Atomistry » Magnesium » PDB 2bhd-2bt1 » 2boy
Atomistry »
  Magnesium »
    PDB 2bhd-2bt1 »
      2boy »

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

Go back to Magnesium Binding Sites List in 2boy
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

Go back to Magnesium Binding Sites List in 2boy
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

Go back to Magnesium Binding Sites List in 2boy
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

Go back to Magnesium Binding Sites List in 2boy
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

Go back to Magnesium Binding Sites List in 2boy
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

Go back to Magnesium Binding Sites List in 2boy
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

Go back to Magnesium Binding Sites List in 2boy
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

Go back to Magnesium Binding Sites List in 2boy
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

Go back to Magnesium Binding Sites List in 2boy
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

Go back to Magnesium Binding Sites List in 2boy
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy