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Manganese in PDB 3m8z: Phosphopentomutase From Bacillus Cereus Bound with Ribose-5-Phosphate

Enzymatic activity of Phosphopentomutase From Bacillus Cereus Bound with Ribose-5-Phosphate

All present enzymatic activity of Phosphopentomutase From Bacillus Cereus Bound with Ribose-5-Phosphate:
5.4.2.7;

Protein crystallography data

The structure of Phosphopentomutase From Bacillus Cereus Bound with Ribose-5-Phosphate, PDB code: 3m8z 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 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.588, 76.755, 107.083, 90.00, 108.66, 90.00
R / Rfree (%) 16.8 / 19.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Phosphopentomutase From Bacillus Cereus Bound with Ribose-5-Phosphate (pdb code 3m8z). 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 with Ribose-5-Phosphate, PDB code: 3m8z:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 3m8z

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Manganese binding site 1 out of 9 in the Phosphopentomutase From Bacillus Cereus Bound with Ribose-5-Phosphate


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 with Ribose-5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn395

b:17.2
occ:1.00
 OD1 A:ASP286 2.1 19.1 1.0
NE2 A:HIS291 2.2 13.5 1.0
NE2 A:HIS339 2.2 20.2 1.0
O1X A:HSX402 2.3 21.8 0.5
O2X A:HSX402 2.4 20.6 0.5
O1P A:THR85 2.4 23.2 0.2
OD2 A:ASP156 2.4 23.9 0.5
OD2 A:ASP286 2.7 16.5 1.0
CG A:ASP286 2.7 17.3 1.0
P' A:HSX402 2.8 22.1 0.5
OD1 A:ASP156 2.8 24.9 0.5
CG A:ASP156 3.0 25.9 0.5
CE1 A:HIS339 3.1 24.2 1.0
CD2 A:HIS291 3.1 15.2 1.0
CE1 A:HIS291 3.1 15.7 1.0
CD2 A:HIS339 3.2 19.3 1.0
P A:THR85 3.5 23.4 0.2
O2P A:THR85 3.6 23.8 0.2
O5' A:HSX402 4.0 21.9 0.5
O3X A:HSX402 4.0 21.9 0.5
C5' A:HSX402 4.1 20.4 0.5
CB A:ASP156 4.1 26.8 0.5
O3' A:HSX402 4.1 17.6 0.5
CB A:ASP286 4.2 16.1 1.0
ND1 A:HIS339 4.2 23.8 1.0
ND1 A:HIS291 4.2 15.3 1.0
CG A:HIS291 4.3 16.8 1.0
CG A:HIS339 4.3 19.3 1.0
ND2 A:ASN330 4.3 18.3 1.0
OG1 A:THR85 4.5 21.5 0.2
OD2 A:ASP156 4.5 28.5 0.5
CB A:ASP156 4.5 25.9 0.5
CE1 A:HIS328 4.5 14.1 1.0
OG1 A:THR85 4.5 21.2 0.8
O3P A:THR85 4.6 22.2 0.2
O A:HOH531 4.7 25.7 1.0
C4' A:HSX402 4.7 20.1 0.5
CG A:ASP156 4.8 27.3 0.5
NE2 A:HIS328 4.8 15.5 1.0
C3' A:HSX402 4.9 19.5 0.5

Manganese binding site 2 out of 9 in 3m8z

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Manganese binding site 2 out of 9 in the Phosphopentomutase From Bacillus Cereus Bound with Ribose-5-Phosphate


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 with Ribose-5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn396

b:17.7
occ:1.00
 OD2 A:ASP327 2.0 16.0 1.0
OG1 A:THR85 2.0 21.2 0.8
OD1 A:ASP13 2.1 14.3 1.0
NE2 A:HIS328 2.3 15.5 1.0
OG1 A:THR85 2.4 21.5 0.2
OD2 A:ASP13 2.4 16.0 1.0
CG A:ASP13 2.5 14.0 1.0
CG A:ASP327 2.8 14.9 1.0
O2P A:THR85 2.9 23.8 0.2
OD1 A:ASP327 3.0 14.9 1.0
CD2 A:HIS328 3.1 15.7 1.0
CB A:THR85 3.2 20.0 0.8
CE1 A:HIS328 3.3 14.1 1.0
P A:THR85 3.3 23.4 0.2
CB A:THR85 3.4 20.0 0.2
CG2 A:THR85 3.5 19.6 0.8
O2X A:HSX402 3.5 20.6 0.5
CA A:THR85 3.6 19.4 0.8
CA A:THR85 3.6 19.6 0.2
CG2 A:THR85 3.8 19.9 0.2
O1P A:THR85 4.0 23.2 0.2
CB A:ASP13 4.0 13.4 1.0
N A:THR85 4.2 20.0 0.8
N A:THR85 4.2 20.1 0.2
CG A:HIS328 4.2 14.7 1.0
N A:SER14 4.3 13.8 1.0
CB A:ASP327 4.3 14.1 1.0
ND1 A:HIS328 4.3 13.6 1.0
O3P A:THR85 4.5 22.2 0.2
O A:HOH709 4.5 36.3 1.0
CA A:ASP13 4.5 13.4 1.0
OD2 A:ASP286 4.5 16.5 1.0
CG A:ASP286 4.5 17.3 1.0
C A:ASP13 4.6 13.3 1.0
NE2 A:HIS89 4.6 16.8 1.0
CD2 A:HIS89 4.8 12.8 1.0
C5' A:HSX402 4.8 20.4 0.5
CB A:ASP286 4.9 16.1 1.0
OD1 A:ASP286 4.9 19.1 1.0
C A:THR85 4.9 18.2 0.8
C A:THR85 4.9 18.4 0.2
C A:ASP84 4.9 21.1 1.0
CA A:SER14 5.0 13.8 1.0
P' A:HSX402 5.0 22.1 0.5
CB A:SER14 5.0 14.4 1.0

Manganese binding site 3 out of 9 in 3m8z

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Manganese binding site 3 out of 9 in the Phosphopentomutase From Bacillus Cereus Bound with Ribose-5-Phosphate


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 with Ribose-5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn397

b:24.8
occ:0.75
 OD1 A:ASP28 2.1 20.0 1.0
O A:HOH485 2.2 31.8 1.0
NE2 A:HIS334 2.2 22.6 1.0
O A:HOH856 2.2 35.1 1.0
O A:HOH610 2.4 26.9 1.0
O A:GLY27 2.5 26.1 1.0
CD2 A:HIS334 3.0 23.3 1.0
CE1 A:HIS334 3.3 23.0 1.0
CG A:ASP28 3.3 21.0 1.0
C A:GLY27 3.3 25.9 1.0
CA A:ASP28 3.8 22.5 1.0
N A:ASP28 3.9 24.2 1.0
O A:PHE26 4.0 27.6 1.0
CB A:ASP28 4.1 21.1 1.0
CG A:HIS334 4.2 22.0 1.0
OD2 A:ASP28 4.2 20.2 1.0
OD2 A:ASP338 4.3 25.1 0.4
ND1 A:HIS334 4.3 23.0 1.0
CA A:GLY27 4.3 27.4 1.0
CG2 A:THR340 4.4 17.6 1.0
NZ A:LYS83 4.4 20.9 1.0
O A:HIS339 4.6 17.6 1.0
O A:PRO335 4.6 24.7 1.0
O A:HOH702 4.8 38.2 1.0
C A:PHE26 4.9 27.9 1.0

Manganese binding site 4 out of 9 in 3m8z

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Manganese binding site 4 out of 9 in the Phosphopentomutase From Bacillus Cereus Bound with Ribose-5-Phosphate


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 with Ribose-5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn395

b:18.4
occ:1.00
 NE2 B:HIS339 2.1 16.9 1.0
NE2 B:HIS291 2.2 18.5 1.0
O1P B:TPO85 2.2 22.5 0.4
OD2 B:ASP156 2.2 29.2 1.0
OD1 B:ASP286 2.2 19.5 1.0
OD1 B:ASP156 2.8 30.4 1.0
CG B:ASP156 2.9 27.7 1.0
CG B:ASP286 2.9 18.7 1.0
OD2 B:ASP286 2.9 19.8 1.0
CE1 B:HIS339 3.0 18.1 1.0
CD2 B:HIS291 3.1 19.5 1.0
CD2 B:HIS339 3.1 18.3 1.0
CE1 B:HIS291 3.2 20.5 1.0
P B:TPO85 3.4 23.5 0.4
O2P B:TPO85 3.7 23.1 0.4
O B:HOH838 3.8 38.9 1.0
ND1 B:HIS339 4.2 18.9 1.0
CG B:HIS339 4.3 18.2 1.0
ND1 B:HIS291 4.3 20.3 1.0
CG B:HIS291 4.3 19.9 1.0
CB B:ASP286 4.3 17.6 1.0
CB B:ASP156 4.3 25.4 1.0
O3P B:TPO85 4.4 23.3 0.4
O B:HOH592 4.4 29.0 1.0
OG1 B:TPO85 4.4 20.6 1.0
ND2 B:ASN330 4.5 19.0 1.0
O B:HOH660 4.5 31.4 1.0
CE1 B:HIS328 4.6 17.0 1.0
NE2 B:HIS328 4.8 16.0 1.0
MN B:MN396 4.9 17.9 1.0
CA B:ASP156 5.0 24.8 1.0

Manganese binding site 5 out of 9 in 3m8z

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Manganese binding site 5 out of 9 in the Phosphopentomutase From Bacillus Cereus Bound with Ribose-5-Phosphate


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 with Ribose-5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn396

b:17.9
occ:1.00
 OD1 B:ASP13 2.1 15.9 1.0
OD2 B:ASP327 2.1 15.1 1.0
OG1 B:TPO85 2.2 20.6 1.0
NE2 B:HIS328 2.2 16.0 1.0
O2P B:TPO85 2.4 23.1 0.4
OD2 B:ASP13 2.5 17.5 1.0
CG B:ASP13 2.6 16.6 1.0
P B:TPO85 2.9 23.5 0.4
CG B:ASP327 2.9 14.8 1.0
OD1 B:ASP327 3.1 14.3 1.0
CD2 B:HIS328 3.1 16.2 1.0
CE1 B:HIS328 3.2 17.0 1.0
CB B:TPO85 3.3 18.6 1.0
CG2 B:TPO85 3.5 19.0 1.0
O1P B:TPO85 3.7 22.5 0.4
CA B:TPO85 3.7 18.1 1.0
CB B:ASP13 4.1 15.8 1.0
O3P B:TPO85 4.2 23.3 0.4
CG B:HIS328 4.2 16.5 1.0
ND1 B:HIS328 4.3 16.7 1.0
CE1 B:HIS339 4.4 18.1 1.0
CB B:ASP327 4.4 14.4 1.0
N B:SER14 4.4 15.9 1.0
N B:TPO85 4.4 18.2 1.0
CG B:ASP286 4.5 18.7 1.0
O B:HOH661 4.6 27.7 1.0
OD2 B:ASP286 4.6 19.8 1.0
CA B:ASP13 4.6 15.7 1.0
NE2 B:HIS89 4.7 16.5 1.0
OD1 B:ASP286 4.7 19.5 1.0
NE2 B:HIS339 4.7 16.9 1.0
C B:ASP13 4.8 16.0 1.0
CB B:ASP286 4.9 17.6 1.0
CD2 B:HIS89 4.9 13.3 1.0
C B:TPO85 4.9 17.4 1.0
MN B:MN395 4.9 18.4 1.0

Manganese binding site 6 out of 9 in 3m8z

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Manganese binding site 6 out of 9 in the Phosphopentomutase From Bacillus Cereus Bound with Ribose-5-Phosphate


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 with Ribose-5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn397

b:37.9
occ:0.75
 O B:HOH800 2.2 38.1 1.0
O B:HOH982 2.3 31.1 1.0
O B:HOH715 2.8 47.4 1.0
OE2 B:GLU318 4.0 35.4 1.0
O B:HOH510 4.1 29.5 1.0

Manganese binding site 7 out of 9 in 3m8z

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Manganese binding site 7 out of 9 in the Phosphopentomutase From Bacillus Cereus Bound with Ribose-5-Phosphate


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 with Ribose-5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn395

b:24.6
occ:1.00
 NE2 C:HIS339 2.1 27.2 1.0
NE2 C:HIS291 2.1 25.4 1.0
OD1 C:ASP286 2.2 27.7 1.0
O1P C:TPO85 2.4 26.3 0.4
OD2 C:ASP156 2.4 43.6 1.0
OD1 C:ASP156 2.7 42.1 1.0
CG C:ASP286 2.9 26.7 1.0
OD2 C:ASP286 2.9 27.6 1.0
CG C:ASP156 2.9 41.6 1.0
CE1 C:HIS339 3.0 27.8 1.0
CD2 C:HIS291 3.1 25.6 1.0
CE1 C:HIS291 3.1 26.2 1.0
CD2 C:HIS339 3.1 27.5 1.0
O3P C:TPO85 3.3 28.7 0.4
P C:TPO85 3.3 28.4 0.4
O C:HOH443 4.0 38.6 1.0
O C:HOH533 4.1 33.2 1.0
ND1 C:HIS339 4.1 28.2 1.0
ND1 C:HIS291 4.2 25.6 1.0
CG C:HIS291 4.2 26.9 1.0
CG C:HIS339 4.2 27.4 1.0
CB C:ASP286 4.3 26.0 1.0
O2P C:TPO85 4.3 27.0 0.4
ND2 C:ASN330 4.3 26.4 1.0
CB C:ASP156 4.4 39.2 1.0
OG1 C:TPO85 4.4 25.5 1.0
CE1 C:HIS328 4.5 23.1 1.0
O C:HOH855 4.7 39.0 1.0
NE2 C:HIS328 4.8 20.3 1.0

Manganese binding site 8 out of 9 in 3m8z

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Manganese binding site 8 out of 9 in the Phosphopentomutase From Bacillus Cereus Bound with Ribose-5-Phosphate


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 with Ribose-5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn396

b:24.4
occ:1.00
 OD2 C:ASP327 2.1 23.5 1.0
OD1 C:ASP13 2.1 22.6 1.0
OG1 C:TPO85 2.2 25.5 1.0
NE2 C:HIS328 2.2 20.3 1.0
OD2 C:ASP13 2.5 22.6 1.0
CG C:ASP13 2.6 23.5 1.0
O3P C:TPO85 2.7 28.7 0.4
CG C:ASP327 2.9 23.1 1.0
CD2 C:HIS328 3.0 21.9 1.0
OD1 C:ASP327 3.1 22.5 1.0
P C:TPO85 3.2 28.4 0.4
CB C:TPO85 3.2 25.3 1.0
CE1 C:HIS328 3.3 23.1 1.0
CA C:TPO85 3.6 24.9 1.0
CG2 C:TPO85 3.6 24.7 1.0
O1P C:TPO85 3.9 26.3 0.4
CB C:ASP13 4.0 22.9 1.0
N C:TPO85 4.2 25.6 1.0
CG C:HIS328 4.2 22.8 1.0
ND1 C:HIS328 4.3 22.5 1.0
O2P C:TPO85 4.3 27.0 0.4
N C:SER14 4.3 24.0 1.0
CB C:ASP327 4.4 23.0 1.0
NE2 C:HIS89 4.5 21.3 1.0
CA C:ASP13 4.6 23.6 1.0
CG C:ASP286 4.6 26.7 1.0
CE1 C:HIS339 4.6 27.8 1.0
OD2 C:ASP286 4.6 27.6 1.0
C C:ASP13 4.7 23.6 1.0
OD1 C:ASP286 4.8 27.7 1.0
CD2 C:HIS89 4.8 19.4 1.0
C C:TPO85 4.8 24.4 1.0
CB C:ASP286 4.9 26.0 1.0
NE2 C:HIS339 4.9 27.2 1.0

Manganese binding site 9 out of 9 in 3m8z

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Manganese binding site 9 out of 9 in the Phosphopentomutase From Bacillus Cereus Bound with Ribose-5-Phosphate


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 with Ribose-5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn397

b:34.6
occ:1.00
 O C:HOH424 2.1 34.2 1.0
OD1 C:ASP28 2.1 29.6 1.0
NE2 C:HIS334 2.2 29.5 1.0
O C:HOH483 2.2 30.5 1.0
O C:HOH444 2.3 26.9 1.0
O C:GLY27 2.5 34.1 1.0
CD2 C:HIS334 3.1 28.8 1.0
CE1 C:HIS334 3.2 29.8 1.0
CG C:ASP28 3.3 30.6 1.0
C C:GLY27 3.3 34.3 1.0
CA C:ASP28 3.8 32.3 1.0
N C:ASP28 3.9 33.5 1.0
O C:PHE26 4.0 35.9 1.0
O C:HOH448 4.1 27.8 1.0
CB C:ASP28 4.1 31.2 1.0
O C:HOH746 4.1 46.0 1.0
OD2 C:ASP28 4.2 28.8 1.0
CG C:HIS334 4.3 28.5 1.0
ND1 C:HIS334 4.3 28.9 1.0
CA C:GLY27 4.3 35.6 1.0
NZ C:LYS83 4.3 26.5 1.0
CG2 C:THR340 4.6 29.3 1.0
O C:HIS339 4.6 28.2 1.0
O C:HOH429 4.7 41.9 1.0
C C:PHE26 4.9 36.2 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 17:02:24 2024

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