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

Manganese in PDB 6oix: Structure of Escherichia Coli Dgtpase Bound to Gtp

Enzymatic activity of Structure of Escherichia Coli Dgtpase Bound to Gtp

All present enzymatic activity of Structure of Escherichia Coli Dgtpase Bound to Gtp:
3.1.5.1;

Protein crystallography data

The structure of Structure of Escherichia Coli Dgtpase Bound to Gtp, PDB code: 6oix 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) 31.75 / 3.15
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 191.587, 191.587, 292.870, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 20.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Escherichia Coli Dgtpase Bound to Gtp (pdb code 6oix). 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 Gtp, PDB code: 6oix:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 6oix

Go back to Manganese Binding Sites List in 6oix
Manganese binding site 1 out of 6 in the Structure of Escherichia Coli Dgtpase Bound to Gtp


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 Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:0.4
occ:1.00
OD1 A:ASP268 2.8 0.3 1.0
NE2 A:HIS69 2.8 99.4 1.0
NE2 A:HIS117 3.0 97.0 0.8
O3' A:GTP601 3.4 0.9 0.9
CD2 A:HIS69 3.5 98.1 1.0
CD2 A:HIS117 3.7 96.5 0.8
CG A:ASP268 3.7 1.0 1.0
OD2 A:ASP268 3.9 0.7 1.0
CE1 A:HIS69 3.9 0.8 1.0
OD1 A:ASP118 4.0 0.0 1.0
CE1 A:HIS117 4.1 95.8 0.8
O1B A:GTP601 4.3 0.9 0.9
NE2 A:GLN53 4.4 0.4 1.0
CG A:ASP118 4.5 0.5 1.0
OD2 A:ASP118 4.6 0.6 1.0
C3' A:GTP601 4.6 0.6 0.9
CG A:HIS69 4.7 96.4 1.0
CG A:HIS117 4.9 93.0 0.8
ND1 A:HIS69 4.9 0.1 1.0

Manganese binding site 2 out of 6 in 6oix

Go back to Manganese Binding Sites List in 6oix
Manganese binding site 2 out of 6 in the Structure of Escherichia Coli Dgtpase Bound to Gtp


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 Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn602

b:0.0
occ:1.00
NE2 B:HIS117 2.8 0.4 0.8
OD1 B:ASP268 2.9 0.8 1.0
NE2 B:HIS69 3.2 0.1 1.0
CD2 B:HIS117 3.4 0.4 0.8
OD2 B:ASP118 3.7 0.3 1.0
OD1 B:ASP118 3.7 0.6 1.0
CG B:ASP268 3.8 0.3 1.0
CD2 B:HIS69 3.8 0.6 1.0
OD2 B:ASP268 3.9 0.4 1.0
CG B:ASP118 4.0 0.4 1.0
CE1 B:HIS117 4.0 0.7 0.8
C5' B:GTP601 4.1 0.3 1.0
O B:HOH702 4.1 90.6 1.0
O3' B:GTP601 4.1 0.8 1.0
CE1 B:HIS69 4.3 0.0 1.0
C4' B:GTP601 4.6 0.9 1.0
CG B:HIS117 4.7 0.1 0.8
OE1 B:GLN53 4.7 0.3 1.0
C3' B:GTP601 4.8 0.2 1.0
O3A B:GTP601 4.9 0.9 1.0
O5' B:GTP601 4.9 0.4 1.0
NH1 B:ARG66 5.0 0.0 1.0

Manganese binding site 3 out of 6 in 6oix

Go back to Manganese Binding Sites List in 6oix
Manganese binding site 3 out of 6 in the Structure of Escherichia Coli Dgtpase Bound to Gtp


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 Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn602

b:0.7
occ:1.00
NE2 C:HIS117 2.9 93.7 0.8
OD1 C:ASP268 3.0 0.7 1.0
NE2 C:HIS69 3.2 90.2 1.0
O3' C:GTP601 3.3 0.7 0.9
O1B C:GTP601 3.4 0.6 0.9
CD2 C:HIS117 3.7 93.6 0.8
CG C:ASP268 3.8 0.3 1.0
CD2 C:HIS69 3.9 89.9 1.0
OD1 C:ASP118 3.9 0.3 1.0
OD2 C:ASP118 3.9 1.0 1.0
OD2 C:ASP268 3.9 0.5 1.0
CE1 C:HIS117 4.0 93.2 0.8
CE1 C:HIS69 4.2 91.4 1.0
CG C:ASP118 4.3 0.2 1.0
NE2 C:GLN53 4.3 0.2 1.0
C3' C:GTP601 4.5 0.7 0.9
C4' C:GTP601 4.8 0.7 0.9
PB C:GTP601 4.8 0.4 0.9
CG C:HIS117 4.9 90.1 0.8
NH1 C:ARG66 5.0 0.5 1.0
O5' C:GTP601 5.0 0.6 0.9

Manganese binding site 4 out of 6 in 6oix

Go back to Manganese Binding Sites List in 6oix
Manganese binding site 4 out of 6 in the Structure of Escherichia Coli Dgtpase Bound to Gtp


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 Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn602

b:0.4
occ:1.00
OD1 D:ASP268 2.6 0.8 1.0
NE2 D:HIS117 2.8 0.6 1.0
NE2 D:HIS69 3.0 0.3 1.0
O3' D:GTP601 3.4 0.5 1.0
CG D:ASP268 3.5 0.1 1.0
CD2 D:HIS117 3.7 0.1 1.0
OD2 D:ASP268 3.7 0.7 1.0
CD2 D:HIS69 3.8 0.0 1.0
O1B D:GTP601 3.9 0.4 1.0
CE1 D:HIS117 3.9 0.8 1.0
OD2 D:ASP118 4.0 0.4 1.0
CE1 D:HIS69 4.0 0.1 1.0
OD1 D:ASP118 4.1 0.3 1.0
CG D:ASP118 4.4 0.1 1.0
NE2 D:GLN53 4.4 0.1 1.0
C3' D:GTP601 4.6 0.3 1.0
O3A D:GTP601 4.8 0.7 1.0
C4' D:GTP601 4.8 0.1 1.0
CG D:HIS117 4.9 0.5 1.0
CB D:ASP268 4.9 0.8 1.0
PB D:GTP601 4.9 0.8 1.0
CG D:HIS69 4.9 0.2 1.0

Manganese binding site 5 out of 6 in 6oix

Go back to Manganese Binding Sites List in 6oix
Manganese binding site 5 out of 6 in the Structure of Escherichia Coli Dgtpase Bound to Gtp


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 Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn602

b:0.3
occ:1.00
OD1 E:ASP268 3.0 0.5 1.0
NE2 E:HIS117 3.2 0.3 0.9
O1B E:GTP601 3.2 1.0 0.9
O3' E:GTP601 3.6 0.1 0.9
NE2 E:HIS69 3.7 99.0 1.0
CG E:ASP268 3.8 0.1 1.0
OD2 E:ASP268 3.8 0.4 1.0
C5' E:GTP601 3.8 0.6 0.9
CD2 E:HIS117 3.8 0.3 0.9
OD1 E:ASP118 3.9 0.9 1.0
OD2 E:ASP118 4.2 0.1 1.0
C4' E:GTP601 4.2 0.2 0.9
CE1 E:HIS117 4.3 0.8 0.9
CD2 E:HIS69 4.4 98.3 1.0
PB E:GTP601 4.4 0.4 0.9
CG E:ASP118 4.4 0.8 1.0
C3' E:GTP601 4.5 0.4 0.9
NE2 E:GLN53 4.6 0.2 1.0
CE1 E:HIS69 4.7 99.8 1.0
O3B E:GTP601 4.7 0.4 0.9
O5' E:GTP601 4.9 0.8 0.9
O3A E:GTP601 4.9 0.7 0.9
NH1 E:ARG66 4.9 0.0 1.0

Manganese binding site 6 out of 6 in 6oix

Go back to Manganese Binding Sites List in 6oix
Manganese binding site 6 out of 6 in the Structure of Escherichia Coli Dgtpase Bound to Gtp


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 Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn602

b:0.4
occ:1.00
O1B F:GTP601 3.0 0.6 0.9
OD1 F:ASP268 3.2 0.5 1.0
NE2 F:HIS69 3.3 1.0 1.0
NE2 F:HIS117 3.3 95.4 0.8
C5' F:GTP601 3.5 0.6 0.9
O3' F:GTP601 3.7 0.7 0.9
C4' F:GTP601 3.9 0.4 0.9
CD2 F:HIS69 3.9 99.5 1.0
OD1 F:ASP118 4.0 0.4 1.0
OD2 F:ASP118 4.0 0.8 1.0
NE2 F:GLN53 4.1 0.9 1.0
CD2 F:HIS117 4.1 95.9 0.8
CG F:ASP268 4.1 0.5 1.0
CE1 F:HIS69 4.2 0.6 1.0
PB F:GTP601 4.2 0.8 0.9
OD2 F:ASP268 4.2 0.6 1.0
CE1 F:HIS117 4.3 93.8 0.8
CG F:ASP118 4.4 0.6 1.0
C3' F:GTP601 4.4 0.3 0.9
O3A F:GTP601 4.5 1.0 0.9
NH2 F:ARG66 4.7 0.1 1.0
O5' F:GTP601 4.7 0.3 0.9
CD F:GLN53 5.0 0.7 1.0
O2B F:GTP601 5.0 0.3 0.9
OE1 F:GLN53 5.0 0.9 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

W in 8QLN
W in 8RJA
V in 8WTN
Te in 8QLN
Re in 9GHX
Rb in 8Z5C
Ni in 9C0T
Ni in 9C0S
Ni in 9GP1
Ni in 9FYO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy