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Manganese in PDB 6oiw: Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol

Enzymatic activity of Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol

All present enzymatic activity of Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol:
3.1.5.1;

Protein crystallography data

The structure of Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol, PDB code: 6oiw was solved by C.O.Barnes, Y.Wu, G.Calero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.48 / 3.35
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 191.240, 191.240, 298.610, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.2

Other elements in 6oiw:

The structure of Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Manganese Binding Sites:

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

Manganese binding site 1 out of 6 in 6oiw

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Manganese binding site 1 out of 6 in the Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:0.6
occ:1.00
 NE2 A:HIS117 2.4 0.2 1.0
OD1 A:ASP268 2.5 0.7 1.0
NE2 A:HIS69 2.6 0.2 1.0
OD2 A:ASP268 2.9 0.0 1.0
CD2 A:HIS117 2.9 0.2 1.0
CG A:ASP268 3.1 0.7 1.0
CD2 A:HIS69 3.2 0.5 1.0
OD2 A:ASP118 3.3 0.9 1.0
CE1 A:HIS117 3.7 0.3 1.0
O A:HOH702 3.7 87.7 1.0
CE1 A:HIS69 3.8 0.1 1.0
CG A:ASP118 4.1 0.6 1.0
CG A:HIS117 4.2 0.4 1.0
OD1 A:ASP118 4.3 0.5 1.0
CG A:HIS69 4.5 99.8 1.0
CB A:ASP268 4.5 91.8 1.0
CD2 A:TYR272 4.6 0.9 1.0
ND1 A:HIS117 4.6 1.0 1.0
NH1 A:ARG66 4.6 0.5 1.0
OE1 A:GLN53 4.7 0.0 1.0
ND1 A:HIS69 4.7 0.4 1.0
S1A A:T8T603 4.8 0.3 1.0
O3A A:T8T603 4.9 1.0 1.0

Manganese binding site 2 out of 6 in 6oiw

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Manganese binding site 2 out of 6 in the Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn601

b:0.3
occ:1.00
 OD1 B:ASP268 2.0 0.8 1.0
NE2 B:HIS117 2.0 0.1 1.0
CE1 B:HIS117 2.2 0.2 1.0
CE1 B:HIS69 2.7 0.1 1.0
CG B:ASP268 2.7 0.2 1.0
OD2 B:ASP268 2.9 1.0 1.0
O1B B:T8T602 3.0 0.2 1.0
OD2 B:ASP118 3.2 0.4 1.0
NE2 B:HIS69 3.3 0.4 1.0
CD2 B:HIS117 3.4 0.9 1.0
ND1 B:HIS117 3.5 0.7 1.0
ND1 B:HIS69 3.7 0.9 1.0
CG B:ASP118 4.0 0.5 1.0
CB B:ASP268 4.0 0.4 1.0
CG B:HIS117 4.1 0.7 1.0
OD1 B:ASP118 4.3 0.9 1.0
PB B:T8T602 4.3 0.4 1.0
CD2 B:TYR272 4.3 0.8 1.0
CD2 B:HIS69 4.5 0.2 1.0
CA B:ASP268 4.6 0.0 1.0
O B:ASP268 4.6 0.4 1.0
CG B:HIS69 4.7 0.5 1.0
O2B B:T8T602 4.8 0.2 1.0
C5' B:T8T602 4.8 0.2 1.0
CG2 B:VAL73 4.9 0.9 1.0
C B:ASP268 5.0 0.3 1.0
CE2 B:TYR272 5.0 0.8 1.0
O3B B:T8T602 5.0 0.4 1.0

Manganese binding site 3 out of 6 in 6oiw

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Manganese binding site 3 out of 6 in the Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn601

b:0.5
occ:1.00
 NE2 C:HIS117 2.0 0.7 1.0
OD1 C:ASP268 2.2 0.2 1.0
CD2 C:HIS117 2.7 0.8 1.0
NE2 C:HIS69 2.8 98.4 1.0
CG C:ASP268 3.2 0.9 1.0
CE1 C:HIS117 3.2 0.8 1.0
OD1 C:ASP118 3.3 0.4 1.0
OD2 C:ASP118 3.5 0.8 1.0
OD2 C:ASP268 3.5 0.5 1.0
CD2 C:HIS69 3.6 98.1 1.0
CG C:ASP118 3.7 0.1 1.0
CE1 C:HIS69 3.9 98.9 1.0
CG C:HIS117 3.9 0.4 1.0
O C:HOH701 4.2 94.8 1.0
ND1 C:HIS117 4.2 0.5 1.0
CB C:ASP268 4.5 0.6 1.0
O2B C:T8T602 4.6 0.2 1.0
CD2 C:TYR272 4.7 0.7 1.0
C5' C:T8T602 4.7 0.3 1.0
CG C:HIS69 4.8 96.7 1.0
OE1 C:GLN53 4.9 0.5 1.0
CG2 C:VAL73 4.9 86.3 1.0
ND1 C:HIS69 5.0 99.4 1.0

Manganese binding site 4 out of 6 in 6oiw

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Manganese binding site 4 out of 6 in the Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn601

b:0.1
occ:1.00
 OD1 D:ASP268 2.4 0.9 1.0
NE2 D:HIS117 2.7 0.5 1.0
O1B D:T8T602 2.9 0.4 1.0
OD2 D:ASP118 2.9 0.7 1.0
NE2 D:HIS69 2.9 0.4 1.0
CD2 D:HIS117 3.0 0.6 1.0
CG D:ASP268 3.2 0.2 1.0
OD2 D:ASP268 3.3 0.8 1.0
OD1 D:ASP118 3.5 0.5 1.0
CG D:ASP118 3.6 0.1 1.0
CD2 D:HIS69 3.6 0.0 1.0
CE1 D:HIS117 3.9 0.1 1.0
CE1 D:HIS69 4.1 0.1 1.0
PB D:T8T602 4.1 1.0 1.0
O2B D:T8T602 4.1 0.9 1.0
CG D:HIS117 4.3 0.4 1.0
CB D:ASP268 4.5 0.2 1.0
ND1 D:HIS117 4.7 0.7 1.0
NH1 D:ARG66 4.7 0.9 1.0
CG D:HIS69 4.8 0.8 1.0
C5' D:T8T602 4.9 0.8 1.0
CD2 D:TYR272 5.0 0.9 1.0

Manganese binding site 5 out of 6 in 6oiw

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Manganese binding site 5 out of 6 in the Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn602

b:0.8
occ:1.00
 OD1 E:ASP268 2.4 0.7 1.0
NE2 E:HIS117 2.5 0.8 1.0
CG E:ASP268 3.3 0.6 1.0
OD2 E:ASP118 3.3 1.0 1.0
CD2 E:HIS117 3.4 0.8 1.0
NE2 E:HIS69 3.4 0.0 1.0
OD2 E:ASP268 3.4 0.7 1.0
CE1 E:HIS117 3.6 0.3 1.0
O2A E:T8T603 3.6 0.3 1.0
OD1 E:ASP118 3.6 0.3 1.0
O5' E:T8T603 3.7 0.5 1.0
CG E:ASP118 3.8 0.2 1.0
C5' E:T8T603 3.8 0.1 1.0
CD2 E:HIS69 4.0 0.1 1.0
PA E:T8T603 4.1 0.1 1.0
O3A E:T8T603 4.3 0.6 1.0
O1B E:T8T603 4.3 0.5 1.0
CE1 E:HIS69 4.5 0.7 1.0
CG E:HIS117 4.6 0.5 1.0
NE2 E:GLN53 4.7 0.3 1.0
ND1 E:HIS117 4.7 0.6 1.0
CB E:ASP268 4.7 0.1 1.0
CD2 E:TYR272 4.7 0.3 1.0
OE1 E:GLN53 4.7 0.7 1.0
C4' E:T8T603 4.8 0.5 1.0
PB E:T8T603 4.8 0.9 1.0

Manganese binding site 6 out of 6 in 6oiw

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Manganese binding site 6 out of 6 in the Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn602

b:0.2
occ:1.00
 OD1 F:ASP268 2.2 0.4 1.0
NE2 F:HIS117 2.6 0.4 1.0
NE2 F:HIS69 2.7 0.8 1.0
O1B F:T8T603 3.1 0.8 0.9
CG F:ASP268 3.3 0.8 1.0
CD2 F:HIS69 3.5 1.0 1.0
CE1 F:HIS117 3.5 0.7 1.0
OD2 F:ASP118 3.6 0.0 1.0
CD2 F:HIS117 3.6 0.9 1.0
OD2 F:ASP268 3.7 0.6 1.0
CE1 F:HIS69 3.8 0.8 1.0
CD2 F:TYR272 4.1 0.7 1.0
C5' F:T8T603 4.2 0.3 0.9
CB F:ASP268 4.5 0.3 1.0
OE1 F:GLN53 4.6 0.3 1.0
PB F:T8T603 4.6 0.6 0.9
CG F:ASP118 4.6 0.7 1.0
ND1 F:HIS117 4.7 0.7 1.0
CE2 F:TYR272 4.7 0.4 1.0
CG F:HIS117 4.7 0.3 1.0
CG F:HIS69 4.7 99.7 1.0
CG F:TYR272 4.8 0.0 1.0
CB F:TYR272 4.8 0.6 1.0
ND1 F:HIS69 4.8 0.6 1.0
C4' F:T8T603 4.8 0.5 0.9
O F:ASP268 4.9 0.2 1.0
OD1 F:ASP118 4.9 0.5 1.0
NE2 F:GLN53 5.0 0.0 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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