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Magnesium in PDB 2boy: Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP

Enzymatic activity of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP

All present enzymatic activity of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP:
1.13.11.1;

Protein crystallography data

The structure of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP, PDB code: 2boy was solved by M.Ferraroni, I.P.Solyanikova, M.P.Kolomytseva, A.Scozzafava, L.A.Golovleva, F.Briganti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 84.51 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 83.179, 86.610, 93.447, 85.37, 66.53, 76.94
R / Rfree (%) 17.6 / 21.9

Other elements in 2boy:

The structure of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP (pdb code 2boy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP, PDB code: 2boy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in 2boy

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Magnesium binding site 1 out of 16 in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1258

b:48.1
occ:1.00
 O A:HOH2094 1.9 38.9 1.0
O A:HOH2095 2.0 28.8 1.0
O A:HOH2088 2.1 33.7 1.0
O A:HOH2030 2.3 40.4 1.0
O A:ASN67 4.0 23.7 1.0
O A:HOH2098 4.2 39.2 1.0
O A:HOH2099 4.3 26.1 1.0
O A:HOH2103 4.3 28.9 1.0
O A:GLU65 4.3 26.6 1.0
O A:ALA64 4.3 20.1 1.0
O A:HOH2104 4.4 32.1 1.0
CB A:ASN67 4.4 22.7 1.0
N A:ASN67 4.8 23.8 1.0
C A:ASN67 4.9 23.5 1.0
C A:GLU65 4.9 25.4 1.0
OE2 A:GLU65 4.9 35.8 0.5
CA A:ASN67 5.0 22.8 1.0

Magnesium binding site 2 out of 16 in 2boy

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Magnesium binding site 2 out of 16 in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1259

b:38.0
occ:1.00
 O A:HOH2028 1.8 35.3 1.0
O A:HOH2087 2.0 30.9 1.0
O A:HOH2033 2.1 40.8 1.0
O A:HOH2090 2.1 44.0 1.0
O A:HOH2029 2.2 37.4 1.0
O A:HOH2093 2.2 36.0 1.0
O A:SER66 4.1 24.1 1.0
O A:HOH2096 4.1 31.1 1.0
OE1 A:GLU202 4.1 31.0 1.0
OD1 A:ASN67 4.2 20.9 1.0
O A:ALA63 4.2 23.0 1.0
O A:HOH2223 4.2 25.1 1.0
O A:HOH2225 4.3 28.6 1.0
C A:SER66 4.4 24.2 1.0
O A:HOH2097 4.4 32.2 1.0
CB A:SER66 4.5 26.5 1.0
O A:HOH2220 4.5 47.3 1.0
N A:ASN67 4.6 23.8 1.0
CA A:ASN67 4.6 22.8 1.0
CD A:GLU202 4.8 31.6 1.0
O A:HOH2027 5.0 39.2 1.0

Magnesium binding site 3 out of 16 in 2boy

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Magnesium binding site 3 out of 16 in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1258

b:54.4
occ:1.00
 O B:HOH2088 2.0 32.8 1.0
O B:HOH2084 2.1 37.2 1.0
O B:HOH2085 2.2 40.7 1.0
O B:HOH2090 2.3 29.1 1.0
O B:HOH2093 4.2 34.3 1.0
O B:ASN67 4.2 24.3 1.0
O B:ALA64 4.3 22.5 1.0
O B:GLU65 4.6 24.1 1.0
CB B:ASN67 4.6 22.1 1.0
N B:ASN67 5.0 22.7 1.0

Magnesium binding site 4 out of 16 in 2boy

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Magnesium binding site 4 out of 16 in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1259

b:28.3
occ:1.00
 O B:HOH2083 2.0 27.0 1.0
O B:HOH2026 2.0 29.4 1.0
O B:HOH2027 2.0 33.4 1.0
O B:HOH2089 2.1 28.3 1.0
O B:HOH2030 2.1 28.4 1.0
O B:HOH2198 2.2 32.6 1.0
O B:HOH2091 3.8 26.5 1.0
O B:HOH2204 4.1 27.1 1.0
O B:ALA63 4.1 20.9 1.0
O B:HOH2099 4.1 37.4 1.0
O B:SER66 4.1 22.5 1.0
OD1 B:ASN67 4.2 19.8 1.0
OE1 B:GLU202 4.2 28.2 1.0
O B:HOH2196 4.3 22.4 1.0
O B:HOH2202 4.4 26.7 1.0
C B:SER66 4.4 23.1 1.0
CB B:SER66 4.5 24.4 1.0
O B:HOH2029 4.6 29.8 1.0
CA B:ASN67 4.6 22.9 1.0
N B:ASN67 4.6 22.7 1.0
CD B:GLU202 4.8 27.7 1.0
O B:HOH2100 5.0 27.4 1.0

Magnesium binding site 5 out of 16 in 2boy

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Magnesium binding site 5 out of 16 in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1260

b:52.7
occ:1.00
 O B:HOH2144 2.0 39.9 1.0
O G:HOH2087 2.3 44.1 1.0
O B:HOH2145 2.3 44.5 1.0
O B:HOH2148 3.2 50.2 1.0
OD1 B:ASP142 4.2 32.8 1.0
O B:HOH2147 4.2 24.9 1.0
O B:PHE135 4.4 28.8 1.0
OH G:TYR143 4.4 37.1 1.0
CD1 B:PHE135 4.4 25.9 1.0
O G:GLY82 4.5 28.7 1.0
CA B:PRO138 4.5 36.4 1.0
O B:PRO138 4.6 37.4 1.0
CA B:PHE135 4.6 26.6 1.0
CB B:PRO138 4.6 36.2 1.0
C B:PHE135 5.0 28.1 1.0

Magnesium binding site 6 out of 16 in 2boy

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Magnesium binding site 6 out of 16 in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1258

b:45.0
occ:1.00
 O C:HOH2023 1.9 40.9 1.0
O C:HOH2059 1.9 32.3 1.0
O C:HOH2024 2.1 30.4 1.0
O C:HOH2166 2.2 37.4 1.0
O C:HOH2168 2.3 34.0 1.0
O C:SER66 4.0 23.5 1.0
OE1 C:GLU202 4.1 32.5 1.0
O C:HOH2062 4.1 30.2 1.0
OD1 C:ASN67 4.2 19.1 1.0
O C:ALA63 4.2 24.5 1.0
C C:SER66 4.3 25.1 1.0
O C:HOH2170 4.3 29.2 1.0
O C:HOH2169 4.3 28.6 1.0
CB C:SER66 4.4 27.1 1.0
N C:ASN67 4.6 24.2 1.0
CA C:ASN67 4.6 22.6 1.0
O C:HOH2061 4.7 35.3 1.0
CD C:GLU202 4.9 33.5 1.0
CA C:SER66 4.9 26.4 1.0

Magnesium binding site 7 out of 16 in 2boy

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Magnesium binding site 7 out of 16 in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1259

b:55.4
occ:1.00
 O C:HOH2074 2.0 28.4 1.0
O F:HOH2151 2.3 43.0 1.0
O C:HOH2073 2.5 27.5 1.0
O C:HOH2044 2.5 38.6 1.0
O F:HOH2155 2.6 42.7 1.0
O F:HOH2153 2.7 38.2 1.0
O C:PRO77 4.0 21.6 1.0
CB C:PRO48 4.0 22.0 1.0
O F:PRO138 4.3 28.3 1.0
O C:HOH2071 4.3 20.0 1.0
O C:HOH2078 4.3 29.6 1.0
CA C:PRO77 4.4 19.7 1.0
CG C:PRO48 4.5 22.2 1.0
O C:HOH2072 4.5 42.0 1.0
O F:HOH2152 4.6 38.7 1.0
C C:PRO77 4.6 19.8 1.0
O F:LEU140 4.7 20.7 1.0
CB C:PRO77 4.8 19.9 1.0
O F:THR139 4.9 26.0 1.0

Magnesium binding site 8 out of 16 in 2boy

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Magnesium binding site 8 out of 16 in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1260

b:51.2
occ:1.00
 O C:HOH2057 2.2 36.5 1.0
O C:HOH2060 2.2 32.1 1.0
O C:ASN67 4.1 21.6 1.0
O C:HOH2064 4.2 22.4 1.0
O C:ALA64 4.2 24.2 1.0
CB C:ASN67 4.3 22.6 1.0
O C:HOH2065 4.4 31.8 1.0
O C:GLU65 4.5 28.5 1.0
O C:HOH2021 4.5 41.0 1.0
N C:ASN67 4.8 24.2 1.0
C C:ASN67 4.9 22.6 1.0
CA C:ASN67 5.0 22.6 1.0

Magnesium binding site 9 out of 16 in 2boy

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Magnesium binding site 9 out of 16 in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1261

b:53.7
occ:1.00
 O A:HOH2159 2.4 48.3 1.0
O A:HOH2157 2.6 39.6 1.0
O A:HOH2066 4.2 41.4 1.0
OD1 A:ASP142 4.2 27.8 1.0
CB A:PRO138 4.3 25.2 1.0
O A:HOH2164 4.3 33.5 1.0
O A:PRO138 4.8 23.9 1.0
CA A:PRO138 4.8 24.6 1.0

Magnesium binding site 10 out of 16 in 2boy

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Magnesium binding site 10 out of 16 in the Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase From Rhodococcus Opacus 1CP within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1258

b:47.1
occ:1.00
 O D:HOH2083 2.0 38.3 1.0
O D:HOH2023 2.0 32.5 1.0
O D:HOH2076 2.1 35.4 1.0
O D:HOH2024 2.2 41.5 1.0
O D:HOH2027 2.3 34.8 1.0
O D:ASN67 4.2 21.5 1.0
O D:ALA64 4.3 24.3 1.0
OE2 C:GLU153 4.3 28.6 1.0
O D:GLU65 4.3 28.1 1.0
O D:HOH2088 4.3 29.3 1.0
O C:HOH2135 4.4 22.4 1.0
O D:HOH2077 4.4 42.4 1.0
O D:HOH2085 4.4 28.4 1.0
CB D:ASN67 4.5 20.5 1.0
N D:ASN67 4.8 21.8 1.0
C D:GLU65 4.9 26.5 1.0
CD C:GLU153 5.0 31.6 1.0
C D:ASN67 5.0 22.0 1.0

Reference:

M.Ferraroni, M.P.Kolomytseva, I.P.Solyanikova, A.Scozzafava, L.A.Golovleva, F.Briganti. Crystal Structure of 3-Chlorocatechol 1,2-Dioxygenase Key Enzyme of A New Modified Ortho-Pathway From the Gram-Positive Rhodococcus Opacus 1CP Grown on 2-Chlorophenol. J. Mol. Biol. V. 360 788 2006.
ISSN: ISSN 0022-2836
PubMed: 16793061
DOI: 10.1016/J.JMB.2006.05.046
Page generated: Tue Aug 13 21:58:46 2024

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