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Manganese in PDB 3un3: Phosphopentomutase T85Q Variant Soaked with Glucose 1,6-Bisphosphate

Enzymatic activity of Phosphopentomutase T85Q Variant Soaked with Glucose 1,6-Bisphosphate

All present enzymatic activity of Phosphopentomutase T85Q Variant Soaked with Glucose 1,6-Bisphosphate:
5.4.2.7;

Protein crystallography data

The structure of Phosphopentomutase T85Q Variant Soaked with Glucose 1,6-Bisphosphate, PDB code: 3un3 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 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.560, 76.781, 106.770, 90.00, 108.55, 90.00
R / Rfree (%) 16.5 / 19.1

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Manganese atom in the Phosphopentomutase T85Q Variant Soaked with Glucose 1,6-Bisphosphate (pdb code 3un3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Phosphopentomutase T85Q Variant Soaked with Glucose 1,6-Bisphosphate, PDB code: 3un3:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 3un3

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Manganese binding site 1 out of 12 in the Phosphopentomutase T85Q Variant 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 Phosphopentomutase T85Q Variant Soaked with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn395

b:16.3
occ:1.00
 NE2 A:HIS339 2.1 16.1 1.0
OD1 A:ASP286 2.1 16.8 1.0
NE2 A:HIS291 2.2 15.1 1.0
OD2 A:ASP156 2.3 17.9 0.5
OD2 A:ASP286 2.5 16.5 1.0
O A:HOH922 2.6 13.0 1.0
CG A:ASP286 2.6 15.8 1.0
CE1 A:HIS339 3.1 17.1 1.0
CD2 A:HIS339 3.1 16.6 1.0
CD2 A:HIS291 3.1 15.9 1.0
CE1 A:HIS291 3.2 16.6 1.0
CG A:ASP156 3.2 21.3 0.5
OD1 A:ASP156 3.5 19.5 0.5
O A:HOH891 3.8 34.5 1.0
CB A:ASP286 4.1 14.7 1.0
ND2 A:ASN330 4.2 16.5 1.0
ND1 A:HIS339 4.2 16.4 1.0
CG A:HIS339 4.3 15.9 1.0
ND1 A:HIS291 4.3 15.9 1.0
CG A:HIS291 4.3 17.4 1.0
CE1 A:HIS328 4.4 15.5 1.0
CB A:ASP156 4.6 22.7 1.0
NE2 A:HIS328 4.6 15.2 1.0
O A:HOH647 4.6 29.9 1.0
MN A:MN396 4.8 16.4 1.0
O A:HOH446 5.0 29.6 1.0
OD1 A:ASP13 5.0 13.8 1.0

Manganese binding site 2 out of 12 in 3un3

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Manganese binding site 2 out of 12 in the Phosphopentomutase T85Q Variant 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 Phosphopentomutase T85Q Variant Soaked with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn396

b:16.4
occ:1.00
 OD2 A:ASP327 2.1 15.5 1.0
OD1 A:ASP13 2.1 13.8 1.0
OE1 A:GLN85 2.2 26.4 1.0
NE2 A:HIS328 2.3 15.2 1.0
OD2 A:ASP13 2.5 17.2 1.0
CG A:ASP13 2.6 14.5 1.0
O A:HOH922 2.7 13.0 1.0
CG A:ASP327 3.0 15.1 1.0
CD A:GLN85 3.2 23.9 1.0
CD2 A:HIS328 3.2 15.2 1.0
OD1 A:ASP327 3.2 15.9 1.0
CE1 A:HIS328 3.3 15.5 1.0
NE2 A:GLN85 3.7 25.7 1.0
CB A:ASP13 4.0 13.8 1.0
CA A:GLN85 4.2 18.5 1.0
CG A:GLN85 4.3 20.9 1.0
CB A:GLN85 4.3 19.1 1.0
CG A:HIS328 4.3 15.2 1.0
ND1 A:HIS328 4.3 13.7 1.0
N A:SER14 4.4 13.2 1.0
CB A:ASP327 4.4 13.7 1.0
NE2 A:HIS89 4.4 17.1 1.0
OD2 A:ASP286 4.5 16.5 1.0
CE1 A:HIS339 4.5 17.1 1.0
CG A:ASP286 4.5 15.8 1.0
CA A:ASP13 4.6 13.6 1.0
CD2 A:HIS89 4.7 13.8 1.0
C A:ASP13 4.7 13.7 1.0
NE2 A:HIS339 4.8 16.1 1.0
MN A:MN395 4.8 16.3 1.0
OD1 A:ASP286 4.8 16.8 1.0
CB A:ASP286 4.9 14.7 1.0
N A:GLN85 4.9 18.1 1.0

Manganese binding site 3 out of 12 in 3un3

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Manganese binding site 3 out of 12 in the Phosphopentomutase T85Q Variant 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 Phosphopentomutase T85Q Variant Soaked with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn397

b:25.6
occ:0.75
 O A:HOH426 2.0 30.3 1.0
NE2 A:HIS334 2.1 23.2 1.0
OD1 A:ASP28 2.1 22.2 1.0
O A:HOH547 2.3 28.5 1.0
O A:GLY27 2.4 26.1 1.0
CD2 A:HIS334 2.9 23.4 1.0
CE1 A:HIS334 3.2 24.1 1.0
C A:GLY27 3.3 26.0 1.0
CG A:ASP28 3.4 21.3 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 27.8 1.0
O A:HOH533 4.1 24.9 1.0
CB A:ASP28 4.1 21.1 1.0
CG A:HIS334 4.1 22.7 1.0
ND1 A:HIS334 4.2 23.6 1.0
OD2 A:ASP28 4.3 20.6 1.0
CA A:GLY27 4.4 27.6 1.0
CG2 A:THR340 4.4 17.9 1.0
NZ A:LYS83 4.5 18.2 1.0
O A:PRO335 4.5 24.3 1.0
O A:HIS339 4.8 17.0 1.0
C A:PHE26 4.9 27.7 1.0

Manganese binding site 4 out of 12 in 3un3

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Manganese binding site 4 out of 12 in the Phosphopentomutase T85Q Variant 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 Phosphopentomutase T85Q Variant Soaked with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn395

b:17.5
occ:1.00
 OD2 B:ASP156 2.1 25.0 1.0
NE2 B:HIS291 2.2 17.7 1.0
NE2 B:HIS339 2.2 15.4 1.0
OD1 B:ASP286 2.2 16.3 1.0
OD2 B:ASP286 2.6 16.8 1.0
O B:HOH923 2.7 16.3 1.0
CG B:ASP286 2.7 16.6 1.0
CE1 B:HIS291 3.1 18.5 1.0
CG B:ASP156 3.1 25.6 1.0
CE1 B:HIS339 3.1 17.4 1.0
CD2 B:HIS339 3.2 17.2 1.0
CD2 B:HIS291 3.2 17.7 1.0
OD1 B:ASP156 3.4 26.1 1.0
O B:HOH467 3.9 36.6 1.0
ND1 B:HIS291 4.2 18.8 1.0
CB B:ASP286 4.2 15.8 1.0
ND1 B:HIS339 4.3 16.6 1.0
CG B:HIS291 4.3 18.1 1.0
CG B:HIS339 4.3 16.8 1.0
ND2 B:ASN330 4.3 18.0 1.0
CE1 B:HIS328 4.5 17.2 1.0
CB B:ASP156 4.5 22.8 1.0
O B:HOH873 4.6 31.7 1.0
NE2 B:HIS328 4.7 16.9 1.0
MN B:MN396 4.9 16.5 1.0

Manganese binding site 5 out of 12 in 3un3

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Manganese binding site 5 out of 12 in the Phosphopentomutase T85Q Variant 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 Phosphopentomutase T85Q Variant Soaked with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn396

b:16.5
occ:1.00
 OD2 B:ASP327 2.1 17.0 1.0
OD1 B:ASP13 2.1 13.9 1.0
OE1 B:GLN85 2.2 27.8 1.0
NE2 B:HIS328 2.3 16.9 1.0
OD2 B:ASP13 2.5 17.5 1.0
O B:HOH923 2.6 16.3 1.0
CG B:ASP13 2.6 15.7 1.0
CG B:ASP327 3.0 14.1 1.0
CD B:GLN85 3.1 26.0 1.0
CD2 B:HIS328 3.2 16.8 1.0
OD1 B:ASP327 3.3 16.7 1.0
CE1 B:HIS328 3.3 17.2 1.0
NE2 B:GLN85 3.6 27.4 1.0
CB B:ASP13 4.1 15.1 1.0
CA B:GLN85 4.2 19.6 1.0
CG B:HIS328 4.3 16.7 1.0
CG B:GLN85 4.3 23.1 1.0
ND1 B:HIS328 4.3 17.4 1.0
CB B:GLN85 4.4 21.1 1.0
CB B:ASP327 4.4 14.4 1.0
N B:SER14 4.4 14.9 1.0
OD2 B:ASP286 4.4 16.8 1.0
NE2 B:HIS89 4.5 16.5 1.0
CG B:ASP286 4.5 16.6 1.0
CE1 B:HIS339 4.5 17.4 1.0
CA B:ASP13 4.6 14.8 1.0
NE2 B:HIS339 4.8 15.4 1.0
C B:ASP13 4.8 15.4 1.0
CD2 B:HIS89 4.8 13.2 1.0
OD1 B:ASP286 4.8 16.3 1.0
MN B:MN395 4.9 17.5 1.0
CB B:ASP286 4.9 15.8 1.0
N B:GLN85 4.9 19.1 1.0

Manganese binding site 6 out of 12 in 3un3

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Manganese binding site 6 out of 12 in the Phosphopentomutase T85Q Variant 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 Phosphopentomutase T85Q Variant Soaked with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn397

b:34.7
occ:0.75
 O B:HOH908 2.2 39.8 1.0
O B:HOH907 2.2 43.9 1.0
O B:HOH656 2.5 45.8 1.0
OE2 B:GLU318 4.1 35.8 1.0
O B:HOH503 4.2 29.4 1.0

Manganese binding site 7 out of 12 in 3un3

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Manganese binding site 7 out of 12 in the Phosphopentomutase T85Q Variant 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 Phosphopentomutase T85Q Variant Soaked with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn398

b:23.2
occ:0.50
 O B:HOH896 1.9 30.5 1.0
O C:HOH895 2.1 30.7 1.0
O C:HOH906 2.2 36.2 1.0
O B:HOH894 2.3 33.1 1.0
OE1 B:GLU248 2.4 21.4 1.0
O B:HOH412 2.8 14.1 1.0
CD B:GLU248 3.1 19.1 1.0
OE2 B:GLU248 3.2 18.8 1.0
O1X C:G16399 4.2 19.1 0.5
O1P C:G16399 4.2 20.3 0.5
NZ B:LYS218 4.3 21.4 1.0
CG B:GLU248 4.4 16.6 1.0
O5 C:G16399 4.4 20.5 0.5
O3X C:G16399 4.5 21.3 0.5
CA B:GLU248 4.7 15.8 1.0
O B:HOH465 4.8 30.6 1.0
C6 C:G16399 4.8 20.7 0.5
P' C:G16399 5.0 21.6 0.5
O B:GLY247 5.0 16.4 1.0

Manganese binding site 8 out of 12 in 3un3

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Manganese binding site 8 out of 12 in the Phosphopentomutase T85Q Variant 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 Phosphopentomutase T85Q Variant Soaked with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn399

b:26.5
occ:0.50
 O2X C:G16399 1.9 20.6 0.5
O B:HOH660 2.0 34.8 1.0
O C:HOH893 2.1 34.1 1.0
P' C:G16399 3.2 21.6 0.5
O3X C:G16399 3.5 21.3 0.5
O1X C:G16399 4.1 19.1 0.5
O C:HOH562 4.2 35.1 1.0
OD1 B:ASP246 4.2 18.9 1.0
OD2 B:ASP246 4.2 21.0 1.0
O1 C:G16399 4.4 20.7 0.5
CG B:ASP246 4.5 19.7 1.0
O B:HOH825 4.6 29.0 1.0
CE C:LYS229 4.7 23.8 1.0
O B:ASP246 4.7 15.6 1.0
NZ B:LYS218 4.8 21.4 1.0
O B:HOH874 4.8 24.4 1.0
NZ C:LYS229 4.9 27.0 1.0

Manganese binding site 9 out of 12 in 3un3

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Manganese binding site 9 out of 12 in the Phosphopentomutase T85Q Variant 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 9 of Phosphopentomutase T85Q Variant Soaked with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn395

b:21.7
occ:1.00
 OD2 C:ASP156 2.1 37.6 1.0
NE2 C:HIS339 2.1 23.0 1.0
NE2 C:HIS291 2.1 22.3 1.0
OD1 C:ASP286 2.2 23.6 1.0
OD2 C:ASP286 2.6 24.3 1.0
CG C:ASP286 2.7 22.5 1.0
O C:HOH401 2.8 27.5 1.0
CG C:ASP156 3.1 36.0 1.0
CE1 C:HIS339 3.1 22.7 1.0
CE1 C:HIS291 3.1 23.0 1.0
CD2 C:HIS291 3.1 23.1 1.0
CD2 C:HIS339 3.2 23.9 1.0
OD1 C:ASP156 3.3 36.5 1.0
O C:HOH462 3.9 48.1 1.0
CB C:ASP286 4.2 22.6 1.0
O C:HOH611 4.2 33.4 1.0
ND1 C:HIS339 4.2 23.0 1.0
ND1 C:HIS291 4.2 24.4 1.0
ND2 C:ASN330 4.3 24.7 1.0
CG C:HIS291 4.3 24.3 1.0
CG C:HIS339 4.3 23.2 1.0
CB C:ASP156 4.5 33.6 1.0
CE1 C:HIS328 4.5 22.1 1.0
O C:HOH469 4.6 31.5 1.0
NE2 C:HIS328 4.7 20.9 1.0
MN C:MN396 4.9 22.7 1.0

Manganese binding site 10 out of 12 in 3un3

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Manganese binding site 10 out of 12 in the Phosphopentomutase T85Q Variant 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 10 of Phosphopentomutase T85Q Variant Soaked with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn396

b:22.7
occ:1.00
 OD2 C:ASP327 2.0 21.9 1.0
OE1 C:GLN85 2.1 23.8 0.5
OD1 C:ASP13 2.1 22.8 1.0
NE2 C:HIS328 2.3 20.9 1.0
OD2 C:ASP13 2.5 22.1 1.0
O C:HOH401 2.5 27.5 1.0
CG C:ASP13 2.6 21.9 1.0
CG C:ASP327 3.0 21.9 1.0
CD2 C:HIS328 3.1 21.8 1.0
CD C:GLN85 3.2 22.7 0.5
OD1 C:ASP327 3.2 23.9 1.0
CE1 C:HIS328 3.3 22.1 1.0
NE2 C:GLN85 3.8 22.3 0.5
CB C:ASP13 4.0 21.7 1.0
CA C:GLN85 4.1 22.8 0.5
CA C:GLN85 4.1 22.7 0.5
CB C:GLN85 4.1 23.1 0.5
CG C:HIS328 4.3 22.9 1.0
CG C:GLN85 4.3 23.3 0.5
CG C:GLN85 4.3 22.8 0.5
CB C:GLN85 4.3 23.0 0.5
CB C:ASP327 4.4 21.6 1.0
ND1 C:HIS328 4.4 22.8 1.0
N C:SER14 4.4 22.8 1.0
NE2 C:HIS89 4.4 21.6 1.0
CE1 C:HIS339 4.5 22.7 1.0
OD2 C:ASP286 4.5 24.3 1.0
CA C:ASP13 4.6 22.1 1.0
CG C:ASP286 4.6 22.5 1.0
C C:ASP13 4.7 22.6 1.0
CD2 C:HIS89 4.8 18.9 1.0
N C:GLN85 4.8 23.3 0.5
N C:GLN85 4.8 23.2 0.5
NE2 C:HIS339 4.9 23.0 1.0
CB C:ASP286 4.9 22.6 1.0
OD1 C:ASP286 4.9 23.6 1.0
MN C:MN395 4.9 21.7 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 18:07:36 2024

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