Atomistry » Magnesium » PDB 2ybb-2yni » 2yfd
Atomistry »
  Magnesium »
    PDB 2ybb-2yni »
      2yfd »

Magnesium in PDB 2yfd: Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mg and Dump

Enzymatic activity of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mg and Dump

All present enzymatic activity of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mg and Dump:
3.6.1.19;

Protein crystallography data

The structure of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mg and Dump, PDB code: 2yfd was solved by A.M.D.Goncalves, D.De Sanctis, S.M.Mcsweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.934 / 1.77
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.090, 149.529, 52.376, 90.00, 90.00, 90.00
R / Rfree (%) 18.43 / 21.14

Other elements in 2yfd:

The structure of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mg and Dump also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mg and Dump (pdb code 2yfd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mg and Dump, PDB code: 2yfd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2yfd

Go back to Magnesium Binding Sites List in 2yfd
Magnesium binding site 1 out of 4 in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mg and Dump


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mg and Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1146

b:35.4
occ:1.00
 OE1 A:GLU50 2.5 36.3 1.0
OD2 A:ASP82 2.5 21.7 1.0
OE1 A:GLU79 2.6 40.2 1.0
OE1 A:GLU47 2.6 25.2 1.0
HB2 A:ASP82 3.2 14.5 1.0
HB3 A:ASP82 3.3 14.5 1.0
CG A:ASP82 3.4 21.4 1.0
CB A:ASP82 3.5 14.5 1.0
O A:HOH2031 3.5 31.2 1.0
HA A:GLU79 3.5 12.7 1.0
CD A:GLU50 3.6 34.1 1.0
CD A:GLU47 3.7 25.5 1.0
CD A:GLU79 3.8 40.1 1.0
OE2 A:GLU47 3.9 25.9 1.0
HB2 A:GLU50 4.2 19.4 1.0
OE2 A:GLU50 4.2 33.4 1.0
HA A:GLU47 4.3 12.7 1.0
HB3 A:GLU50 4.4 19.4 1.0
OE2 A:GLU79 4.4 50.5 1.0
OD1 A:ASP82 4.5 17.4 1.0
CA A:GLU79 4.6 12.7 1.0
HB3 A:GLU79 4.6 17.0 1.0
CB A:GLU50 4.7 19.4 1.0
CG A:GLU50 4.8 22.1 1.0
HD2 A:HIS78 4.9 18.2 1.0
HB3 A:GLU47 4.9 15.1 1.0
CG A:GLU79 4.9 23.5 1.0
CB A:GLU79 4.9 17.0 1.0

Magnesium binding site 2 out of 4 in 2yfd

Go back to Magnesium Binding Sites List in 2yfd
Magnesium binding site 2 out of 4 in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mg and Dump


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mg and Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1145

b:29.9
occ:1.00
 OE1 B:GLU79 2.1 18.8 1.0
O B:HOH2048 2.2 20.6 1.0
OE1 B:GLU47 2.3 14.0 1.0
OD2 B:ASP82 2.3 14.6 1.0
OE2 B:GLU50 2.9 55.1 1.0
CD B:GLU79 3.1 25.5 1.0
O B:HOH2075 3.2 21.9 1.0
CD B:GLU47 3.3 16.6 1.0
CG B:ASP82 3.3 11.9 1.0
OE2 B:GLU79 3.4 27.4 1.0
HB3 B:ASP82 3.4 8.4 1.0
HB2 B:ASP82 3.5 8.4 1.0
H5' A:UMP1147 3.6 19.4 1.0
CB B:ASP82 3.6 8.4 1.0
O A:HOH2097 3.6 18.7 1.0
HA B:GLU79 3.7 7.0 1.0
OE2 B:GLU47 3.7 18.1 1.0
CD B:GLU50 3.7 49.2 1.0
HB2 B:GLU50 3.8 20.2 1.0
HG3 B:GLU50 4.0 33.0 1.0
HB3 B:GLU50 4.1 20.2 1.0
HA B:GLU47 4.2 10.2 1.0
CG B:GLU50 4.2 33.0 1.0
CB B:GLU50 4.3 20.2 1.0
CG B:GLU79 4.4 19.0 1.0
OD1 B:ASP82 4.5 13.3 1.0
HB3 B:GLU79 4.5 10.6 1.0
OP2 A:UMP1147 4.6 19.3 1.0
C5' A:UMP1147 4.6 19.4 1.0
H3' A:UMP1147 4.6 12.2 1.0
CA B:GLU79 4.6 7.0 1.0
CG B:GLU47 4.7 12.4 1.0
OE1 B:GLU50 4.7 53.5 1.0
H5'' A:UMP1147 4.7 19.4 1.0
CB B:GLU79 4.7 10.6 1.0
HB3 B:GLU47 4.8 11.6 1.0
HD2 B:HIS78 4.9 14.1 1.0
OP3 A:UMP1147 4.9 14.2 1.0
HG3 B:GLU47 4.9 12.4 1.0
HG3 B:GLU79 5.0 19.0 1.0

Magnesium binding site 3 out of 4 in 2yfd

Go back to Magnesium Binding Sites List in 2yfd
Magnesium binding site 3 out of 4 in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mg and Dump


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mg and Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1144

b:21.8
occ:1.00
 OE1 C:GLU50 2.3 36.0 1.0
OE1 C:GLU79 2.3 27.2 1.0
OE1 C:GLU47 2.4 21.5 1.0
OD2 C:ASP82 2.4 25.6 1.0
O C:HOH2043 2.6 38.3 1.0
CD C:GLU79 3.3 25.6 1.0
CD C:GLU47 3.4 26.9 1.0
CG C:ASP82 3.4 25.1 1.0
HB3 C:ASP82 3.4 19.8 1.0
CD C:GLU50 3.5 35.7 1.0
HB2 C:ASP82 3.5 19.8 1.0
OE2 C:GLU79 3.6 30.9 1.0
CB C:ASP82 3.7 19.8 1.0
OE2 C:GLU47 3.7 24.8 1.0
HB2 C:GLU50 3.8 20.7 1.0
HA C:GLU79 3.8 15.1 1.0
HA C:GLU47 4.0 18.6 1.0
HB3 C:GLU50 4.1 20.7 1.0
OE2 C:GLU50 4.2 39.3 1.0
CB C:GLU50 4.3 20.7 1.0
CG C:GLU50 4.5 24.7 1.0
OD1 C:ASP82 4.5 22.0 1.0
CG C:GLU79 4.7 18.3 1.0
HB3 C:GLU79 4.7 16.7 1.0
CG C:GLU47 4.8 21.9 1.0
HB3 C:GLU47 4.8 18.6 1.0
CA C:GLU79 4.8 15.1 1.0
CB C:GLU79 4.9 16.7 1.0

Magnesium binding site 4 out of 4 in 2yfd

Go back to Magnesium Binding Sites List in 2yfd
Magnesium binding site 4 out of 4 in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mg and Dump


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mg and Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1145

b:28.1
occ:1.00
 OE1 D:GLU79 2.0 15.9 1.0
OE1 D:GLU47 2.2 15.3 1.0
O D:HOH2042 2.3 17.3 1.0
OD2 D:ASP82 2.4 14.7 1.0
OE1 D:GLU50 2.8 25.9 0.5
OE2 D:GLU50 2.9 35.4 0.5
HG3 D:GLU50 2.9 19.4 0.5
CD D:GLU50 3.0 23.8 0.5
CD D:GLU79 3.0 21.9 1.0
CD D:GLU47 3.2 15.2 1.0
O D:HOH2068 3.3 19.0 1.0
HB2 D:ASP82 3.3 9.2 1.0
CG D:ASP82 3.3 12.3 1.0
HB3 D:ASP82 3.3 9.2 1.0
OE2 D:GLU79 3.4 27.4 1.0
HA D:GLU79 3.5 8.7 1.0
CB D:ASP82 3.6 9.2 1.0
OE2 D:GLU47 3.6 18.3 1.0
HB2 D:GLU50 3.7 15.4 0.5
O C:HOH2096 3.7 19.3 1.0
HB2 D:GLU50 3.7 15.4 0.5
H5' C:UMP1145 3.7 16.1 1.0
HB3 D:GLU50 3.8 15.4 0.5
CG D:GLU50 3.9 19.4 0.5
HB3 D:GLU50 4.0 15.4 0.5
HA D:GLU47 4.0 13.2 1.0
CB D:GLU50 4.0 15.4 0.5
CG D:GLU50 4.1 20.5 0.5
CB D:GLU50 4.2 15.6 0.5
CG D:GLU79 4.3 15.6 1.0
HB3 D:GLU79 4.4 13.4 1.0
H5'' C:UMP1145 4.5 16.1 1.0
OD1 D:ASP82 4.5 10.4 1.0
CA D:GLU79 4.5 8.7 1.0
CG D:GLU47 4.5 8.8 1.0
HG2 D:GLU50 4.5 19.4 0.5
HG2 D:GLU50 4.6 19.4 0.5
C5' C:UMP1145 4.6 16.1 1.0
CB D:GLU79 4.6 13.4 1.0
H3' C:UMP1145 4.7 11.8 1.0
OE1 D:GLU50 4.7 21.4 0.5
HB3 D:GLU47 4.7 11.0 1.0
OP2 C:UMP1145 4.7 18.4 1.0
CD D:GLU50 4.8 21.3 0.5
HG3 D:GLU47 4.8 8.8 1.0
HG3 D:GLU79 4.9 15.6 1.0
HD2 D:HIS78 4.9 10.3 1.0
CA D:GLU47 4.9 13.2 1.0
CB D:GLU47 5.0 11.0 1.0
HG3 D:GLU50 5.0 19.4 0.5
OP3 C:UMP1145 5.0 13.3 1.0

Reference:

A.M.D.Goncalves, D.Desanctis, S.M.Mcsweeney. Structural and Functional Insights Into DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans. J.Biol.Chem. V. 286 30691 2011.
ISSN: ISSN 0021-9258
PubMed: 21733847
DOI: 10.1074/JBC.M111.247999
Page generated: Wed Aug 14 07:30:21 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy