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Magnesium in PDB 3ro8: Crystal Structure of the Catalytic Domain of XYNA1 From Paenibacillus Sp. Jdr-2

Enzymatic activity of Crystal Structure of the Catalytic Domain of XYNA1 From Paenibacillus Sp. Jdr-2

All present enzymatic activity of Crystal Structure of the Catalytic Domain of XYNA1 From Paenibacillus Sp. Jdr-2:
3.2.1.8;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of XYNA1 From Paenibacillus Sp. Jdr-2, PDB code: 3ro8 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) 42.61 / 1.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.072, 93.172, 182.947, 90.00, 99.96, 90.00
R / Rfree (%) 14.2 / 18.5

Other elements in 3ro8:

The structure of Crystal Structure of the Catalytic Domain of XYNA1 From Paenibacillus Sp. Jdr-2 also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of XYNA1 From Paenibacillus Sp. Jdr-2 (pdb code 3ro8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of the Catalytic Domain of XYNA1 From Paenibacillus Sp. Jdr-2, PDB code: 3ro8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 3ro8

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Magnesium binding site 1 out of 12 in the Crystal Structure of the Catalytic Domain of XYNA1 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 Crystal Structure of the Catalytic Domain of XYNA1 From Paenibacillus Sp. Jdr-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:18.4
occ:1.00
 O A:ASP14 2.3 17.4 1.0
O A:HOH611 2.3 31.4 1.0
O A:ALA296 2.4 15.6 1.0
O A:ILE299 2.4 15.8 1.0
O A:HOH895 2.4 27.7 1.0
O A:HOH859 2.5 30.8 1.0
C A:ALA296 3.5 14.3 1.0
C A:ILE299 3.5 14.3 1.0
C A:ASP14 3.6 17.2 1.0
O A:HOH800 4.0 44.9 1.0
CA A:PHE15 4.1 15.6 1.0
N A:ILE299 4.1 14.3 1.0
CB A:PHE15 4.2 15.6 1.0
CA A:ALA296 4.2 14.8 1.0
N A:PHE15 4.3 15.3 1.0
CA A:ILE299 4.4 14.6 1.0
O A:HOH861 4.4 32.1 1.0
N A:ALA300 4.4 14.9 1.0
CA A:ALA300 4.4 13.9 1.0
CB A:ALA296 4.5 15.8 1.0
N A:ASP297 4.5 16.3 1.0
C A:ASP297 4.5 16.4 1.0
CA A:ASP14 4.6 18.7 1.0
CA A:ASP297 4.6 18.5 1.0
O A:HOH852 4.8 43.9 1.0
O A:HOH680 4.8 44.5 1.0
O A:ASP297 4.8 18.1 1.0
CD2 A:PHE15 4.8 16.6 1.0
N A:HIS298 4.9 14.3 1.0
O A:HOH592 4.9 30.2 1.0
CB A:ILE299 4.9 14.0 1.0
C A:ALA300 5.0 15.0 1.0

Magnesium binding site 2 out of 12 in 3ro8

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Magnesium binding site 2 out of 12 in the Crystal Structure of the Catalytic Domain of XYNA1 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 Crystal Structure of the Catalytic Domain of XYNA1 From Paenibacillus Sp. Jdr-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:27.8
occ:1.00
 O A:HOH609 2.8 36.5 1.0
OG A:SER184 3.0 26.2 1.0
N A:SER184 3.3 21.6 1.0
C A:ASN182 3.5 20.7 1.0
N A:PRO183 3.5 21.0 1.0
CA A:ASN182 3.5 19.2 1.0
CD A:PRO183 3.5 21.4 1.0
CB A:SER184 3.6 23.7 1.0
CA A:SER184 4.0 22.7 1.0
O A:ASN182 4.0 20.1 1.0
CB A:ASN182 4.1 20.2 1.0
CB E:ASP297 4.2 23.4 1.0
OD1 E:ASP297 4.2 34.5 1.0
CG A:PRO183 4.2 21.3 1.0
O E:ASP297 4.2 20.5 1.0
C A:PRO183 4.3 20.6 1.0
CG E:ASP297 4.3 30.6 1.0
O E:HOH854 4.4 57.3 1.0
CA A:PRO183 4.4 20.8 1.0
OD1 A:ASN182 4.6 24.7 1.0
CA E:ASP297 4.6 20.9 1.0
NE1 A:TRP185 4.7 24.1 1.0
N A:TRP185 4.7 21.1 1.0
CD1 A:TRP185 4.7 23.3 1.0
N A:ASN182 4.7 19.8 1.0
C A:SER184 4.8 23.4 1.0
O A:GLU181 4.8 24.2 1.0
CG A:ASN182 4.8 19.8 1.0
O A:HOH665 4.9 69.8 1.0
OD2 E:ASP297 4.9 36.5 1.0
C E:ASP297 4.9 18.7 1.0

Magnesium binding site 3 out of 12 in 3ro8

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Magnesium binding site 3 out of 12 in the Crystal Structure of the Catalytic Domain of XYNA1 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 Crystal Structure of the Catalytic Domain of XYNA1 From Paenibacillus Sp. Jdr-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:19.8
occ:1.00
 O B:HOH947 2.3 29.4 1.0
O B:ALA296 2.3 16.8 1.0
O B:ASP14 2.3 18.8 1.0
O B:ILE299 2.4 16.3 1.0
O B:HOH541 2.4 25.4 1.0
O B:HOH640 2.7 31.0 1.0
C B:ALA296 3.5 16.6 1.0
C B:ILE299 3.5 15.2 1.0
C B:ASP14 3.5 16.7 1.0
CB B:PHE15 4.1 15.7 1.0
CA B:PHE15 4.1 15.5 1.0
O B:HOH637 4.2 29.8 1.0
N B:ILE299 4.2 14.9 1.0
CA B:ALA296 4.2 15.8 1.0
N B:PHE15 4.3 15.8 1.0
CA B:ILE299 4.4 14.2 1.0
N B:ALA300 4.4 13.8 1.0
CB B:ALA296 4.4 17.1 1.0
CA B:ALA300 4.4 14.4 1.0
N B:ASP297 4.5 16.8 1.0
O B:HOH919 4.5 31.6 1.0
C B:ASP297 4.6 16.3 1.0
O B:HOH779 4.6 30.8 1.0
CA B:ASP14 4.6 18.9 1.0
CA B:ASP297 4.6 17.6 1.0
CD2 B:PHE15 4.7 14.7 1.0
O B:HOH780 4.8 35.1 1.0
O B:ASP297 4.8 19.4 1.0
N B:HIS298 4.8 14.1 1.0
CB B:ILE299 4.9 14.2 1.0
O B:HOH677 4.9 37.6 1.0
CG B:PHE15 4.9 15.2 1.0
C B:ALA300 5.0 15.5 1.0

Magnesium binding site 4 out of 12 in 3ro8

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Magnesium binding site 4 out of 12 in the Crystal Structure of the Catalytic Domain of XYNA1 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 Crystal Structure of the Catalytic Domain of XYNA1 From Paenibacillus Sp. Jdr-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:23.9
occ:1.00
 O C:HOH812 2.9 36.3 1.0
OG1 B:THR62 3.1 24.9 1.0
O C:HOH841 3.1 36.4 1.0
O B:HOH567 3.2 26.2 1.0
N B:THR62 3.5 17.6 1.0
CB B:THR62 3.5 19.5 1.0
O C:HOH592 3.5 37.5 1.0
CA B:THR60 3.5 18.1 1.0
CB B:THR60 3.6 17.6 1.0
ND2 C:ASN243 3.6 34.0 1.0
N B:PHE61 3.7 16.9 1.0
C B:THR60 3.7 17.5 1.0
CG2 B:THR60 4.0 20.8 1.0
O B:HOH585 4.1 32.7 1.0
CA B:THR62 4.1 18.6 1.0
O B:HOH513 4.3 32.7 1.0
OD1 C:ASN243 4.4 27.2 1.0
CG C:ASN243 4.4 23.8 1.0
O B:THR60 4.5 18.8 1.0
C B:PHE61 4.5 17.3 1.0
O C:HOH896 4.6 21.8 1.0
CA B:PHE61 4.7 17.1 1.0
CG2 B:THR62 4.8 23.9 1.0
OG1 B:THR60 4.9 20.0 1.0
N B:THR60 4.9 18.9 1.0
O B:PHE59 4.9 22.1 1.0

Magnesium binding site 5 out of 12 in 3ro8

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Magnesium binding site 5 out of 12 in the Crystal Structure of the Catalytic Domain of XYNA1 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 5 of Crystal Structure of the Catalytic Domain of XYNA1 From Paenibacillus Sp. Jdr-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:14.7
occ:0.45
 MG C:MG401 0.0 14.7 0.5
MG C:MG401 2.0 25.9 0.6
O C:ASP14 2.1 23.3 1.0
O C:ALA296 2.2 21.1 1.0
O C:ILE299 2.3 17.6 1.0
C C:ALA296 3.3 19.7 1.0
C C:ASP14 3.3 21.2 1.0
C C:ILE299 3.5 15.3 1.0
CD G:PRO274 3.5 27.8 1.0
CA C:ALA296 3.8 19.6 1.0
CB C:PHE15 3.9 18.8 1.0
CD2 G:LEU273 3.9 30.2 1.0
CA C:PHE15 3.9 16.9 1.0
CB C:ALA296 4.0 22.5 1.0
CG G:PRO274 4.1 28.1 1.0
N C:PHE15 4.1 18.8 1.0
N C:ILE299 4.2 16.2 1.0
CA C:ILE299 4.3 14.9 1.0
CD2 C:PHE15 4.3 19.3 1.0
O C:HOH551 4.4 22.9 1.0
CA C:ASP14 4.4 21.3 1.0
N C:ASP297 4.5 21.3 1.0
O C:HOH655 4.5 37.4 1.0
N C:ALA300 4.5 15.7 1.0
CA C:ALA300 4.6 15.6 1.0
CG C:PHE15 4.6 19.0 1.0
CB C:ILE299 4.7 15.6 1.0
C C:ASP297 4.7 19.1 1.0
CA C:ASP297 4.7 21.9 1.0
N C:HIS298 4.9 17.9 1.0
N G:PRO274 4.9 24.9 1.0
CA G:LEU273 4.9 22.2 1.0

Magnesium binding site 6 out of 12 in 3ro8

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Magnesium binding site 6 out of 12 in the Crystal Structure of the Catalytic Domain of XYNA1 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 6 of Crystal Structure of the Catalytic Domain of XYNA1 From Paenibacillus Sp. Jdr-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:25.9
occ:0.55
 MG C:MG401 0.0 25.9 0.6
MG C:MG401 2.0 14.7 0.5
O C:HOH551 2.7 22.9 1.0
O C:ASP14 3.1 23.3 1.0
O C:ILE299 3.3 17.6 1.0
O C:HOH655 3.3 37.4 1.0
CD G:PRO274 3.3 27.8 1.0
CD2 G:LEU273 3.6 30.2 1.0
CA G:LEU273 3.8 22.2 1.0
O C:ALA296 4.0 21.1 1.0
CA C:PHE15 4.0 16.9 1.0
C C:ASP14 4.0 21.2 1.0
O C:HOH623 4.1 32.4 1.0
CG G:PRO274 4.2 28.1 1.0
O G:THR272 4.3 24.8 1.0
CA C:ALA300 4.3 15.6 1.0
O C:ALA300 4.3 15.6 1.0
C C:ILE299 4.3 15.3 1.0
N G:PRO274 4.3 24.9 1.0
N C:PHE15 4.4 18.8 1.0
CB C:PHE15 4.4 18.8 1.0
CB G:LEU273 4.4 21.7 1.0
CG G:LEU273 4.5 26.6 1.0
O G:HOH560 4.6 38.3 1.0
N G:LEU273 4.6 21.4 1.0
C G:LEU273 4.6 24.2 1.0
C C:ALA300 4.7 15.6 1.0
C G:THR272 4.7 22.5 1.0
N C:ALA300 4.8 15.7 1.0

Magnesium binding site 7 out of 12 in 3ro8

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Magnesium binding site 7 out of 12 in the Crystal Structure of the Catalytic Domain of XYNA1 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 7 of Crystal Structure of the Catalytic Domain of XYNA1 From Paenibacillus Sp. Jdr-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:21.7
occ:1.00
 O D:HOH900 2.1 33.5 1.0
O D:ASP14 2.2 21.1 1.0
O D:ALA296 2.3 20.9 1.0
O D:ILE299 2.4 18.4 1.0
O D:HOH775 2.4 32.9 1.0
C D:ASP14 3.4 21.1 1.0
C D:ALA296 3.5 20.8 1.0
C D:ILE299 3.5 17.6 1.0
CA D:PHE15 4.0 18.9 1.0
CB D:PHE15 4.1 18.3 1.0
CA D:ALA296 4.2 20.1 1.0
O D:HOH698 4.2 32.8 1.0
N D:PHE15 4.2 19.6 1.0
N D:ILE299 4.2 17.6 1.0
CB D:ALA296 4.3 21.3 1.0
CA D:ILE299 4.4 16.9 1.0
CA D:ASP14 4.5 21.3 1.0
N D:ASP297 4.5 22.0 1.0
N D:ALA300 4.5 16.4 1.0
CA D:ALA300 4.5 16.8 1.0
O D:HOH815 4.6 57.0 1.0
CA D:ASP297 4.7 21.8 1.0
CD2 D:PHE15 4.7 19.1 1.0
O D:HOH709 4.7 35.5 1.0
C D:ASP297 4.7 20.8 1.0
CB D:ILE299 4.8 17.4 1.0
CG D:PHE15 4.9 17.4 1.0
N D:HIS298 4.9 18.8 1.0
O D:ALA300 5.0 17.0 1.0
O D:HOH858 5.0 54.4 1.0

Magnesium binding site 8 out of 12 in 3ro8

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Magnesium binding site 8 out of 12 in the Crystal Structure of the Catalytic Domain of XYNA1 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 8 of Crystal Structure of the Catalytic Domain of XYNA1 From Paenibacillus Sp. Jdr-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:20.2
occ:1.00
 O E:ASP14 2.3 20.8 1.0
O E:ALA296 2.4 19.9 1.0
O E:ILE299 2.4 18.5 1.0
O E:HOH866 2.4 32.2 1.0
O E:HOH887 2.4 28.5 1.0
O E:HOH625 2.5 29.6 1.0
C E:ASP14 3.5 20.7 1.0
C E:ALA296 3.5 18.9 1.0
C E:ILE299 3.5 17.1 1.0
CA E:PHE15 4.0 18.1 1.0
O E:HOH762 4.1 46.5 1.0
CB E:PHE15 4.1 18.4 1.0
N E:ILE299 4.1 17.2 1.0
N E:PHE15 4.2 19.2 1.0
CA E:ASP297 4.3 20.9 1.0
CA E:ILE299 4.3 15.9 1.0
C E:ASP297 4.3 18.7 1.0
CA E:ALA296 4.3 19.7 1.0
O E:ASP297 4.4 20.5 1.0
N E:ASP297 4.4 21.1 1.0
CB E:ALA296 4.5 21.3 1.0
N E:ALA300 4.5 16.4 1.0
O E:HOH888 4.5 38.6 1.0
O E:HOH768 4.5 42.1 1.0
CA E:ALA300 4.5 17.4 1.0
CA E:ASP14 4.6 21.3 1.0
CD2 E:PHE15 4.8 18.9 1.0
N E:HIS298 4.8 18.6 1.0
CB E:ILE299 4.9 17.3 1.0
O E:HOH771 4.9 42.6 1.0
O E:HOH829 4.9 45.5 1.0
O E:HOH864 4.9 31.2 1.0
CG E:PHE15 4.9 17.1 1.0
C E:ALA300 5.0 15.7 1.0

Magnesium binding site 9 out of 12 in 3ro8

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Magnesium binding site 9 out of 12 in the Crystal Structure of the Catalytic Domain of XYNA1 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 9 of Crystal Structure of the Catalytic Domain of XYNA1 From Paenibacillus Sp. Jdr-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg404

b:33.2
occ:1.00
 O E:HOH907 2.7 36.8 1.0
O E:HOH545 2.9 22.2 1.0
ND2 E:ASN141 3.1 23.3 1.0
CA E:PRO144 3.7 20.7 1.0
CB E:PRO144 3.7 21.0 1.0
CB E:ASN141 3.8 17.9 1.0
CG E:ASN141 3.9 18.8 1.0
CA E:SER153 4.0 16.5 1.0
N E:SER145 4.0 24.8 1.0
O E:HOH614 4.0 33.3 1.0
O E:ALA152 4.1 22.6 1.0
O E:SER153 4.3 16.0 1.0
C E:PRO144 4.4 23.2 1.0
O E:HOH622 4.6 45.8 1.0
OG E:SER153 4.6 18.3 1.0
C E:SER153 4.6 14.9 1.0
CB E:SER153 4.6 17.1 1.0
O E:HOH788 4.8 39.4 1.0
N E:PRO144 4.8 19.9 1.0
N E:SER153 4.9 16.0 1.0
C E:ALA152 4.9 19.5 1.0
OG E:SER145 4.9 32.7 1.0

Magnesium binding site 10 out of 12 in 3ro8

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Magnesium binding site 10 out of 12 in the Crystal Structure of the Catalytic Domain of XYNA1 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 10 of Crystal Structure of the Catalytic Domain of XYNA1 From Paenibacillus Sp. Jdr-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:20.1
occ:1.00
 O F:ASP14 2.3 20.3 1.0
O F:ALA296 2.3 18.5 1.0
O F:ILE299 2.4 17.4 1.0
O F:HOH824 2.4 26.0 1.0
O F:HOH823 2.5 29.5 1.0
O F:HOH640 2.6 29.3 1.0
C F:ASP14 3.4 20.6 1.0
C F:ALA296 3.4 18.1 1.0
C F:ILE299 3.5 16.0 1.0
CA F:PHE15 4.0 17.4 1.0
N F:ILE299 4.1 17.7 1.0
CB F:PHE15 4.2 19.4 1.0
N F:PHE15 4.2 18.7 1.0
O F:HOH825 4.3 37.4 1.0
N F:ASP297 4.3 18.6 1.0
CA F:ASP297 4.3 19.6 1.0
CA F:ILE299 4.3 17.2 1.0
CA F:ALA296 4.3 18.4 1.0
C F:ASP297 4.4 18.4 1.0
O F:ASP297 4.4 18.2 1.0
CA F:ASP14 4.5 23.0 1.0
CB F:ALA296 4.5 20.4 1.0
N F:ALA300 4.5 15.3 1.0
CA F:ALA300 4.6 15.4 1.0
O F:HOH797 4.7 51.6 1.0
CD2 F:PHE15 4.8 19.7 1.0
O F:HOH819 4.8 47.8 1.0
CB F:ILE299 4.8 16.8 1.0
N F:HIS298 4.9 16.6 1.0
CG F:PHE15 5.0 17.4 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: Thu Aug 15 10:32:54 2024

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