Atomistry » Iron » PDB 6vk8-6wnb » 6vsh
Atomistry »
  Iron »
    PDB 6vk8-6wnb »
      6vsh »

Iron in PDB 6vsh: Crystal Structure of Apo Dicamba Monooxygenase

Protein crystallography data

The structure of Crystal Structure of Apo Dicamba Monooxygenase, PDB code: 6vsh was solved by T.J.Rydel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.26 / 3.00
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 80.170, 80.170, 159.346, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 25.2

Iron Binding Sites:

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

Iron binding site 1 out of 6 in 6vsh

Go back to Iron Binding Sites List in 6vsh
Iron binding site 1 out of 6 in the Crystal Structure of Apo 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 Apo Dicamba Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:36.6
occ:1.00
FE1 A:FES501 0.0 36.6 1.0
S2 A:FES501 2.2 35.5 1.0
S1 A:FES501 2.2 32.2 1.0
SG A:CYS68 2.4 42.6 1.0
SG A:CYS49 2.5 31.7 1.0
FE2 A:FES501 2.9 39.8 1.0
CB A:CYS68 3.0 33.8 1.0
CB A:CYS49 3.3 30.7 1.0
CB A:TYR70 4.1 39.5 1.0
N A:HIS71 4.1 38.6 1.0
CB A:HIS51 4.3 29.6 1.0
CA A:CYS68 4.5 28.2 1.0
CB A:ALA54 4.5 34.2 1.0
CA A:CYS49 4.8 24.4 1.0
N A:TYR70 4.8 34.5 1.0
ND1 A:HIS51 4.8 30.7 1.0
CA A:TYR70 4.9 38.0 1.0
CB A:LEU73 4.9 35.1 1.0
C A:CYS68 4.9 30.3 1.0
CD2 A:HIS71 4.9 39.5 1.0
N A:GLY72 4.9 37.0 1.0
CB A:HIS71 5.0 33.1 1.0
CA A:HIS71 5.0 32.4 1.0
C A:TYR70 5.0 41.4 1.0

Iron binding site 2 out of 6 in 6vsh

Go back to Iron Binding Sites List in 6vsh
Iron binding site 2 out of 6 in the Crystal Structure of Apo 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 Apo Dicamba Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:39.8
occ:1.00
FE2 A:FES501 0.0 39.8 1.0
ND1 A:HIS51 2.2 30.7 1.0
S1 A:FES501 2.2 32.2 1.0
S2 A:FES501 2.2 35.5 1.0
CD2 A:HIS71 2.5 39.5 1.0
FE1 A:FES501 2.9 36.6 1.0
CG A:HIS51 2.9 32.6 1.0
CB A:HIS51 3.1 29.6 1.0
CG A:HIS71 3.2 39.7 1.0
CE1 A:HIS51 3.3 33.3 1.0
CB A:HIS71 3.3 33.1 1.0
NE2 A:HIS71 3.7 45.0 1.0
N A:HIS71 3.9 38.6 1.0
N A:ARG52 4.0 32.1 1.0
CD2 A:HIS51 4.1 41.7 1.0
CA A:HIS71 4.2 32.4 1.0
CB A:TYR70 4.2 39.5 1.0
NE2 A:HIS51 4.3 40.7 1.0
CD1 A:TYR70 4.3 42.7 1.0
CA A:HIS51 4.4 31.1 1.0
SG A:CYS49 4.4 31.7 1.0
ND1 A:HIS71 4.5 45.1 1.0
CB A:ARG52 4.5 28.2 1.0
CG A:TYR70 4.5 42.8 1.0
C A:HIS51 4.7 30.9 1.0
CE1 A:HIS71 4.7 47.3 1.0
CG A:ARG52 4.8 39.8 1.0
C A:TYR70 4.8 41.4 1.0
CA A:ARG52 4.8 33.1 1.0
SG A:CYS68 4.9 42.6 1.0
C A:HIS71 5.0 42.1 1.0

Iron binding site 3 out of 6 in 6vsh

Go back to Iron Binding Sites List in 6vsh
Iron binding site 3 out of 6 in the Crystal Structure of Apo 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 Apo Dicamba Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:33.2
occ:1.00
FE1 B:FES501 0.0 33.2 1.0
S1 B:FES501 2.2 30.9 1.0
S2 B:FES501 2.2 28.5 1.0
SG B:CYS49 2.5 32.3 1.0
SG B:CYS68 2.5 37.2 1.0
CB B:CYS49 3.0 25.7 1.0
FE2 B:FES501 3.0 35.2 1.0
CB B:CYS68 3.2 33.0 1.0
CB B:HIS51 4.2 25.9 1.0
CB B:ALA54 4.2 26.2 1.0
CB B:TYR70 4.3 34.9 1.0
CA B:CYS49 4.5 25.4 1.0
N B:HIS71 4.5 38.0 1.0
CA B:CYS68 4.6 28.7 1.0
CB B:LEU73 4.8 34.4 1.0
CD1 B:LEU73 4.8 26.8 1.0
ND1 B:HIS51 4.8 31.0 1.0
N B:ARG52 4.9 31.8 1.0
CG B:LEU73 4.9 32.5 1.0
N B:ALA54 4.9 26.7 1.0
N B:TYR70 5.0 31.6 1.0
C B:CYS49 5.0 29.3 1.0
CD2 B:LEU56 5.0 26.9 1.0
N B:HIS51 5.0 26.3 1.0
CG B:HIS51 5.0 26.7 1.0

Iron binding site 4 out of 6 in 6vsh

Go back to Iron Binding Sites List in 6vsh
Iron binding site 4 out of 6 in the Crystal Structure of Apo 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 Apo Dicamba Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:35.2
occ:1.00
FE2 B:FES501 0.0 35.2 1.0
S1 B:FES501 2.2 30.9 1.0
S2 B:FES501 2.2 28.5 1.0
ND1 B:HIS51 2.3 31.0 1.0
ND1 B:HIS71 2.4 32.0 1.0
FE1 B:FES501 3.0 33.2 1.0
CG B:HIS71 3.1 42.3 1.0
CB B:HIS71 3.1 38.5 1.0
CG B:HIS51 3.2 26.7 1.0
CE1 B:HIS51 3.3 35.8 1.0
CB B:HIS51 3.4 25.9 1.0
CE1 B:HIS71 3.5 39.5 1.0
N B:HIS71 3.8 38.0 1.0
CB B:TYR70 3.9 34.9 1.0
CA B:HIS71 4.0 35.2 1.0
CD1 B:TYR70 4.2 45.2 1.0
CD2 B:HIS71 4.3 52.7 1.0
N B:ARG52 4.3 31.8 1.0
CG B:TYR70 4.3 42.0 1.0
CD2 B:HIS51 4.4 33.8 1.0
NE2 B:HIS51 4.4 36.1 1.0
NE2 B:HIS71 4.4 51.4 1.0
CB B:ARG52 4.6 29.0 1.0
C B:TYR70 4.7 36.2 1.0
SG B:CYS68 4.7 37.2 1.0
CA B:HIS51 4.7 26.9 1.0
SG B:CYS49 4.7 32.3 1.0
C B:HIS71 4.8 37.3 1.0
CG B:ARG52 4.9 34.2 1.0
C B:HIS51 4.9 32.7 1.0
CA B:TYR70 4.9 35.8 1.0

Iron binding site 5 out of 6 in 6vsh

Go back to Iron Binding Sites List in 6vsh
Iron binding site 5 out of 6 in the Crystal Structure of Apo 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 Apo Dicamba Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:59.2
occ:1.00
FE1 C:FES501 0.0 59.2 1.0
S2 C:FES501 2.2 48.3 1.0
S1 C:FES501 2.2 67.2 1.0
SG C:CYS68 2.6 40.5 1.0
SG C:CYS49 2.7 39.1 1.0
FE2 C:FES501 3.1 0.4 1.0
CB C:CYS49 3.5 39.6 1.0
CB C:TYR70 3.9 56.4 1.0
CB C:CYS68 3.9 57.9 1.0
CB C:HIS51 4.0 54.7 1.0
ND1 C:HIS71 4.1 68.3 1.0
ND1 C:HIS51 4.1 49.9 1.0
CB C:ALA54 4.2 36.2 1.0
N C:HIS71 4.3 61.5 1.0
N C:ARG52 4.4 47.5 1.0
CG C:HIS51 4.5 54.8 1.0
CD1 C:TYR70 4.6 58.4 1.0
N C:ALA54 4.6 35.2 1.0
CG C:TYR70 4.7 58.9 1.0
CA C:TYR70 4.9 56.2 1.0
CA C:CYS49 4.9 34.9 1.0
CE1 C:HIS71 4.9 66.7 1.0
CB C:HIS71 5.0 70.8 1.0
CG C:HIS71 5.0 75.5 1.0

Iron binding site 6 out of 6 in 6vsh

Go back to Iron Binding Sites List in 6vsh
Iron binding site 6 out of 6 in the Crystal Structure of Apo 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 Apo Dicamba Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:0.4
occ:1.00
FE2 C:FES501 0.0 0.4 1.0
S1 C:FES501 2.2 67.2 1.0
S2 C:FES501 2.2 48.3 1.0
ND1 C:HIS51 2.6 49.9 1.0
CB C:HIS71 2.7 70.8 1.0
ND1 C:HIS71 2.7 68.3 1.0
CG C:HIS71 3.0 75.5 1.0
FE1 C:FES501 3.1 59.2 1.0
CE1 C:HIS51 3.4 57.1 1.0
CG C:HIS51 3.5 54.8 1.0
CA C:HIS71 3.7 65.1 1.0
N C:HIS71 3.8 61.5 1.0
CB C:HIS51 3.8 54.7 1.0
CE1 C:HIS71 3.9 66.7 1.0
C C:HIS71 4.1 65.5 1.0
CG C:LEU73 4.2 58.6 1.0
CD2 C:HIS71 4.3 72.8 1.0
CD1 B:LEU318 4.4 49.5 1.0
NE2 C:HIS51 4.5 52.8 1.0
CD1 C:LEU73 4.5 55.8 1.0
CD2 C:HIS51 4.6 51.5 1.0
O C:HIS71 4.6 68.5 1.0
N C:GLY72 4.6 65.3 1.0
NE2 C:HIS71 4.7 64.4 1.0
SG C:CYS49 4.8 39.1 1.0
N C:LEU73 4.8 56.0 1.0
SG C:CYS68 4.9 40.5 1.0
CB C:LEU73 4.9 55.5 1.0
C C:TYR70 5.0 60.6 1.0

Reference:

R.L.D'ordine, T.J.Rydel, M.J.Storek, E.J.Sturman, F.Moshiri, R.K.Bartlett, G.R.Brown, R.J.Eilers, C.Dart, Y.Qi, S.Flasinski, S.Franklin. Dicamba Monooxygenase: Structural Insights Into A Dynamic Rieske Oxygenase That Catalyzes An Exocyclic Monooxygenation. J. Mol. Biol. V. 392 481 2009.
ISSN: ISSN 0022-2836
PubMed: 19616009
DOI: 10.1016/J.JMB.2009.07.022
Page generated: Wed Aug 7 13:35:34 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