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Iron in PDB 3gke: Crystal Structure of Dicamba Monooxygenase

Protein crystallography data

The structure of Crystal Structure of Dicamba Monooxygenase, PDB code: 3gke was solved by M.A.Wilson, R.Dumitru, W.Z.Jiang, D.P.Weeks, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.15 / 1.75
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 81.026, 81.026, 158.154, 90.00, 90.00, 120.00
R / Rfree (%) 16.3 / 19.8

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Dicamba Monooxygenase (pdb code 3gke). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Dicamba Monooxygenase, PDB code: 3gke:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3gke

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Iron binding site 1 out of 8 in the Crystal Structure of Dicamba Monooxygenase


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 Dicamba Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:27.0
occ:1.00
 FE1 A:FES500 0.0 27.0 1.0
ND1 A:HIS51 2.1 29.8 1.0
ND1 A:HIS71 2.2 26.3 1.0
S1 A:FES500 2.2 28.2 1.0
S2 A:FES500 2.2 24.8 1.0
FE2 A:FES500 2.7 26.5 1.0
CE1 A:HIS51 3.1 30.7 1.0
CG A:HIS51 3.1 28.2 1.0
CE1 A:HIS71 3.1 26.4 1.0
CG A:HIS71 3.1 27.2 1.0
CB A:HIS51 3.4 26.6 1.0
CB A:HIS71 3.4 26.3 1.0
N A:HIS71 3.8 26.1 1.0
CB A:TYR70 4.0 26.4 1.0
CA A:HIS71 4.2 25.8 1.0
NE2 A:HIS51 4.2 29.8 1.0
NE2 A:HIS71 4.2 26.3 1.0
N A:ARG52 4.2 26.3 1.0
CD2 A:HIS51 4.2 31.8 1.0
CD2 A:HIS71 4.2 31.6 1.0
SG A:CYS49 4.4 26.4 1.0
CG A:TYR70 4.4 25.9 1.0
SG A:CYS68 4.4 26.6 1.0
CB A:ARG52 4.5 23.6 1.0
CD1 A:TYR70 4.5 23.9 1.0
C A:TYR70 4.6 29.1 1.0
CA A:HIS51 4.7 28.5 1.0
C A:HIS71 4.8 31.7 1.0
C A:HIS51 4.9 28.8 1.0
CA A:TYR70 4.9 25.5 1.0
CA A:ARG52 4.9 25.8 1.0
CG A:ARG52 5.0 30.3 1.0

Iron binding site 2 out of 8 in 3gke

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Iron binding site 2 out of 8 in the Crystal Structure of Dicamba Monooxygenase


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 Dicamba Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:26.5
occ:1.00
 FE2 A:FES500 0.0 26.5 1.0
S1 A:FES500 2.2 28.2 1.0
S2 A:FES500 2.2 24.8 1.0
SG A:CYS68 2.3 26.6 1.0
SG A:CYS49 2.3 26.4 1.0
FE1 A:FES500 2.7 27.0 1.0
CB A:CYS49 3.1 23.9 1.0
CB A:CYS68 3.1 24.7 1.0
CB A:HIS51 4.1 26.6 1.0
CB A:TYR70 4.3 26.4 1.0
ND1 A:HIS51 4.3 29.8 1.0
N A:HIS71 4.5 26.1 1.0
ND1 A:HIS71 4.5 26.3 1.0
CA A:CYS49 4.5 22.3 1.0
CB A:ALA54 4.6 26.7 1.0
CA A:CYS68 4.6 28.1 1.0
CG A:HIS51 4.7 28.2 1.0
N A:ARG52 4.7 26.3 1.0
CD1 A:LEU73 4.8 27.4 1.0
N A:TYR70 4.9 26.1 1.0
CG A:LEU73 4.9 29.9 1.0
CB A:LEU73 5.0 28.2 1.0
N A:HIS51 5.0 28.5 1.0

Iron binding site 3 out of 8 in 3gke

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Iron binding site 3 out of 8 in the Crystal Structure of Dicamba Monooxygenase


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 Dicamba Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:21.1
occ:1.00
 NE2 A:HIS165 2.0 25.8 1.0
OD2 A:ASP294 2.0 24.5 1.0
OXT A:ACT354 2.1 26.7 1.0
NE2 A:HIS160 2.1 25.6 1.0
CG A:ASP294 2.7 24.9 1.0
OD1 A:ASP294 2.8 25.6 1.0
C A:ACT354 2.9 31.7 1.0
CE1 A:HIS165 3.0 22.4 1.0
O A:ACT354 3.0 27.7 1.0
CE1 A:HIS160 3.1 26.5 1.0
CD2 A:HIS165 3.1 21.8 1.0
CD2 A:HIS160 3.1 26.9 1.0
OD1 A:ASN154 3.7 23.8 1.0
O A:HOH385 4.0 20.5 1.0
ND1 A:HIS165 4.1 22.4 1.0
CG A:HIS165 4.2 22.5 1.0
ND1 A:HIS160 4.2 23.4 1.0
CB A:ASP294 4.2 26.6 1.0
CG A:HIS160 4.2 27.0 1.0
ND2 A:ASN154 4.3 21.9 1.0
CH3 A:ACT354 4.3 31.6 1.0
CG A:ASN154 4.4 23.8 1.0
CD2 A:LEU290 4.5 29.4 1.0
O A:ALA289 4.7 22.6 1.0

Iron binding site 4 out of 8 in 3gke

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Iron binding site 4 out of 8 in the Crystal Structure of Dicamba Monooxygenase


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 Dicamba Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:20.0
occ:1.00
 FE1 B:FES500 0.0 20.0 1.0
S1 B:FES500 2.2 21.7 1.0
S2 B:FES500 2.2 22.6 1.0
SG B:CYS49 2.3 20.1 1.0
SG B:CYS68 2.3 19.5 1.0
FE2 B:FES500 2.7 21.4 1.0
CB B:CYS49 3.1 19.1 1.0
CB B:CYS68 3.2 14.4 1.0
CB B:HIS51 4.1 18.5 1.0
CB B:ALA54 4.3 17.8 1.0
ND1 B:HIS51 4.3 21.6 1.0
CB B:TYR70 4.4 20.8 1.0
ND1 B:HIS71 4.5 22.5 1.0
N B:HIS71 4.5 22.3 1.0
CA B:CYS49 4.5 19.4 1.0
CA B:CYS68 4.6 18.2 1.0
CG B:HIS51 4.7 24.1 1.0
N B:ARG52 4.7 20.2 1.0
CD1 B:LEU73 4.9 21.9 1.0
CD2 B:LEU56 4.9 19.1 1.0
N B:HIS51 4.9 18.1 1.0
CG B:LEU73 5.0 20.6 1.0
N B:ALA54 5.0 20.8 1.0
CB B:LEU73 5.0 19.3 1.0
N B:TYR70 5.0 20.2 1.0

Iron binding site 5 out of 8 in 3gke

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Iron binding site 5 out of 8 in the Crystal Structure of Dicamba Monooxygenase


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 Dicamba Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:21.4
occ:1.00
 FE2 B:FES500 0.0 21.4 1.0
ND1 B:HIS51 2.1 21.6 1.0
ND1 B:HIS71 2.1 22.5 1.0
S2 B:FES500 2.2 22.6 1.0
S1 B:FES500 2.2 21.7 1.0
FE1 B:FES500 2.7 20.0 1.0
CE1 B:HIS71 3.0 24.5 1.0
CE1 B:HIS51 3.1 24.1 1.0
CG B:HIS51 3.1 24.1 1.0
CG B:HIS71 3.2 24.7 1.0
CB B:HIS51 3.4 18.5 1.0
CB B:HIS71 3.6 19.4 1.0
N B:HIS71 3.8 22.3 1.0
NE2 B:HIS71 4.2 25.9 1.0
NE2 B:HIS51 4.2 23.4 1.0
CB B:TYR70 4.2 20.8 1.0
CA B:HIS71 4.2 22.9 1.0
N B:ARG52 4.2 20.2 1.0
CD2 B:HIS51 4.2 22.7 1.0
CD2 B:HIS71 4.3 30.0 1.0
SG B:CYS49 4.4 20.1 1.0
SG B:CYS68 4.5 19.5 1.0
CD1 B:TYR70 4.5 20.5 1.0
CB B:ARG52 4.5 21.7 1.0
CG B:ARG52 4.5 32.0 1.0
CG B:TYR70 4.6 22.1 1.0
C B:TYR70 4.7 22.4 1.0
CA B:HIS51 4.7 19.7 1.0
C B:HIS71 4.9 21.4 1.0
C B:HIS51 4.9 21.1 1.0
CA B:ARG52 5.0 18.7 1.0

Iron binding site 6 out of 8 in 3gke

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Iron binding site 6 out of 8 in the Crystal Structure of Dicamba Monooxygenase


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 Dicamba Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:30.1
occ:1.00
 OD2 B:ASP294 1.9 35.5 1.0
NE2 B:HIS165 2.0 34.8 1.0
O1 B:OXY600 2.1 42.5 1.0
NE2 B:HIS160 2.2 32.3 1.0
O2 B:OXY600 2.6 41.5 1.0
CG B:ASP294 2.6 36.7 1.0
OD1 B:ASP294 2.7 33.0 1.0
CE1 B:HIS165 2.9 37.2 1.0
CD2 B:HIS165 3.1 39.5 1.0
CD2 B:HIS160 3.1 35.2 1.0
CE1 B:HIS160 3.1 31.9 1.0
OD1 B:ASN154 3.6 28.4 1.0
ND1 B:HIS165 4.1 37.3 1.0
O B:HOH466 4.1 24.8 1.0
CB B:ASP294 4.1 33.0 1.0
CG B:HIS165 4.2 39.9 1.0
ND2 B:ASN154 4.2 26.7 1.0
ND1 B:HIS160 4.3 30.7 1.0
CG B:HIS160 4.3 29.8 1.0
CG B:ASN154 4.3 29.8 1.0
CD2 B:LEU290 4.7 42.2 1.0
O B:ALA289 4.9 32.9 1.0

Iron binding site 7 out of 8 in 3gke

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Iron binding site 7 out of 8 in the Crystal Structure of Dicamba Monooxygenase


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 Dicamba Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe500

b:22.0
occ:1.00
 FE1 C:FES500 0.0 22.0 1.0
ND1 C:HIS71 2.1 18.8 1.0
ND1 C:HIS51 2.1 22.8 1.0
S2 C:FES500 2.2 23.0 1.0
S1 C:FES500 2.2 21.8 1.0
FE2 C:FES500 2.7 21.1 1.0
CE1 C:HIS71 3.0 23.4 1.0
CG C:HIS51 3.1 25.4 1.0
CG C:HIS71 3.1 22.0 1.0
CE1 C:HIS51 3.1 23.6 1.0
CB C:HIS51 3.4 22.4 1.0
CB C:HIS71 3.4 20.3 1.0
N C:HIS71 3.7 22.0 1.0
CB C:TYR70 4.0 21.5 1.0
CA C:HIS71 4.1 23.0 1.0
NE2 C:HIS71 4.2 21.3 1.0
N C:ARG52 4.2 22.4 1.0
CD2 C:HIS71 4.2 27.2 1.0
NE2 C:HIS51 4.2 25.6 1.0
CD2 C:HIS51 4.2 20.9 1.0
CG C:TYR70 4.4 18.4 1.0
SG C:CYS49 4.5 20.6 1.0
SG C:CYS68 4.5 20.9 1.0
CB C:ARG52 4.5 22.4 1.0
CD1 C:TYR70 4.5 21.1 1.0
C C:TYR70 4.5 21.3 1.0
CA C:HIS51 4.6 21.6 1.0
C C:HIS51 4.8 21.8 1.0
CG C:ARG52 4.8 24.0 1.0
C C:HIS71 4.8 26.0 1.0
CA C:TYR70 4.9 21.2 1.0
CA C:ARG52 4.9 23.8 1.0

Iron binding site 8 out of 8 in 3gke

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Iron binding site 8 out of 8 in the Crystal Structure of Dicamba Monooxygenase


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 Dicamba Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe500

b:21.1
occ:1.00
 FE2 C:FES500 0.0 21.1 1.0
S2 C:FES500 2.2 23.0 1.0
S1 C:FES500 2.2 21.8 1.0
SG C:CYS49 2.3 20.6 1.0
SG C:CYS68 2.3 20.9 1.0
FE1 C:FES500 2.7 22.0 1.0
CB C:CYS49 3.1 21.4 1.0
CB C:CYS68 3.2 18.1 1.0
CB C:HIS51 4.0 22.4 1.0
CB C:TYR70 4.3 21.5 1.0
N C:HIS71 4.4 22.0 1.0
ND1 C:HIS51 4.4 22.8 1.0
CB C:ALA54 4.5 23.8 1.0
ND1 C:HIS71 4.5 18.8 1.0
CA C:CYS49 4.5 19.0 1.0
CA C:CYS68 4.6 18.6 1.0
N C:ARG52 4.7 22.4 1.0
CG C:HIS51 4.7 25.4 1.0
N C:TYR70 4.9 22.4 1.0
CD1 C:LEU73 4.9 24.4 1.0
N C:HIS51 4.9 22.8 1.0
CB C:LEU73 4.9 21.5 1.0
CG C:LEU73 4.9 23.9 1.0
CD2 C:LEU56 5.0 21.1 1.0

Reference:

R.Dumitru, W.Z.Jiang, D.P.Weeks, M.A.Wilson. Crystal Structure of Dicamba Monooxygenase: A Rieske Nonheme Oxygenase That Catalyzes Oxidative Demethylation. J.Mol.Biol. V. 392 498 2009.
ISSN: ISSN 0022-2836
PubMed: 19616011
DOI: 10.1016/J.JMB.2009.07.021
Page generated: Sun Aug 4 10:43:25 2024

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