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Manganese in PDB 4lrc: Phosphopentomutase V158L Variant

Enzymatic activity of Phosphopentomutase V158L Variant

All present enzymatic activity of Phosphopentomutase V158L Variant:
5.4.2.7;

Protein crystallography data

The structure of Phosphopentomutase V158L Variant, PDB code: 4lrc 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) 38.78 / 1.89
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.718, 76.796, 107.175, 90.00, 108.70, 90.00
R / Rfree (%) 15.5 / 19.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Phosphopentomutase V158L Variant (pdb code 4lrc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Phosphopentomutase V158L Variant, PDB code: 4lrc:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4lrc

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Manganese binding site 1 out of 8 in the Phosphopentomutase V158L Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Phosphopentomutase V158L Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:12.5
occ:1.00
 OD1 A:ASP13 2.1 10.6 1.0
OD2 A:ASP327 2.1 13.1 1.0
NE2 A:HIS328 2.1 10.6 1.0
OG1 A:TPO85 2.2 28.5 1.0
OD2 A:ASP13 2.5 12.0 1.0
CG A:ASP13 2.5 10.7 1.0
O2P A:TPO85 2.6 58.9 1.0
CG A:ASP327 2.9 12.1 1.0
OD1 A:ASP327 3.0 11.5 1.0
P A:TPO85 3.0 54.2 1.0
CD2 A:HIS328 3.1 10.7 1.0
CE1 A:HIS328 3.1 11.0 1.0
CB A:TPO85 3.2 19.0 1.0
CG2 A:TPO85 3.5 15.8 1.0
CA A:TPO85 3.7 15.9 1.0
O1P A:TPO85 3.9 30.2 1.0
CB A:ASP13 4.0 11.1 1.0
O3P A:TPO85 4.2 55.3 1.0
ND1 A:HIS328 4.2 10.7 1.0
CG A:HIS328 4.2 11.0 1.0
CB A:ASP327 4.3 11.6 1.0
N A:SER14 4.3 9.6 1.0
CE1 A:HIS339 4.3 14.8 1.0
N A:TPO85 4.4 14.0 1.0
CG A:ASP286 4.5 13.8 1.0
O A:HOH625 4.5 36.0 1.0
CE1 A:HIS89 4.5 10.4 1.0
CA A:ASP13 4.6 11.1 1.0
OD2 A:ASP286 4.6 13.2 1.0
C A:ASP13 4.7 11.4 1.0
OD1 A:ASP286 4.7 14.4 1.0
NE2 A:HIS339 4.8 13.8 1.0
CB A:ASP286 4.9 12.1 1.0
C A:TPO85 4.9 13.7 1.0
ND1 A:HIS89 4.9 9.6 1.0
CA A:SER14 5.0 10.8 1.0

Manganese binding site 2 out of 8 in 4lrc

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Manganese binding site 2 out of 8 in the Phosphopentomutase V158L Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Phosphopentomutase V158L Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:12.4
occ:1.00
 O1P A:TPO85 1.9 30.2 1.0
OD2 A:ASP156 2.1 18.4 0.8
OD1 A:ASP286 2.1 14.4 1.0
NE2 A:HIS291 2.2 12.1 1.0
NE2 A:HIS339 2.2 13.8 1.0
OD2 A:ASP286 2.8 13.2 1.0
CG A:ASP286 2.8 13.8 1.0
CG A:ASP156 2.8 18.3 0.9
OD1 A:ASP156 2.8 17.5 0.8
CD2 A:HIS291 3.1 13.2 1.0
CE1 A:HIS339 3.1 14.8 1.0
CE1 A:HIS291 3.2 12.3 1.0
CD2 A:HIS339 3.2 12.7 1.0
P A:TPO85 3.3 54.2 1.0
O2P A:TPO85 3.7 58.9 1.0
O A:HOH725 3.8 35.0 1.0
ND1 A:HIS339 4.3 13.7 1.0
CB A:ASP286 4.3 12.1 1.0
CG A:HIS291 4.3 14.5 1.0
ND1 A:HIS291 4.3 13.4 1.0
CG A:HIS339 4.3 12.0 1.0
CB A:ASP156 4.3 19.0 1.0
O3P A:TPO85 4.3 55.3 1.0
OG1 A:TPO85 4.3 28.5 1.0
O A:HOH535 4.3 19.7 1.0
ND2 A:ASN330 4.4 14.9 1.0
O A:HOH583 4.4 24.4 1.0
CE1 A:HIS328 4.6 11.0 1.0
CA A:ASP156 4.9 17.8 1.0
NE2 A:HIS328 4.9 10.6 1.0

Manganese binding site 3 out of 8 in 4lrc

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Manganese binding site 3 out of 8 in the Phosphopentomutase V158L Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Phosphopentomutase V158L Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:38.8
occ:1.00
 OD1 A:ASP28 2.2 19.3 1.0
O A:HOH677 2.2 35.0 1.0
NE2 A:HIS334 2.3 21.1 1.0
O A:HOH582 2.3 24.8 1.0
O A:GLY27 2.6 28.7 1.0
CD2 A:HIS334 2.9 21.8 1.0
CG A:ASP28 3.4 17.4 1.0
CE1 A:HIS334 3.4 23.8 1.0
C A:GLY27 3.4 24.8 1.0
CA A:ASP28 3.8 19.6 1.0
O A:HOH571 4.0 21.4 1.0
N A:ASP28 4.0 20.0 1.0
O A:PHE26 4.0 30.2 1.0
CG A:HIS334 4.2 21.1 1.0
CB A:ASP28 4.2 17.4 1.0
OD2 A:ASP28 4.2 17.8 1.0
NZ A:LYS83 4.3 14.6 1.0
ND1 A:HIS334 4.4 22.4 1.0
CA A:GLY27 4.4 23.9 1.0
CG2 A:THR340 4.5 14.6 1.0
O A:HIS339 4.6 13.8 1.0
O A:PRO335 4.7 19.8 1.0
C A:PHE26 4.9 24.8 1.0
O A:HOH699 4.9 40.6 1.0

Manganese binding site 4 out of 8 in 4lrc

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Manganese binding site 4 out of 8 in the Phosphopentomutase V158L Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Phosphopentomutase V158L Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:14.5
occ:1.00
 OD2 B:ASP327 2.1 14.8 1.0
OG1 B:TPO85 2.1 29.1 1.0
OD1 B:ASP13 2.2 10.0 1.0
NE2 B:HIS328 2.2 13.2 1.0
OD2 B:ASP13 2.4 12.4 1.0
CG B:ASP13 2.5 11.8 1.0
O2P B:TPO85 2.6 67.6 1.0
CG B:ASP327 2.9 12.0 1.0
CD2 B:HIS328 3.0 13.3 1.0
OD1 B:ASP327 3.0 10.9 1.0
P B:TPO85 3.1 61.5 1.0
CE1 B:HIS328 3.2 13.2 1.0
CB B:TPO85 3.2 20.3 1.0
CG2 B:TPO85 3.5 18.1 1.0
CA B:TPO85 3.7 16.8 1.0
O1P B:TPO85 3.9 41.7 1.0
CB B:ASP13 4.0 12.3 1.0
CG B:HIS328 4.2 12.3 1.0
ND1 B:HIS328 4.2 13.2 1.0
CB B:ASP327 4.3 11.7 1.0
O3P B:TPO85 4.3 53.2 1.0
O B:HOH594 4.4 36.5 1.0
N B:SER14 4.4 13.1 1.0
N B:TPO85 4.4 15.5 1.0
CE1 B:HIS339 4.4 16.3 1.0
CE1 B:HIS89 4.5 12.4 1.0
CG B:ASP286 4.5 15.7 1.0
CA B:ASP13 4.6 12.2 1.0
OD1 B:ASP286 4.7 16.5 1.0
OD2 B:ASP286 4.7 15.2 1.0
C B:ASP13 4.8 13.7 1.0
NE2 B:HIS339 4.8 14.7 1.0
ND1 B:HIS89 4.9 11.8 1.0
CB B:ASP286 4.9 13.8 1.0
C B:TPO85 4.9 15.5 1.0

Manganese binding site 5 out of 8 in 4lrc

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Manganese binding site 5 out of 8 in the Phosphopentomutase V158L Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Phosphopentomutase V158L Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:13.2
occ:1.00
 OD1 B:ASP286 2.1 16.5 1.0
O1P B:TPO85 2.1 41.7 1.0
OD2 B:ASP156 2.1 25.1 1.0
NE2 B:HIS291 2.1 15.6 1.0
NE2 B:HIS339 2.1 14.7 1.0
CG B:ASP286 2.8 15.7 1.0
OD2 B:ASP286 2.8 15.2 1.0
CG B:ASP156 2.9 29.4 1.0
OD1 B:ASP156 3.0 30.3 1.0
CE1 B:HIS339 3.1 16.3 1.0
CD2 B:HIS291 3.1 19.3 1.0
CE1 B:HIS291 3.1 17.6 1.0
CD2 B:HIS339 3.2 14.6 1.0
P B:TPO85 3.3 61.5 1.0
O2P B:TPO85 3.7 67.6 1.0
ND1 B:HIS291 4.2 17.7 1.0
CB B:ASP286 4.2 13.8 1.0
ND1 B:HIS339 4.2 15.3 1.0
CG B:HIS291 4.2 18.7 1.0
O3P B:TPO85 4.3 53.2 1.0
CG B:HIS339 4.3 15.1 1.0
O B:HOH558 4.4 28.4 1.0
ND2 B:ASN330 4.4 18.4 1.0
OG1 B:TPO85 4.4 29.1 1.0
CB B:ASP156 4.4 24.4 1.0
O B:HOH555 4.4 20.2 1.0
CE1 B:HIS328 4.6 13.2 1.0
NE2 B:HIS328 4.8 13.2 1.0
CA B:ASP156 4.9 22.4 1.0

Manganese binding site 6 out of 8 in 4lrc

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Manganese binding site 6 out of 8 in the Phosphopentomutase V158L Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Phosphopentomutase V158L Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:19.9
occ:1.00
 OD2 C:ASP327 2.0 21.2 1.0
OD1 C:ASP13 2.1 21.0 1.0
OG1 C:TPO85 2.2 34.1 1.0
NE2 C:HIS328 2.3 22.1 1.0
OD2 C:ASP13 2.4 21.5 1.0
CG C:ASP13 2.6 22.8 1.0
CG C:ASP327 2.9 23.0 1.0
O1P C:TPO85 2.9 57.3 1.0
OD1 C:ASP327 3.1 20.3 1.0
CD2 C:HIS328 3.1 22.4 1.0
P C:TPO85 3.1 67.7 1.0
CB C:TPO85 3.2 27.1 1.0
CE1 C:HIS328 3.3 23.8 1.0
CG2 C:TPO85 3.5 27.8 1.0
CA C:TPO85 3.5 22.7 1.0
O2P C:TPO85 3.8 58.7 1.0
CB C:ASP13 4.0 20.8 1.0
N C:TPO85 4.2 20.8 1.0
CG C:HIS328 4.3 21.9 1.0
CB C:ASP327 4.3 23.3 1.0
ND1 C:HIS328 4.3 22.8 1.0
N C:SER14 4.4 19.2 1.0
O3P C:TPO85 4.4 71.0 1.0
CE1 C:HIS89 4.5 17.1 1.0
CE1 C:HIS339 4.5 31.1 1.0
CA C:ASP13 4.5 22.0 1.0
CG C:ASP286 4.5 24.5 1.0
C C:ASP13 4.7 20.1 1.0
OD1 C:ASP286 4.7 24.9 1.0
OD2 C:ASP286 4.7 25.7 1.0
C C:TPO85 4.8 21.3 1.0
ND1 C:HIS89 4.9 16.5 1.0
CB C:ASP286 4.9 23.2 1.0
NE2 C:HIS339 4.9 28.8 1.0
O C:TPO85 5.0 18.5 1.0
C C:ASP84 5.0 22.8 1.0

Manganese binding site 7 out of 8 in 4lrc

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Manganese binding site 7 out of 8 in the Phosphopentomutase V158L Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Phosphopentomutase V158L Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:22.6
occ:1.00
 NE2 C:HIS339 2.1 28.8 1.0
OD2 C:ASP156 2.1 34.3 1.0
OD1 C:ASP286 2.1 24.9 1.0
NE2 C:HIS291 2.1 21.0 1.0
O2P C:TPO85 2.2 58.7 1.0
CG C:ASP286 2.8 24.5 1.0
OD2 C:ASP286 2.8 25.7 1.0
CG C:ASP156 2.9 39.7 1.0
OD1 C:ASP156 2.9 36.4 1.0
CE1 C:HIS291 3.0 23.8 1.0
CE1 C:HIS339 3.1 31.1 1.0
CD2 C:HIS339 3.1 27.8 1.0
CD2 C:HIS291 3.1 22.1 1.0
P C:TPO85 3.6 67.7 1.0
O1P C:TPO85 4.1 57.3 1.0
ND1 C:HIS339 4.2 32.4 1.0
ND1 C:HIS291 4.2 22.0 1.0
CG C:HIS339 4.2 29.6 1.0
CB C:ASP286 4.2 23.2 1.0
CG C:HIS291 4.3 21.7 1.0
CB C:ASP156 4.4 33.6 1.0
ND2 C:ASN330 4.4 27.7 1.0
OG1 C:TPO85 4.5 34.1 1.0
O3P C:TPO85 4.5 71.0 1.0
CE1 C:HIS328 4.6 23.8 1.0
NE2 C:HIS328 4.8 22.1 1.0
CA C:ASP156 5.0 35.2 1.0
O C:ASP286 5.0 27.5 1.0

Manganese binding site 8 out of 8 in 4lrc

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Manganese binding site 8 out of 8 in the Phosphopentomutase V158L Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Phosphopentomutase V158L Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn403

b:41.5
occ:1.00
 OD1 C:ASP28 2.1 30.4 1.0
O C:HOH607 2.2 35.0 1.0
O C:HOH502 2.3 32.8 1.0
NE2 C:HIS334 2.4 22.9 1.0
O C:GLY27 2.4 28.3 1.0
O C:HOH501 2.5 30.8 1.0
CD2 C:HIS334 3.1 23.3 1.0
C C:GLY27 3.2 29.7 1.0
CG C:ASP28 3.3 30.4 1.0
CE1 C:HIS334 3.4 24.5 1.0
CA C:ASP28 3.7 29.5 1.0
N C:ASP28 3.8 29.6 1.0
O C:PHE26 3.9 38.5 1.0
CB C:ASP28 4.0 30.3 1.0
O C:HOH520 4.1 29.4 1.0
CA C:GLY27 4.1 31.9 1.0
OD2 C:ASP28 4.3 29.6 1.0
CG C:HIS334 4.3 20.4 1.0
NZ C:LYS83 4.4 24.5 1.0
ND1 C:HIS334 4.4 26.3 1.0
CG2 C:THR340 4.6 24.1 1.0
O C:HIS339 4.6 25.2 1.0
O C:HOH557 4.8 38.8 1.0
C C:PHE26 4.8 35.5 1.0
N C:GLY27 4.9 35.1 1.0
O C:PRO335 4.9 25.7 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 20:09:27 2024

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