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Manganese in PDB 4lra: Phosphopentomutase S154G Variant

Enzymatic activity of Phosphopentomutase S154G Variant

All present enzymatic activity of Phosphopentomutase S154G Variant:
5.4.2.7;

Protein crystallography data

The structure of Phosphopentomutase S154G Variant, PDB code: 4lra 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 (°) 91.050, 76.699, 106.794, 90.00, 108.20, 90.00
R / Rfree (%) 17.2 / 21

Manganese Binding Sites:

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

Manganese binding site 1 out of 9 in 4lra

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Manganese binding site 1 out of 9 in the Phosphopentomutase S154G Variant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:21.0
occ:1.00
 O1P A:TPO85 2.1 27.8 0.5
OD2 A:ASP156 2.2 31.8 1.0
NE2 A:HIS339 2.2 20.7 1.0
NE2 A:HIS291 2.2 18.2 1.0
OD1 A:ASP286 2.2 20.6 1.0
OD2 A:ASP286 2.8 20.5 1.0
CG A:ASP286 2.9 20.0 1.0
CG A:ASP156 2.9 31.7 1.0
OD1 A:ASP156 2.9 33.5 1.0
CE1 A:HIS339 3.1 22.1 1.0
CD2 A:HIS291 3.1 19.3 1.0
CD2 A:HIS339 3.2 21.3 1.0
P A:TPO85 3.2 28.1 0.5
CE1 A:HIS291 3.2 19.9 1.0
O2P A:TPO85 3.4 29.1 0.5
O A:HOH705 3.9 36.1 1.0
O3P A:TPO85 4.2 27.4 0.5
ND1 A:HIS339 4.2 21.9 1.0
CG A:HIS291 4.3 20.2 1.0
ND1 A:HIS291 4.3 20.1 1.0
CG A:HIS339 4.3 21.1 1.0
OG1 A:TPO85 4.3 26.0 1.0
CB A:ASP156 4.3 30.7 1.0
CB A:ASP286 4.4 19.2 1.0
O A:HOH592 4.4 29.9 1.0
ND2 A:ASN330 4.4 20.1 1.0
O A:HOH528 4.5 28.2 1.0
CE1 A:HIS328 4.5 20.5 1.0
NE2 A:HIS328 4.8 21.1 1.0
MN A:MN402 4.9 21.4 1.0
O A:HOH616 4.9 39.9 1.0
CA A:ASP156 4.9 30.3 1.0

Manganese binding site 2 out of 9 in 4lra

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Manganese binding site 2 out of 9 in the Phosphopentomutase S154G Variant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:21.4
occ:1.00
 OD2 A:ASP327 2.1 18.4 1.0
OD1 A:ASP13 2.1 18.8 1.0
OG1 A:TPO85 2.1 26.0 1.0
NE2 A:HIS328 2.2 21.1 1.0
OD2 A:ASP13 2.6 19.8 1.0
O2P A:TPO85 2.6 29.1 0.5
CG A:ASP13 2.7 19.5 1.0
CG A:ASP327 2.9 18.1 1.0
P A:TPO85 3.0 28.1 0.5
OD1 A:ASP327 3.1 18.2 1.0
CD2 A:HIS328 3.1 20.6 1.0
CB A:TPO85 3.2 24.7 1.0
CE1 A:HIS328 3.2 20.5 1.0
CG2 A:TPO85 3.5 24.5 1.0
CA A:TPO85 3.7 23.6 1.0
O1P A:TPO85 3.7 27.8 0.5
CB A:ASP13 4.1 18.6 1.0
O3P A:TPO85 4.2 27.4 0.5
CG A:HIS328 4.3 20.0 1.0
ND1 A:HIS328 4.3 20.1 1.0
O A:HOH627 4.3 35.1 1.0
N A:TPO85 4.4 23.4 1.0
CE1 A:HIS339 4.4 22.1 1.0
CB A:ASP327 4.4 17.9 1.0
N A:SER14 4.4 17.6 1.0
CG A:ASP286 4.5 20.0 1.0
OD2 A:ASP286 4.6 20.5 1.0
CA A:ASP13 4.6 18.5 1.0
NE2 A:HIS89 4.7 21.7 1.0
OD1 A:ASP286 4.7 20.6 1.0
NE2 A:HIS339 4.7 20.7 1.0
C A:ASP13 4.8 18.3 1.0
MN A:MN401 4.9 21.0 1.0
CD2 A:HIS89 4.9 20.1 1.0
C A:TPO85 4.9 22.9 1.0
CB A:ASP286 4.9 19.2 1.0

Manganese binding site 3 out of 9 in 4lra

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Manganese binding site 3 out of 9 in the Phosphopentomutase S154G Variant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:48.9
occ:0.75
 OD1 A:ASP28 2.1 27.4 1.0
O A:HOH507 2.1 33.9 1.0
NE2 A:HIS334 2.2 27.5 1.0
O A:HOH508 2.3 32.3 1.0
O A:GLY27 2.7 31.8 1.0
CD2 A:HIS334 3.0 27.0 1.0
CG A:ASP28 3.3 27.0 1.0
CE1 A:HIS334 3.3 28.2 1.0
C A:GLY27 3.4 32.0 1.0
O A:PHE26 3.8 34.2 1.0
CA A:ASP28 3.8 28.4 1.0
N A:ASP28 3.9 29.9 1.0
O A:HOH588 4.1 27.8 1.0
CB A:ASP28 4.2 26.9 1.0
OD2 A:ASP28 4.2 26.1 1.0
CG A:HIS334 4.2 27.0 1.0
NZ A:LYS83 4.3 27.7 1.0
CA A:GLY27 4.3 33.9 1.0
ND1 A:HIS334 4.3 27.9 1.0
CG2 A:THR340 4.6 21.0 1.0
O A:HIS339 4.6 21.7 1.0
C A:PHE26 4.7 33.9 1.0
N A:GLY27 5.0 34.3 1.0
O A:PRO335 5.0 26.8 1.0

Manganese binding site 4 out of 9 in 4lra

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Manganese binding site 4 out of 9 in the Phosphopentomutase S154G Variant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:24.7
occ:1.00
 O1P B:TPO85 2.1 28.6 0.5
NE2 B:HIS339 2.1 22.6 1.0
OD1 B:ASP286 2.1 24.2 1.0
NE2 B:HIS291 2.2 24.5 1.0
OD2 B:ASP156 2.2 36.5 1.0
OD1 B:ASP156 2.6 36.8 1.0
CG B:ASP156 2.7 35.6 1.0
CG B:ASP286 2.8 24.2 1.0
OD2 B:ASP286 2.9 24.1 1.0
CE1 B:HIS339 3.0 22.5 1.0
CD2 B:HIS291 3.1 24.6 1.0
CD2 B:HIS339 3.2 23.2 1.0
CE1 B:HIS291 3.2 25.0 1.0
P B:TPO85 3.4 29.3 0.5
O2P B:TPO85 3.7 28.2 0.5
ND1 B:HIS339 4.2 22.7 1.0
CB B:ASP156 4.2 33.2 1.0
CG B:HIS339 4.3 23.4 1.0
ND1 B:HIS291 4.3 25.9 1.0
CG B:HIS291 4.3 25.6 1.0
CB B:ASP286 4.3 23.0 1.0
O3P B:TPO85 4.3 28.0 0.5
OG1 B:TPO85 4.4 26.4 1.0
O B:HOH672 4.4 31.3 1.0
ND2 B:ASN330 4.5 23.7 1.0
O B:HOH521 4.5 36.2 1.0
CE1 B:HIS328 4.6 20.5 1.0
NE2 B:HIS328 4.7 20.2 1.0
MN B:MN402 4.9 23.9 1.0
CA B:ASP156 4.9 32.9 1.0

Manganese binding site 5 out of 9 in 4lra

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Manganese binding site 5 out of 9 in the Phosphopentomutase S154G Variant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:23.9
occ:1.00
 OD2 B:ASP327 2.1 20.9 1.0
OD1 B:ASP13 2.1 23.1 1.0
OG1 B:TPO85 2.2 26.4 1.0
NE2 B:HIS328 2.2 20.2 1.0
O2P B:TPO85 2.5 28.2 0.5
OD2 B:ASP13 2.5 23.6 1.0
CG B:ASP13 2.6 23.8 1.0
P B:TPO85 2.9 29.3 0.5
CG B:ASP327 3.0 19.9 1.0
OD1 B:ASP327 3.1 19.5 1.0
CD2 B:HIS328 3.1 20.4 1.0
CE1 B:HIS328 3.2 20.5 1.0
CB B:TPO85 3.2 24.9 1.0
CG2 B:TPO85 3.6 24.1 1.0
O1P B:TPO85 3.7 28.6 0.5
CA B:TPO85 3.7 23.6 1.0
CB B:ASP13 4.1 23.1 1.0
O3P B:TPO85 4.2 28.0 0.5
CG B:HIS328 4.3 20.9 1.0
ND1 B:HIS328 4.3 20.9 1.0
O B:HOH606 4.4 33.2 1.0
N B:TPO85 4.4 23.3 1.0
CB B:ASP327 4.4 19.5 1.0
CE1 B:HIS339 4.4 22.5 1.0
N B:SER14 4.5 22.5 1.0
CG B:ASP286 4.5 24.2 1.0
OD2 B:ASP286 4.6 24.1 1.0
NE2 B:HIS89 4.6 20.8 1.0
CA B:ASP13 4.6 22.1 1.0
OD1 B:ASP286 4.7 24.2 1.0
NE2 B:HIS339 4.7 22.6 1.0
C B:ASP13 4.8 22.6 1.0
CD2 B:HIS89 4.8 19.4 1.0
MN B:MN401 4.9 24.7 1.0
CB B:ASP286 4.9 23.0 1.0
C B:TPO85 4.9 22.9 1.0

Manganese binding site 6 out of 9 in 4lra

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Manganese binding site 6 out of 9 in the Phosphopentomutase S154G Variant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn403

b:71.8
occ:0.50
 NE2 B:HIS36 2.9 38.1 1.0
OE1 B:GLU39 3.3 42.6 0.5
O B:HOH742 3.3 49.0 1.0
CD2 B:HIS36 3.3 37.4 1.0
CD B:GLU39 4.1 43.3 0.5
OE2 B:GLU39 4.2 44.9 0.5
CE1 B:HIS36 4.2 36.9 1.0
O B:HOH815 4.5 42.6 1.0
CG B:HIS36 4.7 35.8 1.0

Manganese binding site 7 out of 9 in 4lra

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Manganese binding site 7 out of 9 in the Phosphopentomutase S154G Variant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:32.3
occ:1.00
 O2P C:TPO85 2.1 38.3 0.5
OD1 C:ASP286 2.1 33.4 1.0
NE2 C:HIS291 2.2 31.7 1.0
NE2 C:HIS339 2.2 34.3 1.0
OD2 C:ASP156 2.3 53.5 1.0
OD1 C:ASP156 2.7 50.0 1.0
CG C:ASP286 2.8 35.0 1.0
CG C:ASP156 2.8 50.3 1.0
OD2 C:ASP286 2.9 35.2 1.0
CE1 C:HIS339 3.1 34.2 1.0
CE1 C:HIS291 3.1 31.8 1.0
CD2 C:HIS291 3.2 32.4 1.0
CD2 C:HIS339 3.2 35.2 1.0
P C:TPO85 3.4 38.6 0.5
O3P C:TPO85 3.8 38.3 0.5
ND1 C:HIS291 4.2 32.9 1.0
ND1 C:HIS339 4.3 35.3 1.0
O C:HOH534 4.3 38.2 1.0
CB C:ASP286 4.3 36.0 1.0
CG C:HIS291 4.3 33.2 1.0
O1P C:TPO85 4.3 36.9 0.5
CB C:ASP156 4.3 46.7 1.0
CG C:HIS339 4.3 36.0 1.0
OG1 C:TPO85 4.4 37.3 1.0
ND2 C:ASN330 4.4 34.7 1.0
CE1 C:HIS328 4.5 33.3 1.0
O C:HOH579 4.6 36.4 1.0
O C:HOH628 4.6 43.1 1.0
NE2 C:HIS328 4.7 31.9 1.0
MN C:MN402 4.9 32.7 1.0
CA C:ASP156 5.0 47.9 1.0

Manganese binding site 8 out of 9 in 4lra

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Manganese binding site 8 out of 9 in the Phosphopentomutase S154G Variant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:32.7
occ:1.00
 OD1 C:ASP13 2.0 33.3 1.0
OD2 C:ASP327 2.2 32.8 1.0
OG1 C:TPO85 2.3 37.3 1.0
NE2 C:HIS328 2.3 31.9 1.0
O3P C:TPO85 2.6 38.3 0.5
CG C:ASP13 2.7 33.9 1.0
OD2 C:ASP13 2.8 32.9 1.0
CG C:ASP327 3.0 34.2 1.0
CD2 C:HIS328 3.0 33.0 1.0
P C:TPO85 3.0 38.6 0.5
OD1 C:ASP327 3.1 35.4 1.0
CB C:TPO85 3.3 36.1 1.0
CE1 C:HIS328 3.3 33.3 1.0
CG2 C:TPO85 3.6 35.7 1.0
CA C:TPO85 3.6 36.0 1.0
O2P C:TPO85 3.7 38.3 0.5
CB C:ASP13 4.1 34.9 1.0
CG C:HIS328 4.2 34.9 1.0
N C:TPO85 4.3 35.9 1.0
O1P C:TPO85 4.3 36.9 0.5
ND1 C:HIS328 4.3 35.1 1.0
CB C:ASP327 4.4 34.5 1.0
CE1 C:HIS339 4.4 34.2 1.0
O C:HOH576 4.4 34.9 1.0
CG C:ASP286 4.5 35.0 1.0
N C:SER14 4.5 37.9 1.0
OD2 C:ASP286 4.6 35.2 1.0
CA C:ASP13 4.6 36.4 1.0
OD1 C:ASP286 4.6 33.4 1.0
NE2 C:HIS89 4.7 33.3 1.0
C C:ASP13 4.8 37.4 1.0
CB C:ASP286 4.8 36.0 1.0
NE2 C:HIS339 4.8 34.3 1.0
C C:TPO85 4.9 35.7 1.0
CD2 C:HIS89 4.9 32.8 1.0
MN C:MN401 4.9 32.3 1.0

Manganese binding site 9 out of 9 in 4lra

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Manganese binding site 9 out of 9 in the Phosphopentomutase S154G Variant


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn403

b:58.9
occ:1.00
 OD1 C:ASP28 2.1 47.9 1.0
O C:HOH501 2.3 39.1 1.0
O C:HOH502 2.3 45.2 1.0
NE2 C:HIS334 2.3 47.7 1.0
O C:GLY27 2.5 52.8 1.0
CE1 C:HIS334 3.2 50.0 1.0
C C:GLY27 3.2 53.8 1.0
CD2 C:HIS334 3.3 46.0 1.0
CG C:ASP28 3.3 48.6 1.0
CA C:ASP28 3.9 52.5 1.0
O C:PHE26 3.9 52.4 1.0
N C:ASP28 3.9 53.8 1.0
O C:HOH540 4.1 40.4 1.0
CA C:GLY27 4.2 55.3 1.0
CB C:ASP28 4.2 50.7 1.0
OD2 C:ASP28 4.2 47.7 1.0
ND1 C:HIS334 4.4 50.3 1.0
NZ C:LYS83 4.4 43.4 1.0
CG C:HIS334 4.4 47.7 1.0
O C:HIS339 4.6 41.2 1.0
C C:PHE26 4.7 54.2 1.0
CG2 C:THR340 4.8 47.1 1.0
N C:GLY27 4.9 56.0 1.0
O C:PRO335 5.0 44.2 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 20:08:58 2024

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