Atomistry » Iron » PDB 2ays-2bmm » 2b24
Atomistry »
  Iron »
    PDB 2ays-2bmm »
      2b24 »

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

Go back to Iron Binding Sites List in 2b24
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

Go back to Iron Binding Sites List in 2b24
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

Go back to Iron Binding Sites List in 2b24
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

Go back to Iron Binding Sites List in 2b24
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

Go back to Iron Binding Sites List in 2b24
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

Go back to Iron Binding Sites List in 2b24
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

Go back to Iron Binding Sites List in 2b24
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

Go back to Iron Binding Sites List in 2b24
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: Wed Jul 16 23:47:21 2025

Last articles

Mg in 4YO7
Mg in 4YN0
Mg in 4YMU
Mg in 4YMN
Mg in 4YLP
Mg in 4YMG
Mg in 4YLO
Mg in 4YLN
Mg in 4YLG
Mg in 4YKH
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy