Atomistry » Manganese » PDB 3m0m-3n37 » 3m8z
Atomistry »
  Manganese »
    PDB 3m0m-3n37 »
      3m8z »

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

Go back to Manganese Binding Sites List in 3m8z
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

Go back to Manganese Binding Sites List in 3m8z
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

Go back to Manganese Binding Sites List in 3m8z
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

Go back to Manganese Binding Sites List in 3m8z
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

Go back to Manganese Binding Sites List in 3m8z
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

Go back to Manganese Binding Sites List in 3m8z
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

Go back to Manganese Binding Sites List in 3m8z
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

Go back to Manganese Binding Sites List in 3m8z
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

Go back to Manganese Binding Sites List in 3m8z
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: Tue Dec 15 04:12:21 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy