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Manganese in PDB 4lr8: Phosphopentomutase S154A Variant Soaked with Ribose 5-Phosphate

Enzymatic activity of Phosphopentomutase S154A Variant Soaked with Ribose 5-Phosphate

All present enzymatic activity of Phosphopentomutase S154A Variant Soaked with Ribose 5-Phosphate:
5.4.2.7;

Protein crystallography data

The structure of Phosphopentomutase S154A Variant Soaked with Ribose 5-Phosphate, PDB code: 4lr8 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 (°) 91.168, 76.497, 106.967, 90.00, 108.89, 90.00
R / Rfree (%) 16.4 / 20.2

Manganese Binding Sites:

The binding sites of Manganese atom in the Phosphopentomutase S154A Variant Soaked with Ribose 5-Phosphate (pdb code 4lr8). 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 S154A Variant Soaked with Ribose 5-Phosphate, PDB code: 4lr8:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 4lr8

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Manganese binding site 1 out of 9 in the Phosphopentomutase S154A Variant Soaked 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 S154A Variant Soaked with Ribose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:19.3
occ:1.00
 O1X A:HSX407 2.1 26.3 0.5
OD1 A:ASP286 2.1 19.5 1.0
NE2 A:HIS339 2.2 21.2 1.0
NE2 A:HIS291 2.2 16.1 1.0
O2X A:HSX407 2.4 27.3 0.5
OD2 A:ASP156 2.4 23.9 0.5
OD2 A:ASP286 2.7 19.7 1.0
P' A:HSX407 2.7 28.2 0.5
CG A:ASP286 2.7 19.3 1.0
OD1 A:ASP156 2.8 25.9 0.5
O1P A:TPO85 2.8 29.1 0.3
O2P A:TPO85 2.9 26.6 0.3
CG A:ASP156 3.0 26.8 0.5
CE1 A:HIS339 3.1 22.7 1.0
CE1 A:HIS291 3.1 17.3 1.0
CD2 A:HIS291 3.2 17.7 1.0
CD2 A:HIS339 3.2 20.5 1.0
P A:TPO85 3.3 27.5 0.3
O3X A:HSX407 3.8 27.6 0.5
O5' A:HSX407 3.8 26.0 0.5
C5' A:HSX407 4.0 22.4 0.5
CB A:ASP156 4.1 28.1 0.5
O3' A:HSX407 4.1 16.9 0.5
CB A:ASP286 4.2 18.0 1.0
ND1 A:HIS339 4.2 22.4 1.0
ND1 A:HIS291 4.2 18.7 1.0
ND2 A:ASN330 4.3 17.2 1.0
CG A:HIS291 4.3 19.3 1.0
CG A:HIS339 4.3 19.5 1.0
O3P A:TPO85 4.4 27.7 0.3
CB A:ASP156 4.5 27.0 0.5
CE1 A:HIS328 4.5 15.6 1.0
OG1 A:TPO85 4.6 26.7 1.0
C4' A:HSX407 4.6 20.7 0.5
OD2 A:ASP156 4.6 30.3 0.5
O A:HOH580 4.7 14.2 1.0
CG A:ASP156 4.8 28.8 0.5
NE2 A:HIS328 4.8 16.8 1.0
C3' A:HSX407 4.8 18.9 0.5
MN A:MN402 4.9 18.6 1.0

Manganese binding site 2 out of 9 in 4lr8

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

b:18.6
occ:1.00
 OD2 A:ASP327 2.0 17.8 1.0
OG1 A:TPO85 2.0 26.7 1.0
OD1 A:ASP13 2.1 16.1 1.0
NE2 A:HIS328 2.2 16.8 1.0
OD2 A:ASP13 2.6 17.7 1.0
CG A:ASP13 2.6 16.7 1.0
O1P A:TPO85 2.8 29.1 0.3
CG A:ASP327 2.9 17.6 1.0
P A:TPO85 3.1 27.5 0.3
CD2 A:HIS328 3.1 15.8 1.0
OD1 A:ASP327 3.1 16.7 1.0
CB A:TPO85 3.1 24.5 1.0
CE1 A:HIS328 3.1 15.6 1.0
O1X A:HSX407 3.3 26.3 0.5
CA A:TPO85 3.5 23.2 1.0
CG2 A:TPO85 3.6 25.8 1.0
O2P A:TPO85 3.8 26.6 0.3
CB A:ASP13 4.1 16.3 1.0
N A:TPO85 4.1 23.8 1.0
O3P A:TPO85 4.2 27.7 0.3
ND1 A:HIS328 4.2 14.8 1.0
CG A:HIS328 4.2 16.0 1.0
N A:SER14 4.3 16.0 1.0
CB A:ASP327 4.3 16.5 1.0
OD2 A:ASP286 4.5 19.7 1.0
CG A:ASP286 4.5 19.3 1.0
CA A:ASP13 4.5 16.4 1.0
P' A:HSX407 4.5 28.2 0.5
C5' A:HSX407 4.6 22.4 0.5
C A:ASP13 4.6 16.4 1.0
NE2 A:HIS89 4.7 18.5 1.0
O5' A:HSX407 4.7 26.0 0.5
CE1 A:HIS339 4.8 22.7 1.0
C A:TPO85 4.8 21.8 1.0
CB A:ASP286 4.8 18.0 1.0
OD1 A:ASP286 4.9 19.5 1.0
NE2 A:HIS339 4.9 21.2 1.0
CD2 A:HIS89 4.9 15.8 1.0
MN A:MN401 4.9 19.3 1.0
C A:ASP84 4.9 23.6 1.0
CA A:SER14 4.9 16.5 1.0
CB A:SER14 5.0 16.9 1.0
O3X A:HSX407 5.0 27.6 0.5

Manganese binding site 3 out of 9 in 4lr8

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Manganese binding site 3 out of 9 in the Phosphopentomutase S154A Variant Soaked 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 S154A Variant Soaked with Ribose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:29.0
occ:0.75
 O A:HOH674 2.0 18.6 1.0
OD1 A:ASP28 2.1 26.7 1.0
O A:HOH741 2.2 22.8 1.0
NE2 A:HIS334 2.2 22.6 1.0
O A:HOH634 2.3 15.6 1.0
O A:GLY27 2.5 31.1 1.0
CD2 A:HIS334 3.0 22.1 1.0
CE1 A:HIS334 3.3 22.6 1.0
CG A:ASP28 3.3 25.1 1.0
C A:GLY27 3.3 30.9 1.0
O A:HOH767 3.8 16.5 1.0
CA A:ASP28 3.8 27.5 1.0
N A:ASP28 3.9 29.2 1.0
O A:PHE26 4.0 32.6 1.0
CB A:ASP28 4.1 25.6 1.0
CG A:HIS334 4.2 21.5 1.0
OD2 A:ASP28 4.2 25.0 1.0
OD2 A:ASP338 4.3 25.3 0.4
ND1 A:HIS334 4.3 21.8 1.0
NZ A:LYS83 4.4 25.5 1.0
CA A:GLY27 4.4 32.9 1.0
CG2 A:THR340 4.4 18.4 1.0
O A:PRO335 4.5 25.3 1.0
O A:HIS339 4.6 19.2 1.0
OD1 A:ASP338 4.8 26.4 0.4
C A:PHE26 4.9 32.9 1.0
CG A:ASP338 4.9 24.4 0.4

Manganese binding site 4 out of 9 in 4lr8

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Manganese binding site 4 out of 9 in the Phosphopentomutase S154A Variant Soaked 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 S154A Variant Soaked with Ribose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:20.5
occ:1.00
 NE2 B:HIS339 2.1 19.7 1.0
NE2 B:HIS291 2.1 19.5 1.0
OD1 B:ASP286 2.2 18.5 1.0
OD2 B:ASP156 2.2 35.1 1.0
O2P B:TPO85 2.6 25.9 0.4
OD2 B:ASP286 2.8 19.2 1.0
O1P B:TPO85 2.8 26.5 0.4
CG B:ASP286 2.8 19.4 1.0
CG B:ASP156 3.0 33.0 1.0
OD1 B:ASP156 3.0 35.6 1.0
CE1 B:HIS339 3.1 20.8 1.0
CD2 B:HIS291 3.1 19.1 1.0
P B:TPO85 3.1 26.3 0.4
CD2 B:HIS339 3.1 20.0 1.0
CE1 B:HIS291 3.1 19.5 1.0
O3P B:TPO85 4.0 26.8 0.4
ND1 B:HIS339 4.2 20.3 1.0
ND1 B:HIS291 4.2 21.4 1.0
CG B:HIS291 4.3 20.9 1.0
CG B:HIS339 4.3 20.7 1.0
ND2 B:ASN330 4.3 20.3 1.0
CB B:ASP286 4.3 18.1 1.0
OG1 B:TPO85 4.4 24.1 1.0
CB B:ASP156 4.4 29.1 1.0
CE1 B:HIS328 4.5 17.0 1.0
O B:HOH661 4.6 11.2 1.0
O B:HOH629 4.6 29.9 1.0
NE2 B:HIS328 4.7 17.2 1.0
MN B:MN402 4.9 18.1 1.0
O B:ASP286 4.9 20.9 1.0

Manganese binding site 5 out of 9 in 4lr8

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

b:18.1
occ:1.00
 OD1 B:ASP13 2.1 17.8 1.0
OD2 B:ASP327 2.2 16.6 1.0
NE2 B:HIS328 2.2 17.2 1.0
OG1 B:TPO85 2.2 24.1 1.0
OD2 B:ASP13 2.6 19.9 1.0
O2P B:TPO85 2.7 25.9 0.4
CG B:ASP13 2.7 19.1 1.0
CG B:ASP327 3.0 15.1 1.0
CD2 B:HIS328 3.0 16.5 1.0
OD1 B:ASP327 3.1 13.7 1.0
P B:TPO85 3.1 26.3 0.4
CE1 B:HIS328 3.2 17.0 1.0
CB B:TPO85 3.3 22.4 1.0
CA B:TPO85 3.6 21.2 1.0
CG2 B:TPO85 3.6 22.6 1.0
O1P B:TPO85 4.1 26.5 0.4
CB B:ASP13 4.1 18.1 1.0
O3P B:TPO85 4.2 26.8 0.4
CG B:HIS328 4.2 16.6 1.0
ND1 B:HIS328 4.2 17.3 1.0
N B:TPO85 4.3 21.2 1.0
N B:SER14 4.3 17.6 1.0
CB B:ASP327 4.4 14.6 1.0
OD2 B:ASP286 4.4 19.2 1.0
CG B:ASP286 4.4 19.4 1.0
CE1 B:HIS339 4.4 20.8 1.0
NE2 B:HIS89 4.6 19.2 1.0
CA B:ASP13 4.6 17.5 1.0
O B:HOH662 4.6 21.5 1.0
OD1 B:ASP286 4.7 18.5 1.0
C B:ASP13 4.7 18.0 1.0
NE2 B:HIS339 4.7 19.7 1.0
C B:TPO85 4.8 20.5 1.0
MN B:MN401 4.9 20.5 1.0
CB B:ASP286 4.9 18.1 1.0
CD2 B:HIS89 4.9 17.1 1.0
CA B:SER14 5.0 18.4 1.0
CB B:SER14 5.0 19.4 1.0

Manganese binding site 6 out of 9 in 4lr8

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Manganese binding site 6 out of 9 in the Phosphopentomutase S154A Variant Soaked 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 S154A Variant Soaked with Ribose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn403

b:36.8
occ:0.50
 OD2 B:ASP186 2.1 36.6 1.0
O B:HOH818 2.1 14.2 1.0
O B:HOH819 2.4 25.0 1.0
O B:HOH820 2.7 23.5 1.0
CG B:ASP186 3.2 33.6 1.0
CB B:ASP186 3.7 31.6 1.0
OD1 B:ASP186 4.3 33.6 1.0
NZ B:LYS188 4.3 46.7 1.0
O B:LEU183 4.4 27.0 1.0
OE2 B:GLU115 4.6 49.8 1.0
CE2 B:TYR189 4.7 35.5 1.0
CA B:ASP186 5.0 32.0 1.0

Manganese binding site 7 out of 9 in 4lr8

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Manganese binding site 7 out of 9 in the Phosphopentomutase S154A Variant Soaked 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 S154A Variant Soaked with Ribose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:28.0
occ:1.00
 O3P C:TPO85 1.8 33.5 0.4
OD1 C:ASP286 2.1 28.4 1.0
NE2 C:HIS339 2.2 28.0 1.0
NE2 C:HIS291 2.2 24.8 1.0
OD2 C:ASP156 2.3 53.8 1.0
CG C:ASP286 2.7 28.1 1.0
OD2 C:ASP286 2.8 29.3 1.0
OD1 C:ASP156 2.9 49.2 1.0
CG C:ASP156 3.0 50.0 1.0
CD2 C:HIS291 3.1 25.4 1.0
CE1 C:HIS339 3.1 28.1 1.0
CD2 C:HIS339 3.2 28.6 1.0
CE1 C:HIS291 3.2 25.7 1.0
P C:TPO85 3.2 33.4 0.4
O1P C:TPO85 3.8 33.2 0.4
O2P C:TPO85 4.0 33.8 0.4
CB C:ASP286 4.2 27.1 1.0
ND1 C:HIS339 4.2 29.0 1.0
ND1 C:HIS291 4.3 26.4 1.0
OG1 C:TPO85 4.3 31.4 1.0
CG C:HIS291 4.3 27.3 1.0
CG C:HIS339 4.3 28.9 1.0
ND2 C:ASN330 4.3 28.7 1.0
CB C:ASP156 4.5 46.4 1.0
CE1 C:HIS328 4.6 26.0 1.0
O C:HOH622 4.7 2.0 1.0
NE2 C:HIS328 4.8 26.1 1.0
MN C:MN402 4.9 24.1 1.0

Manganese binding site 8 out of 9 in 4lr8

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Manganese binding site 8 out of 9 in the Phosphopentomutase S154A Variant Soaked 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 S154A Variant Soaked with Ribose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:24.1
occ:1.00
 OD1 C:ASP13 1.9 25.1 1.0
OD2 C:ASP327 2.1 25.6 1.0
OG1 C:TPO85 2.2 31.4 1.0
NE2 C:HIS328 2.2 26.1 1.0
CG C:ASP13 2.6 25.9 1.0
OD2 C:ASP13 2.7 25.3 1.0
CG C:ASP327 2.9 25.2 1.0
O1P C:TPO85 3.1 33.2 0.4
CD2 C:HIS328 3.1 26.4 1.0
OD1 C:ASP327 3.1 24.8 1.0
P C:TPO85 3.2 33.4 0.4
CB C:TPO85 3.2 29.7 1.0
CE1 C:HIS328 3.2 26.0 1.0
CA C:TPO85 3.5 29.4 1.0
O3P C:TPO85 3.5 33.5 0.4
CG2 C:TPO85 3.6 29.2 1.0
CB C:ASP13 4.0 24.9 1.0
N C:TPO85 4.2 30.0 1.0
CG C:HIS328 4.2 27.1 1.0
ND1 C:HIS328 4.3 27.6 1.0
CB C:ASP327 4.3 25.1 1.0
N C:SER14 4.4 26.0 1.0
OD2 C:ASP286 4.4 29.3 1.0
O2P C:TPO85 4.5 33.8 0.4
CA C:ASP13 4.5 25.6 1.0
CG C:ASP286 4.5 28.1 1.0
CE1 C:HIS339 4.5 28.1 1.0
NE2 C:HIS89 4.6 23.5 1.0
C C:ASP13 4.7 26.1 1.0
C C:TPO85 4.8 28.6 1.0
NE2 C:HIS339 4.8 28.0 1.0
OD1 C:ASP286 4.8 28.4 1.0
CD2 C:HIS89 4.8 22.1 1.0
CB C:ASP286 4.8 27.1 1.0
MN C:MN401 4.9 28.0 1.0
CA C:SER14 5.0 26.8 1.0

Manganese binding site 9 out of 9 in 4lr8

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Manganese binding site 9 out of 9 in the Phosphopentomutase S154A Variant Soaked 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 S154A Variant Soaked with Ribose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn403

b:38.5
occ:1.00
 OD1 C:ASP28 2.0 35.3 1.0
O C:HOH564 2.2 12.2 1.0
NE2 C:HIS334 2.3 34.7 1.0
O C:HOH554 2.3 8.7 1.0
O C:HOH528 2.4 8.7 1.0
O C:GLY27 2.4 40.4 1.0
CD2 C:HIS334 3.1 33.5 1.0
C C:GLY27 3.2 41.1 1.0
CG C:ASP28 3.2 35.5 1.0
CE1 C:HIS334 3.3 34.8 1.0
CA C:ASP28 3.7 38.7 1.0
N C:ASP28 3.8 40.5 1.0
CB C:ASP28 4.0 37.1 1.0
O C:PHE26 4.0 42.2 1.0
O C:HOH532 4.1 10.3 1.0
OD2 C:ASP28 4.2 33.1 1.0
CA C:GLY27 4.2 43.1 1.0
NZ C:LYS83 4.3 31.1 1.0
CG C:HIS334 4.3 33.6 1.0
ND1 C:HIS334 4.3 33.8 1.0
CG2 C:THR340 4.5 31.5 1.0
O C:HOH521 4.7 15.4 1.0
O C:HIS339 4.9 30.7 1.0
C C:PHE26 4.9 43.4 1.0
C C:ASP28 5.0 39.8 1.0
O C:PRO335 5.0 33.3 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 20:08:41 2024

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