Iron in PDB 7ppt: Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose
Protein crystallography data
The structure of Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose, PDB code: 7ppt
was solved by
F.Lennartz,
M.S.Weiss,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.55 /
1.42
|
Space group
|
P 63
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.032,
72.032,
98.044,
90,
90,
120
|
R / Rfree (%)
|
18.5 /
20.8
|
Other elements in 7ppt:
The structure of Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose
(pdb code 7ppt). 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 Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose, PDB code: 7ppt:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 7ppt
Go back to
Iron Binding Sites List in 7ppt
Iron binding site 1 out
of 4 in the Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose
![](/pictures/FE/pdb/pp/7ppt-FE-sphere_01.jpg) Mono view
![](/pictures/FE/pdb/pp/7ppt-FE-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe202
b:17.6
occ:0.80
|
O
|
B:OH401
|
1.8
|
15.9
|
1.0
|
OE2
|
A:GLU92
|
1.9
|
19.3
|
1.0
|
O
|
A:HOH331
|
2.2
|
24.0
|
1.0
|
OE2
|
A:GLU126
|
2.2
|
14.4
|
1.0
|
OE1
|
A:GLU95
|
2.3
|
19.3
|
1.0
|
OE2
|
B:GLU53
|
2.3
|
14.9
|
1.0
|
HO
|
B:OH401
|
2.4
|
19.0
|
1.0
|
CD
|
A:GLU92
|
2.7
|
18.3
|
1.0
|
OE1
|
A:GLU92
|
2.8
|
18.2
|
1.0
|
CD
|
A:GLU126
|
2.9
|
19.1
|
1.0
|
CD
|
B:GLU53
|
3.2
|
14.7
|
1.0
|
HD1
|
A:HIS129
|
3.3
|
15.3
|
1.0
|
CD
|
A:GLU95
|
3.3
|
18.9
|
1.0
|
FE
|
B:FE404
|
3.4
|
16.0
|
1.0
|
OE1
|
B:GLU53
|
3.4
|
13.9
|
1.0
|
OE1
|
A:GLU126
|
3.4
|
17.9
|
1.0
|
HH
|
B:TYR27
|
3.5
|
18.6
|
1.0
|
OE2
|
A:GLU95
|
3.6
|
19.0
|
1.0
|
HG3
|
A:GLU126
|
4.0
|
17.3
|
1.0
|
CG
|
A:GLU126
|
4.0
|
14.4
|
1.0
|
HA
|
A:GLU92
|
4.0
|
20.5
|
1.0
|
HE2
|
B:TYR27
|
4.1
|
16.6
|
1.0
|
HB3
|
A:GLU126
|
4.1
|
16.7
|
1.0
|
ND1
|
A:HIS129
|
4.1
|
12.7
|
1.0
|
CG
|
A:GLU92
|
4.1
|
17.4
|
1.0
|
OH
|
B:TYR27
|
4.3
|
15.5
|
1.0
|
HB1
|
B:ALA23
|
4.3
|
14.9
|
1.0
|
HA
|
A:GLU126
|
4.4
|
14.4
|
1.0
|
HB2
|
B:ALA23
|
4.4
|
14.9
|
1.0
|
HG2
|
A:GLU92
|
4.4
|
20.8
|
1.0
|
OE2
|
B:GLU20
|
4.5
|
13.1
|
1.0
|
HG3
|
B:GLU53
|
4.5
|
16.7
|
1.0
|
CG
|
B:GLU53
|
4.5
|
13.9
|
1.0
|
CB
|
A:GLU126
|
4.5
|
13.9
|
1.0
|
HB2
|
A:GLU95
|
4.6
|
21.7
|
1.0
|
CG
|
A:GLU95
|
4.6
|
18.4
|
1.0
|
OE1
|
B:GLU20
|
4.7
|
13.9
|
1.0
|
HG3
|
A:GLU92
|
4.7
|
20.8
|
1.0
|
CB
|
B:ALA23
|
4.7
|
12.4
|
1.0
|
HB3
|
A:GLU92
|
4.7
|
20.2
|
1.0
|
HB2
|
A:HIS129
|
4.8
|
14.2
|
1.0
|
HB3
|
B:ALA23
|
4.8
|
14.9
|
1.0
|
HE1
|
A:HIS129
|
4.8
|
17.5
|
1.0
|
CB
|
A:GLU92
|
4.8
|
16.8
|
1.0
|
HG2
|
A:GLU126
|
4.8
|
17.3
|
1.0
|
CA
|
A:GLU92
|
4.8
|
17.1
|
1.0
|
CE2
|
B:TYR27
|
4.8
|
13.8
|
1.0
|
HE2
|
A:TYR100
|
4.9
|
20.6
|
1.0
|
CE1
|
A:HIS129
|
4.9
|
14.6
|
1.0
|
CD
|
B:GLU20
|
4.9
|
13.3
|
1.0
|
HB3
|
A:GLU95
|
4.9
|
21.7
|
1.0
|
CB
|
A:GLU95
|
5.0
|
18.1
|
1.0
|
|
Iron binding site 2 out
of 4 in 7ppt
Go back to
Iron Binding Sites List in 7ppt
Iron binding site 2 out
of 4 in the Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose
![](/pictures/FE/pdb/pp/7ppt-FE-sphere_02.jpg) Mono view
![](/pictures/FE/pdb/pp/7ppt-FE-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe203
b:17.3
occ:1.00
|
OE1
|
B:GLU126
|
2.0
|
25.4
|
1.0
|
OE1
|
A:GLU53
|
2.1
|
15.5
|
1.0
|
O
|
A:OH204
|
2.1
|
15.4
|
1.0
|
OE2
|
A:GLU20
|
2.1
|
14.0
|
1.0
|
OE1
|
A:GLU20
|
2.2
|
14.9
|
1.0
|
ND1
|
A:HIS56
|
2.2
|
13.8
|
1.0
|
CD
|
A:GLU20
|
2.5
|
14.2
|
1.0
|
HO
|
A:OH204
|
2.9
|
18.5
|
1.0
|
CD
|
B:GLU126
|
2.9
|
22.8
|
1.0
|
CD
|
A:GLU53
|
3.0
|
16.1
|
1.0
|
CE1
|
A:HIS56
|
3.0
|
14.2
|
1.0
|
HE1
|
A:HIS56
|
3.1
|
17.1
|
1.0
|
OE2
|
B:GLU126
|
3.2
|
23.8
|
1.0
|
CG
|
A:HIS56
|
3.3
|
13.5
|
1.0
|
HA
|
A:GLU53
|
3.3
|
17.9
|
1.0
|
FE
|
B:FE403
|
3.4
|
20.4
|
0.9
|
HB2
|
A:HIS56
|
3.4
|
15.6
|
1.0
|
OE2
|
A:GLU53
|
3.5
|
17.0
|
1.0
|
HB3
|
A:HIS56
|
3.6
|
15.6
|
1.0
|
CB
|
A:HIS56
|
3.7
|
13.0
|
1.0
|
HH
|
B:TYR100
|
3.8
|
20.0
|
1.0
|
HE2
|
B:TYR100
|
3.9
|
20.0
|
1.0
|
CG
|
A:GLU20
|
4.0
|
14.4
|
1.0
|
HE1
|
B:HIS129
|
4.1
|
20.5
|
1.0
|
HB3
|
A:GLU53
|
4.1
|
17.8
|
1.0
|
CA
|
A:GLU53
|
4.2
|
14.9
|
1.0
|
NE2
|
A:HIS56
|
4.2
|
14.3
|
1.0
|
CG
|
A:GLU53
|
4.2
|
15.2
|
1.0
|
CG
|
B:GLU126
|
4.3
|
14.4
|
1.0
|
CD2
|
A:HIS56
|
4.3
|
13.8
|
1.0
|
HG
|
B:LEU122
|
4.4
|
17.1
|
1.0
|
HG3
|
A:GLU20
|
4.4
|
17.4
|
1.0
|
HD1
|
B:HIS129
|
4.4
|
20.7
|
1.0
|
CB
|
A:GLU53
|
4.4
|
14.8
|
1.0
|
HG2
|
A:GLU20
|
4.4
|
17.4
|
1.0
|
HG3
|
B:GLU126
|
4.4
|
17.3
|
1.0
|
HG2
|
B:GLU126
|
4.5
|
17.3
|
1.0
|
OE1
|
B:GLU95
|
4.5
|
20.6
|
1.0
|
HA
|
A:GLU20
|
4.5
|
16.9
|
1.0
|
HB3
|
A:GLU20
|
4.6
|
16.9
|
1.0
|
OH
|
B:TYR100
|
4.6
|
16.7
|
1.0
|
CE2
|
B:TYR100
|
4.7
|
16.7
|
1.0
|
CE1
|
B:HIS129
|
4.8
|
17.1
|
1.0
|
HG2
|
A:GLU53
|
4.8
|
18.3
|
1.0
|
CB
|
A:GLU20
|
4.8
|
14.1
|
1.0
|
HD23
|
B:LEU122
|
4.8
|
20.6
|
1.0
|
HG3
|
A:GLU53
|
4.8
|
18.3
|
1.0
|
N
|
A:GLU53
|
4.9
|
14.6
|
1.0
|
O
|
A:GLY52
|
4.9
|
14.1
|
1.0
|
ND1
|
B:HIS129
|
4.9
|
17.3
|
1.0
|
O
|
B:HOH503
|
4.9
|
37.3
|
1.0
|
HE2
|
A:HIS56
|
5.0
|
17.1
|
1.0
|
|
Iron binding site 3 out
of 4 in 7ppt
Go back to
Iron Binding Sites List in 7ppt
Iron binding site 3 out
of 4 in the Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose
![](/pictures/FE/pdb/pp/7ppt-FE-sphere_03.jpg) Mono view
![](/pictures/FE/pdb/pp/7ppt-FE-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe403
b:20.4
occ:0.90
|
HO
|
A:OH204
|
1.0
|
18.5
|
1.0
|
O
|
A:OH204
|
1.9
|
15.4
|
1.0
|
OE1
|
B:GLU92
|
1.9
|
21.4
|
1.0
|
OE2
|
B:GLU126
|
2.1
|
23.8
|
1.0
|
O
|
B:HOH503
|
2.2
|
37.3
|
1.0
|
OE2
|
A:GLU53
|
2.2
|
17.0
|
1.0
|
OE1
|
B:GLU95
|
2.2
|
20.6
|
1.0
|
CD
|
B:GLU92
|
2.8
|
20.8
|
1.0
|
CD
|
B:GLU126
|
2.9
|
22.8
|
1.0
|
OE2
|
B:GLU92
|
3.1
|
21.1
|
1.0
|
CD
|
A:GLU53
|
3.1
|
16.1
|
1.0
|
CD
|
B:GLU95
|
3.2
|
21.2
|
1.0
|
HD1
|
B:HIS129
|
3.3
|
20.7
|
1.0
|
FE
|
A:FE203
|
3.4
|
17.3
|
1.0
|
OE1
|
A:GLU53
|
3.4
|
15.5
|
1.0
|
OE1
|
B:GLU126
|
3.4
|
25.4
|
1.0
|
HH
|
A:TYR27
|
3.4
|
21.2
|
1.0
|
OE2
|
B:GLU95
|
3.5
|
21.9
|
1.0
|
HA
|
B:GLU92
|
3.8
|
23.3
|
1.0
|
HG3
|
B:GLU126
|
4.0
|
17.3
|
1.0
|
CG
|
B:GLU126
|
4.0
|
14.4
|
1.0
|
HB3
|
B:GLU126
|
4.0
|
19.2
|
1.0
|
ND1
|
B:HIS129
|
4.1
|
17.3
|
1.0
|
HE2
|
A:TYR27
|
4.2
|
19.2
|
1.0
|
CG
|
B:GLU92
|
4.2
|
19.6
|
1.0
|
HB1
|
A:ALA23
|
4.2
|
17.1
|
1.0
|
OH
|
A:TYR27
|
4.2
|
17.7
|
1.0
|
HA
|
B:GLU126
|
4.4
|
17.9
|
1.0
|
HB2
|
A:ALA23
|
4.4
|
17.1
|
1.0
|
CB
|
B:GLU126
|
4.5
|
16.0
|
1.0
|
CG
|
A:GLU53
|
4.5
|
15.2
|
1.0
|
HG3
|
A:GLU53
|
4.5
|
18.3
|
1.0
|
HB2
|
B:GLU95
|
4.5
|
24.4
|
1.0
|
HG2
|
B:GLU92
|
4.5
|
23.6
|
1.0
|
OE2
|
A:GLU20
|
4.5
|
14.0
|
1.0
|
CG
|
B:GLU95
|
4.6
|
21.0
|
1.0
|
CA
|
B:GLU92
|
4.6
|
19.4
|
1.0
|
OE1
|
A:GLU20
|
4.6
|
14.9
|
1.0
|
HB3
|
B:GLU92
|
4.7
|
23.2
|
1.0
|
CB
|
A:ALA23
|
4.7
|
14.2
|
1.0
|
CB
|
B:GLU92
|
4.7
|
19.4
|
1.0
|
HE1
|
B:HIS129
|
4.8
|
20.5
|
1.0
|
HB3
|
A:ALA23
|
4.8
|
17.1
|
1.0
|
HG2
|
B:GLU126
|
4.8
|
17.3
|
1.0
|
HG3
|
B:GLU92
|
4.8
|
23.6
|
1.0
|
HB2
|
B:HIS129
|
4.9
|
21.1
|
1.0
|
HB3
|
B:GLU95
|
4.9
|
24.4
|
1.0
|
CE1
|
B:HIS129
|
4.9
|
17.1
|
1.0
|
CB
|
B:GLU95
|
4.9
|
20.4
|
1.0
|
CE2
|
A:TYR27
|
4.9
|
16.0
|
1.0
|
CD
|
A:GLU20
|
4.9
|
14.2
|
1.0
|
HE2
|
B:TYR100
|
5.0
|
20.0
|
1.0
|
CA
|
B:GLU126
|
5.0
|
14.9
|
1.0
|
|
Iron binding site 4 out
of 4 in 7ppt
Go back to
Iron Binding Sites List in 7ppt
Iron binding site 4 out
of 4 in the Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose
![](/pictures/FE/pdb/pp/7ppt-FE-sphere_04.jpg) Mono view
![](/pictures/FE/pdb/pp/7ppt-FE-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe404
b:16.0
occ:1.00
|
OE1
|
A:GLU126
|
2.0
|
17.9
|
1.0
|
OE1
|
B:GLU53
|
2.1
|
13.9
|
1.0
|
O
|
B:OH401
|
2.1
|
15.9
|
1.0
|
OE2
|
B:GLU20
|
2.1
|
13.1
|
1.0
|
OE1
|
B:GLU20
|
2.2
|
13.9
|
1.0
|
ND1
|
B:HIS56
|
2.2
|
11.8
|
1.0
|
CD
|
B:GLU20
|
2.5
|
13.3
|
1.0
|
HO
|
B:OH401
|
2.5
|
19.0
|
1.0
|
CD
|
A:GLU126
|
3.0
|
19.1
|
1.0
|
CD
|
B:GLU53
|
3.0
|
14.7
|
1.0
|
CE1
|
B:HIS56
|
3.1
|
11.9
|
1.0
|
HE1
|
B:HIS56
|
3.2
|
14.3
|
1.0
|
OE2
|
A:GLU126
|
3.3
|
14.4
|
1.0
|
CG
|
B:HIS56
|
3.3
|
12.3
|
1.0
|
FE
|
A:FE202
|
3.4
|
17.6
|
0.8
|
HA
|
B:GLU53
|
3.4
|
16.8
|
1.0
|
HB2
|
B:HIS56
|
3.4
|
14.6
|
1.0
|
OE2
|
B:GLU53
|
3.5
|
14.9
|
1.0
|
HB3
|
B:HIS56
|
3.6
|
14.6
|
1.0
|
CB
|
B:HIS56
|
3.7
|
12.2
|
1.0
|
HH
|
A:TYR100
|
3.8
|
20.6
|
1.0
|
HE2
|
A:TYR100
|
3.9
|
20.6
|
1.0
|
CG
|
B:GLU20
|
4.0
|
14.0
|
1.0
|
HE1
|
A:HIS129
|
4.0
|
17.5
|
1.0
|
HB3
|
B:GLU53
|
4.2
|
16.6
|
1.0
|
HD1
|
A:HIS129
|
4.2
|
15.3
|
1.0
|
CA
|
B:GLU53
|
4.2
|
14.0
|
1.0
|
CG
|
B:GLU53
|
4.3
|
13.9
|
1.0
|
CG
|
A:GLU126
|
4.3
|
14.4
|
1.0
|
NE2
|
B:HIS56
|
4.3
|
12.2
|
1.0
|
HG
|
A:LEU122
|
4.4
|
14.7
|
1.0
|
HG3
|
B:GLU20
|
4.4
|
16.8
|
1.0
|
CD2
|
B:HIS56
|
4.4
|
12.5
|
1.0
|
HG2
|
B:GLU20
|
4.4
|
16.8
|
1.0
|
HG3
|
A:GLU126
|
4.4
|
17.3
|
1.0
|
CB
|
B:GLU53
|
4.4
|
13.8
|
1.0
|
HG2
|
A:GLU126
|
4.5
|
17.3
|
1.0
|
HA
|
B:GLU20
|
4.5
|
16.6
|
1.0
|
OE1
|
A:GLU95
|
4.6
|
19.3
|
1.0
|
HB3
|
B:GLU20
|
4.6
|
16.4
|
1.0
|
CE1
|
A:HIS129
|
4.6
|
14.6
|
1.0
|
OH
|
A:TYR100
|
4.7
|
17.2
|
1.0
|
CE2
|
A:TYR100
|
4.7
|
17.1
|
1.0
|
ND1
|
A:HIS129
|
4.7
|
12.7
|
1.0
|
HD23
|
A:LEU122
|
4.7
|
16.6
|
1.0
|
O
|
A:HOH331
|
4.8
|
24.0
|
1.0
|
HG2
|
B:GLU53
|
4.8
|
16.7
|
1.0
|
CB
|
B:GLU20
|
4.8
|
13.7
|
1.0
|
HG3
|
B:GLU53
|
4.9
|
16.7
|
1.0
|
O
|
B:GLY52
|
4.9
|
12.5
|
1.0
|
N
|
B:GLU53
|
4.9
|
13.6
|
1.0
|
|
Reference:
F.Lennartz,
J.H.Jeoung,
S.Ruenger,
H.Dobbek,
M.S.Weiss.
Determining the Oxidation State of Elements By X-Ray Crystallography. Acta Crystallogr D Struct V. 78 238 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35102889
DOI: 10.1107/S2059798321013048
Page generated: Thu Aug 8 17:14:10 2024
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