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Manganese in PDB 3m8y: Phosphopentomutase From Bacillus Cereus After Glucose-1,6-Bisphosphate Activation

Enzymatic activity of Phosphopentomutase From Bacillus Cereus After Glucose-1,6-Bisphosphate Activation

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

Protein crystallography data

The structure of Phosphopentomutase From Bacillus Cereus After Glucose-1,6-Bisphosphate Activation, PDB code: 3m8y was solved by T.D.Panosian, D.P.Nannemann, G.Watkins, 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) 20.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.153, 76.661, 107.758, 90.00, 108.92, 90.00
R / Rfree (%) 15.3 / 19.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Phosphopentomutase From Bacillus Cereus After Glucose-1,6-Bisphosphate Activation (pdb code 3m8y). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 10 binding sites of Manganese where determined in the Phosphopentomutase From Bacillus Cereus After Glucose-1,6-Bisphosphate Activation, PDB code: 3m8y:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 3m8y

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Manganese binding site 1 out of 10 in the Phosphopentomutase From Bacillus Cereus After Glucose-1,6-Bisphosphate Activation


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 After Glucose-1,6-Bisphosphate Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn395

b:22.1
occ:1.00
 O1P A:TPO85 2.1 30.8 1.0
OD1 A:ASP286 2.2 21.1 1.0
NE2 A:HIS291 2.2 20.3 1.0
NE2 A:HIS339 2.2 21.5 1.0
OD2 A:ASP156 2.3 26.9 1.0
OD1 A:ASP156 2.5 28.5 1.0
CG A:ASP156 2.7 26.9 1.0
OD2 A:ASP286 2.8 17.0 1.0
CG A:ASP286 2.9 18.9 1.0
CD2 A:HIS291 3.1 21.1 1.0
CE1 A:HIS339 3.1 21.4 1.0
CE1 A:HIS291 3.2 19.5 1.0
CD2 A:HIS339 3.3 21.0 1.0
P A:TPO85 3.4 31.3 1.0
O2P A:TPO85 3.8 33.2 1.0
O A:HOH408 4.0 37.2 1.0
CB A:ASP156 4.3 25.3 1.0
ND1 A:HIS339 4.3 20.9 1.0
CG A:HIS291 4.3 21.7 1.0
ND1 A:HIS291 4.3 20.2 1.0
CB A:ASP286 4.3 18.8 1.0
ND2 A:ASN330 4.3 19.7 1.0
OG1 A:TPO85 4.4 28.1 1.0
O A:HOH428 4.4 26.6 1.0
CG A:HIS339 4.4 21.3 1.0
O3P A:TPO85 4.4 31.6 1.0
O A:HOH533 4.5 32.6 1.0
CE1 A:HIS328 4.6 21.0 1.0
NE2 A:HIS328 4.7 22.0 1.0
MN A:MN396 4.9 20.4 1.0

Manganese binding site 2 out of 10 in 3m8y

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Manganese binding site 2 out of 10 in the Phosphopentomutase From Bacillus Cereus After Glucose-1,6-Bisphosphate Activation


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 After Glucose-1,6-Bisphosphate Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn396

b:20.4
occ:1.00
 O2P A:TPO85 1.9 33.2 1.0
OD1 A:ASP13 2.0 21.0 1.0
OD2 A:ASP327 2.1 19.4 1.0
NE2 A:HIS328 2.2 22.0 1.0
CG A:ASP13 2.6 20.4 1.0
OD2 A:ASP13 2.6 20.7 1.0
CG A:ASP327 2.9 19.6 1.0
OD1 A:ASP327 3.0 18.6 1.0
OG1 A:TPO85 3.0 28.1 1.0
CD2 A:HIS328 3.1 20.4 1.0
P A:TPO85 3.1 31.3 1.0
CE1 A:HIS328 3.3 21.0 1.0
CG2 A:TPO85 3.7 25.6 1.0
CB A:TPO85 3.8 25.6 1.0
O1P A:TPO85 3.9 30.8 1.0
CB A:ASP13 4.1 18.2 1.0
CA A:TPO85 4.1 23.9 1.0
CG A:HIS328 4.2 20.3 1.0
O3P A:TPO85 4.3 31.6 1.0
ND1 A:HIS328 4.3 20.3 1.0
NZ A:LYS240 4.3 29.8 1.0
N A:SER14 4.3 18.0 1.0
CB A:ASP327 4.3 18.8 1.0
CG A:ASP286 4.4 18.9 1.0
OD2 A:ASP286 4.4 17.0 1.0
CE1 A:HIS339 4.4 21.4 1.0
OD1 A:ASP286 4.5 21.1 1.0
CA A:ASP13 4.6 18.2 1.0
N A:TPO85 4.7 23.8 1.0
C A:ASP13 4.7 18.1 1.0
NE2 A:HIS89 4.7 21.3 1.0
NE2 A:HIS339 4.8 21.5 1.0
CB A:ASP286 4.8 18.8 1.0
MN A:MN395 4.9 22.1 1.0
CA A:SER14 4.9 18.1 1.0
CB A:SER14 4.9 18.0 1.0
CE A:LYS240 4.9 28.4 1.0
CD2 A:HIS89 5.0 18.2 1.0

Manganese binding site 3 out of 10 in 3m8y

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Manganese binding site 3 out of 10 in the Phosphopentomutase From Bacillus Cereus After Glucose-1,6-Bisphosphate Activation


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 After Glucose-1,6-Bisphosphate Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn397

b:26.2
occ:0.75
 O A:HOH681 2.0 31.2 1.0
O A:HOH680 2.1 31.5 1.0
OD1 A:ASP28 2.2 27.8 1.0
O A:HOH534 2.2 26.1 1.0
NE2 A:HIS334 2.2 26.8 1.0
O A:GLY27 2.5 33.3 1.0
CD2 A:HIS334 3.0 27.1 1.0
CE1 A:HIS334 3.3 29.2 1.0
CG A:ASP28 3.4 27.4 1.0
C A:GLY27 3.4 33.6 1.0
CA A:ASP28 3.9 30.0 1.0
O A:PHE26 4.0 35.1 1.0
N A:ASP28 4.1 32.0 1.0
OD2 A:ASP338 4.1 31.3 1.0
OD1 A:ASP338 4.1 30.4 1.0
CB A:ASP28 4.2 28.3 1.0
CG A:HIS334 4.2 26.6 1.0
OD2 A:ASP28 4.3 27.0 1.0
CG2 A:THR340 4.3 22.7 1.0
NZ A:LYS83 4.3 25.5 1.0
ND1 A:HIS334 4.4 27.2 1.0
CG A:ASP338 4.5 29.8 1.0
CA A:GLY27 4.5 35.6 1.0
O A:HIS339 4.5 23.9 1.0
O A:PRO335 4.6 29.1 1.0
C A:PHE26 4.9 35.0 1.0

Manganese binding site 4 out of 10 in 3m8y

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Manganese binding site 4 out of 10 in the Phosphopentomutase From Bacillus Cereus After Glucose-1,6-Bisphosphate Activation


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 After Glucose-1,6-Bisphosphate Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn395

b:22.8
occ:1.00
 O1P B:TPO85 2.0 29.5 1.0
NE2 B:HIS339 2.1 22.1 1.0
NE2 B:HIS291 2.2 19.0 1.0
OD1 B:ASP286 2.2 21.9 1.0
OD2 B:ASP156 2.3 29.0 1.0
OD1 B:ASP156 2.6 33.1 1.0
CG B:ASP156 2.8 30.7 1.0
CG B:ASP286 2.9 21.2 1.0
OD2 B:ASP286 2.9 20.7 1.0
CE1 B:HIS339 3.0 21.9 1.0
CD2 B:HIS291 3.1 20.1 1.0
CE1 B:HIS291 3.2 20.6 1.0
CD2 B:HIS339 3.2 22.8 1.0
P B:TPO85 3.4 28.1 1.0
O2P B:TPO85 3.9 29.8 1.0
O B:HOH673 4.1 40.7 1.0
ND1 B:HIS339 4.2 22.0 1.0
ND1 B:HIS291 4.3 21.7 1.0
CG B:HIS291 4.3 22.1 1.0
O3P B:TPO85 4.3 31.0 1.0
CG B:HIS339 4.3 23.0 1.0
OG1 B:TPO85 4.4 26.1 1.0
CB B:ASP286 4.4 20.6 1.0
CB B:ASP156 4.4 28.0 1.0
O B:HOH437 4.4 33.9 1.0
ND2 B:ASN330 4.4 24.6 1.0
O B:HOH552 4.5 34.3 1.0
CE1 B:HIS328 4.6 21.0 1.0
NE2 B:HIS328 4.7 20.4 1.0
MN B:MN396 4.9 21.3 1.0

Manganese binding site 5 out of 10 in 3m8y

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Manganese binding site 5 out of 10 in the Phosphopentomutase From Bacillus Cereus After Glucose-1,6-Bisphosphate Activation


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 After Glucose-1,6-Bisphosphate Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn396

b:21.3
occ:1.00
 O2P B:TPO85 1.9 29.8 1.0
OD2 B:ASP327 2.2 18.5 1.0
NE2 B:HIS328 2.2 20.4 1.0
OD1 B:ASP13 2.2 20.9 1.0
OD2 B:ASP13 2.5 23.4 1.0
CG B:ASP13 2.6 21.6 1.0
CG B:ASP327 2.9 17.9 1.0
CD2 B:HIS328 3.0 18.9 1.0
OD1 B:ASP327 3.0 18.0 1.0
OG1 B:TPO85 3.1 26.1 1.0
P B:TPO85 3.1 28.1 1.0
CE1 B:HIS328 3.2 21.0 1.0
CG2 B:TPO85 3.5 21.4 1.0
CB B:TPO85 3.7 22.6 1.0
O1P B:TPO85 3.8 29.5 1.0
CA B:TPO85 4.1 21.2 1.0
NZ B:LYS240 4.1 28.0 1.0
CB B:ASP13 4.1 20.9 1.0
CG B:HIS328 4.2 19.7 1.0
ND1 B:HIS328 4.2 19.3 1.0
N B:SER14 4.3 20.0 1.0
O3P B:TPO85 4.3 31.0 1.0
CG B:ASP286 4.3 21.2 1.0
CB B:ASP327 4.4 17.4 1.0
OD2 B:ASP286 4.4 20.7 1.0
CE1 B:HIS339 4.4 21.9 1.0
OD1 B:ASP286 4.5 21.9 1.0
CA B:ASP13 4.7 19.5 1.0
NE2 B:HIS89 4.7 20.8 1.0
C B:ASP13 4.7 20.3 1.0
CB B:ASP286 4.7 20.6 1.0
N B:TPO85 4.8 21.5 1.0
NE2 B:HIS339 4.8 22.1 1.0
MN B:MN395 4.9 22.8 1.0
CA B:SER14 4.9 20.7 1.0
CB B:SER14 4.9 22.1 1.0
CE B:LYS240 4.9 27.1 1.0

Manganese binding site 6 out of 10 in 3m8y

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Manganese binding site 6 out of 10 in the Phosphopentomutase From Bacillus Cereus After Glucose-1,6-Bisphosphate Activation


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 After Glucose-1,6-Bisphosphate Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn397

b:40.4
occ:0.75
 O B:HOH541 2.4 46.3 1.0
O B:HOH615 2.9 49.6 1.0
O B:HOH433 4.0 31.0 1.0
OE2 B:GLU318 4.1 44.5 1.0

Manganese binding site 7 out of 10 in 3m8y

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Manganese binding site 7 out of 10 in the Phosphopentomutase From Bacillus Cereus After Glucose-1,6-Bisphosphate Activation


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 After Glucose-1,6-Bisphosphate Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn398

b:41.0
occ:0.50
 O B:HOH755 1.9 45.1 1.0
OD1 B:ASP28 2.1 30.9 1.0
O B:HOH411 2.3 34.6 1.0
O B:HOH621 2.4 43.0 1.0
NE2 B:HIS334 2.4 30.2 1.0
O B:GLY27 2.8 34.7 1.0
CD2 B:HIS334 3.1 29.3 1.0
CG B:ASP28 3.3 28.8 1.0
C B:GLY27 3.3 33.9 1.0
CE1 B:HIS334 3.5 31.5 1.0
O B:PHE26 3.8 35.7 1.0
CA B:ASP28 3.8 30.1 1.0
N B:ASP28 3.8 31.8 1.0
CB B:ASP28 4.1 28.4 1.0
OD2 B:ASP28 4.2 27.4 1.0
O B:HOH539 4.2 35.4 1.0
CA B:GLY27 4.2 35.5 1.0
NZ B:LYS83 4.2 24.0 1.0
CG B:HIS334 4.3 30.1 1.0
ND1 B:HIS334 4.5 31.7 1.0
C B:PHE26 4.7 35.0 1.0
CG2 B:THR340 4.8 25.1 1.0
O B:HIS339 4.9 24.6 1.0
O B:PRO335 4.9 31.8 1.0
N B:GLY27 4.9 35.4 1.0

Manganese binding site 8 out of 10 in 3m8y

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Manganese binding site 8 out of 10 in the Phosphopentomutase From Bacillus Cereus After Glucose-1,6-Bisphosphate Activation


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 After Glucose-1,6-Bisphosphate Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn395

b:32.4
occ:1.00
 OD1 C:ASP286 2.1 25.8 1.0
O1P C:TPO85 2.2 39.1 1.0
NE2 C:HIS339 2.2 29.6 1.0
NE2 C:HIS291 2.2 31.1 1.0
OD1 C:ASP156 2.6 58.3 1.0
OD2 C:ASP156 2.6 62.9 1.0
CG C:ASP286 2.9 27.5 1.0
OD2 C:ASP286 3.0 29.6 1.0
CG C:ASP156 3.0 58.4 1.0
CE1 C:HIS339 3.1 29.0 1.0
CE1 C:HIS291 3.2 32.1 1.0
CD2 C:HIS291 3.2 31.9 1.0
CD2 C:HIS339 3.2 29.8 1.0
P C:TPO85 3.3 37.4 1.0
O3P C:TPO85 3.6 38.2 1.0
O C:HOH417 3.9 45.4 1.0
O C:HOH608 4.2 43.5 1.0
ND1 C:HIS339 4.3 28.4 1.0
CB C:ASP286 4.3 27.8 1.0
ND1 C:HIS291 4.3 33.0 1.0
O2P C:TPO85 4.3 39.1 1.0
CG C:HIS339 4.4 30.0 1.0
CG C:HIS291 4.4 33.3 1.0
OG1 C:TPO85 4.4 34.5 1.0
ND2 C:ASN330 4.4 30.6 1.0
CE1 C:HIS328 4.5 27.4 1.0
CB C:ASP156 4.5 53.8 1.0
O C:HOH754 4.6 55.1 1.0
NE2 C:HIS328 4.7 28.4 1.0
MN C:MN396 4.8 27.6 1.0

Manganese binding site 9 out of 10 in 3m8y

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Manganese binding site 9 out of 10 in the Phosphopentomutase From Bacillus Cereus After Glucose-1,6-Bisphosphate Activation


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 After Glucose-1,6-Bisphosphate Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn396

b:27.6
occ:1.00
 OD1 C:ASP13 2.1 27.5 1.0
OD2 C:ASP327 2.1 25.2 1.0
O3P C:TPO85 2.2 38.2 1.0
NE2 C:HIS328 2.2 28.4 1.0
OG1 C:TPO85 2.5 34.5 1.0
CG C:ASP13 2.7 27.3 1.0
OD2 C:ASP13 2.7 27.6 1.0
CG C:ASP327 3.0 25.9 1.0
P C:TPO85 3.0 37.4 1.0
CD2 C:HIS328 3.1 28.1 1.0
OD1 C:ASP327 3.2 26.2 1.0
CE1 C:HIS328 3.2 27.4 1.0
CB C:TPO85 3.4 32.1 1.0
CG2 C:TPO85 3.6 30.7 1.0
O1P C:TPO85 3.8 39.1 1.0
CA C:TPO85 3.8 31.5 1.0
CB C:ASP13 4.2 26.2 1.0
O2P C:TPO85 4.2 39.1 1.0
CG C:HIS328 4.2 27.0 1.0
ND1 C:HIS328 4.3 27.6 1.0
N C:SER14 4.4 26.8 1.0
CG C:ASP286 4.4 27.5 1.0
CB C:ASP327 4.4 24.9 1.0
N C:TPO85 4.5 32.0 1.0
OD2 C:ASP286 4.5 29.6 1.0
CE1 C:HIS339 4.5 29.0 1.0
OD1 C:ASP286 4.6 25.8 1.0
NZ C:LYS240 4.6 35.8 1.0
CA C:ASP13 4.7 26.3 1.0
NE2 C:HIS339 4.7 29.6 1.0
NE2 C:HIS89 4.7 24.9 1.0
C C:ASP13 4.7 27.0 1.0
CB C:ASP286 4.8 27.8 1.0
MN C:MN395 4.8 32.4 1.0
CB C:SER14 5.0 27.9 1.0

Manganese binding site 10 out of 10 in 3m8y

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Manganese binding site 10 out of 10 in the Phosphopentomutase From Bacillus Cereus After Glucose-1,6-Bisphosphate Activation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Phosphopentomutase From Bacillus Cereus After Glucose-1,6-Bisphosphate Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn397

b:44.4
occ:1.00
 OD1 C:ASP28 2.1 39.8 1.0
O C:HOH477 2.1 35.0 1.0
NE2 C:HIS334 2.2 36.7 1.0
O C:HOH431 2.2 36.0 1.0
O C:GLY27 2.5 41.1 1.0
O C:HOH708 2.5 43.7 1.0
CD2 C:HIS334 3.0 35.4 1.0
CE1 C:HIS334 3.2 36.4 1.0
C C:GLY27 3.3 41.5 1.0
CG C:ASP28 3.3 38.0 1.0
CA C:ASP28 3.8 39.5 1.0
N C:ASP28 3.9 40.9 1.0
O C:PHE26 3.9 41.4 1.0
CB C:ASP28 4.2 38.2 1.0
CG C:HIS334 4.2 35.6 1.0
O C:HOH450 4.2 51.7 1.0
CA C:GLY27 4.2 43.2 1.0
ND1 C:HIS334 4.2 36.2 1.0
OD2 C:ASP28 4.2 36.2 1.0
NZ C:LYS83 4.4 33.4 1.0
CG2 C:THR340 4.5 32.6 1.0
C C:PHE26 4.8 42.5 1.0
O C:HIS339 4.8 32.2 1.0
O C:PRO335 5.0 36.1 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: Sat Oct 5 17:01:56 2024

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