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Magnesium 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:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Second Native Structure of Xylanase A1 From Paenibacillus Sp. Jdr-2, PDB code: 4e4p:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4e4p

Go back to Magnesium Binding Sites List in 4e4p
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg401

b:38.1
occ:1.00
 O A:HOH604 2.2 2.4 1.0
O A:ALA296 2.3 45.1 1.0
O A:ILE299 2.3 36.3 1.0
O A:HOH588 2.3 2.0 0.5
O A:ASP14 2.4 58.6 1.0
C A:ILE299 3.3 39.6 1.0
C A:ALA296 3.5 47.8 1.0
C A:ASP14 3.6 59.6 1.0
O A:HOH588 3.7 3.2 0.5
N A:ILE299 3.9 42.7 1.0
CA A:PHE15 4.2 51.7 1.0
N A:ALA300 4.2 39.3 1.0
CA A:ILE299 4.2 40.2 1.0
CB A:PHE15 4.2 50.3 1.0
CA A:ALA300 4.2 39.2 1.0
CA A:ALA296 4.3 47.3 1.0
N A:PHE15 4.3 55.3 1.0
C A:ASP297 4.4 50.2 1.0
N A:ASP297 4.5 50.7 1.0
CA A:ASP297 4.5 52.9 1.0
O A:ASP297 4.6 50.3 1.0
N A:HIS298 4.6 47.9 1.0
CB A:ILE299 4.6 40.3 1.0
CB A:ALA296 4.7 49.5 1.0
CA A:ASP14 4.7 65.9 1.0
C A:ALA300 4.8 38.3 1.0
O A:ALA300 4.8 37.4 1.0
C A:HIS298 4.9 44.0 1.0
CD2 A:PHE15 5.0 52.6 1.0

Magnesium binding site 2 out of 4 in 4e4p

Go back to Magnesium Binding Sites List in 4e4p
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg403

b:43.2
occ:1.00
 O A:THR60 2.7 38.0 1.0
O A:HOH612 2.7 18.4 1.0
N A:ALA64 3.1 41.4 1.0
CL A:CL402 3.3 33.4 0.8
N A:ALA63 3.4 43.6 1.0
C A:PHE61 3.4 39.5 1.0
C A:THR60 3.5 37.8 1.0
CA A:PHE61 3.5 37.0 1.0
N A:THR62 3.6 40.7 1.0
CB A:ALA63 3.7 46.0 1.0
O A:PHE61 3.8 39.4 1.0
CA A:ALA63 3.8 44.6 1.0
CB A:ALA64 3.9 36.6 1.0
N A:PHE61 3.9 36.4 1.0
C A:ALA63 4.0 42.6 1.0
O A:ALA51 4.0 39.7 1.0
CD2 A:LEU52 4.1 32.0 1.0
CA A:ALA64 4.1 39.7 1.0
C A:THR62 4.2 44.1 1.0
CL A:CL402 4.4 30.0 0.2
CA A:THR62 4.4 43.5 1.0
O A:ALA46 4.5 37.3 1.0
OG1 A:THR60 4.6 41.5 1.0
CB A:THR60 4.7 40.0 1.0
CA A:THR60 4.8 38.8 1.0
CB A:PHE61 5.0 35.4 1.0
C A:ALA51 5.0 36.7 1.0

Magnesium binding site 3 out of 4 in 4e4p

Go back to Magnesium Binding Sites List in 4e4p
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg401

b:41.0
occ:1.00
 O B:ASP14 2.3 53.4 1.0
O B:ALA296 2.3 49.7 1.0
O B:ILE299 2.4 37.7 1.0
O B:HOH593 2.5 3.9 1.0
O B:HOH579 2.5 16.9 1.0
C B:ASP14 3.5 55.5 1.0
C B:ALA296 3.5 51.8 1.0
C B:ILE299 3.6 40.9 1.0
N B:ILE299 4.2 44.7 1.0
C B:ASP297 4.3 52.9 1.0
CA B:ASP297 4.3 56.6 1.0
CA B:PHE15 4.3 49.3 1.0
N B:ASP297 4.3 54.9 1.0
N B:PHE15 4.4 51.9 1.0
CA B:ASP14 4.4 61.5 1.0
CA B:ILE299 4.4 41.8 1.0
CA B:ALA296 4.5 51.0 1.0
CB B:PHE15 4.5 47.2 1.0
N B:ALA300 4.5 38.2 1.0
O B:ASP297 4.6 52.2 1.0
CA B:ALA300 4.6 39.2 1.0
N B:HIS298 4.7 49.6 1.0
CB B:ALA296 4.7 53.8 1.0

Magnesium binding site 4 out of 4 in 4e4p

Go back to Magnesium Binding Sites List in 4e4p
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg403

b:41.7
occ:1.00
 O B:HOH609 2.6 21.3 1.0
O B:THR60 2.7 39.2 1.0
N B:ALA64 2.9 40.2 1.0
C B:PHE61 3.3 40.3 1.0
N B:ALA63 3.3 43.5 1.0
CL B:CL402 3.4 33.9 0.7
CA B:PHE61 3.5 37.1 1.0
N B:THR62 3.6 41.6 1.0
CB B:ALA63 3.6 46.5 1.0
C B:THR60 3.6 38.7 1.0
O B:PHE61 3.6 40.7 1.0
CB B:ALA64 3.7 37.3 1.0
CA B:ALA63 3.7 44.8 1.0
C B:ALA63 3.8 42.3 1.0
CA B:ALA64 3.9 39.8 1.0
N B:PHE61 3.9 37.7 1.0
CD2 B:LEU52 4.0 32.8 1.0
C B:THR62 4.1 44.8 1.0
O B:ALA51 4.3 39.1 1.0
CA B:THR62 4.4 44.5 1.0
CL B:CL402 4.5 35.9 0.3
O B:ALA46 4.5 35.9 1.0
OG1 B:THR60 4.8 42.8 1.0
CA B:THR60 4.9 40.2 1.0
CB B:THR60 4.9 41.9 1.0
CB B:PHE61 4.9 36.4 1.0
N B:ASP65 5.0 41.2 1.0
O B:ALA63 5.0 44.1 1.0
O B:THR62 5.0 43.1 1.0
C B:ALA64 5.0 40.3 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: Mon Aug 11 11:56:07 2025

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