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Manganese in PDB 3uo0: Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with Glucose 1,6-Bisphosphate

Enzymatic activity of Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with Glucose 1,6-Bisphosphate

All present enzymatic activity of Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with Glucose 1,6-Bisphosphate:
5.4.2.7;

Protein crystallography data

The structure of Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with Glucose 1,6-Bisphosphate, PDB code: 3uo0 was solved by T.M.Iverson, W.R.Birmingham, T.D.Panosian, D.P.Nannemann, B.O.Bachmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.819, 77.075, 108.335, 90.00, 108.94, 90.00
R / Rfree (%) 18.2 / 21.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with Glucose 1,6-Bisphosphate (pdb code 3uo0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with Glucose 1,6-Bisphosphate, PDB code: 3uo0:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3uo0

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Manganese binding site 1 out of 8 in the Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with 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 Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn395

b:25.7
occ:1.00
 O3P A:TPO85 1.9 33.5 1.0
OD1 A:ASP286 2.1 25.3 1.0
NE2 A:HIS339 2.2 25.5 1.0
NE2 A:HIS291 2.2 25.9 1.0
OD2 A:ASP156 2.3 33.1 1.0
OD1 A:ASP156 2.8 33.9 1.0
CG A:ASP286 2.9 24.8 1.0
CG A:ASP156 2.9 33.1 1.0
OD2 A:ASP286 2.9 24.6 1.0
CE1 A:HIS339 3.1 25.4 1.0
CE1 A:HIS291 3.2 26.6 1.0
CD2 A:HIS291 3.3 26.1 1.0
P A:TPO85 3.3 32.3 1.0
CD2 A:HIS339 3.3 25.8 1.0
O1P A:TPO85 3.7 33.1 1.0
O A:HOH570 4.0 41.1 1.0
O2P A:TPO85 4.2 32.5 1.0
OG1 A:TPO85 4.3 31.1 1.0
ND1 A:HIS339 4.3 25.9 1.0
ND1 A:HIS291 4.3 27.0 1.0
CB A:ASP286 4.3 24.5 1.0
CG A:HIS291 4.4 26.9 1.0
CG A:HIS339 4.4 26.2 1.0
O A:HOH406 4.4 40.7 1.0
CB A:ASP156 4.4 32.5 1.0
ND2 A:ASN330 4.5 26.2 1.0
O A:HOH502 4.5 69.7 1.0
CE1 A:HIS328 4.5 24.9 1.0
NE2 A:HIS328 4.6 25.1 1.0
MN A:MN396 4.8 25.0 1.0

Manganese binding site 2 out of 8 in 3uo0

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Manganese binding site 2 out of 8 in the Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with 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 Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn396

b:25.0
occ:1.00
 O1P A:TPO85 2.0 33.1 1.0
OD1 A:ASP13 2.0 24.4 1.0
OD2 A:ASP327 2.2 24.1 1.0
NE2 A:HIS328 2.3 25.1 1.0
CG A:ASP13 2.7 23.9 1.0
OD2 A:ASP13 2.7 24.5 1.0
CG A:ASP327 3.0 24.3 1.0
OG1 A:TPO85 3.0 31.1 1.0
CD2 A:HIS328 3.1 24.9 1.0
OD1 A:ASP327 3.1 23.9 1.0
P A:TPO85 3.1 32.3 1.0
CE1 A:HIS328 3.2 24.9 1.0
CG2 A:TPO85 3.6 30.0 1.0
CB A:TPO85 3.8 29.9 1.0
O3P A:TPO85 3.9 33.5 1.0
CB A:ASP13 4.1 23.3 1.0
CA A:TPO85 4.2 29.2 1.0
CG A:HIS328 4.2 25.1 1.0
ND1 A:HIS328 4.2 24.8 1.0
NZ A:LYS240 4.3 28.4 1.0
O2P A:TPO85 4.3 32.5 1.0
CG A:ASP286 4.3 24.8 1.0
N A:SER14 4.4 23.2 1.0
CB A:ASP327 4.4 24.1 1.0
OD1 A:ASP286 4.5 25.3 1.0
OD2 A:ASP286 4.5 24.6 1.0
CA A:ASP13 4.6 23.1 1.0
CE1 A:HIS339 4.6 25.4 1.0
C A:ASP13 4.7 23.2 1.0
CB A:ASP286 4.8 24.5 1.0
NE2 A:HIS339 4.8 25.5 1.0
MN A:MN395 4.8 25.7 1.0
NE2 A:HIS89 4.8 27.4 1.0
N A:TPO85 4.8 29.3 1.0
CB A:SER14 5.0 23.7 1.0
CA A:SER14 5.0 23.4 1.0

Manganese binding site 3 out of 8 in 3uo0

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Manganese binding site 3 out of 8 in the Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with 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 Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn397

b:30.6
occ:0.75
 OD1 A:ASP28 2.1 33.6 1.0
O A:HOH432 2.1 44.4 1.0
O A:HOH466 2.1 35.8 1.0
NE2 A:HIS334 2.2 31.4 1.0
O A:HOH465 2.2 37.4 1.0
O A:GLY27 2.5 37.5 1.0
CD2 A:HIS334 3.1 31.1 1.0
CE1 A:HIS334 3.3 31.7 1.0
CG A:ASP28 3.3 33.5 1.0
C A:GLY27 3.4 37.9 1.0
CA A:ASP28 3.9 35.5 1.0
N A:ASP28 4.0 36.9 1.0
CB A:ASP28 4.1 34.0 1.0
O A:PHE26 4.1 37.5 1.0
OD2 A:ASP28 4.2 32.8 1.0
CG A:HIS334 4.3 30.9 1.0
OD1 A:ASP338 4.3 33.2 1.0
ND1 A:HIS334 4.3 31.3 1.0
CG2 A:THR340 4.4 27.8 1.0
OD2 A:ASP338 4.5 33.5 1.0
CA A:GLY27 4.5 39.4 1.0
O A:PRO335 4.5 32.5 1.0
NZ A:LYS83 4.5 35.1 1.0
O A:HIS339 4.7 28.3 1.0
CG A:ASP338 4.8 32.3 1.0
C A:PHE26 5.0 38.1 1.0

Manganese binding site 4 out of 8 in 3uo0

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Manganese binding site 4 out of 8 in the Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with 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 Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn395

b:25.3
occ:1.00
 O1P B:TPO85 2.0 31.2 1.0
NE2 B:HIS339 2.2 24.8 1.0
OD1 B:ASP286 2.2 26.6 1.0
NE2 B:HIS291 2.2 26.9 1.0
OD2 B:ASP156 2.3 39.1 1.0
OD1 B:ASP156 2.9 39.9 1.0
CG B:ASP156 3.0 38.3 1.0
CG B:ASP286 3.0 26.3 1.0
CE1 B:HIS339 3.0 24.7 1.0
OD2 B:ASP286 3.1 26.8 1.0
CE1 B:HIS291 3.1 27.4 1.0
CD2 B:HIS291 3.3 27.3 1.0
CD2 B:HIS339 3.3 25.6 1.0
P B:TPO85 3.3 30.3 1.0
O3P B:TPO85 3.7 30.0 1.0
ND1 B:HIS339 4.2 25.1 1.0
OG1 B:TPO85 4.3 29.0 1.0
ND1 B:HIS291 4.3 28.3 1.0
O2P B:TPO85 4.3 30.7 1.0
O B:HOH542 4.3 47.1 1.0
CG B:HIS339 4.3 25.8 1.0
O B:HOH591 4.3 40.1 1.0
CG B:HIS291 4.4 28.2 1.0
CB B:ASP286 4.4 25.7 1.0
CB B:ASP156 4.4 35.6 1.0
O B:HOH498 4.5 38.5 1.0
CE1 B:HIS328 4.5 23.6 1.0
ND2 B:ASN330 4.6 26.7 1.0
NE2 B:HIS328 4.6 23.6 1.0
MN B:MN396 4.8 26.3 1.0

Manganese binding site 5 out of 8 in 3uo0

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Manganese binding site 5 out of 8 in the Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with 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 Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn396

b:26.3
occ:1.00
 O3P B:TPO85 2.0 30.0 1.0
OD1 B:ASP13 2.2 28.0 1.0
NE2 B:HIS328 2.2 23.6 1.0
OD2 B:ASP327 2.2 22.9 1.0
OD2 B:ASP13 2.7 28.0 1.0
CG B:ASP13 2.7 27.5 1.0
CD2 B:HIS328 3.0 23.4 1.0
CG B:ASP327 3.1 22.7 1.0
OG1 B:TPO85 3.1 29.0 1.0
P B:TPO85 3.1 30.3 1.0
CE1 B:HIS328 3.2 23.6 1.0
OD1 B:ASP327 3.2 22.2 1.0
CG2 B:TPO85 3.5 27.5 1.0
CB B:TPO85 3.7 27.9 1.0
O1P B:TPO85 4.0 31.2 1.0
CG B:HIS328 4.1 23.9 1.0
CB B:ASP13 4.2 26.9 1.0
ND1 B:HIS328 4.2 23.8 1.0
CA B:TPO85 4.2 27.3 1.0
NZ B:LYS240 4.2 26.1 1.0
O2P B:TPO85 4.3 30.7 1.0
N B:SER14 4.4 25.8 1.0
CG B:ASP286 4.4 26.3 1.0
CB B:ASP327 4.5 22.6 1.0
OD2 B:ASP286 4.5 26.8 1.0
OD1 B:ASP286 4.6 26.6 1.0
CE1 B:HIS339 4.6 24.7 1.0
CA B:ASP13 4.7 25.7 1.0
NE2 B:HIS339 4.8 24.8 1.0
CB B:ASP286 4.8 25.7 1.0
C B:ASP13 4.8 26.2 1.0
MN B:MN395 4.8 25.3 1.0
NE2 B:HIS89 4.8 24.3 1.0
N B:TPO85 4.9 27.5 1.0

Manganese binding site 6 out of 8 in 3uo0

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Manganese binding site 6 out of 8 in the Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with 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 Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn395

b:39.0
occ:1.00
 O3P C:TPO85 2.1 38.6 1.0
OD1 C:ASP286 2.2 33.0 1.0
NE2 C:HIS291 2.2 34.4 1.0
NE2 C:HIS339 2.2 32.7 1.0
OD2 C:ASP156 2.6 67.5 1.0
OD1 C:ASP156 2.8 62.4 1.0
CG C:ASP286 2.9 33.4 1.0
OD2 C:ASP286 2.9 34.0 1.0
CE1 C:HIS339 3.0 32.4 1.0
CG C:ASP156 3.0 63.2 1.0
CE1 C:HIS291 3.1 34.8 1.0
CD2 C:HIS291 3.2 35.2 1.0
P C:TPO85 3.3 37.4 1.0
CD2 C:HIS339 3.3 33.1 1.0
O1P C:TPO85 3.4 37.3 1.0
ND1 C:HIS339 4.2 32.7 1.0
ND1 C:HIS291 4.3 35.8 1.0
OG1 C:TPO85 4.3 36.2 1.0
O2P C:TPO85 4.3 38.0 1.0
CG C:HIS291 4.3 36.0 1.0
CB C:ASP286 4.3 33.6 1.0
CG C:HIS339 4.4 33.2 1.0
CE1 C:HIS328 4.5 32.3 1.0
CB C:ASP156 4.6 59.1 1.0
NE2 C:HIS328 4.6 31.9 1.0
ND2 C:ASN330 4.6 34.4 1.0
MN C:MN396 4.8 33.4 1.0

Manganese binding site 7 out of 8 in 3uo0

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Manganese binding site 7 out of 8 in the Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with 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 Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn396

b:33.4
occ:1.00
 OD1 C:ASP13 2.1 33.7 1.0
OD2 C:ASP327 2.2 30.7 1.0
NE2 C:HIS328 2.2 31.9 1.0
O1P C:TPO85 2.3 37.3 1.0
OG1 C:TPO85 2.5 36.2 1.0
CG C:ASP13 2.8 33.5 1.0
OD2 C:ASP13 2.8 33.6 1.0
P C:TPO85 3.0 37.4 1.0
CG C:ASP327 3.1 31.4 1.0
CE1 C:HIS328 3.1 32.3 1.0
CD2 C:HIS328 3.1 32.0 1.0
OD1 C:ASP327 3.3 31.9 1.0
CG2 C:TPO85 3.3 34.9 1.0
CB C:TPO85 3.3 35.5 1.0
CA C:TPO85 3.9 35.4 1.0
O3P C:TPO85 3.9 38.6 1.0
ND1 C:HIS328 4.1 32.7 1.0
CG C:HIS328 4.2 32.6 1.0
O2P C:TPO85 4.2 38.0 1.0
CB C:ASP13 4.2 33.8 1.0
N C:SER14 4.5 34.4 1.0
CG C:ASP286 4.5 33.4 1.0
CB C:ASP327 4.5 31.4 1.0
N C:TPO85 4.5 36.2 1.0
OD1 C:ASP286 4.5 33.0 1.0
CE1 C:HIS339 4.6 32.4 1.0
OD2 C:ASP286 4.7 34.0 1.0
CA C:ASP13 4.7 33.9 1.0
MN C:MN395 4.8 39.0 1.0
NE2 C:HIS339 4.8 32.7 1.0
CB C:ASP286 4.8 33.6 1.0
NE2 C:HIS89 4.9 30.3 1.0
C C:ASP13 4.9 34.5 1.0

Manganese binding site 8 out of 8 in 3uo0

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Manganese binding site 8 out of 8 in the Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with 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 Phosphorylated Bacillus Cereus Phosphopentomutase Soaked with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn397

b:50.4
occ:1.00
 OD1 C:ASP28 2.1 42.5 1.0
O C:HOH471 2.1 39.8 1.0
O C:HOH470 2.2 40.9 1.0
NE2 C:HIS334 2.3 40.3 1.0
O C:GLY27 2.4 45.6 1.0
O C:HOH472 2.5 39.3 1.0
CD2 C:HIS334 3.1 39.6 1.0
CG C:ASP28 3.3 42.4 1.0
C C:GLY27 3.3 46.0 1.0
CE1 C:HIS334 3.3 41.2 1.0
CA C:ASP28 3.8 44.6 1.0
N C:ASP28 3.9 45.7 1.0
O C:PHE26 4.1 45.4 1.0
CB C:ASP28 4.1 43.2 1.0
O C:HOH416 4.2 42.3 1.0
OD2 C:ASP28 4.2 41.7 1.0
CG C:HIS334 4.3 40.2 1.0
CA C:GLY27 4.3 47.3 1.0
ND1 C:HIS334 4.4 41.1 1.0
NZ C:LYS83 4.6 41.1 1.0
CG2 C:THR340 4.6 38.0 1.0
O C:HIS339 4.7 36.0 1.0
O C:HOH415 4.8 42.8 1.0
O C:PRO335 4.9 39.7 1.0
C C:PHE26 4.9 46.3 1.0

Reference:

T.M.Iverson, T.D.Panosian, W.R.Birmingham, D.P.Nannemann, B.O.Bachmann. Molecular Differences Between A Mutase and A Phosphatase: Investigations of the Activation Step in Bacillus Cereus Phosphopentomutase. Biochemistry V. 51 1964 2012.
ISSN: ISSN 0006-2960
PubMed: 22329805
DOI: 10.1021/BI201761H
Page generated: Sat Oct 5 18:08:35 2024

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