Atomistry » Manganese » PDB 2ypq-3au8 » 3a9t
Atomistry »
  Manganese »
    PDB 2ypq-3au8 »
      3a9t »

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

Go back to Manganese Binding Sites List in 3a9t
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

Go back to Manganese Binding Sites List in 3a9t
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

Go back to Manganese Binding Sites List in 3a9t
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

Go back to Manganese Binding Sites List in 3a9t
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

Go back to Manganese Binding Sites List in 3a9t
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 Aug 16 11:21:48 2025

Last articles

Mo in 8BTS
Mo in 8BQR
Mo in 8BQQ
Mo in 8BQP
Mo in 7Z5J
Mo in 7ZUB
Mo in 7Z0T
Mo in 7WY3
Mo in 7WY2
Mo in 7WY1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy