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Calcium in PDB 2cdp: Structure of A CBM6 in Complex with Neoagarohexaose

Protein crystallography data

The structure of Structure of A CBM6 in Complex with Neoagarohexaose, PDB code: 2cdp 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) 19.62 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.720, 54.996, 195.908, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 25.3

Other elements in 2cdp:

The structure of Structure of A CBM6 in Complex with Neoagarohexaose also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of A CBM6 in Complex with Neoagarohexaose (pdb code 2cdp). 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 A CBM6 in Complex with Neoagarohexaose, PDB code: 2cdp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2cdp

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Calcium binding site 1 out of 8 in the Structure of A CBM6 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 A CBM6 in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1139

b:24.4
occ:1.00
 OE1 A:GLU8 2.2 28.8 1.0
O A:THR36 2.3 23.1 1.0
OE1 A:GLU10 2.4 24.6 1.0
OD1 A:ASP132 2.4 20.7 1.0
O A:ASP132 2.4 16.4 1.0
O A:HOH2040 2.7 26.1 1.0
OE2 A:GLU10 2.8 24.0 1.0
CD A:GLU10 2.9 24.1 1.0
C A:ASP132 3.3 17.1 1.0
C A:THR36 3.4 22.4 1.0
CD A:GLU8 3.5 29.0 1.0
CG A:ASP132 3.6 21.9 1.0
CA A:ASP132 3.8 17.5 1.0
N A:THR36 4.1 24.0 1.0
CA A:THR36 4.1 22.7 1.0
CB A:GLU8 4.3 20.2 1.0
CB A:ASP132 4.3 18.2 1.0
OE2 A:GLU8 4.3 32.7 1.0
N A:ALA9 4.4 17.7 1.0
N A:LYS133 4.4 16.8 1.0
CB A:THR36 4.4 23.2 1.0
N A:ALA37 4.4 21.4 1.0
CG A:GLU8 4.4 22.3 1.0
CB A:LYS133 4.4 17.0 1.0
CG A:GLU10 4.5 21.4 1.0
CA A:GLU8 4.5 18.8 1.0
CA A:ALA37 4.6 20.3 1.0
OD2 A:ASP132 4.6 24.3 1.0
O A:HOH2039 4.6 25.6 1.0
CA A:LYS133 4.8 18.0 1.0
C A:GLU8 4.8 17.2 1.0
N A:GLU10 4.9 19.5 1.0

Calcium binding site 2 out of 8 in 2cdp

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Calcium binding site 2 out of 8 in the Structure of A CBM6 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 A CBM6 in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1140

b:21.9
occ:1.00
 OD1 A:ASN42 2.3 19.3 1.0
O A:PRO26 2.3 25.2 1.0
OD2 A:ASP45 2.4 20.4 1.0
OD2 A:ASP21 2.4 27.7 1.0
O A:TYR40 2.4 17.7 1.0
O A:HOH2020 2.4 25.9 1.0
CG A:ASN42 3.4 18.5 1.0
CG A:ASP45 3.4 19.6 1.0
CG A:ASP21 3.4 33.2 1.0
C A:PRO26 3.5 26.1 1.0
C A:TYR40 3.5 17.5 1.0
OD1 A:ASP45 3.8 18.9 1.0
N A:ASN42 3.8 15.6 1.0
CB A:ASN42 3.9 17.8 1.0
CB A:ASP21 4.0 31.9 1.0
O A:HOH2026 4.1 25.7 1.0
CA A:PRO26 4.2 28.6 1.0
CB A:TYR40 4.3 18.8 1.0
OD1 A:ASP21 4.4 27.3 1.0
CA A:VAL41 4.4 16.8 1.0
N A:VAL41 4.4 15.6 1.0
CA A:TYR40 4.5 16.8 1.0
O A:PHE19 4.5 29.5 1.0
N A:VAL27 4.5 24.2 1.0
C A:VAL41 4.5 16.8 1.0
ND2 A:ASN42 4.5 17.3 1.0
CA A:ASN42 4.5 18.1 1.0
CB A:ASP45 4.6 16.6 1.0
CA A:VAL27 4.7 22.8 1.0
CB A:PRO26 4.8 29.1 1.0
CG2 A:VAL27 4.9 20.9 1.0

Calcium binding site 3 out of 8 in 2cdp

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Calcium binding site 3 out of 8 in the Structure of A CBM6 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 A CBM6 in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1139

b:23.5
occ:1.00
 O B:THR36 2.3 19.8 1.0
OD1 B:ASP132 2.3 19.4 1.0
O B:ASP132 2.4 17.3 1.0
OE1 B:GLU8 2.4 21.9 1.0
OE1 B:GLU10 2.5 18.2 1.0
O B:HOH2023 2.6 27.3 1.0
OE2 B:GLU10 2.9 23.0 1.0
CD B:GLU10 3.0 21.4 1.0
C B:ASP132 3.3 15.4 1.0
C B:THR36 3.4 20.8 1.0
CG B:ASP132 3.5 18.8 1.0
CD B:GLU8 3.6 21.4 1.0
CA B:ASP132 3.9 15.6 1.0
CB B:GLU8 4.1 18.8 1.0
N B:THR36 4.2 22.6 1.0
CA B:THR36 4.3 21.1 1.0
NZ B:LYS133 4.3 15.7 0.5
N B:ALA9 4.3 18.4 1.0
CB B:ASP132 4.3 16.0 1.0
N B:LYS133 4.4 15.4 1.0
N B:ALA37 4.4 19.5 1.0
CG B:GLU8 4.4 18.4 1.0
OD2 B:ASP132 4.5 20.2 1.0
O B:HOH2122 4.5 31.6 1.0
CB B:LYS133 4.5 16.1 0.5
CA B:GLU8 4.5 17.6 1.0
OE2 B:GLU8 4.5 23.8 1.0
CB B:LYS133 4.5 16.4 0.5
CB B:THR36 4.5 21.7 1.0
CA B:ALA37 4.5 17.8 1.0
CG B:GLU10 4.5 19.5 1.0
CE B:LYS133 4.6 18.2 0.5
CA B:LYS133 4.8 15.7 0.5
CA B:LYS133 4.8 15.8 0.5
C B:GLU8 4.8 18.0 1.0
N B:GLU10 4.9 17.8 1.0

Calcium binding site 4 out of 8 in 2cdp

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Calcium binding site 4 out of 8 in the Structure of A CBM6 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 A CBM6 in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1140

b:17.4
occ:1.00
 O B:HOH2011 2.2 28.8 1.0
OD2 B:ASP45 2.3 17.0 1.0
O B:TYR40 2.3 17.5 1.0
OD1 B:ASN42 2.4 21.0 1.0
O B:HOH2032 2.6 25.7 1.0
CG B:ASP45 3.3 18.7 1.0
C B:TYR40 3.4 16.2 1.0
CG B:ASN42 3.4 14.8 1.0
OD1 B:ASP45 3.7 19.5 1.0
N B:ASN42 3.8 15.7 1.0
C B:PRO26 3.8 25.8 1.0
CB B:ASN42 3.9 16.0 1.0
N B:VAL27 3.9 23.4 1.0
CA B:PRO26 3.9 27.1 1.0
CB B:TYR40 4.2 19.0 1.0
N B:PRO26 4.2 28.4 1.0
O B:PRO26 4.2 24.3 1.0
CA B:TYR40 4.3 17.2 1.0
N B:VAL41 4.3 15.3 1.0
CA B:VAL41 4.4 15.1 1.0
C B:VAL41 4.5 15.2 1.0
CA B:ASN42 4.5 14.8 1.0
CA B:VAL27 4.6 20.8 1.0
CB B:ASP45 4.6 14.2 1.0
CG2 B:VAL27 4.7 19.2 1.0
ND2 B:ASN42 4.7 18.1 1.0
O B:HOH2008 4.8 34.3 1.0

Calcium binding site 5 out of 8 in 2cdp

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Calcium binding site 5 out of 8 in the Structure of A CBM6 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 A CBM6 in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1139

b:27.5
occ:1.00
 OE1 C:GLU8 2.2 23.4 1.0
O C:THR36 2.3 23.2 1.0
OD1 C:ASP132 2.4 22.5 1.0
OE1 C:GLU10 2.4 24.1 1.0
O C:ASP132 2.4 19.3 1.0
OE2 C:GLU10 2.7 30.6 1.0
CD C:GLU10 2.9 27.7 1.0
C C:ASP132 3.4 19.2 1.0
C C:THR36 3.4 23.5 1.0
CD C:GLU8 3.5 21.7 1.0
CG C:ASP132 3.6 23.6 1.0
CA C:ASP132 3.8 20.0 1.0
CB C:GLU8 4.1 20.5 1.0
O C:HOH2120 4.2 35.6 1.0
N C:THR36 4.3 26.2 1.0
CB C:ASP132 4.3 21.2 1.0
CG C:GLU8 4.3 19.9 1.0
CA C:THR36 4.3 25.5 1.0
N C:ALA37 4.3 23.2 1.0
OE2 C:GLU8 4.4 23.1 1.0
CA C:ALA37 4.4 23.1 1.0
CB C:THR36 4.4 25.9 1.0
CG C:GLU10 4.4 21.9 1.0
N C:ALA9 4.5 18.6 1.0
CE C:LYS133 4.5 26.6 1.0
N C:LYS133 4.5 19.4 1.0
OD2 C:ASP132 4.5 24.6 1.0
CA C:GLU8 4.6 19.1 1.0
CB C:LYS133 4.7 19.7 1.0
NZ C:LYS133 4.8 25.6 1.0
C C:GLU8 4.9 19.8 1.0
N C:GLU10 4.9 19.5 1.0
CA C:LYS133 5.0 19.4 1.0

Calcium binding site 6 out of 8 in 2cdp

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Calcium binding site 6 out of 8 in the Structure of A CBM6 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 A CBM6 in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1140

b:24.4
occ:1.00
 OD2 C:ASP45 2.3 19.3 1.0
O C:TYR40 2.3 20.2 1.0
OD1 C:ASN42 2.4 21.6 1.0
O C:HOH2028 2.8 26.2 1.0
CG C:ASP45 3.3 17.2 1.0
C C:TYR40 3.4 19.1 1.0
CG C:ASN42 3.5 21.7 1.0
C C:PRO26 3.8 30.1 1.0
OD1 C:ASP45 3.8 19.1 1.0
N C:VAL27 3.9 27.1 1.0
N C:ASN42 3.9 17.9 1.0
CA C:PRO26 4.0 31.4 1.0
CB C:ASN42 4.0 17.6 1.0
CB C:TYR40 4.2 19.7 1.0
O C:PRO26 4.2 29.9 1.0
N C:PRO26 4.3 32.2 1.0
CA C:TYR40 4.3 20.0 1.0
N C:VAL41 4.4 17.6 1.0
CA C:VAL41 4.5 17.9 1.0
O C:HOH2017 4.6 28.8 1.0
C C:VAL41 4.6 17.0 1.0
CB C:ASP45 4.6 16.3 1.0
CA C:ASN42 4.6 17.3 1.0
CA C:VAL27 4.6 25.0 1.0
ND2 C:ASN42 4.7 17.3 1.0
CG2 C:VAL27 4.7 22.9 1.0

Calcium binding site 7 out of 8 in 2cdp

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Calcium binding site 7 out of 8 in the Structure of A CBM6 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 A CBM6 in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1139

b:30.5
occ:1.00
 O D:THR36 2.3 25.5 1.0
OE1 D:GLU8 2.3 26.8 1.0
OD1 D:ASP132 2.3 25.1 1.0
OE1 D:GLU10 2.5 27.0 1.0
O D:ASP132 2.5 22.6 1.0
OE2 D:GLU10 2.7 28.8 1.0
O D:HOH2033 2.7 32.3 1.0
CD D:GLU10 2.9 29.0 1.0
C D:ASP132 3.3 21.9 1.0
C D:THR36 3.4 27.3 1.0
CD D:GLU8 3.5 26.2 1.0
CG D:ASP132 3.5 27.7 1.0
CA D:ASP132 3.8 22.9 1.0
O D:HOH2005 3.9 40.0 1.0
CA D:THR36 4.2 28.8 1.0
CB D:GLU8 4.2 22.8 1.0
N D:THR36 4.2 31.9 1.0
CB D:ASP132 4.3 22.6 1.0
N D:ALA37 4.3 25.5 1.0
CG D:GLU8 4.4 22.9 1.0
OE2 D:GLU8 4.4 27.7 1.0
N D:LYS133 4.4 23.3 1.0
CB D:THR36 4.4 30.2 1.0
N D:ALA9 4.4 20.4 1.0
CG D:GLU10 4.4 24.9 1.0
CB D:LYS133 4.5 24.8 1.0
OD2 D:ASP132 4.5 27.4 1.0
CA D:ALA37 4.5 24.9 1.0
CA D:GLU8 4.5 22.1 1.0
CA D:LYS133 4.8 23.5 1.0
C D:GLU8 4.8 21.2 1.0
N D:GLU10 5.0 19.9 1.0

Calcium binding site 8 out of 8 in 2cdp

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Calcium binding site 8 out of 8 in the Structure of A CBM6 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 A CBM6 in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1140

b:17.4
occ:1.00
 O D:TYR40 2.0 20.2 1.0
O D:PRO26 2.2 23.9 0.5
OD2 D:ASP45 2.3 20.3 1.0
OD1 D:ASN42 2.4 22.2 1.0
O D:HOH2019 2.8 31.7 1.0
O D:HOH2022 2.8 42.5 1.0
C D:TYR40 3.1 19.6 1.0
C D:PRO26 3.3 24.3 0.5
CG D:ASP45 3.4 15.7 1.0
CG D:ASN42 3.4 22.5 1.0
N D:ASN42 3.6 19.4 1.0
OD1 D:ASP45 3.9 19.6 1.0
CB D:ASN42 4.0 20.4 1.0
CB D:TYR40 4.0 20.4 1.0
N D:VAL41 4.1 19.2 1.0
CA D:TYR40 4.1 21.1 1.0
CA D:VAL41 4.1 18.9 1.0
O D:HOH2024 4.1 33.3 1.0
CA D:PRO26 4.2 24.6 0.5
C D:VAL41 4.3 18.8 1.0
N D:VAL27 4.3 25.0 1.0
CA D:ASN42 4.4 19.7 1.0
O D:PHE19 4.6 27.9 0.5
CA D:VAL27 4.6 25.1 1.0
ND2 D:ASN42 4.6 21.1 1.0
CB D:ASP45 4.6 15.2 1.0
CB D:PRO26 4.7 24.9 0.5
CG2 D:VAL27 4.7 23.5 1.0
CB D:PHE19 4.8 28.6 0.5

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 04:49:04 2025

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