 12.7 1.0
C C:THR36 3.4 18.2 1.0
CG C:ASP132 3.5 16.3 1.0
CA C:ASP132 3.8 13.4 1.0
N C:THR36 4.1 21.8 1.0
CB C:GLU8 4.2 15.6 1.0
CA C:THR36 4.2 20.0 1.0
CG C:GLU8 4.2 16.6 1.0
CB C:ASP132 4.2 14.7 1.0
OE2 C:GLU8 4.3 14.7 1.0
CE C:LYS133 4.3 8.3 0.5
N C:ALA37 4.3 17.4 1.0
O C:HOH2029 4.4 18.7 1.0
CG C:GLU10 4.4 16.4 1.0
OD2 C:ASP132 4.4 17.3 1.0
CB C:THR36 4.5 20.9 1.0
N C:LYS133 4.5 12.7 1.0
N C:ALA9 4.5 14.8 1.0
CA C:ALA37 4.6 16.1 1.0
O C:HOH2002 4.6 25.2 1.0
CA C:GLU8 4.6 15.6 1.0
CB C:LYS133 4.7 14.0 0.5
CB C:LYS133 4.7 13.1 0.5
O C:HOH2007 4.8 32.5 1.0
N C:GLU10 4.9 14.4 1.0
NZ C:LYS133 5.0 12.2 0.5
CA C:LYS133 5.0 12.7 0.5
CA C:LYS133 5.0 13.2 0.5
C C:GLU8 5.0 15.8 1.0

Calcium binding site 6 out of 8 in 2cdo

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Calcium binding site 6 out of 8 in the Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1140

b:17.1
occ:1.00
 OD2 C:ASP21 2.2 27.4 1.0
O C:TYR40 2.2 14.8 1.0
O C:PRO26 2.3 21.2 1.0
OD2 C:ASP45 2.3 13.4 1.0
O C:HOH2015 2.4 20.9 1.0
OD1 C:ASN42 2.5 16.7 1.0
CG C:ASP45 3.3 14.8 1.0
CG C:ASP21 3.3 37.3 1.0
C C:TYR40 3.4 15.5 1.0
C C:PRO26 3.4 21.5 1.0
CG C:ASN42 3.5 14.5 1.0
OD1 C:ASP45 3.7 15.8 1.0
N C:ASN42 4.0 10.9 1.0
CB C:ASN42 4.0 12.2 1.0
O C:HOH2022 4.0 19.2 1.0
CB C:ASP21 4.0 37.8 1.0
CB C:TYR40 4.2 16.7 1.0
CA C:PRO26 4.3 23.1 1.0
OD1 C:ASP21 4.3 37.5 1.0
N C:VAL41 4.3 14.6 1.0
CA C:TYR40 4.4 15.6 1.0
N C:VAL27 4.4 19.3 1.0
CA C:VAL41 4.5 12.7 1.0
C C:VAL41 4.6 12.1 1.0
CB C:ASP45 4.6 12.3 1.0
CA C:ASN42 4.6 11.8 1.0
CA C:VAL27 4.7 17.7 1.0
ND2 C:ASN42 4.7 11.7 1.0
O C:PHE19 4.8 38.1 1.0
CG2 C:VAL27 4.9 12.9 1.0
CB C:PRO26 4.9 23.5 1.0

Calcium binding site 7 out of 8 in 2cdo

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Calcium binding site 7 out of 8 in the Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1139

b:13.8
occ:1.00
 OD1 D:ASP132 2.2 15.9 1.0
OE1 D:GLU8 2.3 13.7 1.0
O D:THR36 2.3 16.2 1.0
O D:HOH2039 2.4 13.4 1.0
OE1 D:GLU10 2.5 15.6 1.0
OE2 D:GLU10 2.5 16.8 1.0
O D:ASP132 2.6 11.5 1.0
CD D:GLU10 2.9 17.1 1.0
CD D:GLU8 3.4 14.3 1.0
C D:THR36 3.4 17.2 1.0
C D:ASP132 3.4 12.0 1.0
CG D:ASP132 3.5 15.3 1.0
CA D:ASP132 3.9 11.8 1.0
NZ D:LYS133 3.9 26.9 1.0
O D:HOH2130 4.1 21.5 1.0
N D:THR36 4.2 21.0 1.0
CB D:GLU8 4.2 11.3 1.0
CA D:THR36 4.2 19.0 1.0
OE2 D:GLU8 4.3 14.9 1.0
CB D:ASP132 4.3 11.5 1.0
CG D:GLU8 4.3 12.1 1.0
OD2 D:ASP132 4.4 17.4 1.0
CB D:THR36 4.4 18.7 1.0
N D:ALA37 4.4 15.2 1.0
CG D:GLU10 4.5 11.7 1.0
N D:LYS133 4.5 12.7 1.0
N D:ALA9 4.5 10.2 1.0
CA D:GLU8 4.5 11.2 1.0
CB D:LYS133 4.6 14.2 1.0
CA D:ALA37 4.6 14.8 1.0
O D:HOH2003 4.7 29.9 1.0
O D:HOH2006 4.8 21.7 1.0
CA D:LYS133 4.9 13.8 1.0
C D:GLU8 4.9 10.2 1.0

Calcium binding site 8 out of 8 in 2cdo

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Calcium binding site 8 out of 8 in the Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Agarase Carbohydrate Binding Module in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1140

b:11.4
occ:1.00
 O D:PRO26 2.3 12.4 1.0
O D:TYR40 2.3 8.2 1.0
OD2 D:ASP45 2.3 9.0 1.0
OD2 D:ASP21 2.4 16.1 1.0
ND2 D:ASN42 2.4 7.2 1.0
O D:HOH2016 2.5 11.6 1.0
CG D:ASP45 3.3 10.0 1.0
CG D:ASP21 3.4 18.7 1.0
C D:PRO26 3.4 12.3 1.0
C D:TYR40 3.4 9.8 1.0
CG D:ASN42 3.6 9.2 1.0
OD1 D:ASP45 3.6 10.6 1.0
N D:ASN42 3.9 9.7 1.0
O D:HOH2024 4.0 11.2 1.0
CB D:ASN42 4.0 9.6 1.0
CB D:ASP21 4.1 16.6 1.0
CA D:PRO26 4.1 13.7 1.0
CB D:TYR40 4.2 10.5 1.0
N D:VAL41 4.3 9.2 1.0
CA D:VAL41 4.3 9.0 1.0
OD1 D:ASP21 4.3 17.4 1.0
CA D:TYR40 4.4 9.7 1.0
N D:VAL27 4.4 12.1 1.0
C D:VAL41 4.5 9.6 1.0
O D:PHE19 4.5 15.4 1.0
CB D:ASP45 4.6 6.7 1.0
OD1 D:ASN42 4.6 13.4 1.0
CA D:ASN42 4.6 9.4 1.0
CA D:VAL27 4.7 10.8 1.0
CB D:PRO26 4.7 13.5 1.0
CB D:PHE19 5.0 15.4 1.0

Reference:

J.Henshaw, A.Horne, A.L.Van Bueren, V.A.Money, D.N.Bolam, M.Czjzek, N.A.Ekborg, R.M.Weiner, S.W.Hutcheson, G.J.Davies, A.B.Boraston, H.J.Gilbert. Family 6 Carbohydrate Binding Modules in Beta- Agarases Display Exquisite Selectivity For the Non- Reducing Termini of Agarose Chains. J.Biol.Chem. V. 281 17099 2006.
ISSN: ISSN 0021-9258
PubMed: 16601125
DOI: 10.1074/JBC.M600702200
Page generated: Tue Jul 8 04:48:43 2025

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