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Manganese in PDB 3a9r: X-Ray Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex with (4R)-2-Methylpentane-2,4-Diol

Enzymatic activity of X-Ray Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex with (4R)-2-Methylpentane-2,4-Diol

All present enzymatic activity of X-Ray Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex with (4R)-2-Methylpentane-2,4-Diol:
5.3.1.3;

Protein crystallography data

The structure of X-Ray Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex with (4R)-2-Methylpentane-2,4-Diol, PDB code: 3a9r 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) 41.83 / 1.77
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 144.751, 127.447, 110.885, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex with (4R)-2-Methylpentane-2,4-Diol (pdb code 3a9r). 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 Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex with (4R)-2-Methylpentane-2,4-Diol, PDB code: 3a9r:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3a9r

Go back to Manganese Binding Sites List in 3a9r
Manganese binding site 1 out of 6 in the X-Ray Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex with (4R)-2-Methylpentane-2,4-Diol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex with (4R)-2-Methylpentane-2,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:47.3
occ:1.00
 NE2 A:HIS532 2.4 16.4 1.0
OD2 A:ASP366 2.4 27.6 1.0
OD1 A:ASP366 2.8 25.8 1.0
O4 A:MRD601 2.9 27.4 1.0
OE1 A:GLU342 2.9 17.5 1.0
CG A:ASP366 3.0 24.8 1.0
CD2 A:HIS532 3.3 14.0 1.0
CE1 A:HIS532 3.5 15.2 1.0
OG A:SER398 3.5 17.6 1.0
OD1 A:ASN397 3.6 16.7 1.0
CD A:GLU342 3.6 18.5 1.0
OE2 A:GLU342 3.7 19.5 1.0
CB A:SER398 4.1 16.9 1.0
C4 A:MRD601 4.1 25.4 1.0
OD1 A:ASN531 4.3 20.7 1.0
N A:SER398 4.3 15.6 1.0
CB A:ASP366 4.5 19.7 1.0
CG A:HIS532 4.5 12.8 1.0
C3 A:MRD601 4.6 23.8 1.0
ND1 A:HIS532 4.6 14.9 1.0
C5 A:MRD601 4.6 25.6 1.0
CE1 A:PHE364 4.6 13.2 1.0
CG A:ASN397 4.8 15.5 1.0
CA A:SER398 4.9 16.6 1.0
CG A:GLU342 4.9 13.7 1.0

Manganese binding site 2 out of 6 in 3a9r

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Manganese binding site 2 out of 6 in the X-Ray Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex with (4R)-2-Methylpentane-2,4-Diol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex with (4R)-2-Methylpentane-2,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn801

b:44.2
occ:1.00
 O A:HOH806 1.9 38.9 1.0
O A:HOH802 1.9 34.6 1.0
O A:HOH804 2.0 20.3 1.0
O A:HOH805 2.1 16.9 1.0
O A:HOH803 2.3 27.0 1.0
OD1 A:ASP453 2.5 18.3 1.0
CG A:ASP453 3.4 19.8 1.0
OD2 A:ASP453 3.6 20.1 1.0
OD2 A:ASP496 4.0 19.7 1.0
O A:HOH907 4.1 15.4 1.0
O A:HOH1033 4.2 25.5 1.0
O A:PHE454 4.3 13.4 1.0
NE2 A:HIS492 4.4 17.6 1.0
O A:PRO501 4.4 17.8 1.0
O A:HOH903 4.4 40.1 1.0
O A:HOH933 4.4 32.2 1.0
C A:PHE454 4.5 14.9 1.0
N A:PHE454 4.6 16.4 1.0
CA A:PHE454 4.7 15.5 1.0
C A:ASP453 4.8 16.4 1.0
CB A:ASP453 4.8 17.2 1.0
CB A:LEU455 4.9 17.2 1.0
CG A:ASP496 4.9 19.5 1.0
N A:LEU455 5.0 15.3 1.0

Manganese binding site 3 out of 6 in 3a9r

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Manganese binding site 3 out of 6 in the X-Ray Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex with (4R)-2-Methylpentane-2,4-Diol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex with (4R)-2-Methylpentane-2,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:48.4
occ:1.00
 NE2 B:HIS532 2.3 15.7 1.0
OD2 B:ASP366 2.4 30.4 1.0
OD1 B:ASP366 2.8 28.2 1.0
OE1 B:GLU342 2.9 19.8 1.0
O4 B:MRD601 2.9 32.3 1.0
CG B:ASP366 3.0 27.9 1.0
CD2 B:HIS532 3.3 15.0 1.0
CE1 B:HIS532 3.3 13.6 1.0
CD B:GLU342 3.6 21.4 1.0
OG B:SER398 3.7 24.3 1.0
OD1 B:ASN397 3.7 15.9 1.0
OE2 B:GLU342 3.7 22.6 1.0
C4 B:MRD601 4.1 30.2 1.0
CB B:SER398 4.1 20.8 1.0
OD1 B:ASN531 4.1 22.6 1.0
N B:SER398 4.4 17.4 1.0
C5 B:MRD601 4.4 29.6 1.0
CG B:HIS532 4.4 14.1 1.0
CB B:ASP366 4.4 22.4 1.0
ND1 B:HIS532 4.4 15.5 1.0
C3 B:MRD601 4.6 27.8 1.0
CE1 B:PHE364 4.8 12.4 1.0
CG B:GLU342 4.9 17.6 1.0
CG B:ASN397 4.9 15.6 1.0
CA B:SER398 4.9 19.6 1.0

Manganese binding site 4 out of 6 in 3a9r

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Manganese binding site 4 out of 6 in the X-Ray Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex with (4R)-2-Methylpentane-2,4-Diol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex with (4R)-2-Methylpentane-2,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn801

b:49.4
occ:1.00
 O B:HOH806 1.9 33.4 1.0
O B:HOH802 1.9 30.8 1.0
O B:HOH804 1.9 28.0 1.0
O B:HOH805 2.1 27.6 1.0
OD1 B:ASP453 2.6 20.8 1.0
O B:HOH803 2.8 33.7 1.0
CG B:ASP453 3.5 23.0 1.0
OD2 B:ASP453 3.7 22.1 1.0
OD2 B:ASP496 4.0 21.1 1.0
O B:HOH912 4.1 17.5 1.0
NE2 B:HIS492 4.2 21.2 1.0
O B:HOH1019 4.3 33.4 1.0
O B:HOH734 4.3 45.7 1.0
O B:PHE454 4.4 16.6 1.0
O B:PRO501 4.4 21.1 1.0
C B:PHE454 4.4 17.0 1.0
O B:HOH1091 4.5 33.4 1.0
N B:PHE454 4.6 16.7 1.0
CA B:PHE454 4.7 17.1 1.0
C B:ASP453 4.8 17.2 1.0
CB B:LEU455 4.8 17.1 1.0
CG B:ASP496 4.9 20.9 1.0
N B:LEU455 4.9 17.0 1.0
CB B:ASP453 4.9 18.2 1.0

Manganese binding site 5 out of 6 in 3a9r

Go back to Manganese Binding Sites List in 3a9r
Manganese binding site 5 out of 6 in the X-Ray Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex with (4R)-2-Methylpentane-2,4-Diol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of X-Ray Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex with (4R)-2-Methylpentane-2,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn701

b:44.4
occ:1.00
 NE2 C:HIS532 2.2 17.1 1.0
OD2 C:ASP366 2.3 26.5 1.0
OE1 C:GLU342 2.7 20.4 1.0
O4 C:MRD601 2.8 32.7 1.0
CG C:ASP366 3.1 22.0 1.0
CE1 C:HIS532 3.1 17.2 1.0
OD1 C:ASP366 3.1 24.9 1.0
CD2 C:HIS532 3.2 15.2 1.0
CD C:GLU342 3.5 19.8 1.0
OD1 C:ASN397 3.7 15.8 1.0
OE2 C:GLU342 3.7 22.1 1.0
OG C:SER398 3.7 22.4 1.0
C4 C:MRD601 4.2 32.9 1.0
CB C:SER398 4.2 21.2 1.0
ND1 C:HIS532 4.2 15.0 1.0
CG C:HIS532 4.3 13.9 1.0
OD1 C:ASN531 4.3 22.8 1.0
CE1 C:PHE364 4.5 13.3 1.0
N C:SER398 4.5 17.6 1.0
CB C:ASP366 4.5 18.6 1.0
C5 C:MRD601 4.6 32.2 1.0
CG C:GLU342 4.7 17.5 1.0
C3 C:MRD601 4.7 30.7 1.0
CG C:ASN397 4.9 17.2 1.0
CG2 C:THR341 5.0 14.1 1.0

Manganese binding site 6 out of 6 in 3a9r

Go back to Manganese Binding Sites List in 3a9r
Manganese binding site 6 out of 6 in the X-Ray Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex with (4R)-2-Methylpentane-2,4-Diol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of X-Ray Structures of Bacillus Pallidus D-Arabinose Isomerasecomplex with (4R)-2-Methylpentane-2,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn801

b:48.2
occ:1.00
 O C:HOH802 1.9 33.8 1.0
O C:HOH804 2.0 26.8 1.0
O C:HOH803 2.0 35.0 1.0
O C:HOH806 2.1 36.5 1.0
O C:HOH805 2.1 21.9 1.0
OD1 C:ASP453 2.5 25.2 1.0
CG C:ASP453 3.4 25.0 1.0
OD2 C:ASP453 3.5 25.7 1.0
O C:HOH1039 4.1 27.7 1.0
OD2 C:ASP496 4.3 23.3 1.0
O C:HOH789 4.3 27.3 1.0
O C:HOH899 4.3 17.5 1.0
NE2 C:HIS492 4.4 22.2 1.0
O C:PHE454 4.5 18.2 1.0
O C:PRO501 4.5 20.5 1.0
C C:PHE454 4.5 18.8 1.0
O C:HOH751 4.5 27.2 1.0
N C:PHE454 4.6 18.6 1.0
CA C:PHE454 4.7 18.4 1.0
C C:ASP453 4.8 18.8 1.0
CB C:ASP453 4.8 20.9 1.0
CB C:LEU455 4.9 20.0 1.0
N C:LEU455 4.9 19.2 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: Tue Dec 15 04:07:36 2020

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