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Manganese in PDB 3a9s: X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol

Enzymatic activity of X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol

All present enzymatic activity of X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol:
5.3.1.3;

Protein crystallography data

The structure of X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol, PDB code: 3a9s was solved by K.Takeda, H.Yoshida, K.Izumori, S.Kamitori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.70 / 1.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 144.317, 127.271, 110.315, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 18.7

Manganese Binding Sites:

Pages:

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

Binding sites:

The binding sites of Manganese atom in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol (pdb code 3a9s). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol, PDB code: 3a9s:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 3a9s

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Manganese binding site 1 out of 12 in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:20.8
occ:0.33
 MN A:MN701 0.0 20.8 0.3
MN A:MN701 1.6 25.6 0.3
MN A:MN701 2.0 29.9 0.3
OD2 A:ASP366 2.3 18.4 1.0
NE2 A:HIS532 2.4 12.3 1.0
O A:HOH702 2.4 22.3 1.0
OE1 A:GLU342 2.5 14.4 0.7
O1 A:GOL601 2.7 17.1 1.0
OE1 A:GLU342 2.9 14.3 0.3
CG A:ASP366 3.1 16.8 1.0
OD1 A:ASP366 3.2 15.8 1.0
CD2 A:HIS532 3.2 10.1 1.0
OE2 A:GLU342 3.2 13.2 0.3
CD A:GLU342 3.4 13.2 1.0
CE1 A:HIS532 3.4 11.5 1.0
OE2 A:GLU342 3.5 16.2 0.7
OG A:SER398 3.7 12.2 1.0
OD1 A:ASN397 3.9 10.5 1.0
C1 A:GOL601 4.0 17.7 1.0
O2 A:GOL601 4.1 14.8 1.0
CB A:SER398 4.3 12.5 1.0
ND2 A:ASN531 4.3 14.7 1.0
CG A:HIS532 4.4 8.6 1.0
ND1 A:HIS532 4.4 8.5 1.0
C2 A:GOL601 4.6 15.5 1.0
CB A:ASP366 4.6 12.8 1.0
N A:SER398 4.6 10.4 1.0
CE1 A:PHE364 4.7 9.5 1.0
CG A:GLU342 4.8 11.4 1.0

Manganese binding site 2 out of 12 in 3a9s

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Manganese binding site 2 out of 12 in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:25.6
occ:0.33
 MN A:MN701 0.0 25.6 0.3
MN A:MN701 1.6 20.8 0.3
MN A:MN701 2.1 29.9 0.3
OE1 A:GLU342 2.5 14.4 0.7
OD1 A:ASN397 2.6 10.5 1.0
OG A:SER398 2.6 12.2 1.0
OD2 A:ASP366 3.0 18.4 1.0
OE2 A:GLU342 3.2 13.2 0.3
OE1 A:GLU342 3.2 14.3 0.3
CD A:GLU342 3.3 13.2 1.0
NE2 A:HIS532 3.4 12.3 1.0
CB A:SER398 3.5 12.5 1.0
N A:SER398 3.6 10.4 1.0
OE2 A:GLU342 3.7 16.2 0.7
CG A:ASN397 3.7 8.6 1.0
O1 A:GOL601 3.8 17.1 1.0
CG A:ASP366 3.8 16.8 1.0
CG2 A:THR341 3.9 8.7 1.0
O A:HOH702 3.9 22.3 1.0
OD1 A:ASP366 4.0 15.8 1.0
CE1 A:PHE364 4.0 9.5 1.0
CE1 A:HIS532 4.0 11.5 1.0
CD2 A:HIS532 4.1 10.1 1.0
CA A:SER398 4.2 11.6 1.0
CG A:GLU342 4.4 11.4 1.0
O2 A:GOL601 4.4 14.8 1.0
ND2 A:ASN397 4.5 9.9 1.0
C A:ASN397 4.6 11.5 1.0
CA A:ASN397 4.6 10.5 1.0
O A:HOH708 4.7 20.4 1.0
CB A:THR341 4.7 8.4 1.0
CD1 A:PHE364 4.7 8.1 1.0
CB A:ASN397 4.8 10.5 1.0
CZ A:PHE364 4.8 8.2 1.0
C1 A:GOL601 4.9 17.7 1.0
ND1 A:HIS532 5.0 8.5 1.0

Manganese binding site 3 out of 12 in 3a9s

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Manganese binding site 3 out of 12 in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:29.9
occ:0.33
 MN A:MN701 0.0 29.9 0.3
MN A:MN701 2.0 20.8 0.3
MN A:MN701 2.1 25.6 0.3
OE2 A:GLU342 2.1 13.2 0.3
OG A:SER398 2.3 12.2 1.0
O2 A:GOL601 2.3 14.8 1.0
O1 A:GOL601 2.3 17.1 1.0
OE2 A:GLU342 2.6 16.2 0.7
CB A:SER398 2.8 12.5 1.0
OE1 A:GLU342 2.8 14.4 0.7
CD A:GLU342 2.9 13.2 1.0
C1 A:GOL601 3.1 17.7 1.0
O A:HOH702 3.2 22.3 1.0
C2 A:GOL601 3.2 15.5 1.0
OE1 A:GLU342 3.3 14.3 0.3
OD1 A:ASP366 3.8 15.8 1.0
OD2 A:ASP366 3.9 18.4 1.0
CA A:SER398 4.0 11.6 1.0
N A:SER398 4.1 10.4 1.0
CG A:GLU342 4.2 11.4 1.0
O A:HOH708 4.3 20.4 1.0
CG A:ASP366 4.3 16.8 1.0
NE2 A:HIS532 4.3 12.3 1.0
OD1 A:ASN397 4.3 10.5 1.0
NE2 A:GLN307 4.3 14.2 1.0
C3 A:GOL601 4.5 15.1 1.0
CG2 A:THR341 5.0 8.7 1.0

Manganese binding site 4 out of 12 in 3a9s

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Manganese binding site 4 out of 12 in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn801

b:13.6
occ:1.00
 O A:HOH804 2.1 13.5 1.0
O A:HOH806 2.1 15.5 1.0
O A:HOH805 2.2 11.3 1.0
O A:HOH802 2.2 12.5 1.0
OD1 A:ASP453 2.2 11.9 1.0
O A:HOH803 2.2 12.2 1.0
CG A:ASP453 3.2 14.7 1.0
OD2 A:ASP453 3.4 15.0 1.0
OD2 A:ASP496 4.1 14.2 1.0
O A:HOH794 4.1 11.6 1.0
O A:HOH947 4.2 17.3 1.0
O A:PRO501 4.3 12.4 1.0
O A:HOH917 4.3 25.1 1.0
O A:PHE454 4.3 10.8 1.0
O A:HOH1016 4.4 28.0 1.0
O A:HOH1383 4.5 41.0 1.0
O A:HOH949 4.5 25.2 1.0
C A:PHE454 4.5 9.9 1.0
N A:PHE454 4.5 11.7 1.0
NE2 A:HIS492 4.5 12.2 1.0
CB A:ASP453 4.6 13.3 1.0
C A:ASP453 4.6 12.6 1.0
CA A:PHE454 4.7 10.6 1.0
O A:ASP453 4.9 13.6 1.0

Manganese binding site 5 out of 12 in 3a9s

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Manganese binding site 5 out of 12 in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:22.4
occ:0.33
 MN B:MN701 0.0 22.4 0.3
MN B:MN701 1.6 19.6 0.3
MN B:MN701 1.9 25.1 0.3
O B:HOH702 2.2 23.3 1.0
NE2 B:HIS532 2.3 12.2 1.0
OD2 B:ASP366 2.4 19.2 1.0
OE1 B:GLU342 2.5 15.2 0.7
O1 B:GOL601 2.6 23.1 1.0
OE1 B:GLU342 3.0 15.3 0.3
OE2 B:GLU342 3.1 13.1 0.3
CG B:ASP366 3.1 18.7 1.0
OD1 B:ASP366 3.2 19.6 1.0
CE1 B:HIS532 3.2 12.3 1.0
CD2 B:HIS532 3.3 13.0 1.0
CD B:GLU342 3.3 14.7 1.0
OE2 B:GLU342 3.5 17.1 0.7
OG B:SER398 3.8 14.1 1.0
C1 B:GOL601 3.9 21.3 1.0
O2 B:GOL601 4.0 16.9 1.0
OD1 B:ASN397 4.1 12.9 1.0
ND2 B:ASN531 4.2 15.1 1.0
ND1 B:HIS532 4.3 12.0 1.0
CG B:HIS532 4.4 11.3 1.0
CB B:SER398 4.4 13.8 1.0
C2 B:GOL601 4.4 20.2 1.0
CB B:ASP366 4.6 14.3 1.0
CG B:GLU342 4.7 12.6 1.0
N B:SER398 4.8 12.1 1.0
CE1 B:PHE364 4.8 8.5 1.0

Manganese binding site 6 out of 12 in 3a9s

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Manganese binding site 6 out of 12 in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:19.6
occ:0.33
 MN B:MN701 0.0 19.6 0.3
MN B:MN701 1.6 22.4 0.3
MN B:MN701 2.0 25.1 0.3
OE1 B:GLU342 2.7 15.2 0.7
OD1 B:ASN397 2.7 12.9 1.0
OG B:SER398 2.7 14.1 1.0
OD2 B:ASP366 2.7 19.2 1.0
OE2 B:GLU342 3.1 13.1 0.3
NE2 B:HIS532 3.2 12.2 1.0
CD B:GLU342 3.4 14.7 1.0
OE1 B:GLU342 3.5 15.3 0.3
CB B:SER398 3.5 13.8 1.0
CG B:ASP366 3.6 18.7 1.0
O1 B:GOL601 3.6 23.1 1.0
N B:SER398 3.6 12.1 1.0
OD1 B:ASP366 3.7 19.6 1.0
O B:HOH702 3.7 23.3 1.0
OE2 B:GLU342 3.8 17.1 0.7
CG B:ASN397 3.9 11.3 1.0
CE1 B:HIS532 3.9 12.3 1.0
CD2 B:HIS532 4.0 13.0 1.0
CG2 B:THR341 4.1 9.8 1.0
CE1 B:PHE364 4.1 8.5 1.0
CA B:SER398 4.2 13.1 1.0
O2 B:GOL601 4.3 16.9 1.0
CG B:GLU342 4.5 12.6 1.0
C B:ASN397 4.6 12.8 1.0
CA B:ASN397 4.6 11.3 1.0
ND2 B:ASN397 4.7 11.8 1.0
C1 B:GOL601 4.7 21.3 1.0
O B:HOH914 4.8 23.8 1.0
CD1 B:PHE364 4.8 8.5 1.0
ND1 B:HIS532 4.9 12.0 1.0
CB B:ASN397 4.9 11.4 1.0
CB B:THR341 4.9 8.4 1.0
CZ B:PHE364 4.9 9.1 1.0
CB B:ASP366 4.9 14.3 1.0
CG B:HIS532 4.9 11.3 1.0

Manganese binding site 7 out of 12 in 3a9s

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Manganese binding site 7 out of 12 in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:25.1
occ:0.33
 MN B:MN701 0.0 25.1 0.3
MN B:MN701 1.9 22.4 0.3
MN B:MN701 2.0 19.6 0.3
OE2 B:GLU342 2.0 13.1 0.3
O1 B:GOL601 2.3 23.1 1.0
O2 B:GOL601 2.3 16.9 1.0
OG B:SER398 2.5 14.1 1.0
OE2 B:GLU342 2.6 17.1 0.7
OE1 B:GLU342 2.8 15.2 0.7
CD B:GLU342 2.9 14.7 1.0
CB B:SER398 2.9 13.8 1.0
O B:HOH702 3.0 23.3 1.0
C1 B:GOL601 3.1 21.3 1.0
C2 B:GOL601 3.1 20.2 1.0
OE1 B:GLU342 3.3 15.3 0.3
OD1 B:ASP366 3.7 19.6 1.0
OD2 B:ASP366 3.8 19.2 1.0
NE2 B:HIS532 4.1 12.2 1.0
CG B:ASP366 4.1 18.7 1.0
CA B:SER398 4.2 13.1 1.0
N B:SER398 4.2 12.1 1.0
CG B:GLU342 4.2 12.6 1.0
O B:HOH914 4.3 23.8 1.0
OD1 B:ASN397 4.4 12.9 1.0
NE2 B:GLN307 4.4 19.9 1.0
C3 B:GOL601 4.5 19.9 1.0
CE1 B:HIS532 4.8 12.3 1.0
CE B:MET190 5.0 12.5 1.0

Manganese binding site 8 out of 12 in 3a9s

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Manganese binding site 8 out of 12 in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn801

b:14.3
occ:1.00
 O B:HOH804 2.0 15.8 1.0
O B:HOH806 2.1 15.7 1.0
O B:HOH805 2.2 12.7 1.0
OD1 B:ASP453 2.2 14.2 1.0
O B:HOH803 2.2 12.3 1.0
O B:HOH802 2.2 13.2 1.0
CG B:ASP453 3.2 16.3 1.0
OD2 B:ASP453 3.4 16.2 1.0
O B:HOH818 4.2 11.1 1.0
OD2 B:ASP496 4.2 14.3 1.0
O B:PRO501 4.2 15.2 1.0
O B:HOH981 4.3 20.4 1.0
O B:PHE454 4.4 12.1 1.0
O B:HOH742 4.4 25.6 1.0
N B:PHE454 4.5 11.6 1.0
O B:HOH1048 4.5 27.6 1.0
C B:PHE454 4.5 11.9 1.0
NE2 B:HIS492 4.5 14.6 1.0
CB B:ASP453 4.6 12.9 1.0
C B:ASP453 4.6 12.5 1.0
CA B:PHE454 4.7 12.2 1.0
O B:ASP453 4.9 12.8 1.0

Manganese binding site 9 out of 12 in 3a9s

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Manganese binding site 9 out of 12 in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn701

b:19.9
occ:0.33
 MN C:MN701 0.0 19.9 0.3
MN C:MN701 1.5 20.4 0.3
MN C:MN701 2.0 22.8 0.3
NE2 C:HIS532 2.3 14.1 1.0
OD2 C:ASP366 2.4 18.7 1.0
O C:HOH702 2.4 27.2 1.0
OE1 C:GLU342 2.4 14.1 0.7
O1 C:GOL601 2.7 22.1 1.0
OE1 C:GLU342 2.9 13.6 0.3
OE2 C:GLU342 3.1 10.8 0.3
CG C:ASP366 3.2 17.6 1.0
CD2 C:HIS532 3.2 13.2 1.0
CE1 C:HIS532 3.2 13.8 1.0
OD1 C:ASP366 3.3 18.9 1.0
CD C:GLU342 3.3 12.9 1.0
OE2 C:GLU342 3.5 16.2 0.7
OG C:SER398 3.7 14.8 1.0
OD1 C:ASN397 3.9 13.1 1.0
C1 C:GOL601 4.0 20.0 1.0
O2 C:GOL601 4.1 17.9 1.0
ND2 C:ASN531 4.3 13.8 1.0
ND1 C:HIS532 4.3 11.9 1.0
CG C:HIS532 4.3 11.7 1.0
CB C:SER398 4.4 14.6 1.0
C2 C:GOL601 4.5 19.7 1.0
CB C:ASP366 4.6 12.2 1.0
CG C:GLU342 4.7 9.8 1.0
CE1 C:PHE364 4.7 9.0 1.0
N C:SER398 4.7 13.0 1.0

Manganese binding site 10 out of 12 in 3a9s

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Manganese binding site 10 out of 12 in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn701

b:20.4
occ:0.33
 MN C:MN701 0.0 20.4 0.3
MN C:MN701 1.5 19.9 0.3
MN C:MN701 2.1 22.8 0.3
OE1 C:GLU342 2.6 14.1 0.7
OD1 C:ASN397 2.6 13.1 1.0
OD2 C:ASP366 2.7 18.7 1.0
OG C:SER398 2.7 14.8 1.0
OE2 C:GLU342 3.2 10.8 0.3
NE2 C:HIS532 3.2 14.1 1.0
OE1 C:GLU342 3.4 13.6 0.3
CD C:GLU342 3.5 12.9 1.0
CG C:ASP366 3.6 17.6 1.0
CB C:SER398 3.6 14.6 1.0
N C:SER398 3.6 13.0 1.0
O1 C:GOL601 3.7 22.1 1.0
O C:HOH702 3.8 27.2 1.0
OD1 C:ASP366 3.8 18.9 1.0
CG C:ASN397 3.8 14.1 1.0
CE1 C:HIS532 3.9 13.8 1.0
OE2 C:GLU342 3.9 16.2 0.7
CD2 C:HIS532 3.9 13.2 1.0
CE1 C:PHE364 4.0 9.0 1.0
CG2 C:THR341 4.1 10.5 1.0
CA C:SER398 4.3 13.0 1.0
O2 C:GOL601 4.4 17.9 1.0
CG C:GLU342 4.5 9.8 1.0
C C:ASN397 4.6 13.2 1.0
CA C:ASN397 4.6 12.8 1.0
ND2 C:ASN397 4.6 11.9 1.0
CD1 C:PHE364 4.7 9.7 1.0
C1 C:GOL601 4.8 20.0 1.0
ND1 C:HIS532 4.8 11.9 1.0
CB C:ASN397 4.8 12.2 1.0
CZ C:PHE364 4.8 10.1 1.0
CB C:THR341 4.9 8.5 1.0
CG C:HIS532 4.9 11.7 1.0
O C:HOH862 4.9 27.4 1.0
CB C:ASP366 4.9 12.2 1.0

Reference:

K.Takeda, H.Yoshida, K.Izumori, S.Kamitori. X-Ray Structures of Bacillus Pallidusd-Arabinose Isomerase and Its Complex with L-Fucitol. Biochim.Biophys.Acta V.1804 1359 2010.
ISSN: ISSN 0006-3002
PubMed: 20123133
DOI: 10.1016/J.BBAPAP.2010.01.018
Page generated: Sat Oct 5 15:44:59 2024

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