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

Enzymatic activity of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mn 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 Mn 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 Mn and Dump, PDB code: 2yfc 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) 20.001 / 2.01
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.733, 150.191, 52.423, 90.00, 90.00, 90.00
R / Rfree (%) 17.75 / 21.88

Manganese Binding Sites:

The binding sites of Manganese atom in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mn and Dump (pdb code 2yfc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mn and Dump, PDB code: 2yfc:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 2yfc

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Manganese binding site 1 out of 6 in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mn and Dump


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mn and Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1146

b:30.3
occ:1.00
 OE1 A:GLU50 2.2 29.5 1.0
OD2 A:ASP82 2.3 20.8 1.0
OE1 A:GLU47 2.3 23.1 1.0
OE1 A:GLU79 2.3 29.6 1.0
CG A:ASP82 3.2 24.4 1.0
CD A:GLU79 3.3 29.4 1.0
HB3 A:ASP82 3.3 18.6 1.0
CD A:GLU47 3.3 24.1 1.0
CD A:GLU50 3.4 35.5 1.0
HB2 A:ASP82 3.4 18.6 1.0
OE2 A:GLU79 3.5 34.1 1.0
CB A:ASP82 3.5 18.6 1.0
OE2 A:GLU47 3.6 24.4 1.0
HA A:GLU79 3.7 15.5 1.0
HB2 A:GLU50 3.9 18.5 1.0
OE2 A:GLU50 4.0 46.9 1.0
HA A:GLU47 4.1 18.8 1.0
HB3 A:GLU50 4.2 18.5 1.0
OD1 A:ASP82 4.4 20.4 1.0
CB A:GLU50 4.4 18.5 1.0
CG A:GLU50 4.5 23.1 1.0
HB3 A:GLU47 4.6 15.3 1.0
CG A:GLU79 4.7 17.2 1.0
CG A:GLU47 4.7 17.8 1.0
CA A:GLU79 4.7 15.5 1.0
HB3 A:GLU79 4.8 17.2 1.0
CB A:GLU79 5.0 17.2 1.0
CB A:GLU47 5.0 15.3 1.0

Manganese binding site 2 out of 6 in 2yfc

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Manganese binding site 2 out of 6 in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mn and Dump


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mn and Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1146

b:16.2
occ:1.00
 OE2 B:GLU46 2.2 14.9 1.0
O B:HOH2089 2.2 9.8 1.0
OP1 A:UMP1145 2.2 13.2 1.0
OE2 B:GLU47 2.3 13.5 1.0
OE2 B:GLU50 2.3 21.4 1.0
O B:HOH2088 2.4 22.2 1.0
CD B:GLU46 3.1 19.0 1.0
CD B:GLU50 3.1 22.2 1.0
CD B:GLU47 3.2 17.7 1.0
OE1 B:GLU50 3.2 30.2 1.0
HG2 B:GLU46 3.2 16.5 1.0
HZ2 A:LYS122 3.3 16.4 1.0
H5' A:UMP1145 3.3 15.6 1.0
OE1 B:GLU47 3.4 18.7 1.0
P A:UMP1145 3.4 17.4 1.0
MN B:MN1147 3.6 23.5 1.0
OP2 A:UMP1145 3.6 18.9 1.0
CG B:GLU46 3.7 16.5 1.0
O B:HOH2033 4.0 22.1 1.0
OE1 B:GLU46 4.0 19.1 1.0
HZ3 A:LYS122 4.1 16.4 1.0
NZ A:LYS122 4.1 16.4 1.0
C5' A:UMP1145 4.1 15.6 1.0
O B:HOH2038 4.3 26.9 1.0
HG3 B:GLU46 4.3 16.5 1.0
H5'' A:UMP1145 4.3 15.6 1.0
O B:HOH2030 4.3 27.1 1.0
O5' A:UMP1145 4.4 20.3 1.0
HA B:GLU47 4.4 13.6 1.0
OP3 A:UMP1145 4.5 20.2 1.0
CG B:GLU50 4.5 15.2 1.0
HZ1 A:LYS122 4.6 16.4 1.0
CG B:GLU47 4.6 12.2 1.0
HG2 B:GLU47 4.7 12.2 1.0
HG3 B:GLU50 4.7 15.2 1.0
HB3 B:GLU46 4.9 16.2 1.0
CB B:GLU46 5.0 16.2 1.0

Manganese binding site 3 out of 6 in 2yfc

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Manganese binding site 3 out of 6 in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mn and Dump


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mn and Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1147

b:23.5
occ:1.00
 OE1 B:GLU47 2.1 18.7 1.0
O B:HOH2089 2.1 9.8 1.0
OE1 B:GLU50 2.2 30.2 1.0
OE1 B:GLU79 2.2 15.3 1.0
OD2 B:ASP82 2.2 13.1 1.0
CD B:GLU47 3.2 17.7 1.0
CG B:ASP82 3.2 16.4 1.0
CD B:GLU50 3.3 22.2 1.0
O B:HOH2070 3.3 32.6 1.0
CD B:GLU79 3.3 17.7 1.0
HB3 B:ASP82 3.3 8.7 1.0
HB2 B:ASP82 3.3 8.7 1.0
CB B:ASP82 3.5 8.7 1.0
MN B:MN1146 3.6 16.2 1.0
OE2 B:GLU79 3.6 21.2 1.0
HA B:GLU79 3.7 11.4 1.0
OE2 B:GLU47 3.7 13.5 1.0
H5' A:UMP1145 3.7 15.6 1.0
OE2 B:GLU50 3.8 21.4 1.0
HB2 B:GLU50 4.0 15.4 1.0
HB3 B:GLU50 4.1 15.4 1.0
HA B:GLU47 4.2 13.6 1.0
OD1 B:ASP82 4.4 12.9 1.0
CG B:GLU50 4.4 15.2 1.0
CB B:GLU50 4.4 15.4 1.0
H3' A:UMP1145 4.5 12.9 1.0
CG B:GLU47 4.5 12.2 1.0
OP2 A:UMP1145 4.5 18.9 1.0
HB3 B:GLU47 4.6 10.5 1.0
HB3 B:GLU79 4.6 10.0 1.0
CG B:GLU79 4.6 11.8 1.0
CA B:GLU79 4.7 11.4 1.0
HG3 B:GLU47 4.8 12.2 1.0
H4' A:UMP1145 4.8 12.2 1.0
C5' A:UMP1145 4.8 15.6 1.0
OP1 A:UMP1145 4.8 13.2 1.0
CB B:GLU79 4.9 10.0 1.0
HD2 B:HIS78 4.9 17.6 1.0
CB B:GLU47 4.9 10.5 1.0
O B:HOH2088 5.0 22.2 1.0

Manganese binding site 4 out of 6 in 2yfc

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Manganese binding site 4 out of 6 in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mn and Dump


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mn and Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1145

b:25.9
occ:1.00
 OE1 C:GLU50 2.1 28.3 1.0
OD2 C:ASP82 2.2 21.6 1.0
OE1 C:GLU79 2.3 26.2 1.0
OE1 C:GLU47 2.3 16.2 1.0
O C:HOH2063 2.4 27.0 1.0
CG C:ASP82 3.2 23.3 1.0
HB3 C:ASP82 3.2 18.6 1.0
CD C:GLU47 3.2 24.3 1.0
CD C:GLU50 3.2 35.6 1.0
CD C:GLU79 3.3 23.5 1.0
HB2 C:ASP82 3.4 18.6 1.0
OE2 C:GLU47 3.5 23.1 1.0
CB C:ASP82 3.5 18.6 1.0
OE2 C:GLU79 3.6 26.4 1.0
HA C:GLU79 3.8 13.8 1.0
HB2 C:GLU50 3.9 16.1 1.0
OE2 C:GLU50 3.9 40.6 1.0
HB3 C:GLU50 4.0 16.1 1.0
HA C:GLU47 4.1 21.7 1.0
CB C:GLU50 4.3 16.1 1.0
CG C:GLU50 4.3 26.6 1.0
OD1 C:ASP82 4.3 18.2 1.0
HB3 C:GLU79 4.6 12.1 1.0
CG C:GLU79 4.6 14.9 1.0
CG C:GLU47 4.7 23.0 1.0
HB3 C:GLU47 4.7 17.7 1.0
CA C:GLU79 4.8 13.8 1.0
HG3 C:GLU50 4.9 26.6 1.0
CB C:GLU79 4.9 12.1 1.0
HD2 C:HIS78 4.9 26.8 1.0

Manganese binding site 5 out of 6 in 2yfc

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Manganese binding site 5 out of 6 in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mn and Dump


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mn and Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1145

b:20.6
occ:1.00
 OE1 D:GLU47 2.1 18.7 1.0
OE1 D:GLU79 2.2 13.9 1.0
O D:HOH2073 2.2 10.7 1.0
OE1 D:GLU50 2.2 26.5 1.0
OD2 D:ASP82 2.2 11.5 1.0
O D:HOH2059 3.2 31.6 1.0
CD D:GLU47 3.2 19.1 1.0
CD D:GLU50 3.2 20.7 1.0
CG D:ASP82 3.2 9.6 1.0
CD D:GLU79 3.2 22.6 1.0
HB3 D:ASP82 3.3 8.8 1.0
HB2 D:ASP82 3.4 8.8 1.0
CB D:ASP82 3.5 8.8 1.0
OE2 D:GLU47 3.6 13.3 1.0
MN D:MN1146 3.6 15.7 1.0
OE2 D:GLU79 3.6 26.4 1.0
H5' C:UMP1144 3.7 15.2 1.0
HA D:GLU79 3.7 14.3 1.0
OE2 D:GLU50 3.7 19.8 1.0
HB2 D:GLU50 3.9 10.7 1.0
HB3 D:GLU50 4.1 10.7 1.0
HA D:GLU47 4.2 12.7 1.0
OD1 D:ASP82 4.4 11.8 1.0
CB D:GLU50 4.4 10.7 1.0
CG D:GLU50 4.4 13.4 1.0
HB3 D:GLU79 4.5 12.0 1.0
CG D:GLU47 4.5 14.9 1.0
H3' C:UMP1144 4.5 11.4 1.0
CG D:GLU79 4.6 17.2 1.0
OP2 C:UMP1144 4.6 17.9 1.0
HB3 D:GLU47 4.6 11.6 1.0
CA D:GLU79 4.7 14.3 1.0
C5' C:UMP1144 4.8 15.2 1.0
HG3 D:GLU47 4.8 14.9 1.0
OP1 C:UMP1144 4.8 12.3 1.0
CB D:GLU79 4.8 12.0 1.0
H4' C:UMP1144 4.8 12.9 1.0
CB D:GLU47 5.0 11.6 1.0
HD2 D:HIS78 5.0 13.9 1.0

Manganese binding site 6 out of 6 in 2yfc

Go back to Manganese Binding Sites List in 2yfc
Manganese binding site 6 out of 6 in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mn and Dump


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complexed with Mn and Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1146

b:15.7
occ:1.00
 OE2 D:GLU47 2.1 13.3 1.0
OP1 C:UMP1144 2.2 12.3 1.0
OE2 D:GLU46 2.2 13.7 1.0
OE2 D:GLU50 2.2 19.8 1.0
O D:HOH2073 2.3 10.7 1.0
O D:HOH2074 2.5 21.1 1.0
CD D:GLU50 3.1 20.7 1.0
CD D:GLU46 3.2 20.7 1.0
CD D:GLU47 3.2 19.1 1.0
HZ2 C:LYS122 3.2 11.3 1.0
HG2 D:GLU46 3.2 16.2 1.0
OE1 D:GLU50 3.3 26.5 1.0
H5' C:UMP1144 3.3 15.2 1.0
P C:UMP1144 3.4 15.4 1.0
OE1 D:GLU47 3.5 18.7 1.0
OP2 C:UMP1144 3.6 17.9 1.0
MN D:MN1145 3.6 20.6 1.0
CG D:GLU46 3.8 16.2 1.0
HZ3 C:LYS122 4.0 11.3 1.0
NZ C:LYS122 4.1 11.3 1.0
OE1 D:GLU46 4.1 16.2 1.0
O D:HOH2030 4.1 19.0 1.0
C5' C:UMP1144 4.1 15.2 1.0
H5'' C:UMP1144 4.2 15.2 1.0
HG3 D:GLU46 4.3 16.2 1.0
O B:HOH2048 4.3 27.3 1.0
O5' C:UMP1144 4.4 16.3 1.0
OP3 C:UMP1144 4.4 15.5 1.0
O D:HOH2032 4.4 26.7 1.0
HA D:GLU47 4.5 12.7 1.0
CG D:GLU47 4.5 14.9 1.0
CG D:GLU50 4.5 13.4 1.0
HZ1 C:LYS122 4.6 11.3 1.0
HG2 D:GLU47 4.6 14.9 1.0
HG3 D:GLU50 4.7 13.4 1.0
O C:HOH2054 4.8 40.1 0.5
HB3 D:GLU46 4.9 13.7 1.0
HE3 C:LYS122 5.0 12.0 1.0
CB D:GLU46 5.0 13.7 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: Sat Oct 5 15:31:27 2024

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