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Manganese in PDB 4lr9: Phosphopentomutase S154A Variant Soaked with 2,3-Dideoxyribose 5- Phosphate

Enzymatic activity of Phosphopentomutase S154A Variant Soaked with 2,3-Dideoxyribose 5- Phosphate

All present enzymatic activity of Phosphopentomutase S154A Variant Soaked with 2,3-Dideoxyribose 5- Phosphate:
5.4.2.7;

Protein crystallography data

The structure of Phosphopentomutase S154A Variant Soaked with 2,3-Dideoxyribose 5- Phosphate, PDB code: 4lr9 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 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.329, 76.615, 107.236, 90.00, 108.96, 90.00
R / Rfree (%) 16.9 / 21.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Phosphopentomutase S154A Variant Soaked with 2,3-Dideoxyribose 5- Phosphate (pdb code 4lr9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 10 binding sites of Manganese where determined in the Phosphopentomutase S154A Variant Soaked with 2,3-Dideoxyribose 5- Phosphate, PDB code: 4lr9:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 4lr9

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Manganese binding site 1 out of 10 in the Phosphopentomutase S154A 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 S154A Variant Soaked with 2,3-Dideoxyribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:16.6
occ:1.00
 O1P A:TPO85 1.8 26.3 0.3
NE2 A:HIS339 2.1 17.5 1.0
NE2 A:HIS291 2.1 18.9 1.0
OD1 A:ASP286 2.1 18.2 1.0
OD2 A:ASP156 2.2 31.0 1.0
OD2 A:ASP286 2.7 17.5 1.0
CG A:ASP286 2.8 17.8 1.0
OD1 A:ASP156 2.8 31.7 1.0
CG A:ASP156 2.9 30.6 1.0
CE1 A:HIS339 3.0 18.0 1.0
CD2 A:HIS291 3.0 18.9 1.0
CE1 A:HIS291 3.1 19.2 1.0
CD2 A:HIS339 3.1 17.4 1.0
P A:TPO85 3.2 26.0 0.3
O2P A:TPO85 3.7 26.8 0.3
O3P A:TPO85 4.0 25.3 0.3
ND1 A:HIS339 4.2 17.9 1.0
OG1 A:TPO85 4.2 24.6 1.0
ND1 A:HIS291 4.2 19.6 1.0
O A:HOH594 4.2 35.4 1.0
CG A:HIS291 4.2 19.6 1.0
CG A:HIS339 4.2 17.5 1.0
CB A:ASP286 4.2 17.3 1.0
ND2 A:ASN330 4.3 18.1 1.0
CB A:ASP156 4.4 28.7 1.0
CE1 A:HIS328 4.5 16.2 1.0
NE2 A:HIS328 4.9 16.4 1.0
CA A:ASP156 5.0 27.9 1.0
MN A:MN402 5.0 17.4 1.0
O A:HOH724 5.0 31.3 1.0

Manganese binding site 2 out of 10 in 4lr9

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Manganese binding site 2 out of 10 in the Phosphopentomutase S154A 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 S154A Variant Soaked with 2,3-Dideoxyribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:17.4
occ:1.00
 OD2 A:ASP327 2.1 15.2 1.0
OD1 A:ASP13 2.1 15.9 1.0
NE2 A:HIS328 2.2 16.4 1.0
OG1 A:TPO85 2.2 24.6 1.0
OD2 A:ASP13 2.6 16.2 1.0
CG A:ASP13 2.6 15.8 1.0
CG A:ASP327 2.9 14.9 1.0
OD1 A:ASP327 3.0 14.3 1.0
CB A:TPO85 3.1 23.6 1.0
CE1 A:HIS328 3.1 16.2 1.0
CD2 A:HIS328 3.1 16.0 1.0
O2P A:TPO85 3.3 26.8 0.3
P A:TPO85 3.3 26.0 0.3
CG2 A:TPO85 3.3 23.2 1.0
CA A:TPO85 3.5 22.1 1.0
O1P A:TPO85 3.8 26.3 0.3
CB A:ASP13 4.1 15.4 1.0
ND1 A:HIS328 4.2 16.1 1.0
N A:TPO85 4.2 22.4 1.0
CG A:HIS328 4.2 16.1 1.0
N A:SER14 4.3 15.1 1.0
CB A:ASP327 4.3 14.6 1.0
CG A:ASP286 4.5 17.8 1.0
OD2 A:ASP286 4.5 17.5 1.0
CE1 A:HIS339 4.5 18.0 1.0
CA A:ASP13 4.5 15.0 1.0
O3P A:TPO85 4.6 25.3 0.3
O A:HOH665 4.6 50.1 1.0
NE2 A:HIS89 4.6 18.3 1.0
C A:ASP13 4.7 15.1 1.0
OD1 A:ASP286 4.7 18.2 1.0
C A:TPO85 4.8 21.2 1.0
NE2 A:HIS339 4.8 17.5 1.0
CD2 A:HIS89 4.8 17.1 1.0
CB A:ASP286 4.9 17.3 1.0
CA A:SER14 5.0 15.5 1.0
CB A:SER14 5.0 15.9 1.0
MN A:MN401 5.0 16.6 1.0

Manganese binding site 3 out of 10 in 4lr9

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Manganese binding site 3 out of 10 in the Phosphopentomutase S154A 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 S154A Variant Soaked with 2,3-Dideoxyribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:44.0
occ:0.75
 NE2 A:HIS334 2.3 24.2 1.0
OD1 A:ASP28 2.3 23.8 1.0
O A:GLY27 2.7 29.6 1.0
CD2 A:HIS334 2.9 23.6 1.0
CE1 A:HIS334 3.5 24.2 1.0
C A:GLY27 3.6 29.6 1.0
CG A:ASP28 3.6 23.5 1.0
O A:HOH516 3.9 26.7 1.0
O A:PHE26 4.0 32.1 1.0
CA A:ASP28 4.1 25.7 1.0
N A:ASP28 4.2 27.4 1.0
CG A:HIS334 4.2 23.2 1.0
NZ A:LYS83 4.3 26.9 1.0
ND1 A:HIS334 4.4 23.7 1.0
OD2 A:ASP28 4.4 22.9 1.0
CB A:ASP28 4.5 23.7 1.0
CG2 A:THR340 4.5 18.0 1.0
CA A:GLY27 4.5 31.6 1.0
O A:HIS339 4.7 18.1 1.0
O A:PRO335 4.7 26.3 1.0
O A:HOH738 4.8 35.1 1.0
C A:PHE26 4.9 31.9 1.0

Manganese binding site 4 out of 10 in 4lr9

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Manganese binding site 4 out of 10 in the Phosphopentomutase S154A 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 S154A Variant Soaked with 2,3-Dideoxyribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:17.7
occ:1.00
 O1P B:TPO85 1.8 26.1 0.3
NE2 B:HIS339 2.1 18.6 1.0
OD1 B:ASP286 2.1 21.3 1.0
NE2 B:HIS291 2.1 20.1 1.0
OD2 B:ASP156 2.2 38.3 1.0
CG B:ASP286 2.8 20.9 1.0
OD2 B:ASP286 2.9 20.7 1.0
CE1 B:HIS339 2.9 18.9 1.0
CG B:ASP156 3.1 36.7 1.0
CD2 B:HIS291 3.1 20.4 1.0
CE1 B:HIS291 3.1 20.9 1.0
CD2 B:HIS339 3.2 19.4 1.0
P B:TPO85 3.2 26.0 0.3
OD1 B:ASP156 3.2 38.0 1.0
O3P B:TPO85 3.9 26.4 0.3
O2P B:TPO85 3.9 26.3 0.3
ND1 B:HIS339 4.1 19.2 1.0
CG B:HIS291 4.2 21.0 1.0
ND1 B:HIS291 4.2 21.2 1.0
CG B:HIS339 4.2 19.6 1.0
OG1 B:TPO85 4.3 24.6 1.0
CB B:ASP286 4.3 20.1 1.0
ND2 B:ASN330 4.3 21.0 1.0
O B:HOH566 4.4 33.2 1.0
CB B:ASP156 4.5 33.3 1.0
CE1 B:HIS328 4.5 15.4 1.0
NE2 B:HIS328 4.7 15.1 1.0
MN B:MN402 5.0 18.2 1.0

Manganese binding site 5 out of 10 in 4lr9

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Manganese binding site 5 out of 10 in the Phosphopentomutase S154A 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 S154A Variant Soaked with 2,3-Dideoxyribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:18.2
occ:1.00
 OD1 B:ASP13 2.1 21.3 1.0
OG1 B:TPO85 2.1 24.6 1.0
OD2 B:ASP327 2.1 16.2 1.0
NE2 B:HIS328 2.1 15.1 1.0
OD2 B:ASP13 2.6 21.8 1.0
CG B:ASP13 2.6 21.3 1.0
CD2 B:HIS328 3.0 15.1 1.0
CG B:ASP327 3.0 15.4 1.0
CB B:TPO85 3.0 24.2 1.0
CE1 B:HIS328 3.1 15.4 1.0
OD1 B:ASP327 3.2 15.1 1.0
P B:TPO85 3.2 26.0 0.3
CG2 B:TPO85 3.3 24.2 1.0
O2P B:TPO85 3.4 26.3 0.3
CA B:TPO85 3.4 23.0 1.0
O1P B:TPO85 3.5 26.1 0.3
CB B:ASP13 4.1 20.5 1.0
CG B:HIS328 4.1 15.7 1.0
N B:TPO85 4.2 23.4 1.0
ND1 B:HIS328 4.2 15.6 1.0
N B:SER14 4.4 17.9 1.0
CB B:ASP327 4.4 14.7 1.0
O B:HOH721 4.4 35.3 1.0
O3P B:TPO85 4.5 26.4 0.3
CG B:ASP286 4.5 20.9 1.0
CE1 B:HIS339 4.6 18.9 1.0
OD2 B:ASP286 4.6 20.7 1.0
CA B:ASP13 4.6 18.8 1.0
NE2 B:HIS89 4.6 20.1 1.0
OD1 B:ASP286 4.7 21.3 1.0
C B:TPO85 4.7 22.7 1.0
C B:ASP13 4.7 19.0 1.0
NE2 B:HIS339 4.8 18.6 1.0
CD2 B:HIS89 4.9 18.7 1.0
CB B:ASP286 4.9 20.1 1.0
O B:TPO85 5.0 21.5 1.0
MN B:MN401 5.0 17.7 1.0

Manganese binding site 6 out of 10 in 4lr9

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Manganese binding site 6 out of 10 in the Phosphopentomutase S154A 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 S154A Variant Soaked with 2,3-Dideoxyribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn403

b:49.5
occ:0.75
 OE2 B:GLU318 3.9 38.9 1.0
O B:HOH583 4.0 27.4 1.0
CB B:PRO351 4.9 22.5 1.0

Manganese binding site 7 out of 10 in 4lr9

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Manganese binding site 7 out of 10 in the Phosphopentomutase S154A 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 S154A Variant Soaked with 2,3-Dideoxyribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn404

b:59.0
occ:0.50
 O B:HOH720 2.5 50.9 1.0
NE2 B:HIS36 2.6 27.6 1.0
CD2 B:HIS36 3.5 27.0 1.0
CE1 B:HIS36 3.6 26.6 1.0
O B:HOH751 4.0 47.2 1.0
OE1 B:GLU39 4.3 32.8 0.5
O B:GLY30 4.6 28.5 1.0
CG B:HIS36 4.7 25.8 1.0
ND1 B:HIS36 4.7 25.7 1.0

Manganese binding site 8 out of 10 in 4lr9

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Manganese binding site 8 out of 10 in the Phosphopentomutase S154A 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 S154A Variant Soaked with 2,3-Dideoxyribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:23.0
occ:1.00
 O3P C:TPO85 1.8 26.9 0.3
NE2 C:HIS339 2.0 28.2 1.0
OD1 C:ASP286 2.0 24.4 1.0
NE2 C:HIS291 2.1 23.3 1.0
OD2 C:ASP156 2.4 60.2 1.0
CG C:ASP286 2.8 25.5 1.0
OD2 C:ASP286 2.8 26.1 1.0
CE1 C:HIS339 2.9 28.4 1.0
CE1 C:HIS291 3.0 23.7 1.0
CD2 C:HIS339 3.1 28.5 1.0
CD2 C:HIS291 3.1 23.9 1.0
P C:TPO85 3.1 26.8 0.3
CG C:ASP156 3.3 56.8 1.0
OD1 C:ASP156 3.5 56.4 1.0
O2P C:TPO85 3.7 26.9 0.3
O1P C:TPO85 3.9 26.5 0.3
ND1 C:HIS339 4.1 28.8 1.0
ND1 C:HIS291 4.1 24.2 1.0
CG C:HIS339 4.2 28.4 1.0
CG C:HIS291 4.2 24.7 1.0
OG1 C:TPO85 4.2 26.2 1.0
CB C:ASP286 4.2 25.3 1.0
ND2 C:ASN330 4.2 26.1 1.0
CE1 C:HIS328 4.5 22.4 1.0
CB C:ASP156 4.7 52.3 1.0
O C:HOH610 4.7 25.7 1.0
NE2 C:HIS328 4.8 21.9 1.0
O C:ASP286 5.0 27.3 1.0

Manganese binding site 9 out of 10 in 4lr9

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Manganese binding site 9 out of 10 in the Phosphopentomutase S154A 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 S154A Variant Soaked with 2,3-Dideoxyribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:21.3
occ:1.00
 OD1 C:ASP13 1.9 21.9 1.0
OD2 C:ASP327 2.1 20.8 1.0
NE2 C:HIS328 2.1 21.9 1.0
OG1 C:TPO85 2.3 26.2 1.0
CG C:ASP13 2.6 22.4 1.0
OD2 C:ASP13 2.7 21.7 1.0
CG C:ASP327 3.0 22.0 1.0
CD2 C:HIS328 3.0 22.4 1.0
CB C:TPO85 3.1 26.4 1.0
OD1 C:ASP327 3.1 22.4 1.0
CE1 C:HIS328 3.2 22.4 1.0
CG2 C:TPO85 3.3 25.9 1.0
CA C:TPO85 3.4 26.1 1.0
O3P C:TPO85 3.6 26.9 0.3
P C:TPO85 3.7 26.8 0.3
N C:TPO85 4.0 27.2 1.0
CB C:ASP13 4.0 22.8 1.0
CG C:HIS328 4.1 23.3 1.0
ND1 C:HIS328 4.2 23.3 1.0
N C:SER14 4.4 24.3 1.0
CB C:ASP327 4.4 22.1 1.0
CG C:ASP286 4.5 25.5 1.0
CA C:ASP13 4.5 23.7 1.0
NE2 C:HIS89 4.5 20.6 1.0
O2P C:TPO85 4.6 26.9 0.3
O1P C:TPO85 4.6 26.5 0.3
CE1 C:HIS339 4.6 28.4 1.0
OD2 C:ASP286 4.6 26.1 1.0
C C:ASP13 4.7 24.3 1.0
C C:TPO85 4.7 25.6 1.0
OD1 C:ASP286 4.7 24.4 1.0
CD2 C:HIS89 4.8 20.2 1.0
C C:ASP84 4.8 28.7 1.0
CB C:ASP286 4.8 25.3 1.0
NE2 C:HIS339 4.9 28.2 1.0
O C:TPO85 4.9 25.2 1.0

Manganese binding site 10 out of 10 in 4lr9

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Manganese binding site 10 out of 10 in the Phosphopentomutase S154A 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 10 of Phosphopentomutase S154A Variant Soaked with 2,3-Dideoxyribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn403

b:45.5
occ:1.00
 O C:HOH632 2.2 34.8 1.0
OD1 C:ASP28 2.2 32.3 1.0
NE2 C:HIS334 2.2 31.4 1.0
O C:HOH572 2.3 34.5 1.0
O C:GLY27 2.5 35.1 1.0
O C:HOH659 2.5 30.8 1.0
CD2 C:HIS334 3.1 30.4 1.0
CE1 C:HIS334 3.2 32.5 1.0
C C:GLY27 3.3 35.9 1.0
CG C:ASP28 3.4 32.3 1.0
CA C:ASP28 3.8 34.5 1.0
N C:ASP28 3.9 35.8 1.0
O C:PHE26 4.0 36.5 1.0
O C:HOH520 4.1 27.9 1.0
CB C:ASP28 4.2 33.5 1.0
CA C:GLY27 4.2 37.3 1.0
ND1 C:HIS334 4.3 32.2 1.0
CG C:HIS334 4.3 30.9 1.0
OD2 C:ASP28 4.3 31.7 1.0
NZ C:LYS83 4.4 32.0 1.0
O C:HIS339 4.7 28.2 1.0
O C:HOH653 4.7 49.8 1.0
CG2 C:THR340 4.8 29.8 1.0
C C:PHE26 4.9 37.5 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 20:08:56 2024

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