Atomistry » Magnesium » PDB 4dv6-4e7s » 4e4p
Atomistry »
  Magnesium »
    PDB 4dv6-4e7s »
      4e4p »

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 Dec 14 13:35:01 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy