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Chlorine 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:

Calcium (Ca) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Structure of A CBM6 in Complex with Neoagarohexaose, PDB code: 2cdp:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 2cdp

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Chlorine binding site 1 out of 9 in the Structure of A CBM6 in Complex with Neoagarohexaose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl1142

b:24.0
occ:1.00
 O A:HOH2033 2.9 28.3 1.0
C1 A:EDO1141 3.0 25.7 1.0
O A:HOH2091 3.1 26.8 1.0
C2 A:EDO1141 3.3 21.3 1.0
N A:VAL89 3.3 14.5 1.0
CA A:THR88 3.6 14.9 1.0
O A:VAL89 3.7 15.3 1.0
CB A:THR88 3.8 15.1 1.0
C A:THR88 3.9 14.9 1.0
CA A:VAL89 4.3 15.9 1.0
O1 A:EDO1141 4.4 23.1 1.0
C A:VAL89 4.4 15.6 1.0
O A:LYS87 4.4 15.3 1.0
CG2 A:THR88 4.5 13.9 1.0
CB A:VAL89 4.7 17.9 1.0
O A:HOH2088 4.7 25.3 1.0
O2 A:EDO1141 4.7 28.4 1.0
N A:THR88 4.8 13.8 1.0

Chlorine binding site 2 out of 9 in 2cdp

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Chlorine binding site 2 out of 9 in the Structure of A CBM6 in Complex with Neoagarohexaose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl1143

b:28.3
occ:1.00
 O B:HOH2024 2.7 31.9 1.0
ND2 A:ASN11 3.1 26.9 1.0
N A:GLU8 3.1 19.0 1.0
ND2 B:ASN104 3.2 22.5 1.0
CB B:ASN104 3.7 17.1 1.0
O A:HOH2008 3.7 33.7 1.0
CB A:ASN11 3.8 22.9 1.0
CB A:GLU8 3.8 20.2 1.0
CA A:VAL7 3.9 19.5 1.0
CG A:ASN11 3.9 24.8 1.0
CA A:GLU8 4.0 18.8 1.0
CG B:ASN104 4.0 21.7 1.0
C A:VAL7 4.0 19.2 1.0
CG A:GLU8 4.1 22.3 1.0
O B:HOH2097 4.2 22.2 1.0
O A:ALA6 4.2 21.8 1.0
CG1 A:VAL7 4.2 19.8 1.0
O A:GLU8 4.3 17.6 1.0
C A:GLU8 4.6 17.2 1.0
CB A:VAL7 4.6 20.3 1.0
O B:HOH2095 4.7 36.1 1.0
O B:HOH2092 4.7 36.8 1.0
O A:HOH2053 4.8 34.7 1.0
O A:HOH2011 4.9 33.2 1.0
N A:VAL7 4.9 20.3 1.0
C A:ALA6 5.0 20.4 1.0

Chlorine binding site 3 out of 9 in 2cdp

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Chlorine binding site 3 out of 9 in the Structure of A CBM6 in Complex with Neoagarohexaose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of A CBM6 in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1144

b:27.2
occ:1.00
 O A:HOH2117 2.9 22.5 1.0
O A:HOH2059 2.9 25.4 1.0
O A:HOH2113 3.0 27.4 1.0
N A:TYR109 3.1 14.9 1.0
CA A:VAL108 3.8 14.5 1.0
CB A:TYR109 4.0 15.7 1.0
C A:VAL108 4.0 14.9 1.0
CA A:TYR109 4.1 14.8 1.0
CG2 A:VAL108 4.1 15.0 1.0
CD A:LYS87 4.2 20.7 1.0
NZ A:LYS87 4.4 23.9 1.0
O A:SER107 4.5 16.6 1.0
CB A:VAL108 4.5 15.2 1.0
O A:TYR109 4.6 15.9 1.0
O A:HOH2092 4.6 27.1 1.0
CE A:LYS87 4.6 22.7 1.0
O C:HOH2011 4.8 39.0 1.0
C A:TYR109 4.8 15.9 1.0
N A:VAL108 4.9 15.8 1.0
OD1 A:ASN58 4.9 18.9 1.0

Chlorine binding site 4 out of 9 in 2cdp

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Chlorine binding site 4 out of 9 in the Structure of A CBM6 in Complex with Neoagarohexaose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl1142

b:28.0
occ:1.00
 O B:VAL92 2.7 14.4 1.0
O1 B:EDO1141 2.7 23.6 1.0
O B:VAL69 2.9 16.3 1.0
N B:GLY72 2.9 15.7 1.0
OG B:SER67 3.2 14.6 1.0
CA B:GLY72 3.3 16.0 1.0
O B:GLY72 3.3 16.4 1.0
C1 B:EDO1141 3.4 22.3 1.0
CB B:SER67 3.6 13.8 1.0
C B:GLY72 3.7 17.4 1.0
N B:GLY71 3.8 18.2 1.0
C B:VAL92 3.8 15.1 1.0
C B:VAL69 4.0 17.4 1.0
C B:GLY71 4.1 17.1 1.0
CB B:VAL92 4.2 15.6 1.0
O B:GLN128 4.2 14.6 1.0
N B:VAL92 4.3 14.2 1.0
CA B:VAL92 4.3 13.7 1.0
C B:THR70 4.3 19.4 1.0
CA B:THR70 4.4 19.7 1.0
CA B:GLY71 4.5 18.2 1.0
CG2 B:VAL69 4.6 17.1 1.0
C2 B:EDO1141 4.6 20.0 1.0
O2 B:EDO1141 4.6 23.3 1.0
N B:THR70 4.6 17.1 1.0
O A:HOH2122 4.7 19.6 1.0
C B:PRO93 4.7 16.9 1.0
O B:PRO93 4.8 16.2 1.0
N B:ASN94 4.9 16.9 1.0
CG1 B:VAL92 4.9 14.3 1.0
O B:HOH2140 4.9 24.8 1.0
N B:PRO93 4.9 15.8 1.0

Chlorine binding site 5 out of 9 in 2cdp

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Chlorine binding site 5 out of 9 in the Structure of A CBM6 in Complex with Neoagarohexaose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of A CBM6 in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1143

b:23.9
occ:1.00
 O B:HOH2010 3.1 27.4 1.0
N B:ASN58 3.2 19.3 1.0
OD1 B:ASN138 3.3 34.0 1.0
CA B:GLY57 3.8 19.7 1.0
C B:GLY57 4.0 19.2 1.0
CB B:ASN58 4.1 20.0 1.0
CA B:ASN58 4.2 19.2 1.0
O B:ASN58 4.4 19.7 1.0
CG B:ASN138 4.4 32.0 1.0
ND2 B:ASN138 4.8 31.6 1.0
C B:ASN58 4.8 19.9 1.0
O B:HOH2040 5.0 32.8 1.0

Chlorine binding site 6 out of 9 in 2cdp

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Chlorine binding site 6 out of 9 in the Structure of A CBM6 in Complex with Neoagarohexaose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of A CBM6 in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1144

b:26.1
occ:0.75
 O B:HOH2101 2.9 18.4 1.0
O B:HOH2099 3.2 24.4 1.0
O B:HOH2042 3.2 28.2 1.0
N B:TYR109 3.3 17.7 1.0
O B:HOH2070 3.8 25.4 0.5
CB B:TYR109 3.9 18.3 1.0
CA B:VAL108 4.0 17.4 1.0
C B:VAL108 4.1 16.8 1.0
CA B:TYR109 4.2 16.6 1.0
O B:HOH2071 4.4 33.4 1.0
CG2 B:VAL108 4.4 18.7 1.0
O B:SER107 4.5 18.3 1.0
O B:TYR109 4.6 17.9 1.0
CB B:VAL108 4.8 16.4 1.0
OD1 B:ASN58 4.8 27.8 1.0
N B:VAL108 4.8 17.8 1.0
C B:TYR109 4.9 17.1 1.0
CD B:LYS87 4.9 18.2 1.0
NZ B:LYS87 5.0 15.6 1.0
C B:SER107 5.0 18.6 1.0

Chlorine binding site 7 out of 9 in 2cdp

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Chlorine binding site 7 out of 9 in the Structure of A CBM6 in Complex with Neoagarohexaose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of A CBM6 in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1142

b:26.7
occ:0.75
 O C:HOH2116 2.8 32.7 1.0
OG C:SER124 2.9 20.5 1.0
O C:HOH2052 3.4 36.1 1.0
N C:ASN125 3.6 18.6 1.0
ND2 C:ASN125 3.6 26.1 1.0
O C:THR70 3.6 24.1 1.0
CA C:ASN125 3.6 20.0 1.0
CB C:ASN125 3.7 19.6 1.0
CB C:SER124 3.7 20.9 1.0
C C:SER124 3.8 20.2 1.0
CG C:ASN125 4.1 23.4 1.0
CA C:GLY71 4.1 18.9 1.0
O C:SER124 4.2 21.2 1.0
CA C:SER124 4.4 20.1 1.0
C C:THR70 4.6 23.0 1.0
N C:GLY71 4.8 21.2 1.0
O C:HOH2117 4.8 22.8 1.0
O C:GLY71 4.9 17.8 1.0
C C:GLY71 5.0 19.2 1.0

Chlorine binding site 8 out of 9 in 2cdp

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Chlorine binding site 8 out of 9 in the Structure of A CBM6 in Complex with Neoagarohexaose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of A CBM6 in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1143

b:30.3
occ:1.00
 ND2 C:ASN11 3.1 19.6 1.0
N C:GLU8 3.2 20.0 1.0
NE2 A:GLN55 3.4 28.1 1.0
CA C:VAL7 3.6 20.4 1.0
CB C:ASN11 3.9 21.5 1.0
O C:ALA6 3.9 25.4 1.0
C C:VAL7 3.9 20.3 1.0
CG C:ASN11 4.0 20.8 1.0
CB A:SER1 4.0 33.1 1.0
CB C:GLU8 4.1 20.5 1.0
CA C:GLU8 4.2 19.1 1.0
CG1 C:VAL7 4.2 20.6 1.0
CG C:GLU8 4.3 19.9 1.0
CD A:GLN55 4.5 28.3 1.0
CB C:VAL7 4.5 21.0 1.0
O C:GLU8 4.6 20.7 1.0
C2 C:EDO1141 4.6 19.4 1.0
N C:VAL7 4.6 22.0 1.0
C C:ALA6 4.6 23.3 1.0
OE1 A:GLN55 4.7 31.5 1.0
O A:ALA56 4.8 17.6 1.0
C1 C:EDO1141 4.9 17.9 1.0
C C:GLU8 4.9 19.8 1.0
OG A:SER1 5.0 31.3 1.0
CA A:SER1 5.0 32.6 1.0

Chlorine binding site 9 out of 9 in 2cdp

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Chlorine binding site 9 out of 9 in the Structure of A CBM6 in Complex with Neoagarohexaose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structure of A CBM6 in Complex with Neoagarohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1141

b:32.0
occ:1.00
 N D:GLU8 3.1 21.7 1.0
ND2 D:ASN11 3.4 30.5 1.0
CA D:VAL7 3.8 23.1 1.0
CB D:GLU8 3.9 22.8 1.0
C D:VAL7 3.9 21.3 1.0
CB D:ASN11 4.0 22.8 1.0
CA D:GLU8 4.0 22.1 1.0
CG D:GLU8 4.1 22.9 1.0
CG1 D:VAL7 4.2 22.8 1.0
CG D:ASN11 4.2 26.7 1.0
O D:ALA6 4.2 24.9 1.0
O D:GLU8 4.3 19.3 1.0
CB D:VAL7 4.5 22.9 1.0
C D:GLU8 4.7 21.2 1.0
O D:HOH2004 4.8 22.3 1.0
N D:VAL7 4.8 24.1 1.0
C D:ALA6 4.9 25.9 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: Sat Jul 20 06:17:37 2024

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