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Manganese in PDB 3a9t: X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with L-Fucitol

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

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

Protein crystallography data

The structure of X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with L-Fucitol, PDB code: 3a9t 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) 47.76 / 2.61
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 144.858, 127.672, 110.202, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 22

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with L-Fucitol (pdb code 3a9t). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with L-Fucitol, PDB code: 3a9t:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3a9t

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Manganese binding site 1 out of 6 in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with L-Fucitol


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 L-Fucitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:55.8
occ:1.00
 O1 A:FOC601 2.1 39.8 1.0
OD2 A:ASP366 2.2 30.3 1.0
O2 A:FOC601 2.5 34.5 1.0
NE2 A:HIS532 2.6 20.7 1.0
C2 A:FOC601 2.8 34.9 1.0
C1 A:FOC601 2.9 37.1 1.0
CG A:ASP366 3.0 27.8 1.0
OD1 A:ASP366 3.1 31.4 1.0
OE1 A:GLU342 3.2 22.3 1.0
OE2 A:GLU342 3.4 20.9 1.0
CD2 A:HIS532 3.5 16.2 1.0
CE1 A:HIS532 3.7 18.5 1.0
CD A:GLU342 3.7 20.1 1.0
OD1 A:ASN397 3.7 17.1 1.0
OG A:SER398 3.8 29.7 1.0
CB A:SER398 4.1 21.8 1.0
C3 A:FOC601 4.3 33.8 1.0
N A:SER398 4.4 17.9 1.0
CB A:ASP366 4.4 23.3 1.0
O4 A:FOC601 4.6 30.6 1.0
CG A:HIS532 4.7 17.6 1.0
OD1 A:ASN531 4.7 19.4 1.0
ND1 A:HIS532 4.8 18.0 1.0
CE1 A:PHE364 4.8 18.1 1.0
C4 A:FOC601 4.9 32.9 1.0
CA A:SER398 4.9 20.1 1.0
CG A:ASN397 4.9 19.3 1.0
O3 A:FOC601 5.0 33.2 1.0

Manganese binding site 2 out of 6 in 3a9t

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Manganese binding site 2 out of 6 in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with L-Fucitol


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 L-Fucitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn801

b:49.2
occ:1.00
 O A:HOH806 2.3 37.2 1.0
O A:HOH804 2.4 10.7 1.0
OD1 A:ASP453 2.4 22.6 1.0
O A:HOH802 2.5 33.0 1.0
O A:HOH805 2.6 27.1 1.0
O A:HOH803 2.6 22.8 1.0
CG A:ASP453 3.3 22.5 1.0
OD2 A:ASP453 3.4 23.1 1.0
O A:HOH1038 3.7 25.5 1.0
O A:HOH905 4.1 1.6 1.0
O A:PHE454 4.2 15.9 1.0
O A:HOH884 4.3 21.9 1.0
C A:PHE454 4.3 18.1 1.0
O A:PRO501 4.4 17.4 1.0
N A:PHE454 4.4 18.7 1.0
OD2 A:ASP496 4.4 20.8 1.0
CA A:PHE454 4.5 17.8 1.0
C A:ASP453 4.5 20.3 1.0
NE2 A:HIS492 4.6 18.2 1.0
CB A:ASP453 4.7 20.7 1.0
O A:ASP453 4.7 21.1 1.0
N A:LEU455 4.8 17.5 1.0
CB A:LEU455 4.8 15.5 1.0
O A:HOH911 4.9 35.2 1.0

Manganese binding site 3 out of 6 in 3a9t

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Manganese binding site 3 out of 6 in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with L-Fucitol


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 L-Fucitol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:64.5
occ:1.00
 OD2 B:ASP366 2.3 31.7 1.0
O1 B:FOC601 2.3 34.5 1.0
NE2 B:HIS532 2.5 18.3 1.0
O2 B:FOC601 2.6 33.0 1.0
C2 B:FOC601 2.8 31.0 1.0
OE2 B:GLU342 3.0 23.7 1.0
C1 B:FOC601 3.1 33.1 1.0
CG B:ASP366 3.2 27.4 1.0
OE1 B:GLU342 3.3 23.0 1.0
CE1 B:HIS532 3.3 16.5 1.0
OD1 B:ASP366 3.5 29.6 1.0
CD B:GLU342 3.5 22.3 1.0
OD1 B:ASN397 3.5 25.6 1.0
CD2 B:HIS532 3.5 17.0 1.0
OG B:SER398 3.6 24.5 1.0
CB B:SER398 4.1 22.2 1.0
C3 B:FOC601 4.3 29.9 1.0
N B:SER398 4.3 23.0 1.0
O4 B:FOC601 4.3 29.1 1.0
ND1 B:HIS532 4.5 20.3 1.0
CB B:ASP366 4.6 22.6 1.0
CG B:HIS532 4.6 17.9 1.0
OD1 B:ASN531 4.7 21.3 1.0
CG B:ASN397 4.7 24.9 1.0
CE1 B:PHE364 4.7 14.3 1.0
C4 B:FOC601 4.8 29.0 1.0
CG B:GLU342 4.8 19.7 1.0
CA B:SER398 4.9 22.7 1.0

Manganese binding site 4 out of 6 in 3a9t

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Manganese binding site 4 out of 6 in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with L-Fucitol


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 L-Fucitol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn801

b:46.5
occ:1.00
 O B:HOH804 2.2 31.4 1.0
O B:HOH806 2.4 24.6 1.0
O B:HOH805 2.4 22.7 1.0
O B:HOH803 2.4 13.7 1.0
OD1 B:ASP453 2.5 26.8 1.0
O B:HOH802 2.5 21.4 1.0
CG B:ASP453 3.2 24.5 1.0
OD2 B:ASP453 3.3 25.1 1.0
O B:HOH911 4.0 18.6 1.0
O B:HOH1079 4.0 13.1 1.0
O B:HOH727 4.0 37.6 1.0
O B:PRO501 4.1 23.7 1.0
OD2 B:ASP496 4.1 23.3 1.0
O B:HOH996 4.2 27.1 1.0
NE2 B:HIS492 4.4 16.9 1.0
N B:PHE454 4.6 21.6 1.0
C B:PHE454 4.7 20.0 1.0
CB B:ASP453 4.7 22.9 1.0
O B:PHE454 4.7 20.3 1.0
C B:ASP453 4.7 22.5 1.0
CA B:PHE454 4.8 20.4 1.0
O B:ASP453 5.0 23.8 1.0
CG B:ASP496 5.0 23.8 1.0

Manganese binding site 5 out of 6 in 3a9t

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Manganese binding site 5 out of 6 in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with L-Fucitol


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 L-Fucitol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn701

b:45.3
occ:1.00
 NE2 C:HIS532 2.4 21.1 1.0
O1 C:FOC601 2.4 30.3 1.0
OD2 C:ASP366 2.5 31.9 1.0
O2 C:FOC601 2.8 28.2 1.0
C2 C:FOC601 3.1 28.3 1.0
OE1 C:GLU342 3.1 20.9 1.0
OE2 C:GLU342 3.2 20.1 1.0
CE1 C:HIS532 3.2 20.4 1.0
C1 C:FOC601 3.3 29.2 1.0
CD2 C:HIS532 3.4 20.3 1.0
CG C:ASP366 3.4 27.4 1.0
OD1 C:ASN397 3.4 20.8 1.0
CD C:GLU342 3.5 18.6 1.0
OD1 C:ASP366 3.6 31.2 1.0
OG C:SER398 3.6 26.2 1.0
ND1 C:HIS532 4.4 20.4 1.0
CB C:SER398 4.4 22.8 1.0
N C:SER398 4.4 22.8 1.0
CE1 C:PHE364 4.4 11.9 1.0
CG C:HIS532 4.4 21.6 1.0
C3 C:FOC601 4.6 27.7 1.0
CG C:ASN397 4.6 22.7 1.0
CB C:ASP366 4.7 23.6 1.0
O4 C:FOC601 4.7 26.2 1.0
CG2 C:THR341 4.8 13.9 1.0
OD1 C:ASN531 4.8 24.0 1.0
CG C:GLU342 5.0 16.6 1.0

Manganese binding site 6 out of 6 in 3a9t

Go back to Manganese Binding Sites List in 3a9t
Manganese binding site 6 out of 6 in the X-Ray Structure of Bacillus Pallidus D-Arabinose Isomerase Complex with L-Fucitol


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 L-Fucitol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn801

b:53.5
occ:1.00
 O C:HOH804 2.3 14.2 1.0
OD1 C:ASP453 2.3 22.5 1.0
O C:HOH803 2.4 33.3 1.0
O C:HOH802 2.5 30.1 1.0
O C:HOH806 2.6 28.6 1.0
O C:HOH805 2.7 32.2 1.0
CG C:ASP453 3.1 23.1 1.0
OD2 C:ASP453 3.1 22.9 1.0
O C:HOH1045 3.8 24.4 1.0
O C:HOH744 3.9 12.5 1.0
O C:HOH781 4.0 42.9 1.0
O C:PRO501 4.2 24.7 1.0
OD2 C:ASP496 4.3 24.2 1.0
O C:HOH902 4.4 9.0 1.0
N C:PHE454 4.5 21.8 1.0
CB C:ASP453 4.6 21.3 1.0
NE2 C:HIS492 4.7 23.9 1.0
C C:ASP453 4.7 22.4 1.0
C C:PHE454 4.7 21.2 1.0
O C:PHE454 4.7 21.4 1.0
CA C:PHE454 4.7 21.8 1.0
O C:ASP453 5.0 22.2 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 15:45:04 2024

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