Atomistry » Manganese » PDB 6oe2-6q9f » 6oiw
Atomistry »
  Manganese »
    PDB 6oe2-6q9f »
      6oiw »

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

Go back to Manganese Binding Sites List in 6oiw
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

Go back to Manganese Binding Sites List in 6oiw
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

Go back to Manganese Binding Sites List in 6oiw
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

Go back to Manganese Binding Sites List in 6oiw
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

Go back to Manganese Binding Sites List in 6oiw
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

Go back to Manganese Binding Sites List in 6oiw
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy