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Manganese in PDB 4lrb: Phosphopentomutase S154G Variant Soaked with 2,3-Dideoxyribose 5- Phosphate

Enzymatic activity of Phosphopentomutase S154G Variant Soaked with 2,3-Dideoxyribose 5- Phosphate

All present enzymatic activity of Phosphopentomutase S154G Variant Soaked with 2,3-Dideoxyribose 5- Phosphate:
5.4.2.7;

Protein crystallography data

The structure of Phosphopentomutase S154G Variant Soaked with 2,3-Dideoxyribose 5- Phosphate, PDB code: 4lrb was solved by W.A.Birmingham, C.A.Starbird, T.D.Panosian, D.P.Nannemann, T.M.Iverson, B.O.Bachmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.226, 76.774, 106.486, 90.00, 108.32, 90.00
R / Rfree (%) 16.9 / 20.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Phosphopentomutase S154G Variant Soaked with 2,3-Dideoxyribose 5- Phosphate (pdb code 4lrb). 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 S154G Variant Soaked with 2,3-Dideoxyribose 5- Phosphate, PDB code: 4lrb:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 4lrb

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Manganese binding site 1 out of 9 in the Phosphopentomutase S154G Variant Soaked with 2,3-Dideoxyribose 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 S154G Variant Soaked with 2,3-Dideoxyribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:14.3
occ:1.00
 O1P A:TPO85 2.0 21.8 0.3
NE2 A:HIS291 2.1 13.9 1.0
OD1 A:ASP286 2.1 14.6 1.0
NE2 A:HIS339 2.2 13.5 1.0
OD2 A:ASP156 2.2 24.1 1.0
OD1 A:ASP156 2.7 25.4 1.0
OD2 A:ASP286 2.8 13.8 1.0
CG A:ASP286 2.8 13.8 1.0
CG A:ASP156 2.8 24.4 1.0
CD2 A:HIS291 3.0 14.3 1.0
CE1 A:HIS291 3.1 14.8 1.0
CE1 A:HIS339 3.1 13.8 1.0
CD2 A:HIS339 3.2 13.8 1.0
P A:TPO85 3.3 21.6 0.3
O2P A:TPO85 3.7 22.9 0.3
ND1 A:HIS291 4.2 15.2 1.0
CG A:HIS291 4.2 15.2 1.0
O3P A:TPO85 4.2 21.2 0.3
ND1 A:HIS339 4.3 13.8 1.0
CB A:ASP286 4.3 13.0 1.0
CG A:HIS339 4.3 13.8 1.0
ND2 A:ASN330 4.3 12.4 1.0
OG1 A:TPO85 4.3 20.5 1.0
CB A:ASP156 4.4 23.7 1.0
O A:HOH636 4.4 24.2 1.0
O A:HOH735 4.5 23.9 1.0
CE1 A:HIS328 4.6 11.1 1.0
O A:HOH784 4.8 39.5 1.0
NE2 A:HIS328 4.8 11.0 1.0
MN A:MN402 5.0 14.2 1.0
CA A:ASP156 5.0 23.6 1.0
O A:HOH835 5.0 29.0 1.0

Manganese binding site 2 out of 9 in 4lrb

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Manganese binding site 2 out of 9 in the Phosphopentomutase S154G Variant Soaked with 2,3-Dideoxyribose 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 S154G Variant Soaked with 2,3-Dideoxyribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:14.2
occ:1.00
 OD2 A:ASP327 2.1 12.1 1.0
OD1 A:ASP13 2.1 12.3 1.0
OG1 A:TPO85 2.2 20.5 1.0
NE2 A:HIS328 2.2 11.0 1.0
OD2 A:ASP13 2.5 12.5 1.0
CG A:ASP13 2.6 12.2 1.0
O2P A:TPO85 2.9 22.9 0.3
CG A:ASP327 2.9 11.6 1.0
CD2 A:HIS328 3.0 11.0 1.0
OD1 A:ASP327 3.1 11.4 1.0
P A:TPO85 3.1 21.6 0.3
CB A:TPO85 3.2 19.4 1.0
CE1 A:HIS328 3.2 11.1 1.0
CG2 A:TPO85 3.5 19.4 1.0
CA A:TPO85 3.6 18.6 1.0
O1P A:TPO85 3.7 21.8 0.3
CB A:ASP13 4.1 11.8 1.0
CG A:HIS328 4.2 11.1 1.0
ND1 A:HIS328 4.3 11.1 1.0
N A:TPO85 4.3 18.5 1.0
O3P A:TPO85 4.4 21.2 0.3
CB A:ASP327 4.4 11.2 1.0
N A:SER14 4.4 11.1 1.0
CE1 A:HIS339 4.4 13.8 1.0
CG A:ASP286 4.5 13.8 1.0
O A:HOH668 4.5 35.5 1.0
CA A:ASP13 4.6 11.4 1.0
OD2 A:ASP286 4.6 13.8 1.0
NE2 A:HIS89 4.6 16.5 1.0
OD1 A:ASP286 4.7 14.6 1.0
C A:ASP13 4.7 11.3 1.0
NE2 A:HIS339 4.7 13.5 1.0
C A:TPO85 4.8 17.8 1.0
CD2 A:HIS89 4.9 15.4 1.0
CB A:ASP286 4.9 13.0 1.0
MN A:MN401 5.0 14.3 1.0

Manganese binding site 3 out of 9 in 4lrb

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Manganese binding site 3 out of 9 in the Phosphopentomutase S154G Variant Soaked with 2,3-Dideoxyribose 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 S154G Variant Soaked with 2,3-Dideoxyribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:38.2
occ:0.75
 OD1 A:ASP28 2.0 21.2 1.0
O A:HOH502 2.1 29.4 1.0
O A:HOH501 2.3 24.8 1.0
NE2 A:HIS334 2.3 22.0 1.0
O A:GLY27 2.8 24.5 1.0
CD2 A:HIS334 2.9 21.4 1.0
CG A:ASP28 3.3 20.4 1.0
CE1 A:HIS334 3.5 22.1 1.0
C A:GLY27 3.5 24.5 1.0
CA A:ASP28 3.9 21.8 1.0
O A:PHE26 3.9 25.4 1.0
N A:ASP28 4.0 23.2 1.0
O A:HOH589 4.0 20.1 1.0
OD2 A:ASP28 4.1 19.8 1.0
CB A:ASP28 4.2 20.7 1.0
CG A:HIS334 4.2 20.9 1.0
NZ A:LYS83 4.2 24.8 1.0
ND1 A:HIS334 4.4 21.4 1.0
CA A:GLY27 4.4 26.1 1.0
CG2 A:THR340 4.4 15.0 1.0
O A:HIS339 4.5 14.9 1.0
O A:PRO335 4.7 21.6 1.0
C A:PHE26 4.8 25.7 1.0

Manganese binding site 4 out of 9 in 4lrb

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Manganese binding site 4 out of 9 in the Phosphopentomutase S154G Variant Soaked with 2,3-Dideoxyribose 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 S154G Variant Soaked with 2,3-Dideoxyribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:16.9
occ:1.00
 O1P B:TPO85 2.1 20.3 0.3
NE2 B:HIS339 2.1 14.9 1.0
OD1 B:ASP286 2.1 16.8 1.0
NE2 B:HIS291 2.2 17.8 1.0
OD2 B:ASP156 2.2 30.4 1.0
OD1 B:ASP156 2.7 31.1 1.0
CG B:ASP156 2.8 29.5 1.0
CG B:ASP286 2.8 16.5 1.0
OD2 B:ASP286 2.8 16.6 1.0
CE1 B:HIS339 3.1 14.7 1.0
CD2 B:HIS291 3.1 18.1 1.0
CD2 B:HIS339 3.1 15.4 1.0
CE1 B:HIS291 3.1 18.5 1.0
P B:TPO85 3.4 19.9 0.3
O2P B:TPO85 3.8 19.5 0.3
ND1 B:HIS339 4.2 15.1 1.0
ND1 B:HIS291 4.2 19.4 1.0
CG B:HIS339 4.3 15.4 1.0
CG B:HIS291 4.3 19.0 1.0
CB B:ASP156 4.3 26.8 1.0
CB B:ASP286 4.3 15.5 1.0
O3P B:TPO85 4.4 20.4 0.3
ND2 B:ASN330 4.4 16.6 1.0
OG1 B:TPO85 4.4 18.4 1.0
O B:HOH743 4.5 22.1 1.0
CE1 B:HIS328 4.6 12.8 1.0
O B:HOH549 4.6 27.5 1.0
NE2 B:HIS328 4.8 12.5 1.0
CA B:ASP156 4.9 26.2 1.0
MN B:MN402 4.9 16.3 1.0
O B:HOH739 5.0 49.4 1.0

Manganese binding site 5 out of 9 in 4lrb

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Manganese binding site 5 out of 9 in the Phosphopentomutase S154G Variant Soaked with 2,3-Dideoxyribose 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 S154G Variant Soaked with 2,3-Dideoxyribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:16.3
occ:1.00
 OD2 B:ASP327 2.1 12.2 1.0
OG1 B:TPO85 2.1 18.4 1.0
OD1 B:ASP13 2.2 14.9 1.0
NE2 B:HIS328 2.3 12.5 1.0
OD2 B:ASP13 2.5 14.9 1.0
O2P B:TPO85 2.6 19.5 0.3
CG B:ASP13 2.6 14.8 1.0
P B:TPO85 2.9 19.9 0.3
CG B:ASP327 2.9 11.8 1.0
CD2 B:HIS328 3.1 12.5 1.0
OD1 B:ASP327 3.1 11.7 1.0
CB B:TPO85 3.2 17.7 1.0
CE1 B:HIS328 3.3 12.8 1.0
CG2 B:TPO85 3.5 17.4 1.0
CA B:TPO85 3.7 16.9 1.0
O1P B:TPO85 3.7 20.3 0.3
CB B:ASP13 4.1 14.6 1.0
O3P B:TPO85 4.2 20.4 0.3
CG B:HIS328 4.3 13.1 1.0
ND1 B:HIS328 4.3 13.1 1.0
CB B:ASP327 4.3 11.6 1.0
N B:TPO85 4.4 17.0 1.0
CE1 B:HIS339 4.4 14.7 1.0
O B:HOH655 4.4 25.7 1.0
N B:SER14 4.4 14.3 1.0
CG B:ASP286 4.5 16.5 1.0
NE2 B:HIS89 4.6 11.9 1.0
OD2 B:ASP286 4.6 16.6 1.0
CA B:ASP13 4.6 14.0 1.0
OD1 B:ASP286 4.7 16.8 1.0
NE2 B:HIS339 4.8 14.9 1.0
C B:ASP13 4.8 14.6 1.0
CD2 B:HIS89 4.8 11.6 1.0
C B:TPO85 4.9 16.6 1.0
CB B:ASP286 4.9 15.5 1.0
MN B:MN401 4.9 16.9 1.0

Manganese binding site 6 out of 9 in 4lrb

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Manganese binding site 6 out of 9 in the Phosphopentomutase S154G Variant Soaked with 2,3-Dideoxyribose 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 S154G Variant Soaked with 2,3-Dideoxyribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn403

b:63.2
occ:0.75
 O B:HOH842 3.3 48.7 1.0
O B:HOH757 3.3 30.6 1.0
O B:HOH643 3.4 39.2 1.0
OE2 B:GLU318 4.2 30.5 1.0
O B:HOH653 4.4 29.0 1.0

Manganese binding site 7 out of 9 in 4lrb

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Manganese binding site 7 out of 9 in the Phosphopentomutase S154G Variant Soaked with 2,3-Dideoxyribose 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 S154G Variant Soaked with 2,3-Dideoxyribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:23.4
occ:1.00
 O2P C:TPO85 2.0 28.1 0.3
OD1 C:ASP286 2.0 25.7 1.0
NE2 C:HIS339 2.1 26.5 1.0
NE2 C:HIS291 2.1 26.1 1.0
OD2 C:ASP156 2.3 52.6 1.0
OD1 C:ASP156 2.8 49.0 1.0
CG C:ASP286 2.8 27.0 1.0
OD2 C:ASP286 2.8 27.7 1.0
CG C:ASP156 2.9 48.9 1.0
CE1 C:HIS339 3.0 26.4 1.0
CD2 C:HIS339 3.1 27.8 1.0
CD2 C:HIS291 3.1 26.8 1.0
CE1 C:HIS291 3.1 26.8 1.0
P C:TPO85 3.4 27.6 0.3
O1P C:TPO85 4.0 27.6 0.3
O C:HOH602 4.1 30.0 1.0
O3P C:TPO85 4.1 26.7 0.3
ND1 C:HIS339 4.2 27.4 1.0
CG C:HIS339 4.2 28.4 1.0
CB C:ASP286 4.2 27.6 1.0
ND1 C:HIS291 4.2 27.6 1.0
CG C:HIS291 4.2 27.7 1.0
ND2 C:ASN330 4.3 28.4 1.0
OG1 C:TPO85 4.3 27.5 1.0
CB C:ASP156 4.4 44.6 1.0
CE1 C:HIS328 4.5 26.6 1.0
O C:HOH629 4.6 29.1 1.0
NE2 C:HIS328 4.8 25.4 1.0
CA C:ASP156 4.9 45.4 1.0

Manganese binding site 8 out of 9 in 4lrb

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Manganese binding site 8 out of 9 in the Phosphopentomutase S154G Variant Soaked with 2,3-Dideoxyribose 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 S154G Variant Soaked with 2,3-Dideoxyribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:25.3
occ:1.00
 OD1 C:ASP13 2.0 24.9 1.0
OD2 C:ASP327 2.2 25.0 1.0
OG1 C:TPO85 2.2 27.5 1.0
NE2 C:HIS328 2.2 25.4 1.0
CG C:ASP13 2.6 25.0 1.0
OD2 C:ASP13 2.7 23.9 1.0
CG C:ASP327 2.9 26.1 1.0
CD2 C:HIS328 3.0 26.4 1.0
OD1 C:ASP327 3.0 26.9 1.0
O1P C:TPO85 3.0 27.6 0.3
CB C:TPO85 3.1 26.5 1.0
P C:TPO85 3.2 27.6 0.3
CE1 C:HIS328 3.3 26.6 1.0
CG2 C:TPO85 3.5 25.8 1.0
CA C:TPO85 3.5 26.6 1.0
O2P C:TPO85 3.6 28.1 0.3
CB C:ASP13 4.1 26.0 1.0
N C:TPO85 4.1 27.1 1.0
CG C:HIS328 4.2 28.2 1.0
ND1 C:HIS328 4.3 28.2 1.0
CB C:ASP327 4.4 27.0 1.0
N C:SER14 4.4 29.4 1.0
O3P C:TPO85 4.5 26.7 0.3
CA C:ASP13 4.6 27.7 1.0
CE1 C:HIS339 4.6 26.4 1.0
CG C:ASP286 4.6 27.0 1.0
NE2 C:HIS89 4.6 23.5 1.0
OD2 C:ASP286 4.6 27.7 1.0
C C:TPO85 4.7 26.2 1.0
C C:ASP13 4.7 28.8 1.0
CD2 C:HIS89 4.8 23.2 1.0
OD1 C:ASP286 4.8 25.7 1.0
NE2 C:HIS339 4.9 26.5 1.0
CB C:ASP286 4.9 27.6 1.0
C C:ASP84 5.0 28.3 1.0
O C:TPO85 5.0 26.1 1.0

Manganese binding site 9 out of 9 in 4lrb

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Manganese binding site 9 out of 9 in the Phosphopentomutase S154G Variant Soaked with 2,3-Dideoxyribose 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 S154G Variant Soaked with 2,3-Dideoxyribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn403

b:46.2
occ:1.00
 O C:HOH665 2.1 36.1 1.0
OD1 C:ASP28 2.2 39.3 1.0
NE2 C:HIS334 2.3 41.5 1.0
O C:HOH623 2.3 28.4 1.0
O C:HOH547 2.3 30.5 1.0
O C:GLY27 2.6 44.1 1.0
CD2 C:HIS334 3.1 39.9 1.0
CE1 C:HIS334 3.3 43.8 1.0
C C:GLY27 3.4 45.2 1.0
CG C:ASP28 3.5 40.1 1.0
CA C:ASP28 3.9 44.8 1.0
O C:PHE26 4.0 42.6 1.0
N C:ASP28 4.0 45.6 1.0
O C:HOH554 4.0 29.8 1.0
CB C:ASP28 4.2 43.0 1.0
CG C:HIS334 4.3 41.2 1.0
CA C:GLY27 4.3 46.2 1.0
ND1 C:HIS334 4.3 43.8 1.0
OD2 C:ASP28 4.4 38.9 1.0
NZ C:LYS83 4.4 35.5 1.0
CG2 C:THR340 4.6 38.6 1.0
O C:HIS339 4.6 33.2 1.0
O C:PRO335 4.9 37.2 1.0
C C:PHE26 4.9 44.5 1.0

Reference:

W.R.Birmingham, C.A.Starbird, T.D.Panosian, D.P.Nannemann, T.M.Iverson, B.O.Bachmann. Bioretrosynthetic Construction of A Didanosine Biosynthetic Pathway. Nat.Chem.Biol. V. 10 392 2014.
ISSN: ISSN 1552-4450
PubMed: 24657930
DOI: 10.1038/NCHEMBIO.1494
Page generated: Sat Oct 5 20:08:59 2024

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