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Manganese in PDB 6oiv: Xfel Structure of Escherichia Coli Dgtpase

Enzymatic activity of Xfel Structure of Escherichia Coli Dgtpase

All present enzymatic activity of Xfel Structure of Escherichia Coli Dgtpase:
3.1.5.1;

Protein crystallography data

The structure of Xfel Structure of Escherichia Coli Dgtpase, PDB code: 6oiv 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) 61.20 / 3.06
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 192.589, 192.589, 291.254, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 24.8

Manganese Binding Sites:

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

Manganese binding site 1 out of 6 in 6oiv

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Manganese binding site 1 out of 6 in the Xfel Structure of 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 Xfel Structure of Escherichia Coli Dgtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:69.5
occ:0.93
 NE2 A:HIS117 2.5 34.2 1.0
OD1 A:ASP268 2.6 45.8 1.0
NE2 A:HIS69 3.0 29.7 1.0
CD2 A:HIS117 3.3 34.3 1.0
OD1 A:ASP118 3.4 34.1 1.0
CG A:ASP268 3.4 49.7 1.0
CE1 A:HIS117 3.6 34.1 1.0
OD2 A:ASP268 3.6 61.3 1.0
OD2 A:ASP118 3.7 39.0 1.0
CE1 A:HIS69 3.8 29.2 1.0
CG A:ASP118 3.9 34.1 1.0
CD2 A:HIS69 3.9 30.1 1.0
CG A:HIS117 4.5 32.2 1.0
ND1 A:HIS117 4.7 34.7 1.0
CB A:ASP268 4.7 44.2 1.0
OE1 A:GLN53 4.8 70.2 1.0
ND1 A:HIS69 4.9 29.8 1.0
CG A:HIS69 5.0 28.2 1.0

Manganese binding site 2 out of 6 in 6oiv

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Manganese binding site 2 out of 6 in the Xfel Structure of 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 Xfel Structure of Escherichia Coli Dgtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn601

b:43.2
occ:0.67
 NE2 B:HIS117 2.7 94.8 1.0
OD2 B:ASP118 3.0 95.0 1.0
OD1 B:ASP268 3.1 92.5 1.0
OD1 B:ASP118 3.2 90.8 1.0
NE2 B:HIS69 3.4 79.0 1.0
CD2 B:HIS117 3.4 95.2 1.0
CG B:ASP118 3.5 91.5 1.0
CE1 B:HIS117 3.9 94.6 1.0
NH1 B:ARG66 3.9 0.1 1.0
OD2 B:ASP268 3.9 94.1 1.0
CG B:ASP268 3.9 91.4 1.0
CE1 B:HIS69 4.1 78.9 1.0
CD2 B:HIS69 4.2 79.1 1.0
OE1 B:GLN53 4.6 94.2 1.0
CG B:HIS117 4.7 93.3 1.0
ND1 B:HIS117 4.9 95.3 1.0
CB B:ASP118 5.0 87.2 1.0

Manganese binding site 3 out of 6 in 6oiv

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Manganese binding site 3 out of 6 in the Xfel Structure of 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 Xfel Structure of Escherichia Coli Dgtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn601

b:39.3
occ:0.82
 NE2 C:HIS117 2.5 26.7 1.0
OD1 C:ASP268 2.6 52.3 1.0
CE1 C:HIS69 3.1 28.7 1.0
O C:HOH703 3.2 5.1 1.0
CD2 C:HIS117 3.4 27.6 1.0
CG C:ASP268 3.5 52.4 1.0
CE1 C:HIS117 3.6 26.2 1.0
OD2 C:ASP268 3.6 60.8 1.0
NE2 C:HIS69 3.7 28.7 1.0
OD1 C:ASP118 3.8 54.2 1.0
OD2 C:ASP118 4.1 57.8 1.0
ND1 C:HIS69 4.1 29.3 1.0
CG C:ASP118 4.3 52.9 1.0
NH1 C:ARG66 4.5 0.5 1.0
CG C:HIS117 4.6 26.2 1.0
ND1 C:HIS117 4.6 27.4 1.0
OE1 C:GLN53 4.7 96.1 1.0
CD2 C:HIS69 4.9 28.7 1.0
CB C:ASP268 4.9 38.8 1.0

Manganese binding site 4 out of 6 in 6oiv

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Manganese binding site 4 out of 6 in the Xfel Structure of 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 Xfel Structure of Escherichia Coli Dgtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn601

b:0.1
occ:0.97
 NE2 D:HIS117 2.2 96.8 1.0
CE1 D:HIS69 2.3 78.4 1.0
OD1 D:ASP268 2.4 97.7 1.0
OD2 D:ASP268 2.8 0.9 1.0
NE2 D:HIS69 2.9 78.6 1.0
CG D:ASP268 2.9 97.6 1.0
CE1 D:HIS117 3.1 96.4 1.0
CD2 D:HIS117 3.2 96.9 1.0
ND1 D:HIS69 3.5 79.3 1.0
OD1 D:ASP118 3.5 0.9 1.0
CD2 D:HIS69 4.2 78.8 1.0
ND1 D:HIS117 4.2 96.6 1.0
CB D:ASP268 4.2 88.3 1.0
CG D:HIS117 4.3 94.5 1.0
CG2 D:VAL73 4.3 87.4 1.0
CG D:HIS69 4.4 77.5 1.0
CG D:ASP118 4.6 0.7 1.0
O D:ASP268 4.7 90.5 1.0
CA D:ASP268 4.7 86.6 1.0
OE1 D:GLN53 4.9 0.7 1.0
C D:ASP268 5.0 91.2 1.0

Manganese binding site 5 out of 6 in 6oiv

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Manganese binding site 5 out of 6 in the Xfel Structure of 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 Xfel Structure of Escherichia Coli Dgtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn601

b:43.4
occ:0.76
 OD1 E:ASP268 2.5 41.2 1.0
NE2 E:HIS69 2.5 40.2 1.0
NE2 E:HIS117 2.8 41.8 1.0
O E:HOH702 2.8 3.0 1.0
CE1 E:HIS69 3.2 39.3 1.0
CG E:ASP268 3.5 42.4 1.0
CD2 E:HIS69 3.5 40.4 1.0
CE1 E:HIS117 3.7 40.9 1.0
OD2 E:ASP118 3.7 56.7 1.0
CD2 E:HIS117 3.7 42.0 1.0
OD2 E:ASP268 3.8 54.7 1.0
OD1 E:ASP118 4.3 54.5 1.0
ND1 E:HIS69 4.4 38.8 1.0
CG E:ASP118 4.4 51.6 1.0
CG E:HIS69 4.5 36.6 1.0
NE2 E:GLN53 4.6 37.5 1.0
CB E:ASP268 4.8 30.3 1.0
ND1 E:HIS117 4.9 41.0 1.0
O E:ASP268 4.9 28.2 1.0
CG2 E:VAL73 4.9 13.0 1.0
CG E:HIS117 4.9 38.8 1.0
NH2 E:ARG66 5.0 0.6 1.0
CD1 E:TYR272 5.0 66.5 1.0

Manganese binding site 6 out of 6 in 6oiv

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Manganese binding site 6 out of 6 in the Xfel Structure of 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 Xfel Structure of Escherichia Coli Dgtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn601

b:26.4
occ:0.60
 OD1 F:ASP268 2.0 62.1 1.0
NE2 F:HIS69 2.2 34.3 1.0
NE2 F:HIS117 2.8 21.4 1.0
CE1 F:HIS69 2.8 34.2 1.0
CG F:ASP268 3.2 59.7 1.0
O F:HOH702 3.4 3.0 1.0
CD2 F:HIS69 3.5 34.0 1.0
CE1 F:HIS117 3.6 21.1 1.0
CD2 F:HIS117 3.8 22.0 1.0
OD2 F:ASP268 3.9 66.8 1.0
O F:ASP268 4.0 35.5 1.0
ND1 F:HIS69 4.1 34.4 1.0
OD1 F:ASP118 4.2 22.6 1.0
CB F:ASP268 4.2 39.1 1.0
CG2 F:VAL73 4.3 24.7 1.0
CG F:HIS69 4.4 31.6 1.0
CA F:ASP268 4.6 35.9 1.0
CA F:TYR272 4.8 49.7 1.0
ND1 F:HIS117 4.8 22.4 1.0
C F:ASP268 4.8 36.1 1.0
CD1 F:TYR272 4.9 63.0 1.0
CG F:HIS117 4.9 20.8 1.0
CG F:ASP118 4.9 23.2 1.0
OD2 F:ASP118 4.9 26.5 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 05:43:04 2024

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