Atomistry » Iron » PDB 6zkh-6zzu » 6zmc
Atomistry »
  Iron »
    PDB 6zkh-6zzu »
      6zmc »

Iron in PDB 6zmc: Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 2000 Bar Using the High Pressure Freezing Method

Protein crystallography data

The structure of Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 2000 Bar Using the High Pressure Freezing Method, PDB code: 6zmc was solved by P.Carpentier, M.Atta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.52 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.388, 51.909, 78.978, 90.00, 90.36, 90.00
R / Rfree (%) 18.2 / 24.5

Other elements in 6zmc:

The structure of Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 2000 Bar Using the High Pressure Freezing Method also contains other interesting chemical elements:

Argon (Ar) 1 atom
Calcium (Ca) 2 atoms
Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 2000 Bar Using the High Pressure Freezing Method (pdb code 6zmc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 2000 Bar Using the High Pressure Freezing Method, PDB code: 6zmc:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6zmc

Go back to Iron Binding Sites List in 6zmc
Iron binding site 1 out of 4 in the Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 2000 Bar Using the High Pressure Freezing Method


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 2000 Bar Using the High Pressure Freezing Method within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:82.9
occ:1.00
ND1 B:HIS72 1.9 76.4 1.0
O B:HOH402 2.1 92.3 1.0
O B:HOH412 2.2 82.9 1.0
OE1 B:GLU38 2.2 71.0 1.0
OE1 B:GLU69 2.4 69.2 1.0
O3 B:TRS306 2.4 68.3 1.0
CE1 B:HIS72 2.8 73.0 1.0
CD B:GLU38 3.0 72.4 1.0
CG B:HIS72 3.1 66.8 1.0
OE2 B:GLU38 3.1 78.5 1.0
FE B:FE302 3.3 79.5 1.0
CD B:GLU69 3.6 63.5 1.0
C3 B:TRS306 3.6 77.9 1.0
CB B:HIS72 3.6 67.5 1.0
OE1 B:GLU151 3.7 81.0 1.0
NE2 B:HIS72 3.9 73.3 1.0
OE2 B:GLU69 4.1 82.7 1.0
CD2 B:HIS72 4.1 70.6 1.0
CD B:GLU151 4.3 87.1 1.0
CG B:GLU38 4.4 69.0 1.0
OE2 B:GLU151 4.5 89.0 1.0
CE1 B:HIS154 4.5 73.7 1.0
CA B:GLU69 4.6 57.2 1.0
ND1 B:HIS154 4.6 68.8 1.0
C B:TRS306 4.7 87.8 1.0
N B:TRS306 4.7 81.8 1.0
CG B:GLU69 4.8 67.4 1.0
O2 B:TRS306 4.8 0.3 1.0
CB B:GLU38 5.0 66.1 1.0
OG B:SER150 5.0 0.1 1.0

Iron binding site 2 out of 4 in 6zmc

Go back to Iron Binding Sites List in 6zmc
Iron binding site 2 out of 4 in the Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 2000 Bar Using the High Pressure Freezing Method


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 2000 Bar Using the High Pressure Freezing Method within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:79.5
occ:1.00
ND1 B:HIS154 2.3 68.8 1.0
OE1 B:GLU122 2.4 85.2 1.0
O3 B:TRS306 2.4 68.3 1.0
O B:HOH412 2.6 82.9 1.0
OE2 B:GLU69 2.6 82.7 1.0
OE2 B:GLU151 2.8 89.0 1.0
O2 B:TRS306 3.0 0.3 1.0
CE1 B:HIS154 3.1 73.7 1.0
OE1 B:GLU69 3.1 69.2 1.0
CD B:GLU69 3.2 63.5 1.0
FE B:FE301 3.3 82.9 1.0
CG B:HIS154 3.4 71.7 1.0
C3 B:TRS306 3.4 77.9 1.0
CD B:GLU122 3.5 77.6 1.0
CD B:GLU151 3.5 87.1 1.0
CB B:HIS154 3.8 71.0 1.0
OE1 B:GLU151 3.8 81.0 1.0
OE2 B:GLU122 4.0 81.6 1.0
C2 B:TRS306 4.1 97.2 1.0
O B:HOH402 4.2 92.3 1.0
NE2 B:HIS154 4.3 81.2 1.0
CD2 B:HIS154 4.4 78.0 1.0
C B:TRS306 4.4 87.8 1.0
CG B:GLU69 4.6 67.4 1.0
CA B:GLU151 4.7 74.3 1.0
OE1 B:GLU38 4.7 71.0 1.0
ND1 B:HIS72 4.7 76.4 1.0
CG B:GLU122 4.7 73.5 1.0
CG B:GLU151 4.7 81.6 1.0
CE1 B:HIS72 4.7 73.0 1.0
O B:SER150 4.9 74.9 1.0
CD1 B:LEU65 4.9 66.7 1.0

Iron binding site 3 out of 4 in 6zmc

Go back to Iron Binding Sites List in 6zmc
Iron binding site 3 out of 4 in the Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 2000 Bar Using the High Pressure Freezing Method


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 2000 Bar Using the High Pressure Freezing Method within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:62.6
occ:1.00
O C:HOH405 2.0 69.7 1.0
OE1 C:GLU69 2.1 65.7 1.0
O1 C:TRS303 2.2 64.0 1.0
OE1 C:GLU38 2.3 59.1 1.0
ND1 C:HIS72 2.3 66.1 1.0
O C:HOH417 2.3 72.0 1.0
FE C:FE302 3.0 73.2 1.0
CE1 C:HIS72 3.1 63.4 1.0
CD C:GLU69 3.2 63.6 1.0
CD C:GLU38 3.2 63.8 1.0
C1 C:TRS303 3.3 67.4 1.0
CG C:HIS72 3.4 60.1 1.0
OE2 C:GLU38 3.5 67.0 1.0
OE2 C:GLU69 3.6 69.4 1.0
CB C:HIS72 3.8 59.1 1.0
OE1 C:GLU151 3.9 74.1 1.0
NE2 C:HIS72 4.3 62.5 1.0
CD C:GLU151 4.3 72.1 1.0
OE2 C:GLU151 4.4 72.7 1.0
CD2 C:HIS72 4.4 60.6 1.0
CA C:GLU69 4.5 50.0 1.0
CE1 C:HIS154 4.5 61.4 1.0
CG C:GLU69 4.5 59.3 1.0
C C:TRS303 4.5 78.7 1.0
CG C:GLU38 4.6 62.5 1.0
ND1 C:HIS154 4.6 56.0 1.0
N C:TRS303 4.6 73.0 1.0
O3 C:TRS303 4.8 96.1 1.0
OG C:SER150 4.8 83.2 1.0
CB C:GLU69 4.8 53.3 1.0
CB C:GLU38 4.9 60.6 1.0

Iron binding site 4 out of 4 in 6zmc

Go back to Iron Binding Sites List in 6zmc
Iron binding site 4 out of 4 in the Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 2000 Bar Using the High Pressure Freezing Method


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 2000 Bar Using the High Pressure Freezing Method within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe302

b:73.2
occ:1.00
OE1 C:GLU122 2.2 64.9 1.0
O C:HOH417 2.2 72.0 1.0
OE2 C:GLU69 2.3 69.4 1.0
O1 C:TRS303 2.4 64.0 1.0
ND1 C:HIS154 2.5 56.0 1.0
OE2 C:GLU151 2.5 72.7 1.0
O C:HOH402 2.8 73.2 1.0
O3 C:TRS303 3.0 96.1 1.0
FE C:FE301 3.0 62.6 1.0
CD C:GLU69 3.1 63.6 1.0
C1 C:TRS303 3.1 67.4 1.0
OE1 C:GLU69 3.2 65.7 1.0
CE1 C:HIS154 3.2 61.4 1.0
CD C:GLU122 3.3 70.8 1.0
CD C:GLU151 3.4 72.1 1.0
CG C:HIS154 3.6 61.6 1.0
OE1 C:GLU151 3.6 74.1 1.0
OE2 C:GLU122 3.8 83.8 1.0
CB C:HIS154 4.0 58.6 1.0
O C:HOH405 4.0 69.7 1.0
C3 C:TRS303 4.1 88.8 1.0
C C:TRS303 4.2 78.7 1.0
NE2 C:HIS154 4.5 59.2 1.0
CG C:GLU122 4.5 68.3 1.0
CG C:GLU69 4.6 59.3 1.0
CA C:GLU151 4.6 60.2 1.0
CG C:GLU151 4.6 68.2 1.0
CD2 C:HIS154 4.7 60.1 1.0
OE1 C:GLU38 4.7 59.1 1.0
ND1 C:HIS72 4.8 66.1 1.0
CE1 C:HIS72 4.9 63.4 1.0
O C:SER150 5.0 64.8 1.0

Reference:

P.Carpentier, C.Lepretre, C.Basset, T.Douki, S.Torelli, V.Duarte, D.Hamdane, M.Fontecave, M.Atta. Structural, Biochemical and Functional Analyses of Trna-Monooxygenase Enzyme Miae From Pseudomonas Putida Provide Insights Into Trna/Miae Interaction. Nucleic Acids Res. V. 48 9918 2020.
ISSN: ESSN 1362-4962
PubMed: 32785618
DOI: 10.1093/NAR/GKAA667
Page generated: Wed Aug 7 20:30:18 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