Iron in PDB 6qkj: Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine
Protein crystallography data
The structure of Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine, PDB code: 6qkj
was solved by
A.R.Stampfli,
B.N.Badri,
T.Schirmer,
F.P.Seebeck,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.68 /
2.20
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
108.143,
201.288,
108.332,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.5 /
23.8
|
Other elements in 6qkj:
The structure of Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine
(pdb code 6qkj). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine, PDB code: 6qkj:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6qkj
Go back to
Iron Binding Sites List in 6qkj
Iron binding site 1 out
of 4 in the Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:21.8
occ:1.00
|
NE2
|
A:HIS153
|
2.1
|
23.1
|
1.0
|
NE2
|
A:HIS157
|
2.1
|
22.8
|
1.0
|
NE2
|
A:HIS62
|
2.1
|
20.5
|
1.0
|
NAT
|
A:AVJ502
|
2.1
|
24.4
|
1.0
|
CL
|
A:CL503
|
2.5
|
57.4
|
1.0
|
CL
|
A:CL504
|
2.5
|
44.4
|
1.0
|
CE1
|
A:HIS153
|
3.0
|
23.2
|
1.0
|
CE1
|
A:HIS157
|
3.0
|
23.4
|
1.0
|
CD2
|
A:HIS157
|
3.1
|
22.0
|
1.0
|
CE1
|
A:HIS62
|
3.1
|
21.7
|
1.0
|
CD2
|
A:HIS62
|
3.1
|
20.7
|
1.0
|
CD2
|
A:HIS153
|
3.1
|
23.5
|
1.0
|
CAM
|
A:AVJ502
|
3.1
|
24.2
|
1.0
|
CAZ
|
A:AVJ502
|
3.2
|
24.9
|
1.0
|
ND1
|
A:HIS157
|
4.2
|
24.1
|
1.0
|
ND1
|
A:HIS62
|
4.2
|
20.6
|
1.0
|
CG
|
A:HIS157
|
4.2
|
23.0
|
1.0
|
ND1
|
A:HIS153
|
4.2
|
21.5
|
1.0
|
CG
|
A:HIS62
|
4.2
|
21.6
|
1.0
|
CG
|
A:HIS153
|
4.2
|
22.8
|
1.0
|
CAY
|
A:AVJ502
|
4.3
|
24.4
|
1.0
|
NAR
|
A:AVJ502
|
4.3
|
25.4
|
1.0
|
OG
|
A:SER92
|
4.5
|
27.9
|
0.5
|
CB
|
A:SER92
|
4.6
|
30.8
|
0.5
|
CB
|
A:SER92
|
4.6
|
33.8
|
0.5
|
OG
|
A:SER92
|
4.8
|
34.5
|
0.5
|
|
Iron binding site 2 out
of 4 in 6qkj
Go back to
Iron Binding Sites List in 6qkj
Iron binding site 2 out
of 4 in the Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe505
b:23.1
occ:1.00
|
OE2
|
A:GLU9
|
1.9
|
30.0
|
1.0
|
NE2
|
A:HIS25
|
2.1
|
28.8
|
1.0
|
OE2
|
A:GLU148
|
2.1
|
21.1
|
1.0
|
N3
|
A:IMD506
|
2.2
|
26.6
|
1.0
|
OE1
|
A:GLU148
|
2.6
|
23.7
|
1.0
|
C4
|
A:IMD506
|
2.6
|
26.9
|
1.0
|
CD
|
A:GLU148
|
2.6
|
23.4
|
1.0
|
CD
|
A:GLU9
|
2.7
|
33.9
|
1.0
|
OE1
|
A:GLU9
|
2.8
|
32.6
|
1.0
|
CD2
|
A:HIS25
|
3.0
|
27.6
|
1.0
|
CE1
|
A:HIS25
|
3.1
|
29.9
|
1.0
|
C2
|
A:IMD506
|
3.4
|
26.6
|
1.0
|
C5
|
A:IMD506
|
3.9
|
26.7
|
1.0
|
CG
|
A:GLU9
|
4.1
|
36.0
|
1.0
|
ND1
|
A:HIS25
|
4.1
|
27.3
|
1.0
|
CG
|
A:HIS25
|
4.1
|
28.5
|
1.0
|
CZ3
|
A:TRP22
|
4.2
|
27.3
|
1.0
|
CG
|
A:GLU148
|
4.2
|
24.0
|
1.0
|
CH2
|
A:TRP22
|
4.2
|
28.5
|
1.0
|
N1
|
A:IMD506
|
4.2
|
26.8
|
1.0
|
O
|
A:HOH690
|
4.2
|
30.8
|
1.0
|
CE1
|
A:HIS152
|
4.5
|
24.1
|
1.0
|
CD1
|
A:LEU151
|
4.7
|
26.8
|
1.0
|
O
|
A:HOH611
|
4.7
|
41.4
|
1.0
|
CB
|
A:GLU148
|
4.9
|
23.9
|
1.0
|
ND1
|
A:HIS152
|
5.0
|
28.3
|
1.0
|
|
Iron binding site 3 out
of 4 in 6qkj
Go back to
Iron Binding Sites List in 6qkj
Iron binding site 3 out
of 4 in the Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:24.8
occ:1.00
|
NE2
|
B:HIS157
|
2.1
|
24.0
|
1.0
|
NE2
|
B:HIS153
|
2.1
|
30.6
|
1.0
|
NE2
|
B:HIS62
|
2.1
|
26.1
|
1.0
|
NAT
|
B:AVJ502
|
2.1
|
29.0
|
1.0
|
CL
|
B:CL504
|
2.5
|
56.5
|
1.0
|
CL
|
B:CL503
|
2.7
|
63.0
|
1.0
|
CE1
|
B:HIS157
|
3.0
|
24.9
|
1.0
|
CD2
|
B:HIS157
|
3.1
|
24.8
|
1.0
|
CE1
|
B:HIS62
|
3.1
|
25.6
|
1.0
|
CE1
|
B:HIS153
|
3.1
|
31.8
|
1.0
|
CD2
|
B:HIS62
|
3.1
|
25.4
|
1.0
|
CD2
|
B:HIS153
|
3.1
|
30.6
|
1.0
|
CAZ
|
B:AVJ502
|
3.1
|
28.8
|
1.0
|
CAM
|
B:AVJ502
|
3.1
|
28.2
|
1.0
|
ND1
|
B:HIS157
|
4.1
|
26.0
|
1.0
|
ND1
|
B:HIS62
|
4.2
|
25.9
|
1.0
|
CG
|
B:HIS157
|
4.2
|
25.6
|
1.0
|
ND1
|
B:HIS153
|
4.2
|
31.6
|
1.0
|
CG
|
B:HIS62
|
4.2
|
26.0
|
1.0
|
CG
|
B:HIS153
|
4.2
|
29.6
|
1.0
|
NAR
|
B:AVJ502
|
4.2
|
29.9
|
1.0
|
CAY
|
B:AVJ502
|
4.3
|
28.6
|
1.0
|
OG
|
B:SER92
|
4.4
|
42.7
|
0.5
|
CB
|
B:SER92
|
4.6
|
44.3
|
0.5
|
CB
|
B:SER92
|
4.6
|
44.4
|
0.5
|
OG
|
B:SER92
|
4.7
|
42.4
|
0.5
|
|
Iron binding site 4 out
of 4 in 6qkj
Go back to
Iron Binding Sites List in 6qkj
Iron binding site 4 out
of 4 in the Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe505
b:47.6
occ:1.00
|
OE2
|
B:GLU148
|
2.1
|
59.5
|
1.0
|
NE2
|
B:HIS25
|
2.2
|
44.1
|
1.0
|
N3
|
B:IMD506
|
2.6
|
55.1
|
1.0
|
C4
|
B:IMD506
|
2.7
|
54.0
|
1.0
|
CD
|
B:GLU148
|
2.8
|
50.5
|
1.0
|
OE1
|
B:GLU148
|
2.9
|
50.0
|
1.0
|
CD2
|
B:HIS25
|
2.9
|
42.5
|
1.0
|
CE1
|
B:HIS25
|
3.4
|
41.1
|
1.0
|
C2
|
B:IMD506
|
3.8
|
55.0
|
1.0
|
CZ3
|
B:TRP22
|
3.9
|
48.9
|
1.0
|
C5
|
B:IMD506
|
3.9
|
50.3
|
1.0
|
CH2
|
B:TRP22
|
4.0
|
46.3
|
1.0
|
CG
|
B:HIS25
|
4.1
|
40.4
|
1.0
|
ND1
|
B:HIS25
|
4.3
|
40.0
|
1.0
|
CG
|
B:GLU148
|
4.3
|
43.9
|
1.0
|
CE1
|
B:HIS152
|
4.4
|
29.3
|
1.0
|
N1
|
B:IMD506
|
4.4
|
52.7
|
1.0
|
CD1
|
B:LEU151
|
4.7
|
35.8
|
1.0
|
CE3
|
B:TRP22
|
4.9
|
47.3
|
1.0
|
CB
|
B:GLU148
|
5.0
|
37.9
|
1.0
|
ND1
|
B:HIS152
|
5.0
|
29.5
|
1.0
|
|
Reference:
A.R.Stampfli,
K.V.Goncharenko,
M.Meury,
B.N.Dubey,
T.Schirmer,
F.P.Seebeck.
An Alternative Active Site Architecture For O2ACTIVATION in the Ergothioneine Biosynthetic Egtb From Chloracidobacterium Thermophilum. J.Am.Chem.Soc. V. 141 5275 2019.
ISSN: ESSN 1520-5126
PubMed: 30883103
DOI: 10.1021/JACS.8B13023
Page generated: Wed Aug 7 07:59:30 2024
|