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Manganese in PDB 3un2: Phosphopentomutase T85Q Variant Enzyme

Enzymatic activity of Phosphopentomutase T85Q Variant Enzyme

All present enzymatic activity of Phosphopentomutase T85Q Variant Enzyme:
5.4.2.7;

Protein crystallography data

The structure of Phosphopentomutase T85Q Variant Enzyme, PDB code: 3un2 was solved by T.M.Iverson, W.R.Birmingham, T.D.Panosian, D.P.Nannemann, B.O.Bachmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.897, 76.720, 107.190, 90.00, 108.68, 90.00
R / Rfree (%) 16.7 / 19.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Phosphopentomutase T85Q Variant Enzyme (pdb code 3un2). 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 T85Q Variant Enzyme, PDB code: 3un2:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 3un2

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Manganese binding site 1 out of 9 in the Phosphopentomutase T85Q Variant Enzyme


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Phosphopentomutase T85Q Variant Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn395

b:15.4
occ:1.00
 OD2 A:ASP156 2.1 23.8 1.0
NE2 A:HIS291 2.2 13.9 1.0
OD1 A:ASP286 2.2 16.3 1.0
NE2 A:HIS339 2.2 13.9 1.0
OD2 A:ASP286 2.6 15.1 1.0
CG A:ASP286 2.7 14.9 1.0
O A:HOH410 2.8 16.0 1.0
CG A:ASP156 3.1 24.0 1.0
CE1 A:HIS291 3.1 15.9 1.0
CD2 A:HIS291 3.1 14.8 1.0
CE1 A:HIS339 3.1 16.9 1.0
CD2 A:HIS339 3.2 14.6 1.0
OD1 A:ASP156 3.3 25.6 1.0
O A:HOH541 3.9 32.3 1.0
CB A:ASP286 4.2 13.3 1.0
ND2 A:ASN330 4.2 16.4 1.0
ND1 A:HIS291 4.2 16.1 1.0
ND1 A:HIS339 4.3 15.7 1.0
CG A:HIS291 4.3 16.1 1.0
CG A:HIS339 4.3 14.5 1.0
CE1 A:HIS328 4.5 13.8 1.0
CB A:ASP156 4.5 22.6 1.0
O A:HOH411 4.5 26.0 1.0
NE2 A:HIS328 4.8 15.1 1.0
MN A:MN396 4.9 17.4 1.0
O A:HOH438 4.9 29.8 1.0

Manganese binding site 2 out of 9 in 3un2

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Manganese binding site 2 out of 9 in the Phosphopentomutase T85Q Variant Enzyme


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Phosphopentomutase T85Q Variant Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn396

b:17.4
occ:1.00
 OD1 A:ASP13 2.1 14.0 1.0
OD2 A:ASP327 2.1 14.4 1.0
OE1 A:GLN85 2.2 25.7 1.0
NE2 A:HIS328 2.3 15.1 1.0
OD2 A:ASP13 2.5 16.6 1.0
O A:HOH410 2.5 16.0 1.0
CG A:ASP13 2.6 15.0 1.0
CG A:ASP327 3.0 13.9 1.0
CD A:GLN85 3.1 22.8 1.0
CD2 A:HIS328 3.2 14.8 1.0
CE1 A:HIS328 3.2 13.8 1.0
OD1 A:ASP327 3.3 15.5 1.0
NE2 A:GLN85 3.7 24.0 1.0
CB A:ASP13 4.0 13.1 1.0
CA A:GLN85 4.2 18.1 1.0
ND1 A:HIS328 4.3 14.3 1.0
CG A:HIS328 4.3 14.0 1.0
CG A:GLN85 4.3 20.9 1.0
CB A:GLN85 4.3 18.9 1.0
N A:SER14 4.4 13.2 1.0
CB A:ASP327 4.4 12.8 1.0
OD2 A:ASP286 4.5 15.1 1.0
NE2 A:HIS89 4.5 17.4 1.0
CG A:ASP286 4.5 14.9 1.0
CE1 A:HIS339 4.5 16.9 1.0
CA A:ASP13 4.5 13.0 1.0
C A:ASP13 4.7 12.9 1.0
CD2 A:HIS89 4.8 13.5 1.0
OD1 A:ASP286 4.8 16.3 1.0
NE2 A:HIS339 4.8 13.9 1.0
CB A:ASP286 4.9 13.3 1.0
N A:GLN85 4.9 17.6 1.0
MN A:MN395 4.9 15.4 1.0

Manganese binding site 3 out of 9 in 3un2

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Manganese binding site 3 out of 9 in the Phosphopentomutase T85Q Variant Enzyme


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Phosphopentomutase T85Q Variant Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn397

b:35.8
occ:0.75
 O A:HOH729 1.9 31.9 1.0
NE2 A:HIS334 2.0 23.9 1.0
OD1 A:ASP28 2.1 21.7 1.0
O A:HOH722 2.4 33.3 1.0
CD2 A:HIS334 2.6 23.0 1.0
O A:GLY27 2.8 26.6 1.0
CE1 A:HIS334 3.2 23.2 1.0
CG A:ASP28 3.3 20.5 1.0
C A:GLY27 3.6 25.8 1.0
CG A:HIS334 3.8 21.2 1.0
CA A:ASP28 3.9 22.0 1.0
O A:HOH466 4.0 21.9 1.0
ND1 A:HIS334 4.1 23.3 1.0
N A:ASP28 4.1 23.7 1.0
O A:PHE26 4.1 27.4 1.0
CB A:ASP28 4.2 20.1 1.0
OD2 A:ASP28 4.2 19.4 1.0
CG2 A:THR340 4.3 17.9 1.0
NZ A:LYS83 4.4 20.5 1.0
CA A:GLY27 4.6 27.6 1.0
O A:PRO335 4.6 22.4 1.0
O A:HIS339 4.8 15.9 1.0
O A:HOH613 4.9 29.9 1.0
C A:PHE26 4.9 27.5 1.0

Manganese binding site 4 out of 9 in 3un2

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Manganese binding site 4 out of 9 in the Phosphopentomutase T85Q Variant Enzyme


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Phosphopentomutase T85Q Variant Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn395

b:16.8
occ:1.00
 OD2 B:ASP156 2.1 25.5 1.0
NE2 B:HIS339 2.1 15.0 1.0
OD1 B:ASP286 2.2 17.8 1.0
NE2 B:HIS291 2.2 17.8 1.0
O B:HOH402 2.5 20.5 1.0
OD2 B:ASP286 2.6 19.4 1.0
CG B:ASP286 2.7 17.6 1.0
CE1 B:HIS339 3.1 15.8 1.0
CG B:ASP156 3.1 25.7 1.0
CD2 B:HIS339 3.1 16.6 1.0
CE1 B:HIS291 3.1 18.8 1.0
CD2 B:HIS291 3.2 18.6 1.0
OD1 B:ASP156 3.3 26.2 1.0
O B:HOH617 3.9 37.6 1.0
ND1 B:HIS339 4.2 16.8 1.0
CB B:ASP286 4.2 16.6 1.0
ND1 B:HIS291 4.3 18.6 1.0
CG B:HIS339 4.3 17.1 1.0
CG B:HIS291 4.3 18.6 1.0
ND2 B:ASN330 4.3 17.4 1.0
CE1 B:HIS328 4.4 16.4 1.0
CB B:ASP156 4.5 22.7 1.0
O B:HOH685 4.6 27.1 1.0
NE2 B:HIS328 4.7 15.1 1.0
MN B:MN396 4.9 18.7 1.0
O B:HOH416 4.9 35.2 1.0

Manganese binding site 5 out of 9 in 3un2

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Manganese binding site 5 out of 9 in the Phosphopentomutase T85Q Variant Enzyme


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Phosphopentomutase T85Q Variant Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn396

b:18.7
occ:1.00
 OD2 B:ASP327 2.1 16.1 1.0
OD1 B:ASP13 2.2 16.3 1.0
OE1 B:GLN85 2.2 27.8 1.0
NE2 B:HIS328 2.3 15.1 1.0
OD2 B:ASP13 2.5 18.9 1.0
CG B:ASP13 2.6 17.8 1.0
O B:HOH402 2.8 20.5 1.0
CG B:ASP327 3.0 13.1 1.0
CD B:GLN85 3.1 25.4 1.0
CD2 B:HIS328 3.2 16.1 1.0
OD1 B:ASP327 3.2 13.9 1.0
CE1 B:HIS328 3.3 16.4 1.0
NE2 B:GLN85 3.6 27.4 1.0
CB B:ASP13 4.1 16.9 1.0
CA B:GLN85 4.1 18.6 1.0
CG B:GLN85 4.3 22.7 1.0
CG B:HIS328 4.3 16.0 1.0
CB B:GLN85 4.3 20.5 1.0
ND1 B:HIS328 4.3 16.6 1.0
CB B:ASP327 4.4 13.5 1.0
N B:SER14 4.4 15.7 1.0
OD2 B:ASP286 4.5 19.4 1.0
CE1 B:HIS339 4.5 15.8 1.0
NE2 B:HIS89 4.5 17.6 1.0
CG B:ASP286 4.5 17.6 1.0
CA B:ASP13 4.6 15.9 1.0
C B:ASP13 4.8 16.5 1.0
CD2 B:HIS89 4.8 14.1 1.0
NE2 B:HIS339 4.8 15.0 1.0
OD1 B:ASP286 4.8 17.8 1.0
N B:GLN85 4.8 18.2 1.0
MN B:MN395 4.9 16.8 1.0
CB B:ASP286 4.9 16.6 1.0

Manganese binding site 6 out of 9 in 3un2

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Manganese binding site 6 out of 9 in the Phosphopentomutase T85Q Variant Enzyme


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Phosphopentomutase T85Q Variant Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn397

b:49.1
occ:0.50
 NE2 B:HIS36 2.3 29.1 1.0
O B:HOH471 2.8 45.3 1.0
CD2 B:HIS36 3.2 28.0 1.0
O B:HOH675 3.2 42.8 1.0
CE1 B:HIS36 3.4 27.4 1.0
OE1 B:GLU39 4.0 33.5 0.5
O B:HOH919 4.0 56.9 1.0
CG B:HIS36 4.4 25.8 1.0
ND1 B:HIS36 4.5 26.6 1.0
O B:HOH705 4.6 40.5 1.0
O B:GLY30 4.7 26.2 1.0
CD B:GLU39 5.0 33.8 0.5

Manganese binding site 7 out of 9 in 3un2

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Manganese binding site 7 out of 9 in the Phosphopentomutase T85Q Variant Enzyme


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Phosphopentomutase T85Q Variant Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn395

b:24.8
occ:1.00
 OD2 C:ASP156 2.1 42.0 1.0
OD1 C:ASP286 2.1 26.8 1.0
NE2 C:HIS339 2.2 29.3 1.0
NE2 C:HIS291 2.2 28.0 1.0
OD2 C:ASP286 2.6 28.8 1.0
CG C:ASP286 2.7 27.8 1.0
O C:HOH409 2.9 31.3 1.0
CE1 C:HIS339 3.1 28.4 1.0
CG C:ASP156 3.1 40.3 1.0
CD2 C:HIS291 3.2 28.9 1.0
CE1 C:HIS291 3.2 29.6 1.0
CD2 C:HIS339 3.2 29.9 1.0
OD1 C:ASP156 3.5 40.2 1.0
O C:HOH552 3.8 52.0 1.0
CB C:ASP286 4.2 27.9 1.0
O C:HOH986 4.2 37.6 1.0
ND1 C:HIS339 4.3 28.7 1.0
ND2 C:ASN330 4.3 30.8 1.0
ND1 C:HIS291 4.3 30.2 1.0
CG C:HIS339 4.3 29.7 1.0
CG C:HIS291 4.3 30.6 1.0
CB C:ASP156 4.5 37.7 1.0
CE1 C:HIS328 4.5 29.1 1.0
O C:HOH723 4.7 37.4 1.0
NE2 C:HIS328 4.7 27.8 1.0
MN C:MN396 4.9 26.8 1.0

Manganese binding site 8 out of 9 in 3un2

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Manganese binding site 8 out of 9 in the Phosphopentomutase T85Q Variant Enzyme


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Phosphopentomutase T85Q Variant Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn396

b:26.8
occ:1.00
 OD1 C:ASP13 2.1 26.9 1.0
OD2 C:ASP327 2.1 26.3 1.0
NE2 C:HIS328 2.3 27.8 1.0
O C:HOH409 2.4 31.3 1.0
OD2 C:ASP13 2.6 26.3 1.0
CG C:ASP13 2.6 27.0 1.0
CG C:ASP327 3.0 27.0 1.0
CD2 C:HIS328 3.1 28.1 1.0
OD1 C:ASP327 3.2 29.5 1.0
CE1 C:HIS328 3.3 29.1 1.0
OE1 C:GLN85 3.4 34.5 1.0
CB C:GLN85 3.9 27.8 1.0
CA C:GLN85 3.9 27.8 1.0
CB C:ASP13 4.1 27.3 1.0
CD C:GLN85 4.2 32.2 1.0
CG C:GLN85 4.2 29.2 1.0
CG C:HIS328 4.3 29.3 1.0
ND1 C:HIS328 4.4 30.4 1.0
N C:SER14 4.4 29.9 1.0
CB C:ASP327 4.4 27.0 1.0
NE2 C:HIS89 4.4 26.5 1.0
CE1 C:HIS339 4.5 28.4 1.0
CA C:ASP13 4.6 28.7 1.0
CG C:ASP286 4.6 27.8 1.0
OD2 C:ASP286 4.6 28.8 1.0
N C:GLN85 4.7 28.1 1.0
C C:ASP13 4.7 29.7 1.0
CD2 C:HIS89 4.8 23.8 1.0
NE2 C:HIS339 4.9 29.3 1.0
OD1 C:ASP286 4.9 26.8 1.0
CB C:ASP286 4.9 27.9 1.0
MN C:MN395 4.9 24.8 1.0

Manganese binding site 9 out of 9 in 3un2

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Manganese binding site 9 out of 9 in the Phosphopentomutase T85Q Variant Enzyme


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Phosphopentomutase T85Q Variant Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn397

b:43.6
occ:1.00
 O C:HOH431 2.1 41.6 1.0
OD1 C:ASP28 2.1 37.4 1.0
O C:HOH536 2.2 34.7 1.0
NE2 C:HIS334 2.3 43.1 1.0
O C:HOH980 2.3 49.2 1.0
O C:GLY27 2.7 44.3 1.0
CD2 C:HIS334 3.2 41.5 1.0
CG C:ASP28 3.3 38.5 1.0
CE1 C:HIS334 3.3 45.6 1.0
C C:GLY27 3.4 45.0 1.0
CA C:ASP28 3.8 43.5 1.0
N C:ASP28 3.9 44.7 1.0
O C:PHE26 3.9 43.6 1.0
O C:HOH423 4.0 37.4 1.0
CB C:ASP28 4.1 41.5 1.0
OD2 C:ASP28 4.2 36.7 1.0
CA C:GLY27 4.3 46.3 1.0
CG C:HIS334 4.3 42.6 1.0
ND1 C:HIS334 4.4 45.0 1.0
NZ C:LYS83 4.4 35.3 1.0
CG2 C:THR340 4.6 39.2 1.0
O C:HIS339 4.6 34.4 1.0
C C:PHE26 4.8 45.0 1.0
O C:PRO335 5.0 39.5 1.0

Reference:

T.M.Iverson, T.D.Panosian, W.R.Birmingham, D.P.Nannemann, B.O.Bachmann. Molecular Differences Between A Mutase and A Phosphatase: Investigations of the Activation Step in Bacillus Cereus Phosphopentomutase. Biochemistry V. 51 1964 2012.
ISSN: ISSN 0006-2960
PubMed: 22329805
DOI: 10.1021/BI201761H
Page generated: Sat Oct 5 18:06:27 2024

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