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Manganese in PDB 6oi7: Se-Met Structure of Apo- Escherichia Coli Dgtpase

Enzymatic activity of Se-Met Structure of Apo- Escherichia Coli Dgtpase

All present enzymatic activity of Se-Met Structure of Apo- Escherichia Coli Dgtpase:
3.1.5.1;

Protein crystallography data

The structure of Se-Met Structure of Apo- Escherichia Coli Dgtpase, PDB code: 6oi7 was solved by G.Calero, C.O.Barnes, Y.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.97 / 2.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 192.183, 192.183, 287.189, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 23.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Se-Met Structure of Apo- Escherichia Coli Dgtpase (pdb code 6oi7). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Se-Met Structure of Apo- Escherichia Coli Dgtpase, PDB code: 6oi7:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 6oi7

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Manganese binding site 1 out of 6 in the Se-Met Structure of Apo- Escherichia Coli Dgtpase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Se-Met Structure of Apo- Escherichia Coli Dgtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:0.1
occ:0.93
 NE2 A:HIS117 2.2 0.5 1.0
OD1 A:ASP268 2.5 0.4 1.0
CE1 A:HIS69 3.0 77.2 1.0
CD2 A:HIS117 3.1 0.8 1.0
OD1 A:ASP118 3.2 0.6 1.0
CE1 A:HIS117 3.3 0.2 1.0
ND1 A:HIS69 3.4 74.4 1.0
CG A:ASP268 3.7 0.8 1.0
CG A:ASP118 3.9 0.4 1.0
OD2 A:ASP118 4.0 0.1 1.0
OD2 A:ASP268 4.1 0.4 1.0
NE2 A:HIS69 4.2 78.8 1.0
CG A:HIS117 4.3 99.1 1.0
ND1 A:HIS117 4.3 0.1 1.0
CG2 A:VAL73 4.6 63.6 1.0
OE1 A:GLN53 4.6 0.8 1.0
CG A:HIS69 4.7 80.1 1.0
NH1 A:ARG66 4.8 0.3 1.0
CB A:ASP268 4.9 97.7 1.0

Manganese binding site 2 out of 6 in 6oi7

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Manganese binding site 2 out of 6 in the Se-Met Structure of Apo- Escherichia Coli Dgtpase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Se-Met Structure of Apo- Escherichia Coli Dgtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn601

b:0.2
occ:0.67
 NE2 B:HIS117 2.0 0.2 1.0
OD1 B:ASP268 2.4 0.8 1.0
CD2 B:HIS117 2.6 0.3 1.0
NE2 B:HIS69 2.7 0.8 1.0
CG B:ASP268 3.2 0.9 1.0
CE1 B:HIS117 3.2 0.4 1.0
CD2 B:HIS69 3.4 0.1 1.0
OD2 B:ASP268 3.4 0.9 1.0
OD2 B:ASP118 3.5 0.1 1.0
CE1 B:HIS69 3.7 0.8 1.0
OD1 B:ASP118 3.9 0.2 1.0
CG B:HIS117 3.9 0.7 1.0
CG B:ASP118 4.0 0.7 1.0
ND1 B:HIS117 4.1 0.6 1.0
CB B:ASP268 4.6 0.1 1.0
CG B:HIS69 4.6 0.3 1.0
ND1 B:HIS69 4.7 0.2 1.0
CB B:TYR272 4.7 1.0 1.0
OE1 B:GLN53 4.8 0.3 1.0

Manganese binding site 3 out of 6 in 6oi7

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Manganese binding site 3 out of 6 in the Se-Met Structure of Apo- Escherichia Coli Dgtpase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Se-Met Structure of Apo- Escherichia Coli Dgtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn601

b:0.8
occ:0.82
 NE2 C:HIS117 2.2 96.7 1.0
CD2 C:HIS117 2.8 0.3 1.0
OD1 C:ASP268 2.8 94.2 1.0
CE1 C:HIS69 2.9 83.1 1.0
OD1 C:ASP118 3.1 0.9 1.0
CE1 C:HIS117 3.5 95.1 1.0
ND1 C:HIS69 3.5 88.8 1.0
CG C:ASP268 3.6 99.4 1.0
OD2 C:ASP268 3.8 0.2 1.0
CG C:ASP118 3.8 0.2 1.0
OD2 C:ASP118 3.9 0.7 1.0
NE2 C:HIS69 4.0 86.0 1.0
CG C:HIS117 4.1 97.7 1.0
ND1 C:HIS117 4.4 0.7 1.0
OE1 C:GLN53 4.5 0.0 1.0
NH1 C:ARG66 4.5 1.0 1.0
CG C:HIS69 4.8 85.2 1.0
NE2 C:GLN53 4.9 0.3 1.0
CG2 C:VAL73 4.9 61.9 1.0

Manganese binding site 4 out of 6 in 6oi7

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Manganese binding site 4 out of 6 in the Se-Met Structure of Apo- Escherichia Coli Dgtpase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Se-Met Structure of Apo- Escherichia Coli Dgtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn601

b:0.6
occ:0.97
 NE2 D:HIS117 2.5 0.3 1.0
OD1 D:ASP268 2.6 0.3 1.0
CE1 D:HIS69 2.7 0.4 1.0
CD2 D:HIS117 3.3 0.1 1.0
CG D:ASP268 3.4 0.4 1.0
ND1 D:HIS69 3.5 0.8 1.0
OD2 D:ASP118 3.5 0.1 1.0
OD2 D:ASP268 3.5 0.8 1.0
CE1 D:HIS117 3.7 0.4 1.0
NE2 D:HIS69 3.7 0.4 1.0
CG D:ASP118 4.2 0.2 1.0
OD1 D:ASP118 4.4 0.8 1.0
CG D:HIS117 4.5 0.4 1.0
ND1 D:HIS117 4.7 0.0 1.0
CG D:HIS69 4.7 0.5 1.0
CD2 D:HIS69 4.8 0.8 1.0
CB D:ASP268 4.8 0.4 1.0
OE1 D:GLN53 4.9 0.3 1.0
NH1 D:ARG66 4.9 0.8 1.0

Manganese binding site 5 out of 6 in 6oi7

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Manganese binding site 5 out of 6 in the Se-Met Structure of Apo- Escherichia Coli Dgtpase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Se-Met Structure of Apo- Escherichia Coli Dgtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn601

b:0.1
occ:0.76
 NE2 E:HIS117 2.1 0.7 1.0
OD1 E:ASP268 2.7 0.8 1.0
CE1 E:HIS69 2.9 81.0 1.0
CD2 E:HIS117 3.0 0.4 1.0
CE1 E:HIS117 3.2 0.2 1.0
OD2 E:ASP118 3.2 0.1 1.0
ND1 E:HIS69 3.4 78.8 1.0
CG E:ASP268 3.8 0.4 1.0
CG E:ASP118 3.9 0.0 1.0
NE2 E:HIS69 4.0 84.1 1.0
OD1 E:ASP118 4.1 0.4 1.0
CG E:HIS117 4.2 0.1 1.0
ND1 E:HIS117 4.2 0.3 1.0
OD2 E:ASP268 4.3 0.7 1.0
OE1 E:GLN53 4.7 0.1 1.0
CG2 E:VAL73 4.7 76.5 1.0
CG E:HIS69 4.7 78.3 1.0
CB E:ASP268 4.9 0.5 1.0

Manganese binding site 6 out of 6 in 6oi7

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Manganese binding site 6 out of 6 in the Se-Met Structure of Apo- Escherichia Coli Dgtpase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Se-Met Structure of Apo- Escherichia Coli Dgtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn601

b:0.6
occ:0.60
 NE2 F:HIS117 2.1 0.1 1.0
OD1 F:ASP268 2.6 0.7 1.0
CD2 F:HIS117 2.7 0.1 1.0
NE2 F:HIS69 3.0 87.7 1.0
CE1 F:HIS117 3.3 0.0 1.0
CD2 F:HIS69 3.5 80.1 1.0
CG F:ASP268 3.5 0.6 1.0
OD1 F:ASP118 3.6 0.1 1.0
OD2 F:ASP268 3.9 0.5 1.0
CG F:HIS117 4.0 0.2 1.0
CE1 F:HIS69 4.2 93.1 1.0
ND1 F:HIS117 4.2 0.4 1.0
CG F:ASP118 4.3 0.5 1.0
OD2 F:ASP118 4.3 0.5 1.0
CG2 F:VAL73 4.6 64.5 1.0
CB F:ASP268 4.7 90.3 1.0
CG F:HIS69 4.8 76.7 1.0

Reference:

C.O.Barnes, Y.Wu, J.Song, G.Lin, E.L.Baxter, A.S.Brewster, V.Nagarajan, A.Holmes, S.M.Soltis, N.K.Sauter, J.Ahn, A.E.Cohen, G.Calero. The Crystal Structure of Dgtpase Reveals the Molecular Basis of Dgtp Selectivity. Proc.Natl.Acad.Sci.Usa V. 116 9333 2019.
ISSN: ESSN 1091-6490
PubMed: 31019074
DOI: 10.1073/PNAS.1814999116
Page generated: Sun Oct 6 05:43:05 2024

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