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Iron in PDB 2b24: Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp. Bound to Indole

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

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

Protein crystallography data

The structure of Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp. Bound to Indole, PDB code: 2b24 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) 20.42 / 3.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 179.358, 179.358, 245.411, 90.00, 90.00, 90.00
R / Rfree (%) 28.7 / 30

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp. Bound to Indole (pdb code 2b24). 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. Bound to Indole, PDB code: 2b24:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 2b24

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


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. Bound to Indole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:66.3
occ:1.00
 NE2 A:HIS221 2.0 86.6 1.0
OD2 A:ASP372 2.2 78.7 1.0
NE2 A:HIS216 2.2 90.0 1.0
OD1 A:ASP372 2.6 77.0 1.0
CG A:ASP372 2.8 78.0 1.0
CE1 A:HIS221 2.9 87.0 1.0
CD2 A:HIS221 3.0 87.2 1.0
CE1 A:HIS216 3.1 90.3 1.0
CD2 A:HIS216 3.3 90.0 1.0
OD1 A:ASN209 3.8 85.7 1.0
ND1 A:HIS221 4.0 87.4 1.0
CG A:HIS221 4.1 87.4 1.0
ND1 A:HIS216 4.3 90.3 1.0
CB A:ASP372 4.3 78.0 1.0
C3 A:IND503 4.4 72.4 1.0
CG A:HIS216 4.4 90.1 1.0
CZ A:PHE362 4.5 79.3 1.0
CE2 A:PHE362 4.6 79.6 1.0
CG A:ASN209 4.8 85.7 1.0
C2 A:IND503 4.9 71.8 1.0
C9 A:IND503 4.9 72.6 1.0
O A:PHE368 5.0 80.0 1.0
ND2 A:ASN209 5.0 85.8 1.0

Iron binding site 2 out of 9 in 2b24

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


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. Bound to Indole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:64.7
occ:1.00
 FE1 A:FES501 0.0 64.7 1.0
ND1 A:HIS111 1.9 83.5 1.0
S2 A:FES501 2.2 61.0 1.0
S1 A:FES501 2.2 61.0 1.0
ND1 A:HIS90 2.4 88.0 1.0
FE2 A:FES501 2.7 60.7 1.0
CG A:HIS111 2.8 83.9 1.0
CE1 A:HIS111 3.0 84.0 1.0
CB A:HIS111 3.1 84.6 1.0
CG A:HIS90 3.2 88.2 1.0
CB A:HIS90 3.3 88.4 1.0
CE1 A:HIS90 3.4 88.5 1.0
N A:HIS111 3.5 85.1 1.0
CB A:TYR110 3.8 85.4 1.0
CA A:HIS111 3.9 84.9 1.0
CD2 A:HIS111 4.0 84.2 1.0
NE2 A:HIS111 4.0 83.9 1.0
CG A:TYR110 4.2 84.1 1.0
N A:ARG91 4.2 88.8 1.0
CD1 A:TYR110 4.3 83.5 1.0
SG A:CYS108 4.4 87.0 1.0
CD2 A:HIS90 4.4 89.2 1.0
C A:TYR110 4.4 85.3 1.0
NE2 A:HIS90 4.5 88.7 1.0
CB A:ARG91 4.5 88.5 1.0
SG A:CYS88 4.6 84.9 1.0
CA A:HIS90 4.7 88.6 1.0
CA A:TYR110 4.7 85.5 1.0
C A:HIS90 4.8 88.7 1.0
C A:HIS111 4.9 84.8 1.0
CA A:ARG91 5.0 88.7 1.0

Iron binding site 3 out of 9 in 2b24

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


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. Bound to Indole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:60.7
occ:1.00
 FE2 A:FES501 0.0 60.7 1.0
S1 A:FES501 2.2 61.0 1.0
S2 A:FES501 2.2 61.0 1.0
SG A:CYS88 2.3 84.9 1.0
SG A:CYS108 2.4 87.0 1.0
FE1 A:FES501 2.7 64.7 1.0
CB A:CYS88 3.1 86.5 1.0
CB A:CYS108 3.5 88.8 1.0
CB A:HIS90 3.8 88.4 1.0
CB A:TYR110 4.3 85.4 1.0
N A:ARG91 4.4 88.8 1.0
ND1 A:HIS90 4.5 88.0 1.0
N A:HIS111 4.5 85.1 1.0
ND1 A:HIS111 4.5 83.5 1.0
CA A:CYS88 4.6 86.7 1.0
CG A:HIS90 4.6 88.2 1.0
CB A:MET93 4.6 87.7 1.0
CB A:TRP113 4.7 84.4 1.0
N A:HIS90 4.7 88.3 1.0
CA A:HIS90 4.7 88.6 1.0
CG A:TRP113 4.9 83.6 1.0
CA A:CYS108 4.9 88.8 1.0
N A:MET93 4.9 88.0 1.0

Iron binding site 4 out of 9 in 2b24

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


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. Bound to Indole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:69.1
occ:1.00
 NE2 C:HIS221 2.0 86.8 1.0
NE2 C:HIS216 2.1 90.0 1.0
OD2 C:ASP372 2.3 79.1 1.0
OD1 C:ASP372 2.5 77.2 1.0
CG C:ASP372 2.8 78.2 1.0
CE1 C:HIS221 2.9 87.2 1.0
CE1 C:HIS216 3.0 90.4 1.0
CD2 C:HIS221 3.0 87.2 1.0
CD2 C:HIS216 3.2 90.0 1.0
OD1 C:ASN209 3.8 85.8 1.0
ND1 C:HIS221 4.0 87.7 1.0
CG C:HIS221 4.1 87.6 1.0
ND1 C:HIS216 4.2 90.3 1.0
CG C:HIS216 4.3 90.2 1.0
CB C:ASP372 4.3 78.1 1.0
C3 C:IND503 4.3 72.4 1.0
CZ C:PHE362 4.6 79.8 1.0
CG C:ASN209 4.7 85.8 1.0
CE2 C:PHE362 4.8 79.8 1.0
ND2 C:ASN209 4.8 85.8 1.0
C2 C:IND503 4.9 71.8 1.0
C9 C:IND503 4.9 72.7 1.0

Iron binding site 5 out of 9 in 2b24

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


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. Bound to Indole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:62.6
occ:1.00
 FE1 C:FES501 0.0 62.6 1.0
ND1 C:HIS111 2.1 83.4 1.0
S1 C:FES501 2.1 59.6 1.0
S2 C:FES501 2.2 59.7 1.0
ND1 C:HIS90 2.3 87.7 1.0
FE2 C:FES501 2.6 58.2 1.0
CG C:HIS111 3.0 83.8 1.0
CE1 C:HIS111 3.1 83.9 1.0
CG C:HIS90 3.1 88.2 1.0
CB C:HIS90 3.2 88.4 1.0
CB C:HIS111 3.3 84.6 1.0
CE1 C:HIS90 3.4 88.4 1.0
N C:HIS111 3.7 84.9 1.0
CB C:TYR110 3.9 85.2 1.0
CA C:HIS111 4.1 84.7 1.0
CD2 C:HIS111 4.1 84.0 1.0
N C:ARG91 4.1 88.8 1.0
NE2 C:HIS111 4.1 83.8 1.0
CD1 C:TYR110 4.3 83.4 1.0
CG C:TYR110 4.3 84.0 1.0
CD2 C:HIS90 4.3 89.1 1.0
CB C:ARG91 4.4 88.5 1.0
NE2 C:HIS90 4.5 88.7 1.0
CA C:HIS90 4.5 88.4 1.0
SG C:CYS108 4.5 86.7 1.0
C C:TYR110 4.6 85.1 1.0
SG C:CYS88 4.6 84.5 1.0
C C:HIS90 4.7 88.5 1.0
CA C:TYR110 4.8 85.2 1.0
CA C:ARG91 4.9 88.6 1.0
CD1 C:TRP113 5.0 83.1 1.0

Iron binding site 6 out of 9 in 2b24

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


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. Bound to Indole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:58.2
occ:1.00
 FE2 C:FES501 0.0 58.2 1.0
S1 C:FES501 2.2 59.6 1.0
S2 C:FES501 2.2 59.7 1.0
SG C:CYS108 2.2 86.7 1.0
FE1 C:FES501 2.6 62.6 1.0
SG C:CYS88 2.6 84.5 1.0
CB C:CYS88 3.3 86.4 1.0
CB C:CYS108 3.4 88.8 1.0
CB C:HIS90 4.0 88.4 1.0
CB C:TYR110 4.1 85.2 1.0
N C:HIS111 4.3 84.9 1.0
ND1 C:HIS111 4.4 83.4 1.0
CB C:MET93 4.4 87.7 1.0
N C:ARG91 4.6 88.8 1.0
ND1 C:HIS90 4.6 87.7 1.0
CA C:CYS108 4.8 88.8 1.0
CA C:CYS88 4.8 86.6 1.0
CB C:TRP113 4.8 84.2 1.0
CG C:HIS90 4.8 88.2 1.0
N C:TYR110 4.8 86.1 1.0
N C:MET93 4.9 87.9 1.0
CA C:TYR110 4.9 85.2 1.0
C C:CYS108 5.0 88.2 1.0
N C:HIS90 5.0 88.4 1.0
CB C:HIS111 5.0 84.6 1.0
CA C:HIS90 5.0 88.4 1.0

Iron binding site 7 out of 9 in 2b24

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


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. Bound to Indole within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe502

b:66.1
occ:1.00
 NE2 E:HIS221 1.9 86.6 1.0
NE2 E:HIS216 2.1 89.7 1.0
OD2 E:ASP372 2.2 78.7 1.0
OD1 E:ASP372 2.4 77.3 1.0
CG E:ASP372 2.7 78.1 1.0
CE1 E:HIS221 2.8 86.9 1.0
CD2 E:HIS221 2.9 87.3 1.0
CE1 E:HIS216 3.1 90.3 1.0
CD2 E:HIS216 3.1 89.9 1.0
ND1 E:HIS221 3.9 87.3 1.0
OD1 E:ASN209 3.9 85.8 1.0
CG E:HIS221 4.0 87.4 1.0
ND1 E:HIS216 4.2 90.5 1.0
CB E:ASP372 4.2 78.1 1.0
CG E:HIS216 4.2 90.1 1.0
C3 E:IND503 4.6 72.2 1.0
CZ E:PHE362 4.7 79.4 1.0
CG E:ASN209 4.8 85.7 1.0
CE2 E:PHE362 4.8 79.6 1.0
ND2 E:ASN209 4.8 85.9 1.0
O E:PHE368 5.0 79.9 1.0

Iron binding site 8 out of 9 in 2b24

Go back to Iron Binding Sites List in 2b24
Iron binding site 8 out of 9 in the Crystal Structure of Naphthalene 1,2-Dioxygenase From Rhodococcus Sp. Bound to Indole


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. Bound to Indole within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:62.7
occ:1.00
 FE1 E:FES501 0.0 62.7 1.0
ND1 E:HIS111 2.1 83.7 1.0
S2 E:FES501 2.2 59.9 1.0
ND1 E:HIS90 2.2 87.8 1.0
S1 E:FES501 2.2 60.7 1.0
FE2 E:FES501 2.7 58.6 1.0
CG E:HIS111 3.0 84.0 1.0
CG E:HIS90 3.0 88.3 1.0
CB E:HIS90 3.1 88.6 1.0
CE1 E:HIS111 3.1 83.9 1.0
CB E:HIS111 3.2 84.5 1.0
CE1 E:HIS90 3.3 88.3 1.0
N E:HIS111 3.7 84.9 1.0
CA E:HIS111 4.0 84.7 1.0
CD2 E:HIS111 4.1 84.0 1.0
CB E:TYR110 4.1 85.2 1.0
NE2 E:HIS111 4.2 83.6 1.0
N E:ARG91 4.2 88.8 1.0
CD2 E:HIS90 4.2 89.0 1.0
NE2 E:HIS90 4.3 88.5 1.0
CA E:HIS90 4.5 88.5 1.0
SG E:CYS88 4.5 84.5 1.0
CG E:TYR110 4.5 83.9 1.0
CB E:ARG91 4.6 88.3 1.0
CD1 E:TYR110 4.6 83.4 1.0
SG E:CYS108 4.6 86.3 1.0
C E:TYR110 4.6 85.1 1.0
C E:HIS90 4.7 88.6 1.0
CD1 E:TRP113 4.8 83.3 1.0
NE1 E:TRP113 4.9 82.2 1.0
CA E:TYR110 5.0 85.3 1.0
C E:HIS111 5.0 84.6 1.0
CA E:ARG91 5.0 88.5 1.0

Iron binding site 9 out of 9 in 2b24

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


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. Bound to Indole within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:58.6
occ:1.00
 FE2 E:FES501 0.0 58.6 1.0
S1 E:FES501 2.2 60.7 1.0
S2 E:FES501 2.2 59.9 1.0
SG E:CYS108 2.3 86.3 1.0
SG E:CYS88 2.4 84.5 1.0
FE1 E:FES501 2.7 62.7 1.0
CB E:CYS88 3.2 86.5 1.0
CB E:CYS108 3.4 88.7 1.0
CB E:HIS90 3.9 88.6 1.0
CB E:TYR110 4.3 85.2 1.0
N E:HIS111 4.4 84.9 1.0
ND1 E:HIS111 4.5 83.7 1.0
ND1 E:HIS90 4.5 87.8 1.0
N E:ARG91 4.6 88.8 1.0
CB E:TRP113 4.6 84.2 1.0
CB E:MET93 4.7 87.5 1.0
CA E:CYS88 4.7 86.6 1.0
CG E:HIS90 4.7 88.3 1.0
CA E:CYS108 4.8 88.8 1.0
CG E:TRP113 4.8 83.7 1.0
N E:HIS90 4.8 88.4 1.0
CA E:HIS90 4.9 88.5 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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