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Chlorine in PDB 4e4p: Second Native Structure of Xylanase A1 From Paenibacillus Sp. Jdr-2

Enzymatic activity of Second Native Structure of Xylanase A1 From Paenibacillus Sp. Jdr-2

All present enzymatic activity of Second Native Structure of Xylanase A1 From Paenibacillus Sp. Jdr-2:
3.2.1.8;

Protein crystallography data

The structure of Second Native Structure of Xylanase A1 From Paenibacillus Sp. Jdr-2, PDB code: 4e4p was solved by E.Pozharski, F.J.St John, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.92
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 179.518, 58.528, 65.024, 90.00, 108.81, 90.00
R / Rfree (%) 25.3 / 29.5

Other elements in 4e4p:

The structure of Second Native Structure of Xylanase A1 From Paenibacillus Sp. Jdr-2 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Second Native Structure of Xylanase A1 From Paenibacillus Sp. Jdr-2 (pdb code 4e4p). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Second Native Structure of Xylanase A1 From Paenibacillus Sp. Jdr-2, PDB code: 4e4p:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4e4p

Go back to Chlorine Binding Sites List in 4e4p
Chlorine binding site 1 out of 4 in the Second Native Structure of Xylanase A1 From Paenibacillus Sp. Jdr-2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Second Native Structure of Xylanase A1 From Paenibacillus Sp. Jdr-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:33.4
occ:0.75
 CL A:CL402 0.0 33.4 0.8
CL A:CL402 2.2 30.0 0.2
MG A:MG403 3.3 43.2 1.0
N A:ALA63 3.5 43.6 1.0
N A:THR62 3.8 40.7 1.0
CB A:THR62 3.8 45.8 1.0
CB A:ALA63 4.0 46.0 1.0
CB A:THR60 4.1 40.0 1.0
O A:THR60 4.1 38.0 1.0
CA A:THR62 4.2 43.5 1.0
C A:THR60 4.3 37.8 1.0
C A:THR62 4.3 44.1 1.0
CA A:ALA63 4.4 44.6 1.0
OG1 A:THR62 4.5 47.0 1.0
CA A:THR60 4.6 38.8 1.0
C A:PHE61 4.7 39.5 1.0
OG1 A:THR60 4.7 41.5 1.0
N A:PHE61 4.7 36.4 1.0
CG2 A:THR62 5.0 47.1 1.0

Chlorine binding site 2 out of 4 in 4e4p

Go back to Chlorine Binding Sites List in 4e4p
Chlorine binding site 2 out of 4 in the Second Native Structure of Xylanase A1 From Paenibacillus Sp. Jdr-2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Second Native Structure of Xylanase A1 From Paenibacillus Sp. Jdr-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:30.0
occ:0.25
 CL A:CL402 0.0 30.0 0.2
CL A:CL402 2.2 33.4 0.8
OG1 A:THR62 3.2 47.0 1.0
N A:THR62 3.2 40.7 1.0
CB A:THR62 3.3 45.8 1.0
CB A:THR60 3.4 40.0 1.0
CA A:THR60 3.5 38.8 1.0
C A:THR60 3.5 37.8 1.0
N A:PHE61 3.7 36.4 1.0
CA A:THR62 3.8 43.5 1.0
O A:HOH552 3.9 27.8 1.0
O A:THR60 4.1 38.0 1.0
CG2 A:THR60 4.2 42.9 1.0
C A:PHE61 4.3 39.5 1.0
MG A:MG403 4.4 43.2 1.0
CA A:PHE61 4.5 37.0 1.0
N A:ALA63 4.5 43.6 1.0
OG1 A:THR60 4.6 41.5 1.0
C A:THR62 4.8 44.1 1.0
CG2 A:THR62 4.8 47.1 1.0
N A:THR60 4.9 37.0 1.0

Chlorine binding site 3 out of 4 in 4e4p

Go back to Chlorine Binding Sites List in 4e4p
Chlorine binding site 3 out of 4 in the Second Native Structure of Xylanase A1 From Paenibacillus Sp. Jdr-2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Second Native Structure of Xylanase A1 From Paenibacillus Sp. Jdr-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:33.9
occ:0.70
 CL B:CL402 0.0 33.9 0.7
CL B:CL402 2.0 35.9 0.3
MG B:MG403 3.4 41.7 1.0
N B:ALA63 3.4 43.5 1.0
N B:THR62 3.7 41.6 1.0
CB B:THR62 3.8 47.0 1.0
CB B:ALA63 3.8 46.5 1.0
CA B:THR62 4.1 44.5 1.0
O B:THR60 4.1 39.2 1.0
CB B:THR60 4.1 41.9 1.0
C B:THR60 4.3 38.7 1.0
CA B:ALA63 4.3 44.8 1.0
C B:THR62 4.3 44.8 1.0
OG1 B:THR62 4.4 49.6 1.0
C B:PHE61 4.6 40.3 1.0
CA B:THR60 4.7 40.2 1.0
N B:PHE61 4.7 37.7 1.0
OG1 B:THR60 4.8 42.8 1.0

Chlorine binding site 4 out of 4 in 4e4p

Go back to Chlorine Binding Sites List in 4e4p
Chlorine binding site 4 out of 4 in the Second Native Structure of Xylanase A1 From Paenibacillus Sp. Jdr-2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Second Native Structure of Xylanase A1 From Paenibacillus Sp. Jdr-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:35.9
occ:0.30
 CL B:CL402 0.0 35.9 0.3
CL B:CL402 2.0 33.9 0.7
OG1 B:THR62 3.4 49.6 1.0
N B:THR62 3.4 41.6 1.0
CB B:THR60 3.4 41.9 1.0
CB B:THR62 3.5 47.0 1.0
CA B:THR60 3.6 40.2 1.0
C B:THR60 3.6 38.7 1.0
N B:PHE61 3.9 37.7 1.0
CA B:THR62 4.0 44.5 1.0
O B:THR60 4.1 39.2 1.0
CG2 B:THR60 4.1 43.7 1.0
O B:HOH565 4.2 25.7 1.0
C B:PHE61 4.4 40.3 1.0
MG B:MG403 4.5 41.7 1.0
N B:ALA63 4.5 43.5 1.0
OG1 B:THR60 4.6 42.8 1.0
CA B:PHE61 4.7 37.1 1.0
C B:THR62 4.8 44.8 1.0
CG2 B:THR62 4.9 47.7 1.0

Reference:

F.J.St John, J.F.Preston, E.Pozharski. Novel Structural Features of Xylanase A1 From Paenibacillus Sp. Jdr-2. J.Struct.Biol. V. 180 303 2012.
ISSN: ISSN 1047-8477
PubMed: 23000703
DOI: 10.1016/J.JSB.2012.09.007
Page generated: Sun Jul 21 12:32:56 2024

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