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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

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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

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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

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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: Sun Dec 13 18:25:16 2020

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