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Magnesium in PDB 4apz: Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1

Enzymatic activity of Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1

All present enzymatic activity of Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1:
3.6.1.23;

Protein crystallography data

The structure of Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1, PDB code: 4apz was solved by J.Garcia-Nafria, J.Timm, C.Harrison, J.P.Turkenburg, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.44 / 2.01
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 97.060, 97.070, 193.850, 89.72, 88.47, 90.11
R / Rfree (%) 16.909 / 21.185

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Magnesium atom in the Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1 (pdb code 4apz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 48 binding sites of Magnesium where determined in the Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1, PDB code: 4apz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 48 in 4apz

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Magnesium binding site 1 out of 48 in the Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1 within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg1147

b:18.2
occ:1.00
 O5 1:POP1146 2.0 19.2 1.0
O 1:HOH2115 2.0 18.5 1.0
O 1:HOH2118 2.1 19.8 1.0
O 1:HOH2120 2.1 16.2 1.0
O2 1:POP1146 2.2 18.9 1.0
O 1:HOH2111 2.3 15.3 1.0
P2 1:POP1146 3.2 20.2 1.0
P1 1:POP1146 3.2 20.7 1.0
O 1:POP1146 3.5 18.6 1.0
O3 1:POP1146 3.8 21.8 1.0
O4 1:POP1146 3.8 19.8 1.0
NH2 1:ARG135 4.0 18.6 1.0
OD1 Y:ASP27 4.0 17.6 1.0
NE Y:ARG63 4.1 19.7 1.0
O Y:HOH2021 4.1 16.6 1.0
O Y:HOH2024 4.2 15.2 1.0
OE1 Y:GLN112 4.2 15.7 1.0
OG1 1:THR141 4.3 20.0 1.0
NH2 Y:ARG63 4.4 21.1 1.0
O6 1:POP1146 4.4 24.2 1.0
OD2 Y:ASP27 4.5 21.1 1.0
O1 1:POP1146 4.5 20.3 1.0
CG Y:ASP27 4.7 19.1 1.0
CZ Y:ARG63 4.7 21.1 1.0
O5' Z:DUR1145 4.7 18.1 1.0
OD2 Z:ASP82 4.9 21.3 1.0
C5' Z:DUR1145 4.9 17.0 1.0
O 1:HOH2119 4.9 28.4 1.0
CD Y:GLN112 4.9 16.1 1.0
CG Y:ARG63 4.9 18.8 1.0
CD Y:ARG63 5.0 20.4 1.0
CG2 1:THR141 5.0 21.3 1.0

Magnesium binding site 2 out of 48 in 4apz

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Magnesium binding site 2 out of 48 in the Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1 within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1147

b:11.7
occ:1.00
 O 2:HOH2127 2.0 13.4 1.0
O5 2:POP1146 2.0 14.6 1.0
O 2:HOH2133 2.0 15.9 1.0
O 2:HOH2139 2.1 15.3 1.0
O2 2:POP1146 2.1 14.7 1.0
O 2:HOH2137 2.2 25.6 1.0
P1 2:POP1146 3.2 15.5 1.0
P2 2:POP1146 3.3 16.0 1.0
O 2:POP1146 3.5 14.8 1.0
O3 2:POP1146 3.7 16.0 1.0
O4 2:POP1146 3.9 15.9 1.0
O 3:HOH2031 4.0 13.8 1.0
NH2 2:ARG135 4.0 17.0 1.0
OD1 3:ASP27 4.0 20.4 1.0
NE 3:ARG63 4.1 17.9 1.0
O 3:HOH2034 4.1 18.5 1.0
OE1 3:GLN112 4.2 15.6 1.0
OD2 3:ASP27 4.4 17.8 1.0
OG1 2:THR141 4.4 18.5 1.0
NH2 3:ARG63 4.4 17.7 1.0
O6 2:POP1146 4.5 13.9 1.0
O1 2:POP1146 4.5 17.5 1.0
CG 3:ASP27 4.6 19.3 1.0
CZ 3:ARG63 4.7 17.4 1.0
O5' 4:DUR1145 4.7 14.1 1.0
OD2 4:ASP82 4.8 20.1 1.0
C5' 4:DUR1145 4.8 13.1 1.0
CD 3:GLN112 4.9 16.0 1.0
CG 3:ARG63 4.9 16.2 1.0
CD 3:ARG63 4.9 17.2 1.0
O 2:HOH2138 4.9 21.5 1.0
CG2 2:THR141 5.0 18.3 1.0

Magnesium binding site 3 out of 48 in 4apz

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Magnesium binding site 3 out of 48 in the Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1 within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg1147

b:17.7
occ:1.00
 O 2:HOH2085 2.0 19.6 1.0
O5 3:POP1146 2.0 16.7 1.0
O 3:HOH2096 2.1 16.9 1.0
O2 3:POP1146 2.1 15.7 1.0
O 3:HOH2102 2.1 14.0 1.0
O 3:HOH2099 2.2 20.4 1.0
P2 3:POP1146 3.2 16.2 1.0
P1 3:POP1146 3.2 16.5 1.0
O 3:POP1146 3.4 16.6 1.0
O3 3:POP1146 3.7 17.9 1.0
O4 3:POP1146 3.8 17.0 1.0
NH2 3:ARG135 4.0 14.6 1.0
NE 4:ARG63 4.1 14.3 1.0
OD1 4:ASP27 4.1 21.8 1.0
O 2:HOH2084 4.1 18.2 1.0
O 4:HOH2021 4.2 13.2 1.0
OG1 3:THR141 4.4 19.2 1.0
OD2 4:ASP27 4.4 18.4 1.0
NE2 4:GLN112 4.4 16.3 1.0
NH2 4:ARG63 4.4 13.8 1.0
O1 3:POP1146 4.5 18.6 1.0
O6 3:POP1146 4.5 14.7 1.0
CG 4:ASP27 4.7 19.2 1.0
CZ 4:ARG63 4.7 13.6 1.0
O5' 2:DUR1145 4.8 18.2 1.0
OD2 2:ASP82 4.8 18.3 1.0
O 2:HOH2083 4.8 25.2 1.0
C5' 2:DUR1145 4.9 15.9 1.0
CG 4:ARG63 4.9 14.2 1.0

Magnesium binding site 4 out of 48 in 4apz

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Magnesium binding site 4 out of 48 in the Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1 within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Mg1147

b:15.9
occ:1.00
 O 2:HOH2039 2.0 15.8 1.0
O 2:HOH2038 2.1 15.5 1.0
O 4:HOH2084 2.1 15.9 1.0
O5 4:POP1146 2.1 17.3 1.0
O 3:HOH2065 2.1 19.2 1.0
O2 4:POP1146 2.2 14.4 1.0
P1 4:POP1146 3.3 16.4 1.0
P2 4:POP1146 3.3 16.0 1.0
O 4:POP1146 3.6 14.4 1.0
O3 4:POP1146 3.8 14.5 1.0
NH2 4:ARG135 3.8 15.8 1.0
O 2:HOH2037 3.9 17.1 1.0
O4 4:POP1146 4.0 14.1 1.0
OD1 2:ASP27 4.1 16.5 1.0
O 2:HOH2033 4.1 9.4 1.0
NE 2:ARG63 4.1 21.2 1.0
OG1 4:THR141 4.3 20.3 1.0
OD2 2:ASP27 4.4 18.6 1.0
NH2 2:ARG63 4.5 21.0 1.0
O1 4:POP1146 4.5 15.9 1.0
NE2 2:GLN112 4.6 13.4 1.0
O6 4:POP1146 4.6 14.0 1.0
CG 2:ASP27 4.7 18.9 1.0
OD2 3:ASP82 4.7 18.6 1.0
CZ 2:ARG63 4.7 20.7 1.0
O5' 3:DUR1145 4.8 16.9 1.0
CG 2:ARG63 4.9 17.9 1.0
C5' 3:DUR1145 4.9 14.9 1.0
CZ 4:ARG135 4.9 16.3 1.0
CD 2:ARG63 4.9 20.5 1.0
CG2 4:THR141 5.0 20.5 1.0
O 2:HOH2100 5.0 27.8 1.0

Magnesium binding site 5 out of 48 in 4apz

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Magnesium binding site 5 out of 48 in the Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1 within 5.0Å range:
probe atom residue distance (Å) B Occ
5:Mg1147

b:18.0
occ:1.00
 O 5:HOH2101 2.0 17.3 1.0
O 5:HOH2104 2.1 18.4 1.0
O2 5:POP1146 2.1 19.7 1.0
O 5:HOH2109 2.1 17.1 1.0
O5 5:POP1146 2.1 17.0 1.0
O 5:HOH2107 2.2 19.5 1.0
P1 5:POP1146 3.1 20.2 1.0
P2 5:POP1146 3.3 20.8 1.0
O 5:POP1146 3.5 17.1 1.0
O3 5:POP1146 3.6 19.9 1.0
NH2 5:ARG135 3.9 19.0 1.0
O4 5:POP1146 3.9 20.4 1.0
OD1 7:ASP27 4.1 24.9 1.0
NE 7:ARG63 4.2 23.2 1.0
OG1 5:THR141 4.2 21.1 1.0
O 7:HOH2018 4.2 18.9 1.0
OE1 7:GLN112 4.2 20.5 1.0
O 6:HOH2059 4.3 19.6 1.0
OD2 7:ASP27 4.4 23.8 1.0
NH2 7:ARG63 4.4 23.9 1.0
O1 5:POP1146 4.5 19.6 1.0
O6 5:POP1146 4.5 21.0 1.0
CG 7:ASP27 4.7 22.2 1.0
O5' 6:DUR1145 4.7 23.1 1.0
CZ 7:ARG63 4.8 24.0 1.0
OD2 6:ASP82 4.8 26.0 1.0
C5' 6:DUR1145 4.9 22.4 1.0
CG2 5:THR141 4.9 27.8 1.0
CZ 5:ARG135 5.0 20.5 1.0
CG 7:ARG63 5.0 20.9 1.0
O 5:HOH2108 5.0 24.6 1.0

Magnesium binding site 6 out of 48 in 4apz

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Magnesium binding site 6 out of 48 in the Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1 within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Mg1147

b:19.3
occ:1.00
 O 5:HOH2034 1.9 18.9 1.0
O 5:HOH2080 2.0 29.5 1.0
O5 6:POP1146 2.0 22.3 1.0
O2 6:POP1146 2.0 18.2 1.0
O 5:HOH2033 2.1 18.9 1.0
O 6:HOH2091 2.1 20.1 1.0
P2 6:POP1146 3.2 22.8 1.0
P1 6:POP1146 3.2 21.0 1.0
O 6:POP1146 3.4 21.3 1.0
O3 6:POP1146 3.7 19.3 1.0
NH2 6:ARG135 3.8 19.5 1.0
O4 6:POP1146 3.9 24.8 1.0
NE 5:ARG63 4.1 23.1 1.0
O 5:HOH2029 4.2 17.4 1.0
OD1 5:ASP27 4.2 24.4 1.0
O 5:HOH2032 4.2 20.7 1.0
OE1 5:GLN112 4.2 16.4 1.0
OG1 6:THR141 4.3 22.3 1.0
O6 6:POP1146 4.4 22.9 1.0
O5' 7:DUR1145 4.4 24.5 1.0
OD2 5:ASP27 4.4 21.8 1.0
O1 6:POP1146 4.5 20.3 1.0
NH2 5:ARG63 4.5 24.1 1.0
OD2 7:ASP82 4.6 26.8 1.0
CG 5:ASP27 4.8 22.5 1.0
CZ 5:ARG63 4.8 22.6 1.0
C5' 7:DUR1145 4.9 21.7 1.0
CZ 6:ARG135 4.9 19.4 1.0
CD 5:GLN112 4.9 17.7 1.0
CG 5:ARG63 4.9 23.2 1.0

Magnesium binding site 7 out of 48 in 4apz

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Magnesium binding site 7 out of 48 in the Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1 within 5.0Å range:
probe atom residue distance (Å) B Occ
7:Mg1147

b:21.0
occ:1.00
 O2 7:POP1146 2.0 21.0 1.0
O 6:HOH2022 2.1 23.2 1.0
O 6:HOH2021 2.1 23.8 1.0
O 7:HOH2066 2.1 18.4 1.0
O5 7:POP1146 2.1 19.7 1.0
O 5:HOH2070 2.3 30.3 1.0
P1 7:POP1146 3.2 22.8 1.0
P2 7:POP1146 3.2 23.4 1.0
O 7:POP1146 3.5 21.7 1.0
O4 7:POP1146 3.7 21.2 1.0
O3 7:POP1146 3.7 21.0 1.0
NH2 7:ARG135 3.9 20.9 1.0
O 5:HOH2069 3.9 15.8 1.0
O 6:HOH2020 4.0 16.0 1.0
OD1 6:ASP27 4.1 26.7 1.0
NE 6:ARG63 4.1 23.5 1.0
OE1 6:GLN112 4.2 15.8 1.0
OG1 7:THR141 4.3 22.8 1.0
OD2 6:ASP27 4.4 24.1 1.0
O1 7:POP1146 4.4 18.8 1.0
NH2 6:ARG63 4.4 23.1 1.0
O6 7:POP1146 4.5 21.8 1.0
O5' 5:DUR1145 4.6 22.4 1.0
CG 6:ASP27 4.7 24.5 1.0
CZ 6:ARG63 4.7 21.9 1.0
CD 6:GLN112 4.9 16.1 1.0
OD2 5:ASP82 4.9 23.9 1.0
C5' 5:DUR1145 4.9 22.0 1.0
CG 6:ARG63 4.9 21.0 1.0
CZ 7:ARG135 5.0 20.8 1.0
CD 6:ARG63 5.0 22.8 1.0

Magnesium binding site 8 out of 48 in 4apz

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Magnesium binding site 8 out of 48 in the Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1 within 5.0Å range:
probe atom residue distance (Å) B Occ
8:Mg1147

b:17.4
occ:1.00
 O 8:HOH2128 2.0 17.0 1.0
O2 8:POP1146 2.1 14.6 1.0
O 8:HOH2132 2.1 21.1 1.0
O5 8:POP1146 2.1 16.1 1.0
O 8:HOH2134 2.2 29.0 1.0
O 8:HOH2136 2.2 18.4 1.0
P1 8:POP1146 3.3 16.6 1.0
P2 8:POP1146 3.4 17.3 1.0
O 8:POP1146 3.6 15.7 1.0
O3 8:POP1146 3.8 16.3 1.0
NH2 8:ARG135 3.9 18.2 1.0
O4 8:POP1146 4.0 16.5 1.0
O 9:HOH2026 4.0 18.0 1.0
OD1 9:ASP27 4.1 17.4 1.0
O 9:HOH2023 4.1 15.0 1.0
NE 9:ARG63 4.2 18.9 1.0
OE1 9:GLN112 4.2 14.5 1.0
OD2 9:ASP27 4.3 20.7 1.0
OG1 8:THR141 4.3 23.3 1.0
NH2 9:ARG63 4.5 20.8 1.0
O1 8:POP1146 4.6 14.2 1.0
O6 8:POP1146 4.6 17.1 1.0
CG 9:ASP27 4.6 20.2 1.0
OD2 a:ASP82 4.7 21.6 1.0
O5' a:DUR1145 4.7 17.6 1.0
CZ 9:ARG63 4.8 20.0 1.0
C5' a:DUR1145 4.9 16.9 1.0
CG 9:ARG63 5.0 17.5 1.0
CZ 8:ARG135 5.0 18.5 1.0
CD 9:GLN112 5.0 15.2 1.0
CD 9:ARG63 5.0 18.7 1.0

Magnesium binding site 9 out of 48 in 4apz

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Magnesium binding site 9 out of 48 in the Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1 within 5.0Å range:
probe atom residue distance (Å) B Occ
9:Mg1147

b:17.8
occ:1.00
 O 9:HOH2101 2.1 13.6 1.0
O5 9:POP1146 2.1 15.4 1.0
O2 9:POP1146 2.1 16.4 1.0
O 9:HOH2095 2.2 14.1 1.0
O 9:HOH2093 2.2 16.8 1.0
O 8:HOH2094 2.2 17.3 1.0
P1 9:POP1146 3.3 16.0 1.0
P2 9:POP1146 3.3 14.3 1.0
O 9:POP1146 3.7 15.1 1.0
O3 9:POP1146 3.8 14.2 1.0
NH2 9:ARG135 4.0 13.9 1.0
O4 9:POP1146 4.0 16.0 1.0
O a:HOH2048 4.0 13.7 1.0
O 8:HOH2093 4.0 13.2 1.0
NE a:ARG63 4.0 16.3 1.0
OD1 a:ASP27 4.1 19.7 1.0
OE1 a:GLN112 4.1 15.8 1.0
OG1 9:THR141 4.2 17.0 1.0
OD2 a:ASP27 4.4 20.0 1.0
NH2 a:ARG63 4.4 14.1 1.0
O1 9:POP1146 4.5 14.7 1.0
O6 9:POP1146 4.5 14.2 1.0
CG a:ASP27 4.7 19.8 1.0
CZ a:ARG63 4.7 15.3 1.0
O5' 8:DUR1145 4.7 14.7 1.0
O 8:HOH2092 4.8 19.6 1.0
OD2 8:ASP82 4.8 19.6 1.0
C5' 8:DUR1145 4.8 12.8 1.0
CD a:GLN112 4.8 16.6 1.0
CG a:ARG63 4.9 15.2 1.0
CD a:ARG63 4.9 16.9 1.0

Magnesium binding site 10 out of 48 in 4apz

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Magnesium binding site 10 out of 48 in the Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of B. Subtilis Genomic Dutpase Yncf in Complex with Du, Ppi and Mg in P1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1147

b:21.4
occ:1.00
 O5 A:POP1146 2.0 18.6 1.0
O A:HOH2185 2.0 20.8 1.0
O2 A:POP1146 2.1 18.8 1.0
O A:HOH2193 2.1 22.7 1.0
O A:HOH2195 2.2 21.6 1.0
O A:HOH2178 2.2 17.4 1.0
P1 A:POP1146 3.2 21.8 1.0
P2 A:POP1146 3.2 19.6 1.0
O A:POP1146 3.4 20.2 1.0
O3 A:POP1146 3.7 25.0 1.0
O4 A:POP1146 3.7 20.6 1.0
NH2 A:ARG135 3.9 20.7 1.0
NE C:ARG63 4.1 24.1 1.0
O B:HOH2137 4.1 18.2 1.0
OE1 C:GLN112 4.2 17.9 1.0
OD1 C:ASP27 4.2 21.4 1.0
O C:HOH2045 4.2 17.7 1.0
OG1 A:THR141 4.3 18.8 1.0
OD2 C:ASP27 4.4 22.2 1.0
O6 A:POP1146 4.5 18.2 1.0
NH2 C:ARG63 4.5 24.8 1.0
O1 A:POP1146 4.5 20.3 1.0
O5' B:DUR1145 4.7 19.8 1.0
CG C:ASP27 4.7 19.7 1.0
CZ C:ARG63 4.8 24.0 1.0
C5' B:DUR1145 4.8 20.1 1.0
OD2 B:ASP82 4.8 25.9 1.0
CG C:ARG63 4.9 20.8 1.0
CD C:GLN112 4.9 16.2 1.0
CD C:ARG63 5.0 21.2 1.0

Reference:

J.Garcia-Nafria, J.Timm, C.Harrison, J.P.Turkenburg, K.S.Wilson. Tying Down the Arm in Bacillus Dutpase: Structure and Mechanism Acta Crystallogr.,Sect.D V. 69 1367 2013.
ISSN: ISSN 0907-4449
PubMed: 23897460
DOI: 10.1107/S090744491300735X
Page generated: Thu Aug 15 14:39:31 2024

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