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Chlorine in PDB 5nz7: Clostridium Thermocellum Cellodextrin Phosphorylase Ligand Free Form

Protein crystallography data

The structure of Clostridium Thermocellum Cellodextrin Phosphorylase Ligand Free Form, PDB code: 5nz7 was solved by E.C.O'neill, G.Pergolizzi, C.E.M.Stevenson, D.M.Lawson, S.A.Nepogodiev, R.A.Field, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.65 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.640, 151.810, 91.970, 90.00, 114.60, 90.00
R / Rfree (%) 19.1 / 22.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Clostridium Thermocellum Cellodextrin Phosphorylase Ligand Free Form (pdb code 5nz7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Clostridium Thermocellum Cellodextrin Phosphorylase Ligand Free Form, PDB code: 5nz7:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5nz7

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Chlorine binding site 1 out of 6 in the Clostridium Thermocellum Cellodextrin Phosphorylase Ligand Free Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Clostridium Thermocellum Cellodextrin Phosphorylase Ligand Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1001

b:46.0
occ:1.00
 N A:LEU887 3.2 50.7 1.0
N A:GLN490 3.2 45.9 1.0
CB A:PRO886 3.4 47.0 1.0
N A:THR491 3.4 47.0 1.0
OG1 A:THR491 3.5 47.8 1.0
CA A:PRO886 3.5 48.3 1.0
NE2 A:HIS140 3.7 46.3 1.0
CD2 A:HIS140 3.7 45.3 1.0
C A:GLY489 3.8 47.6 1.0
CA A:GLY489 3.8 48.0 1.0
CB A:LEU887 3.9 49.7 1.0
C A:PRO886 3.9 48.7 1.0
CG A:LEU887 3.9 49.4 1.0
CA A:GLN490 4.0 45.8 1.0
N A:GLN492 4.0 52.2 1.0
CB A:GLN490 4.1 45.8 1.0
CD1 A:LEU887 4.1 49.3 1.0
CA A:LEU887 4.1 50.8 1.0
C A:GLN490 4.2 45.4 1.0
CA A:THR491 4.3 48.7 1.0
CB A:THR491 4.5 47.7 1.0
C A:THR491 4.6 49.9 1.0
CB A:GLN492 4.7 57.6 1.0
O A:GLY489 4.7 47.7 1.0
N A:GLY489 4.8 51.8 1.0
N A:PRO886 4.8 48.7 1.0
N A:LEU888 4.9 54.0 1.0
CG A:PRO886 4.9 47.1 1.0
CE1 A:HIS140 5.0 46.0 1.0
C A:LEU887 5.0 53.6 1.0
CA A:GLN492 5.0 55.7 1.0

Chlorine binding site 2 out of 6 in 5nz7

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Chlorine binding site 2 out of 6 in the Clostridium Thermocellum Cellodextrin Phosphorylase Ligand Free Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Clostridium Thermocellum Cellodextrin Phosphorylase Ligand Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1002

b:52.2
occ:1.00
 NH2 A:ARG717 3.0 52.6 1.0
NE A:ARG717 3.0 51.6 1.0
ND2 A:ASN623 3.2 61.5 1.0
O A:HOH1129 3.2 50.8 1.0
ND2 A:ASN751 3.4 46.7 1.0
CZ A:ARG717 3.4 53.0 1.0
CB A:ASN623 3.7 59.1 1.0
CB A:ASN751 3.9 48.7 1.0
CG A:ASN623 3.9 60.8 1.0
CE3 A:TRP622 4.0 54.9 1.0
CZ3 A:TRP622 4.0 56.1 1.0
CD2 A:PHE749 4.0 58.7 1.0
CG A:ASN751 4.1 50.4 1.0
CD A:ARG717 4.2 51.3 1.0
CD1 A:LEU786 4.5 63.0 1.0
SD A:MET666 4.6 54.6 1.0
CB A:PHE749 4.6 51.5 1.0
CG A:PHE749 4.7 54.8 1.0
NH1 A:ARG717 4.8 53.5 1.0
CA A:ASN623 4.8 58.9 1.0
CE2 A:PHE749 4.8 60.8 1.0
N A:ASN751 5.0 46.6 1.0

Chlorine binding site 3 out of 6 in 5nz7

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Chlorine binding site 3 out of 6 in the Clostridium Thermocellum Cellodextrin Phosphorylase Ligand Free Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Clostridium Thermocellum Cellodextrin Phosphorylase Ligand Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1003

b:75.7
occ:1.00
 ND1 A:HIS817 3.2 53.7 1.0
N A:GLY890 3.3 54.3 1.0
CB A:SER889 3.7 57.2 1.0
CB A:HIS817 3.8 45.7 1.0
CG A:HIS817 3.9 49.8 1.0
CA A:SER889 3.9 57.6 1.0
C A:SER889 4.1 58.1 1.0
O A:HOH1138 4.2 49.1 1.0
CE1 A:HIS817 4.2 52.4 1.0
CA A:GLY890 4.2 51.6 1.0
NE A:ARG486 4.5 67.6 1.0
O A:HOH1214 4.6 43.7 1.0
OG A:SER889 4.7 48.1 1.0
NE2 A:GLN874 5.0 47.3 1.0

Chlorine binding site 4 out of 6 in 5nz7

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Chlorine binding site 4 out of 6 in the Clostridium Thermocellum Cellodextrin Phosphorylase Ligand Free Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Clostridium Thermocellum Cellodextrin Phosphorylase Ligand Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1001

b:43.5
occ:1.00
 N B:GLN490 3.1 41.2 1.0
N B:LEU887 3.2 47.6 1.0
N B:THR491 3.4 41.3 1.0
OG1 B:THR491 3.5 40.2 1.0
CB B:PRO886 3.6 43.3 1.0
CD2 B:HIS140 3.7 45.8 1.0
CA B:PRO886 3.7 43.6 1.0
NE2 B:HIS140 3.7 44.9 1.0
C B:GLY489 3.7 43.1 1.0
CA B:GLY489 3.8 44.5 1.0
CB B:LEU887 3.9 44.8 1.0
CA B:GLN490 3.9 41.0 1.0
CG B:LEU887 3.9 45.9 1.0
CB B:GLN490 4.0 41.1 1.0
C B:PRO886 4.0 45.4 1.0
CD1 B:LEU887 4.0 48.1 1.0
N B:GLN492 4.0 44.7 1.0
C B:GLN490 4.1 42.1 1.0
CA B:LEU887 4.2 46.1 1.0
CA B:THR491 4.3 40.9 1.0
CB B:THR491 4.5 41.8 1.0
C B:THR491 4.6 43.5 1.0
O B:GLY489 4.7 41.1 1.0
CB B:GLN492 4.7 51.8 1.0
N B:GLY489 4.7 48.1 1.0
N B:LEU888 4.9 48.3 1.0
CG B:HIS140 5.0 42.2 1.0
CE1 B:HIS140 5.0 43.6 1.0

Chlorine binding site 5 out of 6 in 5nz7

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Chlorine binding site 5 out of 6 in the Clostridium Thermocellum Cellodextrin Phosphorylase Ligand Free Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Clostridium Thermocellum Cellodextrin Phosphorylase Ligand Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1002

b:67.5
occ:1.00
 O B:HOH1192 2.9 57.5 1.0
ND2 B:ASN623 3.1 78.5 1.0
NH2 B:ARG717 3.2 73.0 1.0
ND2 B:ASN751 3.2 64.8 1.0
NE B:ARG717 3.3 75.9 1.0
CZ B:ARG717 3.7 76.7 1.0
CB B:ASN623 3.7 76.3 1.0
CZ3 B:TRP622 3.8 69.8 1.0
CG B:ASN623 3.9 76.7 1.0
CB B:ASN751 3.9 65.0 1.0
CE3 B:TRP622 3.9 69.5 1.0
CD2 B:PHE749 4.0 63.1 1.0
CG B:ASN751 4.1 64.2 1.0
CD1 B:LEU786 4.2 59.6 1.0
CD B:ARG717 4.4 75.5 1.0
CB B:PHE749 4.6 61.9 1.0
CG B:PHE749 4.7 63.6 1.0
SD B:MET666 4.8 69.2 1.0
CE2 B:PHE749 4.8 65.3 1.0
CA B:ASN623 4.9 76.4 1.0
N B:ASN751 4.9 65.0 1.0
CG B:LEU786 4.9 58.0 1.0
CA B:ASN751 5.0 65.4 1.0

Chlorine binding site 6 out of 6 in 5nz7

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Chlorine binding site 6 out of 6 in the Clostridium Thermocellum Cellodextrin Phosphorylase Ligand Free Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Clostridium Thermocellum Cellodextrin Phosphorylase Ligand Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1003

b:72.6
occ:1.00
 CB B:SER889 3.4 54.6 1.0
O B:HOH1145 3.6 66.3 1.0
O B:HOH1154 3.6 55.5 1.0
ND1 B:HIS817 3.7 48.1 1.0
N B:GLY890 3.7 45.4 1.0
CB B:HIS817 3.9 43.2 1.0
CA B:SER889 3.9 51.3 1.0
CG B:HIS817 4.3 46.7 1.0
NE2 B:GLN874 4.3 49.0 1.0
C B:SER889 4.4 48.0 1.0
CG B:GLN874 4.4 47.9 1.0
OG B:SER889 4.4 53.2 1.0
O B:HOH1207 4.7 52.1 1.0
CA B:GLY890 4.7 45.5 1.0
CD B:GLN874 4.8 51.4 1.0
CE1 B:HIS817 4.8 52.4 1.0
NE B:ARG486 5.0 65.2 1.0

Reference:

E.C.O'neill, G.Pergolizzi, C.E.M.Stevenson, D.M.Lawson, S.A.Nepogodiev, R.A.Field. Cellodextrin Phosphorylase From Ruminiclostridium Thermocellum: X-Ray Crystal Structure and Substrate Specificity Analysis. Carbohydr. Res. V. 451 118 2017.
ISSN: ISSN 1873-426X
PubMed: 28760417
DOI: 10.1016/J.CARRES.2017.07.005
Page generated: Fri Jul 26 14:00:39 2024

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