Atomistry » Manganese » PDB 3uag-3vnm » 3uo0
Atomistry »
  Manganese »
    PDB 3uag-3vnm »
      3uo0 »

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

Go back to Manganese Binding Sites List in 3uo0
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

Go back to Manganese Binding Sites List in 3uo0
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

Go back to Manganese Binding Sites List in 3uo0
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

Go back to Manganese Binding Sites List in 3uo0
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

Go back to Manganese Binding Sites List in 3uo0
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

Go back to Manganese Binding Sites List in 3uo0
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

Go back to Manganese Binding Sites List in 3uo0
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

Go back to Manganese Binding Sites List in 3uo0
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy