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Manganese in PDB 4lrf: Phosphopentomutase S154G Variant Soaked with Ribose 5-Phosphate

Enzymatic activity of Phosphopentomutase S154G Variant Soaked with Ribose 5-Phosphate

All present enzymatic activity of Phosphopentomutase S154G Variant Soaked with Ribose 5-Phosphate:
5.4.2.7;

Protein crystallography data

The structure of Phosphopentomutase S154G Variant Soaked with Ribose 5-Phosphate, PDB code: 4lrf 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 (°) 90.922, 76.770, 107.530, 90.00, 108.72, 90.00
R / Rfree (%) 16.3 / 20

Manganese Binding Sites:

Pages:

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

Binding sites:

The binding sites of Manganese atom in the Phosphopentomutase S154G Variant Soaked with Ribose 5-Phosphate (pdb code 4lrf). 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 S154G Variant Soaked with Ribose 5-Phosphate, PDB code: 4lrf:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 4lrf

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Manganese binding site 1 out of 12 in the Phosphopentomutase S154G 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 S154G Variant Soaked with Ribose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:13.3
occ:1.00
 O2X A:HSX407 2.0 21.6 0.5
OD1 A:ASP286 2.1 12.7 1.0
NE2 A:HIS291 2.2 12.6 1.0
NE2 A:HIS339 2.2 13.6 1.0
O1P A:TPO85 2.3 20.5 0.3
OD2 A:ASP156 2.4 22.6 0.5
O1X A:HSX407 2.4 21.6 0.5
P' A:HSX407 2.6 22.0 0.5
OD1 A:ASP156 2.7 23.7 0.5
OD2 A:ASP286 2.8 12.4 1.0
CG A:ASP286 2.8 12.2 1.0
CG A:ASP156 2.9 23.0 0.5
CE1 A:HIS339 3.1 13.9 1.0
CE1 A:HIS291 3.1 13.4 1.0
CD2 A:HIS291 3.1 12.9 1.0
CD2 A:HIS339 3.2 13.8 1.0
P A:TPO85 3.4 20.2 0.3
O2P A:TPO85 3.6 21.3 0.3
O3X A:HSX407 3.7 22.4 0.5
O5' A:HSX407 3.8 21.6 0.5
C5' A:HSX407 4.1 20.2 0.5
CB A:ASP156 4.1 23.1 0.5
O3' A:HSX407 4.2 19.0 0.5
ND1 A:HIS339 4.2 14.0 1.0
ND1 A:HIS291 4.2 13.8 1.0
CB A:ASP286 4.3 11.3 1.0
CG A:HIS291 4.3 13.6 1.0
ND2 A:ASN330 4.3 10.6 1.0
CG A:HIS339 4.3 13.8 1.0
O3P A:TPO85 4.3 19.6 0.3
CB A:ASP156 4.4 22.5 0.5
OG1 A:TPO85 4.5 19.5 1.0
O A:HOH702 4.5 27.5 1.0
CE1 A:HIS328 4.6 9.7 1.0
C4' A:HSX407 4.7 19.7 0.5
NE2 A:HIS328 4.9 9.5 1.0
C3' A:HSX407 4.9 19.1 0.5
O A:HOH575 4.9 36.2 1.0

Manganese binding site 2 out of 12 in 4lrf

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Manganese binding site 2 out of 12 in the Phosphopentomutase S154G 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 S154G Variant Soaked with Ribose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:11.9
occ:1.00
 OD2 A:ASP327 2.0 10.1 1.0
OG1 A:TPO85 2.1 19.5 1.0
OD1 A:ASP13 2.1 9.4 1.0
NE2 A:HIS328 2.2 9.5 1.0
OD2 A:ASP13 2.5 9.7 1.0
CG A:ASP13 2.6 9.4 1.0
O2P A:TPO85 2.7 21.3 0.3
CG A:ASP327 2.9 9.6 1.0
P A:TPO85 3.0 20.2 0.3
OD1 A:ASP327 3.1 9.5 1.0
CD2 A:HIS328 3.1 9.4 1.0
CB A:TPO85 3.2 18.1 1.0
CE1 A:HIS328 3.2 9.7 1.0
O2X A:HSX407 3.5 21.6 0.5
CG2 A:TPO85 3.6 17.9 1.0
CA A:TPO85 3.6 17.5 1.0
O1P A:TPO85 3.7 20.5 0.3
CB A:ASP13 4.0 9.2 1.0
N A:TPO85 4.3 17.6 1.0
CG A:HIS328 4.3 9.7 1.0
O3P A:TPO85 4.3 19.6 0.3
ND1 A:HIS328 4.3 9.8 1.0
N A:SER14 4.3 8.9 1.0
CB A:ASP327 4.3 9.4 1.0
CG A:ASP286 4.5 12.2 1.0
CE1 A:HIS339 4.5 13.9 1.0
OD2 A:ASP286 4.5 12.4 1.0
CA A:ASP13 4.5 9.0 1.0
P' A:HSX407 4.6 22.0 0.5
C A:ASP13 4.6 8.9 1.0
OD1 A:ASP286 4.7 12.7 1.0
NE2 A:HIS89 4.8 13.9 1.0
CB A:ASP286 4.8 11.3 1.0
O3X A:HSX407 4.8 22.4 0.5
C5' A:HSX407 4.8 20.2 0.5
NE2 A:HIS339 4.8 13.6 1.0
C A:TPO85 4.9 16.6 1.0
O5' A:HSX407 4.9 21.6 0.5
CD2 A:HIS89 5.0 13.0 1.0
CA A:SER14 5.0 9.0 1.0
CB A:SER14 5.0 9.2 1.0

Manganese binding site 3 out of 12 in 4lrf

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Manganese binding site 3 out of 12 in the Phosphopentomutase S154G 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 S154G Variant Soaked with Ribose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:16.9
occ:0.75
 O A:HOH671 2.1 22.6 1.0
OD1 A:ASP28 2.1 17.6 1.0
O A:HOH727 2.2 30.5 1.0
O A:HOH527 2.2 18.8 1.0
NE2 A:HIS334 2.2 18.5 1.0
O A:GLY27 2.4 21.4 1.0
CD2 A:HIS334 3.0 18.2 1.0
C A:GLY27 3.3 21.6 1.0
CG A:ASP28 3.3 17.3 1.0
CE1 A:HIS334 3.4 18.8 1.0
CA A:ASP28 3.8 19.1 1.0
N A:ASP28 3.9 20.5 1.0
O A:PHE26 4.0 22.5 1.0
OD2 A:ASP338 4.1 18.8 0.5
CB A:ASP28 4.1 17.8 1.0
CG A:HIS334 4.3 18.0 1.0
OD1 A:ASP338 4.3 18.4 0.5
OD2 A:ASP28 4.3 16.9 1.0
CA A:GLY27 4.3 23.3 1.0
NZ A:LYS83 4.4 24.1 1.0
ND1 A:HIS334 4.4 18.5 1.0
CG2 A:THR340 4.4 13.9 1.0
CG A:ASP338 4.5 18.2 0.5
O A:HIS339 4.6 14.4 1.0
O A:PRO335 4.6 20.8 1.0
C A:PHE26 4.9 23.1 1.0

Manganese binding site 4 out of 12 in 4lrf

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Manganese binding site 4 out of 12 in the Phosphopentomutase S154G 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 S154G Variant Soaked with Ribose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:48.8
occ:1.00
 O A:HOH815 2.2 31.9 1.0
O A:HOH816 2.4 36.5 1.0
O A:HOH818 2.6 28.1 1.0
OE1 A:GLU300 2.6 19.0 1.0
O A:HOH817 2.6 28.8 1.0
OE2 A:GLU300 2.7 19.1 1.0
CD A:GLU300 3.0 18.0 1.0
CG A:GLN296 4.3 15.4 1.0
O A:HOH734 4.4 21.1 1.0
CG A:GLU300 4.4 16.1 1.0
O A:HOH539 4.5 20.5 1.0
NE2 A:GLN296 5.0 15.5 1.0

Manganese binding site 5 out of 12 in 4lrf

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Manganese binding site 5 out of 12 in the Phosphopentomutase S154G 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 S154G Variant Soaked with Ribose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:14.4
occ:1.00
 O1P B:TPO85 2.0 19.6 0.5
NE2 B:HIS339 2.1 14.3 1.0
OD1 B:ASP286 2.2 14.5 1.0
NE2 B:HIS291 2.2 15.5 1.0
OD2 B:ASP156 2.3 26.5 1.0
OD1 B:ASP156 2.6 26.9 1.0
CG B:ASP156 2.8 25.6 1.0
CG B:ASP286 2.8 14.1 1.0
OD2 B:ASP286 2.9 14.4 1.0
CE1 B:HIS339 3.0 14.2 1.0
CD2 B:HIS291 3.1 15.9 1.0
CD2 B:HIS339 3.2 14.8 1.0
CE1 B:HIS291 3.2 16.4 1.0
P B:TPO85 3.4 19.5 0.5
O2P B:TPO85 3.8 19.3 0.5
ND1 B:HIS339 4.2 14.4 1.0
CG B:HIS339 4.3 14.8 1.0
ND1 B:HIS291 4.3 17.0 1.0
OG1 B:TPO85 4.3 17.3 1.0
CB B:ASP156 4.3 23.1 1.0
CG B:HIS291 4.3 16.8 1.0
CB B:ASP286 4.3 13.4 1.0
O3P B:TPO85 4.4 19.9 0.5
O B:HOH734 4.4 20.3 1.0
O B:HOH573 4.5 25.1 1.0
ND2 B:ASN330 4.5 14.7 1.0
CE1 B:HIS328 4.5 11.4 1.0
NE2 B:HIS328 4.8 11.0 1.0
MN B:MN402 4.9 13.0 1.0
CA B:ASP156 5.0 22.6 1.0
O B:HOH790 5.0 45.2 1.0

Manganese binding site 6 out of 12 in 4lrf

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Manganese binding site 6 out of 12 in the Phosphopentomutase S154G 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 S154G Variant Soaked with Ribose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:13.0
occ:1.00
 OD2 B:ASP327 2.1 10.3 1.0
NE2 B:HIS328 2.1 11.0 1.0
OD1 B:ASP13 2.2 13.0 1.0
OG1 B:TPO85 2.2 17.3 1.0
OD2 B:ASP13 2.4 12.8 1.0
CG B:ASP13 2.6 12.8 1.0
O2P B:TPO85 2.6 19.3 0.5
CG B:ASP327 2.9 10.0 1.0
P B:TPO85 3.0 19.5 0.5
CD2 B:HIS328 3.0 10.9 1.0
OD1 B:ASP327 3.1 10.0 1.0
CE1 B:HIS328 3.1 11.4 1.0
CB B:TPO85 3.2 16.0 1.0
CG2 B:TPO85 3.5 15.7 1.0
CA B:TPO85 3.7 14.7 1.0
O1P B:TPO85 3.8 19.6 0.5
CB B:ASP13 4.1 12.3 1.0
ND1 B:HIS328 4.2 11.5 1.0
CG B:HIS328 4.2 11.2 1.0
O3P B:TPO85 4.3 19.9 0.5
N B:SER14 4.3 12.1 1.0
N B:TPO85 4.4 14.6 1.0
CB B:ASP327 4.4 9.8 1.0
CE1 B:HIS339 4.4 14.2 1.0
O B:HOH618 4.4 28.3 1.0
CG B:ASP286 4.5 14.1 1.0
OD2 B:ASP286 4.6 14.4 1.0
CA B:ASP13 4.6 11.8 1.0
NE2 B:HIS89 4.6 11.0 1.0
OD1 B:ASP286 4.6 14.5 1.0
NE2 B:HIS339 4.7 14.3 1.0
C B:ASP13 4.8 12.3 1.0
CB B:ASP286 4.9 13.4 1.0
CD2 B:HIS89 4.9 10.8 1.0
C B:TPO85 4.9 14.0 1.0
MN B:MN401 4.9 14.4 1.0

Manganese binding site 7 out of 12 in 4lrf

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Manganese binding site 7 out of 12 in the Phosphopentomutase S154G 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 S154G Variant Soaked with Ribose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn403

b:36.7
occ:0.75
 O B:HOH848 2.4 41.7 1.0
O B:HOH733 2.5 37.0 1.0
O B:HOH752 2.8 46.5 1.0
O B:HOH607 4.1 22.8 1.0
OE2 B:GLU318 4.1 28.0 1.0

Manganese binding site 8 out of 12 in 4lrf

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Manganese binding site 8 out of 12 in the Phosphopentomutase S154G 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 S154G Variant Soaked with Ribose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn404

b:33.7
occ:0.50
 O B:HOH844 1.6 42.6 1.0
O B:HOH722 2.1 33.8 1.0
O B:HOH804 2.3 36.0 1.0
NE2 B:HIS36 2.4 22.3 1.0
O B:HOH789 2.4 37.7 1.0
CD2 B:HIS36 3.2 21.8 1.0
CE1 B:HIS36 3.4 21.5 1.0
O B:GLY30 4.4 21.8 1.0
CG B:HIS36 4.4 20.7 1.0
ND1 B:HIS36 4.5 20.6 1.0
OE1 B:GLU39 4.6 27.3 0.5
OE2 B:GLU39 4.8 27.4 0.5
OD2 B:ASP32 4.9 20.0 1.0
CB B:ASP32 4.9 19.1 1.0

Manganese binding site 9 out of 12 in 4lrf

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Manganese binding site 9 out of 12 in the Phosphopentomutase S154G 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 S154G Variant Soaked with Ribose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn405

b:28.8
occ:0.50
 O B:HOH849 2.0 34.2 1.0
OD1 B:ASP28 2.1 22.9 1.0
O B:HOH774 2.2 21.3 1.0
NE2 B:HIS334 2.4 22.8 1.0
O B:HOH611 2.4 34.4 1.0
O B:GLY27 2.5 26.4 1.0
CD2 B:HIS334 3.1 22.2 1.0
C B:GLY27 3.2 26.3 1.0
CG B:ASP28 3.3 22.1 1.0
CE1 B:HIS334 3.5 22.9 1.0
O B:PHE26 3.6 27.7 1.0
CA B:ASP28 3.8 23.3 1.0
N B:ASP28 3.9 24.9 1.0
O B:HOH644 4.1 22.5 1.0
OD2 B:ASP28 4.1 21.4 1.0
CB B:ASP28 4.2 22.1 1.0
CA B:GLY27 4.2 28.1 1.0
NZ B:LYS83 4.3 18.8 1.0
CG B:HIS334 4.3 21.9 1.0
ND1 B:HIS334 4.5 22.4 1.0
C B:PHE26 4.5 27.8 1.0
O B:HOH624 4.6 34.8 1.0
CG2 B:THR340 4.8 16.7 1.0
O B:HIS339 4.8 17.0 1.0
N B:GLY27 4.8 28.1 1.0

Manganese binding site 10 out of 12 in 4lrf

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Manganese binding site 10 out of 12 in the Phosphopentomutase S154G 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 10 of Phosphopentomutase S154G Variant Soaked with Ribose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:18.8
occ:1.00
 O2P C:TPO85 2.0 23.5 0.5
NE2 C:HIS339 2.1 17.4 1.0
NE2 C:HIS291 2.2 18.6 1.0
OD1 C:ASP286 2.2 18.5 1.0
OD2 C:ASP156 2.3 49.4 1.0
OD1 C:ASP156 2.7 45.4 1.0
OD2 C:ASP286 2.8 18.4 1.0
CG C:ASP286 2.8 18.3 1.0
CG C:ASP156 2.9 45.6 1.0
CE1 C:HIS339 3.0 17.4 1.0
CD2 C:HIS339 3.1 17.8 1.0
CE1 C:HIS291 3.1 19.2 1.0
CD2 C:HIS291 3.2 18.8 1.0
P C:TPO85 3.3 23.5 0.5
O3P C:TPO85 3.6 23.1 0.5
ND1 C:HIS339 4.1 17.9 1.0
O C:HOH645 4.2 24.6 1.0
CG C:HIS339 4.2 18.1 1.0
OG1 C:TPO85 4.3 21.5 1.0
ND1 C:HIS291 4.3 19.6 1.0
O1P C:TPO85 4.3 23.5 0.5
CG C:HIS291 4.3 19.6 1.0
CB C:ASP286 4.3 18.0 1.0
ND2 C:ASN330 4.4 18.0 1.0
CB C:ASP156 4.4 41.6 1.0
CE1 C:HIS328 4.5 16.2 1.0
O C:HOH659 4.5 29.6 1.0
NE2 C:HIS328 4.8 15.8 1.0
MN C:MN402 4.9 15.9 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 20:11:39 2024

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