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Iron in PDB 2b1x: Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp.

Enzymatic activity of Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp.

All present enzymatic activity of Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp.:
1.14.12.12;

Protein crystallography data

The structure of Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp., PDB code: 2b1x was solved by L.Gakhar, Z.A.Malik, C.C.Allen, D.A.Lipscomb, M.J.Larkin, S.Ramaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.80 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.744, 144.246, 186.207, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 22.4

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp. (pdb code 2b1x). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp., PDB code: 2b1x:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 2b1x

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Iron binding site 1 out of 9 in the Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:19.7
occ:1.00
 NE2 A:HIS216 2.1 12.6 1.0
NE2 A:HIS221 2.1 11.4 1.0
O A:HOH1962 2.2 21.6 1.0
O A:HOH1961 2.3 26.4 1.0
OD2 A:ASP372 2.3 13.3 1.0
OD1 A:ASP372 2.4 13.3 1.0
CG A:ASP372 2.7 12.6 1.0
CD2 A:HIS216 3.0 14.3 1.0
CE1 A:HIS221 3.1 10.3 1.0
CD2 A:HIS221 3.1 10.7 1.0
CE1 A:HIS216 3.2 13.3 1.0
O A:HOH1806 4.1 29.9 1.0
CG A:HIS216 4.2 13.4 1.0
CB A:ASP372 4.2 12.0 1.0
ND1 A:HIS221 4.2 10.4 1.0
ND1 A:HIS216 4.2 13.6 1.0
O A:HOH1713 4.3 19.6 1.0
CG A:HIS221 4.3 10.9 1.0
OD1 A:ASN209 4.4 15.2 1.0
ND2 A:ASN209 4.4 15.2 1.0
O A:HOH1747 4.5 28.5 1.0
O2 A:MPD1700 4.5 25.8 1.0
CE2 A:PHE362 4.6 15.4 1.0
CG A:ASN209 4.8 14.2 1.0
CG2 A:THR220 4.8 9.7 1.0
CZ A:PHE362 4.8 13.4 1.0

Iron binding site 2 out of 9 in 2b1x

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Iron binding site 2 out of 9 in the Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:20.9
occ:1.00
 FE1 A:FES501 0.0 20.9 1.0
ND1 A:HIS90 2.1 9.5 1.0
ND1 A:HIS111 2.1 11.7 1.0
S2 A:FES501 2.2 20.7 1.0
S1 A:FES501 2.2 22.3 1.0
FE2 A:FES501 2.8 20.8 1.0
CE1 A:HIS111 3.0 11.1 1.0
CG A:HIS90 3.1 11.8 1.0
CE1 A:HIS90 3.1 12.2 1.0
CG A:HIS111 3.1 11.5 1.0
CB A:HIS90 3.4 10.2 1.0
CB A:HIS111 3.5 10.8 1.0
N A:HIS111 3.7 11.0 1.0
CB A:TYR110 4.1 11.7 1.0
NE2 A:HIS111 4.1 12.3 1.0
N A:ARG91 4.1 11.9 1.0
CD2 A:HIS111 4.2 11.4 1.0
CA A:HIS111 4.2 11.3 1.0
NE2 A:HIS90 4.2 9.4 1.0
CD2 A:HIS90 4.2 10.2 1.0
SG A:CYS88 4.4 12.9 1.0
CB A:ARG91 4.4 12.4 1.0
CG A:TYR110 4.4 12.8 1.0
SG A:CYS108 4.5 14.4 1.0
CD1 A:TYR110 4.5 11.3 1.0
C A:TYR110 4.6 11.7 1.0
CA A:HIS90 4.6 11.0 1.0
C A:HIS90 4.7 11.6 1.0
CA A:TYR110 4.9 11.5 1.0
CA A:ARG91 4.9 11.8 1.0

Iron binding site 3 out of 9 in 2b1x

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Iron binding site 3 out of 9 in the Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:20.8
occ:1.00
 FE2 A:FES501 0.0 20.8 1.0
S1 A:FES501 2.2 22.3 1.0
SG A:CYS108 2.2 14.4 1.0
S2 A:FES501 2.2 20.7 1.0
SG A:CYS88 2.3 12.9 1.0
FE1 A:FES501 2.8 20.9 1.0
CB A:CYS108 3.1 12.6 1.0
CB A:CYS88 3.1 12.3 1.0
CB A:HIS90 4.1 10.2 1.0
CB A:TYR110 4.3 11.7 1.0
N A:HIS111 4.4 11.0 1.0
ND1 A:HIS90 4.4 9.5 1.0
ND1 A:HIS111 4.5 11.7 1.0
CA A:CYS108 4.5 12.9 1.0
N A:ARG91 4.6 11.9 1.0
CA A:CYS88 4.6 12.4 1.0
CB A:MET93 4.6 12.5 1.0
CB A:TRP113 4.7 10.5 1.0
CG A:HIS90 4.8 11.8 1.0
N A:TYR110 4.9 12.4 1.0
N A:MET93 4.9 11.4 1.0
C A:CYS108 4.9 12.7 1.0
N A:HIS90 5.0 10.3 1.0
CG A:TRP113 5.0 10.9 1.0
CA A:TYR110 5.0 11.5 1.0

Iron binding site 4 out of 9 in 2b1x

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Iron binding site 4 out of 9 in the Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:21.8
occ:1.00
 NE2 C:HIS221 2.1 11.9 1.0
NE2 C:HIS216 2.2 13.0 1.0
O C:HOH1958 2.2 27.1 1.0
OD2 C:ASP372 2.3 14.1 1.0
O C:HOH1957 2.3 17.2 1.0
OD1 C:ASP372 2.4 13.8 1.0
CG C:ASP372 2.7 12.2 1.0
CD2 C:HIS216 3.0 14.1 1.0
CE1 C:HIS221 3.1 10.5 1.0
CD2 C:HIS221 3.2 10.7 1.0
CE1 C:HIS216 3.2 13.5 1.0
O C:HOH1730 3.9 21.1 1.0
CB C:ASP372 4.2 12.0 1.0
ND1 C:HIS221 4.2 10.1 1.0
CG C:HIS216 4.2 13.2 1.0
O C:HOH1794 4.3 22.1 1.0
ND1 C:HIS216 4.3 13.6 1.0
CG C:HIS221 4.3 11.0 1.0
OD1 C:ASN209 4.3 14.9 1.0
ND2 C:ASN209 4.4 15.1 1.0
O2 C:MPD1704 4.6 29.2 1.0
CE2 C:PHE362 4.6 14.9 1.0
CG2 C:THR220 4.7 9.5 1.0
CZ C:PHE362 4.8 13.6 1.0
CG C:ASN209 4.8 14.8 1.0

Iron binding site 5 out of 9 in 2b1x

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Iron binding site 5 out of 9 in the Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:20.4
occ:1.00
 FE1 C:FES501 0.0 20.4 1.0
ND1 C:HIS90 2.1 9.7 1.0
ND1 C:HIS111 2.2 11.9 1.0
S2 C:FES501 2.2 21.1 1.0
S1 C:FES501 2.2 21.4 1.0
FE2 C:FES501 2.8 20.1 1.0
CE1 C:HIS111 3.0 11.7 1.0
CG C:HIS90 3.0 11.2 1.0
CE1 C:HIS90 3.1 11.9 1.0
CG C:HIS111 3.2 12.1 1.0
CB C:HIS90 3.3 10.2 1.0
CB C:HIS111 3.6 10.8 1.0
N C:HIS111 3.8 11.3 1.0
CB C:TYR110 4.1 11.4 1.0
NE2 C:HIS111 4.1 11.4 1.0
N C:ARG91 4.2 12.0 1.0
CD2 C:HIS90 4.2 9.6 1.0
NE2 C:HIS90 4.2 10.1 1.0
CD2 C:HIS111 4.2 11.3 1.0
CA C:HIS111 4.2 11.2 1.0
CB C:ARG91 4.4 12.6 1.0
SG C:CYS88 4.4 13.0 1.0
CG C:TYR110 4.4 12.4 1.0
SG C:CYS108 4.5 13.7 1.0
CD1 C:TYR110 4.5 11.6 1.0
CA C:HIS90 4.5 11.0 1.0
C C:TYR110 4.6 11.7 1.0
C C:HIS90 4.7 11.1 1.0
CA C:TYR110 4.9 11.7 1.0
CA C:ARG91 4.9 11.7 1.0

Iron binding site 6 out of 9 in 2b1x

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Iron binding site 6 out of 9 in the Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:20.1
occ:1.00
 FE2 C:FES501 0.0 20.1 1.0
S2 C:FES501 2.2 21.1 1.0
S1 C:FES501 2.2 21.4 1.0
SG C:CYS108 2.2 13.7 1.0
SG C:CYS88 2.3 13.0 1.0
FE1 C:FES501 2.8 20.4 1.0
CB C:CYS108 3.1 12.3 1.0
CB C:CYS88 3.1 12.7 1.0
CB C:HIS90 4.0 10.2 1.0
CB C:TYR110 4.3 11.4 1.0
ND1 C:HIS90 4.4 9.7 1.0
N C:HIS111 4.5 11.3 1.0
CA C:CYS108 4.5 13.0 1.0
CB C:MET93 4.5 12.7 1.0
ND1 C:HIS111 4.6 11.9 1.0
CA C:CYS88 4.6 12.0 1.0
N C:ARG91 4.6 12.0 1.0
CB C:TRP113 4.7 10.0 1.0
CG C:HIS90 4.7 11.2 1.0
N C:MET93 4.9 11.9 1.0
N C:HIS90 4.9 10.7 1.0
N C:TYR110 4.9 12.3 1.0
CA C:HIS90 5.0 11.0 1.0
CG C:TRP113 5.0 11.4 1.0
C C:CYS108 5.0 12.7 1.0

Iron binding site 7 out of 9 in 2b1x

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Iron binding site 7 out of 9 in the Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe502

b:21.0
occ:1.00
 O E:HOH2010 2.1 22.9 1.0
NE2 E:HIS216 2.1 13.4 1.0
NE2 E:HIS221 2.1 11.8 1.0
O E:HOH2011 2.2 23.6 1.0
OD1 E:ASP372 2.3 12.8 1.0
OD2 E:ASP372 2.3 12.7 1.0
CG E:ASP372 2.7 12.4 1.0
CD2 E:HIS216 3.0 14.4 1.0
CE1 E:HIS221 3.0 10.5 1.0
CD2 E:HIS221 3.2 11.2 1.0
CE1 E:HIS216 3.2 13.3 1.0
O E:HOH1805 3.9 30.5 1.0
O E:HOH1748 4.0 20.5 1.0
ND1 E:HIS221 4.2 9.4 1.0
CB E:ASP372 4.2 11.4 1.0
CG E:HIS216 4.2 13.7 1.0
OD1 E:ASN209 4.2 15.6 1.0
ND1 E:HIS216 4.3 13.7 1.0
CG E:HIS221 4.3 10.7 1.0
ND2 E:ASN209 4.4 15.8 1.0
O E:HOH1816 4.6 35.1 1.0
O2 E:MPD1708 4.6 25.6 1.0
CG2 E:THR220 4.7 9.4 1.0
CG E:ASN209 4.7 14.4 1.0
CE2 E:PHE362 4.8 15.6 1.0
CZ E:PHE362 4.9 13.5 1.0

Iron binding site 8 out of 9 in 2b1x

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Iron binding site 8 out of 9 in the Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:19.9
occ:1.00
 FE1 E:FES501 0.0 19.9 1.0
ND1 E:HIS90 2.2 10.1 1.0
S2 E:FES501 2.2 19.4 1.0
ND1 E:HIS111 2.2 11.4 1.0
S1 E:FES501 2.3 20.4 1.0
FE2 E:FES501 2.7 19.2 1.0
CG E:HIS90 3.0 11.5 1.0
CE1 E:HIS111 3.1 11.8 1.0
CG E:HIS111 3.2 11.7 1.0
CB E:HIS90 3.2 10.4 1.0
CE1 E:HIS90 3.2 11.8 1.0
CB E:HIS111 3.6 10.9 1.0
N E:HIS111 3.7 10.8 1.0
CB E:TYR110 4.1 11.3 1.0
N E:ARG91 4.2 11.9 1.0
CA E:HIS111 4.2 11.0 1.0
NE2 E:HIS111 4.2 11.7 1.0
CD2 E:HIS90 4.2 9.4 1.0
CD2 E:HIS111 4.3 11.7 1.0
NE2 E:HIS90 4.3 9.2 1.0
SG E:CYS88 4.4 13.3 1.0
CG E:TYR110 4.4 12.5 1.0
SG E:CYS108 4.5 13.8 1.0
CA E:HIS90 4.5 11.2 1.0
C E:TYR110 4.5 11.6 1.0
CB E:ARG91 4.5 11.9 1.0
CD1 E:TYR110 4.5 11.9 1.0
C E:HIS90 4.7 11.2 1.0
CA E:TYR110 4.9 11.4 1.0
CA E:ARG91 5.0 11.3 1.0
CD1 E:TRP113 5.0 11.0 1.0

Iron binding site 9 out of 9 in 2b1x

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Iron binding site 9 out of 9 in the Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:19.2
occ:1.00
 FE2 E:FES501 0.0 19.2 1.0
S1 E:FES501 2.2 20.4 1.0
S2 E:FES501 2.2 19.4 1.0
SG E:CYS108 2.3 13.8 1.0
SG E:CYS88 2.3 13.3 1.0
FE1 E:FES501 2.7 19.9 1.0
CB E:CYS108 3.0 12.1 1.0
CB E:CYS88 3.1 12.6 1.0
CB E:HIS90 4.0 10.4 1.0
CB E:TYR110 4.3 11.3 1.0
N E:HIS111 4.4 10.8 1.0
CA E:CYS108 4.5 12.7 1.0
ND1 E:HIS90 4.5 10.1 1.0
CA E:CYS88 4.6 12.5 1.0
ND1 E:HIS111 4.6 11.4 1.0
CB E:MET93 4.6 13.3 1.0
N E:ARG91 4.7 11.9 1.0
CB E:TRP113 4.7 10.5 1.0
CG E:HIS90 4.8 11.5 1.0
N E:TYR110 4.9 12.4 1.0
N E:HIS90 4.9 10.7 1.0
N E:MET93 4.9 11.3 1.0
C E:CYS108 4.9 12.4 1.0
CA E:HIS90 4.9 11.2 1.0
CG E:TRP113 5.0 11.1 1.0

Reference:

L.Gakhar, Z.A.Malik, C.C.Allen, D.A.Lipscomb, M.J.Larkin, S.Ramaswamy. Structure and Increased Thermostability of Rhodococcus Sp. Naphthalene 1,2-Dioxygenase. J.Bacteriol. V. 187 7222 2005.
ISSN: ISSN 0021-9193
PubMed: 16237006
DOI: 10.1128/JB.187.21.7222-7231.2005
Page generated: Sat Aug 3 19:30:42 2024

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