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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

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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

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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: Mon Dec 14 07:48:45 2020

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