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Manganese in PDB 2yf3: Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese

Enzymatic activity of Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese

All present enzymatic activity of Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese:
3.6.1.19;

Protein crystallography data

The structure of Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese, PDB code: 2yf3 was solved by A.M.D.Goncalves, D.Desanctis, S.M.Mcsweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.12 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.109, 111.402, 166.539, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 23.8

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese (pdb code 2yf3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 11 binding sites of Manganese where determined in the Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese, PDB code: 2yf3:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 11 in 2yf3

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Manganese binding site 1 out of 11 in the Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1145

b:17.4
occ:1.00
 OE1 A:GLU50 2.1 19.1 1.0
OD2 A:ASP82 2.1 14.2 1.0
OE1 A:GLU79 2.2 15.2 1.0
OE1 A:GLU47 2.3 15.9 1.0
O A:HOH2127 2.3 16.4 1.0
O A:HOH2128 2.4 19.4 1.0
CD A:GLU79 3.2 18.6 1.0
CG A:ASP82 3.2 15.7 1.0
CD A:GLU47 3.2 16.1 1.0
CD A:GLU50 3.3 23.6 1.0
HB3 A:ASP82 3.4 13.4 1.0
HB2 A:ASP82 3.4 13.4 1.0
OE2 A:GLU79 3.4 21.6 1.0
OE2 A:GLU47 3.4 17.6 1.0
CB A:ASP82 3.6 13.4 1.0
HA A:GLU79 3.8 12.3 1.0
HB2 A:GLU50 3.8 14.6 1.0
O A:HOH2132 3.9 39.0 1.0
O A:HOH2058 3.9 22.7 1.0
O A:HOH2057 3.9 49.5 1.0
OE2 A:GLU50 4.0 30.9 1.0
HA A:GLU47 4.1 12.1 1.0
HB3 A:GLU50 4.1 14.6 1.0
H2 A:GOL1151 4.1 22.5 1.0
O A:HOH2059 4.1 35.9 1.0
CB A:GLU50 4.3 14.6 1.0
OD1 A:ASP82 4.3 15.0 1.0
CG A:GLU50 4.3 20.1 1.0
HO2 A:GOL1151 4.4 20.5 1.0
CG A:GLU79 4.6 12.4 1.0
CG A:GLU47 4.6 13.8 1.0
HB3 A:GLU47 4.7 11.2 1.0
HB3 A:GLU79 4.7 12.5 1.0
CA A:GLU79 4.8 12.3 1.0
CB A:GLU79 4.9 12.5 1.0
C2 A:GOL1151 4.9 22.5 1.0
O2 A:GOL1151 5.0 20.5 1.0
HG2 A:GLU50 5.0 20.1 1.0

Manganese binding site 2 out of 11 in 2yf3

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Manganese binding site 2 out of 11 in the Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1148

b:17.1
occ:1.00
 OE1 B:GLU50 2.0 18.9 1.0
OD2 B:ASP82 2.2 14.8 1.0
OE1 B:GLU79 2.2 14.9 1.0
OE1 B:GLU47 2.3 13.3 1.0
O B:HOH2100 2.3 15.2 1.0
O B:HOH2099 2.4 14.9 1.0
CD B:GLU79 3.1 15.5 1.0
CG B:ASP82 3.2 13.5 1.0
CD B:GLU47 3.2 14.7 1.0
CD B:GLU50 3.3 20.6 1.0
OE2 B:GLU79 3.3 18.9 1.0
HB3 B:ASP82 3.4 11.5 1.0
HB2 B:ASP82 3.4 11.5 1.0
OE2 B:GLU47 3.5 13.3 1.0
CB B:ASP82 3.6 11.5 1.0
HA B:GLU79 3.8 11.2 1.0
O B:HOH2042 3.8 22.7 1.0
HB2 B:GLU50 3.9 12.9 1.0
HB3 B:GLU50 3.9 12.9 1.0
HA B:GLU47 4.0 10.2 1.0
OE2 B:GLU50 4.1 27.8 1.0
O B:HOH2043 4.1 29.7 1.0
CB B:GLU50 4.2 12.9 1.0
CG B:GLU50 4.3 16.6 1.0
OD1 B:ASP82 4.3 12.4 1.0
CG B:GLU79 4.5 12.6 1.0
HD2 B:HIS78 4.6 19.5 1.0
HB3 B:GLU79 4.6 11.0 1.0
CG B:GLU47 4.6 11.1 1.0
CA B:GLU79 4.7 11.2 1.0
CB B:GLU79 4.9 11.0 1.0
HB3 B:GLU47 4.9 10.4 1.0
HG2 B:GLU50 4.9 16.6 1.0
HE2 B:HIS78 4.9 24.1 1.0
CA B:GLU47 5.0 10.2 1.0

Manganese binding site 3 out of 11 in 2yf3

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Manganese binding site 3 out of 11 in the Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1149

b:24.3
occ:0.50
 O B:HOH2102 1.9 29.8 1.0
O B:HOH2101 1.9 33.4 1.0
O B:HOH2103 2.1 37.3 1.0
O B:HOH2104 2.2 27.8 1.0
O B:HOH2105 2.4 30.1 1.0
HB2 B:ASP97 3.2 25.1 1.0
O B:GLU27 3.6 31.0 1.0
O B:HOH2070 4.0 25.4 1.0
O B:HOH2097 4.0 39.9 1.0
HD23 B:LEU141 4.2 23.4 1.0
CB B:ASP97 4.3 25.1 1.0
OD2 B:ASP97 4.3 29.0 1.0
OD1 B:ASP147 4.4 55.3 1.0
HB3 B:GLU27 4.5 35.4 1.0
OD2 B:ASP147 4.5 52.3 1.0
CG B:ASP97 4.6 26.1 1.0
C B:GLU27 4.7 31.9 1.0
HA B:GLU27 4.8 33.0 1.0
HA B:ASP97 4.8 21.9 1.0
HB3 B:ASP97 4.9 25.1 1.0
CG B:ASP147 4.9 53.1 1.0
H B:ASP97 5.0 21.0 1.0

Manganese binding site 4 out of 11 in 2yf3

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Manganese binding site 4 out of 11 in the Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1148

b:8.1
occ:0.50
 O F:HOH2100 1.8 24.0 1.0
O F:HOH2099 1.8 23.4 1.0
O F:HOH2098 2.0 18.6 1.0
O F:HOH2097 2.1 24.3 1.0
O F:HOH2096 2.3 19.3 1.0
O F:HOH2095 2.3 23.2 1.0
HB2 C:ASP97 3.5 14.1 1.0
HG3 C:GLU27 4.0 20.7 1.0
O C:HOH2058 4.1 21.3 1.0
OD1 C:ASP147 4.2 38.7 1.0
O C:HOH2037 4.2 21.6 1.0
O C:HOH2073 4.3 24.5 1.0
O C:HOH2148 4.3 19.8 1.0
OD2 C:ASP97 4.3 17.8 1.0
O C:GLU27 4.3 19.0 1.0
O C:HOH2059 4.4 17.8 1.0
CB C:ASP97 4.5 14.1 1.0
OD2 C:ASP147 4.5 36.6 1.0
HD23 C:LEU141 4.6 17.2 1.0
O C:HOH2057 4.6 23.2 1.0
HG2 C:GLU27 4.6 20.7 1.0
O C:HOH2025 4.7 20.4 1.0
CG C:ASP97 4.7 15.5 1.0
O C:HOH2121 4.7 13.8 1.0
O C:HOH2010 4.7 22.6 1.0
CG C:ASP147 4.8 37.1 1.0
CG C:GLU27 4.9 20.7 1.0
HA C:GLU27 4.9 18.8 1.0

Manganese binding site 5 out of 11 in 2yf3

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Manganese binding site 5 out of 11 in the Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1149

b:15.2
occ:1.00
 OE1 C:GLU50 2.1 16.9 1.0
OE1 C:GLU79 2.2 11.1 1.0
OE1 C:GLU47 2.2 9.7 1.0
OD2 C:ASP82 2.2 10.3 1.0
O C:HOH2151 2.3 13.3 1.0
O C:HOH2150 2.4 13.9 1.0
CD C:GLU79 3.1 14.3 1.0
CD C:GLU47 3.2 12.1 1.0
CG C:ASP82 3.2 11.9 1.0
HB3 C:ASP82 3.3 9.4 1.0
OE2 C:GLU79 3.3 14.5 1.0
CD C:GLU50 3.3 20.7 1.0
OE2 C:GLU47 3.5 13.0 1.0
HB2 C:ASP82 3.5 9.4 1.0
CB C:ASP82 3.5 9.4 1.0
HA C:GLU79 3.8 9.9 1.0
O C:HOH2081 3.8 29.2 1.0
HB2 C:GLU50 3.8 13.0 1.0
O C:HOH2082 4.0 25.4 1.0
HA C:GLU47 4.0 10.6 1.0
OE2 C:GLU50 4.0 30.0 1.0
O C:HOH2158 4.1 28.6 1.0
HB3 C:GLU50 4.1 13.0 1.0
HO2 C:GOL1153 4.1 23.1 1.0
CB C:GLU50 4.3 13.0 1.0
OD1 C:ASP82 4.4 15.3 1.0
CG C:GLU50 4.4 17.1 1.0
CG C:GLU79 4.6 9.6 1.0
CG C:GLU47 4.6 9.9 1.0
H32 C:GOL1153 4.6 18.9 1.0
HB3 C:GLU47 4.6 8.4 1.0
H11 C:GOL1153 4.6 28.2 1.0
HB3 C:GLU79 4.6 8.9 1.0
CA C:GLU79 4.8 9.9 1.0
O C:HOH2115 4.9 17.6 1.0
CB C:GLU79 4.9 8.9 1.0
CB C:GLU47 5.0 8.4 1.0
CA C:GLU47 5.0 10.6 1.0
O2 C:GOL1153 5.0 23.1 1.0

Manganese binding site 6 out of 11 in 2yf3

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Manganese binding site 6 out of 11 in the Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1148

b:14.8
occ:1.00
 OE1 D:GLU50 2.1 19.6 1.0
OE1 D:GLU47 2.1 13.2 1.0
OD2 D:ASP82 2.2 13.1 1.0
OE1 D:GLU79 2.2 11.1 1.0
O F:HOH2093 2.3 13.1 1.0
O F:HOH2094 2.4 14.8 1.0
CD D:GLU47 3.1 17.1 1.0
CD D:GLU79 3.1 13.0 1.0
CG D:ASP82 3.2 11.1 1.0
CD D:GLU50 3.3 20.8 1.0
HB3 D:ASP82 3.3 8.7 1.0
OE2 D:GLU79 3.3 14.0 1.0
OE2 D:GLU47 3.4 17.9 1.0
HB2 D:ASP82 3.5 8.7 1.0
CB D:ASP82 3.6 8.7 1.0
HA D:GLU79 3.7 10.4 1.0
HB2 D:GLU50 3.9 13.1 1.0
O D:HOH2148 3.9 24.5 1.0
O D:HOH2068 3.9 27.7 1.0
H2 D:GOL1153 4.0 24.2 1.0
HB3 D:GLU50 4.0 13.1 1.0
O D:HOH2066 4.0 29.2 1.0
OE2 D:GLU50 4.0 31.9 1.0
HA D:GLU47 4.1 11.8 1.0
CB D:GLU50 4.3 13.1 1.0
OD1 D:ASP82 4.3 10.7 1.0
HO2 D:GOL1153 4.3 25.6 1.0
CG D:GLU50 4.3 15.6 1.0
CG D:GLU47 4.5 12.0 1.0
HE2 D:HIS78 4.5 22.2 1.0
CG D:GLU79 4.5 10.4 1.0
HB3 D:GLU47 4.6 11.6 1.0
HB3 D:GLU79 4.6 10.1 1.0
HD2 D:HIS78 4.7 21.5 1.0
CA D:GLU79 4.7 10.4 1.0
CB D:GLU79 4.9 10.1 1.0
NE2 D:HIS78 4.9 22.2 1.0
CB D:GLU47 4.9 11.6 1.0
HG3 D:GLU50 4.9 15.6 1.0
C2 D:GOL1153 5.0 24.2 1.0
CD2 D:HIS78 5.0 21.5 1.0
O D:HOH2094 5.0 18.0 1.0

Manganese binding site 7 out of 11 in 2yf3

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Manganese binding site 7 out of 11 in the Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1149

b:19.4
occ:0.50
 O D:HOH2140 1.8 28.9 1.0
O D:HOH2143 2.0 25.6 1.0
O D:HOH2141 2.0 23.6 1.0
O D:HOH2142 2.2 32.2 1.0
O D:HOH2144 2.3 29.1 1.0
O D:HOH2139 2.4 25.0 1.0
HB2 D:ASP97 3.6 14.8 1.0
HG3 D:GLU27 3.9 30.1 1.0
O D:HOH2039 4.2 26.5 1.0
OD2 D:ASP97 4.2 19.2 1.0
O D:HOH2023 4.2 26.9 1.0
O D:GLU27 4.4 24.6 1.0
OD1 D:ASP147 4.4 42.1 1.0
OD2 D:ASP147 4.5 39.9 1.0
O D:HOH2040 4.5 33.6 1.0
HG2 D:GLU27 4.5 30.1 1.0
CB D:ASP97 4.5 14.8 1.0
O D:HOH2017 4.5 27.4 1.0
CG D:ASP97 4.6 19.3 1.0
O D:HOH2041 4.7 19.8 1.0
CG D:GLU27 4.8 30.1 1.0
O D:HOH2003 4.8 27.4 1.0
HD23 D:LEU141 4.9 20.0 1.0
CG D:ASP147 4.9 44.3 1.0
O D:HOH2102 4.9 15.5 1.0
HA D:GLU27 4.9 23.9 1.0

Manganese binding site 8 out of 11 in 2yf3

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Manganese binding site 8 out of 11 in the Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn1148

b:28.7
occ:1.00
 O F:HOH2105 1.9 26.8 1.0
O F:HOH2106 1.9 20.3 1.0
O F:HOH2104 2.1 34.8 1.0
O F:HOH2103 2.2 28.5 1.0
O F:HOH2102 2.3 29.8 1.0
O F:HOH2101 2.3 24.1 1.0
HB2 E:ASP97 3.7 25.4 1.0
HG3 E:GLU27 4.1 28.8 1.0
O E:HOH2036 4.1 22.8 1.0
O E:HOH2049 4.2 32.9 1.0
OD2 E:ASP97 4.2 26.1 1.0
O E:HOH2110 4.3 30.5 1.0
O E:GLU27 4.3 27.0 1.0
OD1 E:ASP147 4.3 39.9 1.0
OD2 E:ASP147 4.4 39.1 1.0
O E:HOH2039 4.4 21.7 1.0
O E:HOH2024 4.4 22.6 1.0
O E:HOH2016 4.5 33.8 1.0
O E:HOH2037 4.5 35.0 1.0
CB E:ASP97 4.6 25.4 1.0
CG E:ASP97 4.6 26.7 1.0
O E:HOH2081 4.6 22.4 1.0
HG2 E:GLU27 4.7 28.8 1.0
HD23 E:LEU141 4.7 28.9 1.0
O E:HOH2007 4.8 25.0 1.0
CG E:ASP147 4.8 41.7 1.0
HA E:GLU27 4.9 25.3 1.0
CG E:GLU27 4.9 28.8 1.0

Manganese binding site 9 out of 11 in 2yf3

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Manganese binding site 9 out of 11 in the Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn1149

b:19.9
occ:1.00
 OD2 E:ASP82 2.1 15.0 1.0
OE1 E:GLU79 2.2 18.7 1.0
OE1 E:GLU50 2.2 21.2 1.0
O E:HOH2116 2.3 17.8 1.0
OE1 E:GLU47 2.3 17.1 1.0
O E:HOH2117 2.5 19.9 1.0
CD E:GLU79 3.1 19.4 1.0
CG E:ASP82 3.1 17.8 1.0
CD E:GLU47 3.2 17.0 1.0
CD E:GLU50 3.2 28.8 1.0
OE2 E:GLU79 3.3 21.1 1.0
HB3 E:ASP82 3.3 13.7 1.0
OE2 E:GLU47 3.4 20.4 1.0
HB2 E:ASP82 3.5 13.7 1.0
CB E:ASP82 3.5 13.7 1.0
O E:HOH2058 3.7 25.0 1.0
HA E:GLU79 3.8 16.4 1.0
OE2 E:GLU50 3.8 34.5 1.0
O E:HOH2057 4.0 29.6 1.0
HB2 E:GLU50 4.0 20.6 1.0
HB3 E:GLU50 4.1 20.6 1.0
HA E:GLU47 4.1 16.8 1.0
OD1 E:ASP82 4.3 16.4 1.0
CG E:GLU50 4.3 23.2 1.0
CB E:GLU50 4.4 20.6 1.0
O E:HOH2033 4.5 35.3 1.0
CG E:GLU79 4.6 17.9 1.0
CG E:GLU47 4.6 15.5 1.0
HB3 E:GLU47 4.6 15.8 1.0
HG3 E:GLU50 4.7 23.2 1.0
HB3 E:GLU79 4.7 16.6 1.0
HD2 E:HIS78 4.7 25.1 1.0
CA E:GLU79 4.8 16.4 1.0
CB E:GLU79 4.9 16.6 1.0
CB E:GLU47 5.0 15.8 1.0

Manganese binding site 10 out of 11 in 2yf3

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Manganese binding site 10 out of 11 in the Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of DR2231, the Mazg-Like Protein From Deinococcus Radiodurans, Complex with Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn1147

b:30.9
occ:0.50
 O F:HOH2108 2.1 38.4 1.0
O F:HOH2107 2.1 47.1 1.0
O F:HOH2109 2.2 37.9 1.0
HB2 F:ASP97 3.5 29.8 1.0
O F:HOH2010 4.1 49.8 1.0
OD2 F:ASP147 4.2 51.0 1.0
HG3 F:GLU27 4.3 52.2 1.0
OD2 F:ASP97 4.4 33.0 1.0
O F:HOH2088 4.4 41.7 1.0
O F:GLU27 4.4 42.6 1.0
CB F:ASP97 4.5 29.8 1.0
OD1 F:ASP147 4.6 52.0 1.0
CG F:ASP97 4.7 30.7 1.0
O F:HOH2052 4.8 28.6 1.0
HD23 F:LEU141 4.8 32.8 1.0
CG F:ASP147 4.8 52.5 1.0
HG2 F:GLU27 4.9 52.2 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 15:31:25 2024

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