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Manganese in PDB 3ot9: Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate

Enzymatic activity of Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate

All present enzymatic activity of Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate:
5.4.2.7;

Protein crystallography data

The structure of Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate, PDB code: 3ot9 was solved by T.D.Panosian, D.P.Nannemann, G.Watkins, V.Phalen, B.Wadzinski, B.O.Bachmann, T.M.Iverson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.871, 76.582, 107.051, 90.00, 108.73, 90.00
R / Rfree (%) 16.2 / 19

Manganese Binding Sites:

The binding sites of Manganese atom in the Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate (pdb code 3ot9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 9 binding sites of Manganese where determined in the Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate, PDB code: 3ot9:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 3ot9

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Manganese binding site 1 out of 9 in the Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn395

b:12.2
occ:1.00
 O1P A:TPO85 2.1 14.9 0.3
OD2 A:ASP156 2.1 23.4 1.0
OD1 A:ASP286 2.1 13.4 1.0
NE2 A:HIS339 2.1 13.9 1.0
NE2 A:HIS291 2.2 11.8 1.0
CG A:ASP286 2.8 12.6 1.0
OD2 A:ASP286 2.8 12.9 1.0
CG A:ASP156 2.9 20.9 1.0
OD1 A:ASP156 3.1 24.9 1.0
CE1 A:HIS339 3.1 15.4 1.0
CD2 A:HIS291 3.1 12.4 1.0
CD2 A:HIS339 3.1 14.3 1.0
CE1 A:HIS291 3.2 13.3 1.0
P A:TPO85 3.3 18.2 0.3
O2P A:TPO85 3.7 17.5 0.3
O A:HOH607 3.7 34.8 1.0
ND1 A:HIS339 4.2 15.1 1.0
ND1 A:HIS291 4.3 13.6 1.0
CG A:HIS291 4.3 13.5 1.0
CB A:ASP286 4.3 11.6 1.0
CG A:HIS339 4.3 13.2 1.0
O3P A:TPO85 4.3 15.9 0.3
CB A:ASP156 4.3 18.9 1.0
OG1 A:TPO85 4.4 16.3 1.0
O A:HOH438 4.4 17.9 1.0
ND2 A:ASN330 4.4 14.5 1.0
O A:HOH577 4.4 20.7 1.0
CE1 A:HIS328 4.6 12.8 1.0
O A:HOH511 4.8 27.1 1.0
NE2 A:HIS328 4.9 12.9 1.0
CA A:ASP156 4.9 18.8 1.0
MN A:MN396 5.0 11.9 1.0

Manganese binding site 2 out of 9 in 3ot9

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Manganese binding site 2 out of 9 in the Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn396

b:11.9
occ:1.00
 OD2 A:ASP327 2.0 10.8 1.0
OD1 A:ASP13 2.1 12.4 1.0
OG1 A:TPO85 2.2 16.3 1.0
NE2 A:HIS328 2.2 12.9 1.0
OD2 A:ASP13 2.4 13.0 1.0
CG A:ASP13 2.6 11.3 1.0
O2P A:TPO85 2.7 17.5 0.3
CG A:ASP327 2.9 10.9 1.0
OD1 A:ASP327 3.0 11.1 1.0
P A:TPO85 3.1 18.2 0.3
CD2 A:HIS328 3.1 12.7 1.0
CE1 A:HIS328 3.2 12.8 1.0
CB A:TPO85 3.2 14.8 1.0
CG2 A:TPO85 3.5 14.9 1.0
CA A:TPO85 3.6 14.4 1.0
O1P A:TPO85 3.8 14.9 0.3
CB A:ASP13 4.0 10.7 1.0
CG A:HIS328 4.2 12.4 1.0
ND1 A:HIS328 4.3 11.5 1.0
O3P A:TPO85 4.3 15.9 0.3
N A:TPO85 4.3 14.3 1.0
CB A:ASP327 4.3 11.4 1.0
CE1 A:HIS339 4.4 15.4 1.0
N A:SER14 4.4 10.7 1.0
O A:HOH504 4.4 24.0 1.0
CG A:ASP286 4.5 12.6 1.0
OD2 A:ASP286 4.6 12.9 1.0
CA A:ASP13 4.6 10.4 1.0
NE2 A:HIS89 4.6 14.1 1.0
OD1 A:ASP286 4.6 13.4 1.0
C A:ASP13 4.7 10.8 1.0
NE2 A:HIS339 4.8 13.9 1.0
CD2 A:HIS89 4.8 10.6 1.0
C A:TPO85 4.8 13.6 1.0
CB A:ASP286 4.9 11.6 1.0
MN A:MN395 5.0 12.2 1.0

Manganese binding site 3 out of 9 in 3ot9

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Manganese binding site 3 out of 9 in the Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn397

b:21.4
occ:0.50
 O A:HOH701 1.9 36.0 1.0
NE2 A:HIS334 2.0 21.6 1.0
OD1 A:ASP28 2.1 20.7 1.0
O A:HOH560 2.3 27.5 1.0
O A:GLY27 2.6 25.2 1.0
CD2 A:HIS334 2.8 22.0 1.0
CE1 A:HIS334 3.2 22.2 1.0
CG A:ASP28 3.3 19.6 1.0
C A:GLY27 3.5 25.0 1.0
CA A:ASP28 3.9 21.0 1.0
O A:HOH496 4.0 21.0 1.0
O A:PHE26 4.0 26.7 1.0
N A:ASP28 4.0 23.2 1.0
CG A:HIS334 4.0 20.7 1.0
ND1 A:HIS334 4.2 21.2 1.0
CB A:ASP28 4.2 19.7 1.0
OD2 A:ASP28 4.2 19.2 1.0
NZ A:LYS83 4.3 19.1 1.0
CG2 A:THR340 4.4 14.9 1.0
CA A:GLY27 4.5 26.9 1.0
O A:HIS339 4.6 14.1 1.0
O A:PRO335 4.6 20.8 1.0
O A:HOH828 4.7 40.6 1.0
O A:HOH688 4.9 36.8 1.0
C A:PHE26 4.9 26.9 1.0

Manganese binding site 4 out of 9 in 3ot9

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Manganese binding site 4 out of 9 in the Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn395

b:14.3
occ:1.00
 OD2 B:ASP156 2.1 26.7 1.0
O1P B:TPO85 2.1 19.1 0.4
NE2 B:HIS291 2.1 15.2 1.0
NE2 B:HIS339 2.1 14.0 1.0
OD1 B:ASP286 2.1 16.9 1.0
CG B:ASP286 2.8 15.0 1.0
OD2 B:ASP286 2.8 15.6 1.0
CG B:ASP156 2.9 25.1 1.0
CE1 B:HIS339 3.1 14.0 1.0
OD1 B:ASP156 3.1 28.4 1.0
CD2 B:HIS291 3.1 16.8 1.0
CE1 B:HIS291 3.1 15.8 1.0
CD2 B:HIS339 3.1 14.3 1.0
P B:TPO85 3.4 21.3 0.4
O2P B:TPO85 3.7 19.9 0.4
O B:HOH1048 3.8 33.9 1.0
ND1 B:HIS339 4.2 13.3 1.0
ND1 B:HIS291 4.2 16.6 1.0
CG B:HIS291 4.2 16.3 1.0
CG B:HIS339 4.3 14.0 1.0
CB B:ASP286 4.3 14.1 1.0
O3P B:TPO85 4.3 20.2 0.4
CB B:ASP156 4.3 22.0 1.0
ND2 B:ASN330 4.4 16.5 1.0
OG1 B:TPO85 4.4 16.6 1.0
O B:HOH665 4.4 25.8 1.0
O B:HOH437 4.5 24.1 1.0
CE1 B:HIS328 4.6 14.1 1.0
NE2 B:HIS328 4.8 12.9 1.0
CA B:ASP156 4.9 21.4 1.0
MN B:MN396 5.0 12.8 1.0
O B:HOH489 5.0 21.9 1.0

Manganese binding site 5 out of 9 in 3ot9

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Manganese binding site 5 out of 9 in the Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn396

b:12.8
occ:1.00
 OD2 B:ASP327 2.1 11.1 1.0
OD1 B:ASP13 2.1 12.9 1.0
OG1 B:TPO85 2.2 16.6 1.0
NE2 B:HIS328 2.2 12.9 1.0
OD2 B:ASP13 2.4 14.8 1.0
CG B:ASP13 2.6 13.6 1.0
O2P B:TPO85 2.6 19.9 0.4
CG B:ASP327 2.9 10.3 1.0
P B:TPO85 3.0 21.3 0.4
CD2 B:HIS328 3.1 13.3 1.0
OD1 B:ASP327 3.1 10.2 1.0
CE1 B:HIS328 3.2 14.1 1.0
CB B:TPO85 3.2 15.3 1.0
CG2 B:TPO85 3.5 15.6 1.0
CA B:TPO85 3.7 14.5 1.0
O1P B:TPO85 3.7 19.1 0.4
CB B:ASP13 4.1 13.0 1.0
CG B:HIS328 4.2 13.4 1.0
ND1 B:HIS328 4.2 13.6 1.0
O3P B:TPO85 4.2 20.2 0.4
CE1 B:HIS339 4.3 14.0 1.0
N B:TPO85 4.4 14.4 1.0
CB B:ASP327 4.4 10.4 1.0
N B:SER14 4.4 12.2 1.0
O B:HOH633 4.5 26.5 1.0
CG B:ASP286 4.5 15.0 1.0
OD2 B:ASP286 4.6 15.6 1.0
NE2 B:HIS89 4.6 14.0 1.0
CA B:ASP13 4.6 12.2 1.0
OD1 B:ASP286 4.7 16.9 1.0
NE2 B:HIS339 4.7 14.0 1.0
C B:ASP13 4.8 12.7 1.0
CD2 B:HIS89 4.8 10.8 1.0
C B:TPO85 4.9 13.8 1.0
CB B:ASP286 4.9 14.1 1.0
MN B:MN395 5.0 14.3 1.0

Manganese binding site 6 out of 9 in 3ot9

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Manganese binding site 6 out of 9 in the Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn397

b:35.5
occ:0.75
 O B:HOH843 2.1 39.0 1.0
O B:HOH399 2.6 45.0 1.0
O B:HOH486 2.6 47.9 1.0
O B:HOH1092 4.1 33.2 1.0
O B:HOH531 4.1 27.8 1.0
OE2 B:GLU318 4.2 33.1 1.0

Manganese binding site 7 out of 9 in 3ot9

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Manganese binding site 7 out of 9 in the Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn395

b:20.8
occ:1.00
 OD1 C:ASP286 2.1 25.5 1.0
NE2 C:HIS291 2.1 24.0 1.0
O2P C:TPO85 2.1 24.4 0.3
NE2 C:HIS339 2.1 25.9 1.0
OD2 C:ASP156 2.1 50.4 1.0
CG C:ASP286 2.8 24.8 1.0
OD2 C:ASP286 2.8 25.8 1.0
CG C:ASP156 2.9 46.5 1.0
OD1 C:ASP156 3.0 47.1 1.0
CE1 C:HIS291 3.1 25.2 1.0
CE1 C:HIS339 3.1 25.0 1.0
CD2 C:HIS291 3.1 25.2 1.0
CD2 C:HIS339 3.2 26.1 1.0
P C:TPO85 3.4 25.1 0.3
O C:HOH531 3.8 42.8 1.0
O3P C:TPO85 3.8 25.3 0.3
ND1 C:HIS291 4.2 26.0 1.0
O C:HOH564 4.2 33.5 1.0
ND1 C:HIS339 4.2 25.7 1.0
CG C:HIS291 4.2 26.5 1.0
CB C:ASP286 4.3 24.7 1.0
CG C:HIS339 4.3 25.6 1.0
ND2 C:ASN330 4.3 25.8 1.0
OG1 C:TPO85 4.4 22.9 1.0
CB C:ASP156 4.4 42.8 1.0
O1P C:TPO85 4.4 23.7 0.3
CE1 C:HIS328 4.5 23.9 1.0
O C:HOH585 4.6 46.6 1.0
O C:HOH855 4.7 35.4 1.0
NE2 C:HIS328 4.7 21.7 1.0
MN C:MN396 5.0 20.5 1.0

Manganese binding site 8 out of 9 in 3ot9

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Manganese binding site 8 out of 9 in the Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn396

b:20.5
occ:1.00
 OD1 C:ASP13 2.0 21.9 1.0
OD2 C:ASP327 2.0 21.7 1.0
OG1 C:TPO85 2.1 22.9 1.0
NE2 C:HIS328 2.2 21.7 1.0
OD2 C:ASP13 2.5 22.3 1.0
CG C:ASP13 2.6 22.4 1.0
CG C:ASP327 2.9 22.5 1.0
O3P C:TPO85 2.9 25.3 0.3
CD2 C:HIS328 3.0 23.1 1.0
OD1 C:ASP327 3.1 23.1 1.0
P C:TPO85 3.1 25.1 0.3
CB C:TPO85 3.2 21.9 1.0
CE1 C:HIS328 3.2 23.9 1.0
CA C:TPO85 3.6 22.0 1.0
CG2 C:TPO85 3.6 21.4 1.0
O2P C:TPO85 3.7 24.4 0.3
CB C:ASP13 4.0 22.1 1.0
CG C:HIS328 4.2 23.9 1.0
N C:TPO85 4.2 22.8 1.0
ND1 C:HIS328 4.3 24.4 1.0
CB C:ASP327 4.3 22.3 1.0
N C:SER14 4.4 24.4 1.0
O1P C:TPO85 4.4 23.7 0.3
CE1 C:HIS339 4.4 25.0 1.0
CG C:ASP286 4.5 24.8 1.0
CA C:ASP13 4.6 23.2 1.0
NE2 C:HIS89 4.6 21.1 1.0
OD2 C:ASP286 4.7 25.8 1.0
OD1 C:ASP286 4.7 25.5 1.0
C C:ASP13 4.7 24.1 1.0
C C:TPO85 4.8 21.4 1.0
NE2 C:HIS339 4.8 25.9 1.0
CD2 C:HIS89 4.8 18.9 1.0
CB C:ASP286 4.9 24.7 1.0
MN C:MN395 5.0 20.8 1.0

Manganese binding site 9 out of 9 in 3ot9

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Manganese binding site 9 out of 9 in the Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Phosphopentomutase From Bacillus Cereus Bound to Glucose-1,6- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn397

b:33.4
occ:1.00
 O C:HOH827 2.1 37.3 1.0
O C:HOH437 2.1 32.4 1.0
NE2 C:HIS334 2.1 34.5 1.0
OD1 C:ASP28 2.1 31.8 1.0
O C:HOH405 2.2 30.3 1.0
O C:GLY27 2.5 37.8 1.0
CD2 C:HIS334 3.0 33.4 1.0
CE1 C:HIS334 3.2 36.3 1.0
C C:GLY27 3.3 38.3 1.0
CG C:ASP28 3.4 32.7 1.0
CA C:ASP28 3.8 36.6 1.0
O C:HOH436 3.9 32.1 1.0
N C:ASP28 4.0 37.9 1.0
O C:PHE26 4.0 37.3 1.0
CG C:HIS334 4.2 34.0 1.0
CB C:ASP28 4.2 34.8 1.0
ND1 C:HIS334 4.2 35.6 1.0
OD2 C:ASP28 4.3 30.8 1.0
CA C:GLY27 4.3 39.7 1.0
NZ C:LYS83 4.4 28.4 1.0
O C:HIS339 4.6 28.8 1.0
CG2 C:THR340 4.6 32.0 1.0
O C:HOH991 4.7 57.9 1.0
O C:PRO335 4.8 32.3 1.0
O C:HOH604 4.9 46.3 1.0
C C:PHE26 4.9 38.6 1.0

Reference:

T.D.Panosian, D.P.Nannemann, G.R.Watkins, V.V.Phelan, W.H.Mcdonald, B.E.Wadzinski, B.O.Bachmann, T.M.Iverson. Bacillus Cereus Phosphopentomutase Is An Alkaline Phosphatase Family Member That Exhibits An Altered Entry Point Into the Catalytic Cycle. J.Biol.Chem. V. 286 8043 2011.
ISSN: ISSN 0021-9258
PubMed: 21193409
DOI: 10.1074/JBC.M110.201350
Page generated: Tue Dec 15 04:13:37 2020

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