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:
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
|