Chlorine in PDB 6ncw: Crystal Structure of A GH2 Beta-Galacturonidase From Eisenbergiella Tayi Bound to Glycerol

Enzymatic activity of Crystal Structure of A GH2 Beta-Galacturonidase From Eisenbergiella Tayi Bound to Glycerol

All present enzymatic activity of Crystal Structure of A GH2 Beta-Galacturonidase From Eisenbergiella Tayi Bound to Glycerol:
3.2.1.31;

Protein crystallography data

The structure of Crystal Structure of A GH2 Beta-Galacturonidase From Eisenbergiella Tayi Bound to Glycerol, PDB code: 6ncw was solved by W.G.Walton, S.J.Pellock, M.R.Redinbo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.54 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 65.930, 87.677, 124.375, 93.29, 101.55, 90.37
R / Rfree (%) 16.5 / 20.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of A GH2 Beta-Galacturonidase From Eisenbergiella Tayi Bound to Glycerol (pdb code 6ncw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of A GH2 Beta-Galacturonidase From Eisenbergiella Tayi Bound to Glycerol, PDB code: 6ncw:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6ncw

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Chlorine binding site 1 out of 4 in the Crystal Structure of A GH2 Beta-Galacturonidase From Eisenbergiella Tayi Bound to Glycerol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of A GH2 Beta-Galacturonidase From Eisenbergiella Tayi Bound to Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:21.9
occ:1.00
 N A:ASN531 3.1 19.8 1.0
O A:HOH960 3.3 20.5 1.0
NZ A:LYS532 3.4 20.7 1.0
CH2 A:TRP482 3.5 15.6 1.0
CZ3 A:TRP482 3.6 16.4 1.0
ND2 A:ASN531 3.8 20.1 1.0
CD A:ARG525 3.8 17.9 1.0
NH1 A:ARG525 3.9 18.3 1.0
CA A:ASN530 3.9 17.2 1.0
CB A:ASN531 4.0 17.0 1.0
C A:ASN530 4.0 19.9 1.0
CA A:ASN531 4.0 22.2 1.0
CG A:LYS532 4.1 16.8 1.0
OD1 A:ASN530 4.2 17.7 1.0
NE A:ARG525 4.2 19.4 1.0
CZ A:ARG525 4.2 20.3 1.0
CG A:ASN530 4.2 17.1 1.0
O A:MET529 4.3 20.2 1.0
CE A:LYS532 4.3 22.1 1.0
CG A:ASN531 4.4 18.5 1.0
C A:ASN531 4.4 19.2 1.0
N A:LYS532 4.5 20.0 1.0
O A:SER524 4.5 19.3 1.0
CD A:PRO526 4.6 16.8 1.0
ND2 A:ASN530 4.6 16.3 1.0
CB A:ASN530 4.7 17.4 1.0
CD A:LYS532 4.8 21.9 1.0
CZ2 A:TRP482 4.8 20.0 1.0
CA A:ARG525 4.9 17.1 1.0
CE3 A:TRP482 4.9 16.3 1.0
N A:ASN530 5.0 16.6 1.0
CA A:GLY469 5.0 14.9 1.0

Chlorine binding site 2 out of 4 in 6ncw

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Chlorine binding site 2 out of 4 in the Crystal Structure of A GH2 Beta-Galacturonidase From Eisenbergiella Tayi Bound to Glycerol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of A GH2 Beta-Galacturonidase From Eisenbergiella Tayi Bound to Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:23.2
occ:1.00
 N B:ASN531 3.1 21.1 1.0
NZ B:LYS532 3.3 21.6 1.0
O B:HOH879 3.4 24.5 1.0
CH2 B:TRP482 3.5 18.4 1.0
CZ3 B:TRP482 3.5 16.9 1.0
NH1 B:ARG525 3.8 16.7 1.0
CD B:ARG525 3.8 20.9 1.0
ND2 B:ASN531 3.9 21.2 1.0
CG B:LYS532 3.9 20.8 1.0
CA B:ASN531 4.0 20.4 1.0
CA B:ASN530 4.0 19.0 1.0
CB B:ASN531 4.0 17.5 1.0
C B:ASN530 4.0 17.1 1.0
CE B:LYS532 4.0 21.4 1.0
CZ B:ARG525 4.2 21.6 1.0
NE B:ARG525 4.2 18.9 1.0
OD1 B:ASN530 4.3 19.4 1.0
CG B:ASN530 4.3 19.8 1.0
O B:MET529 4.3 17.1 1.0
C B:ASN531 4.3 17.7 1.0
N B:LYS532 4.4 21.5 1.0
O B:SER524 4.4 20.6 1.0
CG B:ASN531 4.5 18.4 1.0
ND2 B:ASN530 4.6 16.0 1.0
CD B:LYS532 4.6 24.3 1.0
CD B:PRO526 4.7 18.6 1.0
CB B:ASN530 4.8 17.6 1.0
CZ2 B:TRP482 4.8 18.3 1.0
CE3 B:TRP482 4.9 17.9 1.0
CA B:ARG525 4.9 18.5 1.0
CA B:GLY469 5.0 17.2 1.0

Chlorine binding site 3 out of 4 in 6ncw

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Chlorine binding site 3 out of 4 in the Crystal Structure of A GH2 Beta-Galacturonidase From Eisenbergiella Tayi Bound to Glycerol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of A GH2 Beta-Galacturonidase From Eisenbergiella Tayi Bound to Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl601

b:22.4
occ:1.00
 N C:ASN531 3.1 19.3 1.0
NZ C:LYS532 3.2 23.3 1.0
O C:HOH859 3.3 28.4 1.0
CH2 C:TRP482 3.6 20.2 1.0
CZ3 C:TRP482 3.6 17.4 1.0
CD C:ARG525 3.7 19.7 1.0
ND2 C:ASN531 3.8 16.1 1.0
NH1 C:ARG525 3.8 21.0 1.0
CA C:ASN530 3.9 18.0 1.0
C C:ASN530 4.0 18.9 1.0
CA C:ASN531 4.0 18.1 1.0
CG C:LYS532 4.1 20.5 1.0
CB C:ASN531 4.1 16.0 1.0
NE C:ARG525 4.1 21.9 1.0
CE C:LYS532 4.2 19.1 1.0
CZ C:ARG525 4.2 23.2 1.0
CG C:ASN530 4.2 19.6 1.0
OD1 C:ASN530 4.2 19.1 1.0
O C:MET529 4.3 20.1 1.0
O C:SER524 4.3 23.5 1.0
CG C:ASN531 4.4 17.9 1.0
C C:ASN531 4.4 18.2 1.0
N C:LYS532 4.4 20.3 1.0
ND2 C:ASN530 4.5 17.3 1.0
CD C:PRO526 4.6 18.6 1.0
CB C:ASN530 4.6 21.1 1.0
CD C:LYS532 4.8 22.9 1.0
CA C:ARG525 4.9 22.5 1.0
CZ2 C:TRP482 4.9 20.6 1.0
CE3 C:TRP482 5.0 17.8 1.0
N C:ASN530 5.0 19.6 1.0

Chlorine binding site 4 out of 4 in 6ncw

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Chlorine binding site 4 out of 4 in the Crystal Structure of A GH2 Beta-Galacturonidase From Eisenbergiella Tayi Bound to Glycerol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of A GH2 Beta-Galacturonidase From Eisenbergiella Tayi Bound to Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl601

b:19.9
occ:1.00
 N D:ASN531 3.1 19.3 1.0
NZ D:LYS532 3.3 20.9 1.0
O D:HOH956 3.5 21.2 1.0
CH2 D:TRP482 3.5 19.4 1.0
CZ3 D:TRP482 3.6 17.2 1.0
CD D:ARG525 3.8 18.9 1.0
ND2 D:ASN531 3.9 20.4 1.0
CA D:ASN530 3.9 20.7 1.0
CA D:ASN531 3.9 18.1 1.0
C D:ASN530 3.9 18.5 1.0
CB D:ASN531 4.0 15.8 1.0
NH1 D:ARG525 4.0 18.5 1.0
CG D:LYS532 4.0 18.6 1.0
OD1 D:ASN530 4.1 18.8 1.0
NE D:ARG525 4.2 16.5 1.0
CG D:ASN530 4.2 20.9 1.0
O D:MET529 4.3 18.7 1.0
CZ D:ARG525 4.3 20.4 1.0
CE D:LYS532 4.3 21.1 1.0
C D:ASN531 4.3 17.1 1.0
N D:LYS532 4.4 18.0 1.0
O D:SER524 4.4 23.2 1.0
CG D:ASN531 4.5 18.5 1.0
CD D:PRO526 4.6 18.1 1.0
CB D:ASN530 4.7 18.7 1.0
ND2 D:ASN530 4.7 18.0 1.0
CD D:LYS532 4.8 21.1 1.0
CZ2 D:TRP482 4.8 20.2 1.0
CA D:ARG525 4.8 15.8 1.0
CE3 D:TRP482 5.0 17.3 1.0
N D:ASN530 5.0 18.7 1.0

Reference:

S.J.Pellock, W.G.Walton, M.R.Redinbo. Selecting A Single Stereocenter: the Molecular Nuances That Differentiate Beta-Hexuronidases in the Human Gut Microbiome. Biochemistry V. 58 1311 2019.
ISSN: ISSN 1520-4995
PubMed: 30729778
DOI: 10.1021/ACS.BIOCHEM.8B01285
Page generated: Sat Dec 12 13:23:17 2020

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