Iron in PDB 6y45: Crystal Structure of the H33A Variant of Rsrr
Protein crystallography data
The structure of Crystal Structure of the H33A Variant of Rsrr, PDB code: 6y45
was solved by
R.Rohac,
A.Volbeda,
J.C.Fontecilla-Camps,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.14 /
1.68
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
37.920,
117.000,
71.330,
90.00,
95.83,
90.00
|
R / Rfree (%)
|
15.9 /
20.5
|
Other elements in 6y45:
The structure of Crystal Structure of the H33A Variant of Rsrr also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the H33A Variant of Rsrr
(pdb code 6y45). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Crystal Structure of the H33A Variant of Rsrr, PDB code: 6y45:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 6y45
Go back to
Iron Binding Sites List in 6y45
Iron binding site 1 out
of 8 in the Crystal Structure of the H33A Variant of Rsrr
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of the H33A Variant of Rsrr within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:27.6
occ:1.00
|
FE1
|
A:FES201
|
0.0
|
27.6
|
1.0
|
OE2
|
A:GLU8
|
1.9
|
24.1
|
1.0
|
S1
|
A:FES201
|
2.2
|
27.3
|
1.0
|
S2
|
A:FES201
|
2.3
|
27.8
|
1.0
|
SG
|
C:CYS90
|
2.4
|
31.2
|
1.0
|
FE2
|
A:FES201
|
2.7
|
27.2
|
1.0
|
CD
|
A:GLU8
|
3.0
|
26.4
|
1.0
|
CB
|
C:CYS90
|
3.4
|
29.1
|
1.0
|
CG
|
A:GLU8
|
3.5
|
24.9
|
1.0
|
CA
|
C:CYS90
|
3.7
|
27.4
|
1.0
|
N
|
C:GLU92
|
3.8
|
27.1
|
1.0
|
N
|
C:THR91
|
4.1
|
30.3
|
1.0
|
OE1
|
A:GLU8
|
4.1
|
27.9
|
1.0
|
NE2
|
A:HIS12
|
4.2
|
30.3
|
1.0
|
CA
|
C:GLU92
|
4.3
|
30.4
|
1.0
|
C
|
C:CYS90
|
4.3
|
28.7
|
1.0
|
N
|
C:ILE93
|
4.4
|
28.4
|
1.0
|
CB
|
C:CYS110
|
4.4
|
28.0
|
1.0
|
SG
|
C:CYS110
|
4.5
|
29.5
|
1.0
|
CG1
|
C:ILE93
|
4.7
|
30.9
|
1.0
|
CB
|
C:ALA113
|
4.8
|
28.9
|
1.0
|
O
|
C:HOH378
|
4.8
|
36.2
|
1.0
|
CD2
|
A:HIS12
|
4.8
|
25.8
|
1.0
|
C
|
C:GLU92
|
4.8
|
31.3
|
1.0
|
CB
|
A:GLU8
|
4.8
|
24.9
|
1.0
|
C
|
C:THR91
|
4.9
|
29.5
|
1.0
|
CZ
|
C:PHE88
|
4.9
|
27.9
|
1.0
|
CE2
|
C:PHE88
|
4.9
|
27.1
|
1.0
|
|
Iron binding site 2 out
of 8 in 6y45
Go back to
Iron Binding Sites List in 6y45
Iron binding site 2 out
of 8 in the Crystal Structure of the H33A Variant of Rsrr
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of the H33A Variant of Rsrr within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:27.2
occ:1.00
|
FE2
|
A:FES201
|
0.0
|
27.2
|
1.0
|
NE2
|
A:HIS12
|
2.1
|
30.3
|
1.0
|
S2
|
A:FES201
|
2.2
|
27.8
|
1.0
|
S1
|
A:FES201
|
2.2
|
27.3
|
1.0
|
SG
|
C:CYS110
|
2.3
|
29.5
|
1.0
|
FE1
|
A:FES201
|
2.7
|
27.6
|
1.0
|
CE1
|
A:HIS12
|
3.0
|
31.3
|
1.0
|
CB
|
C:CYS110
|
3.1
|
28.0
|
1.0
|
CD2
|
A:HIS12
|
3.2
|
25.8
|
1.0
|
CB
|
C:ILE112
|
4.1
|
29.9
|
1.0
|
ND1
|
A:HIS12
|
4.2
|
30.2
|
1.0
|
OE2
|
A:GLU8
|
4.2
|
24.1
|
1.0
|
CG
|
A:HIS12
|
4.3
|
27.6
|
1.0
|
SG
|
C:CYS90
|
4.5
|
31.2
|
1.0
|
CA
|
C:CYS110
|
4.6
|
29.0
|
1.0
|
CD1
|
C:ILE112
|
4.6
|
35.7
|
1.0
|
CG2
|
C:ILE112
|
4.7
|
29.7
|
1.0
|
CG
|
A:GLU8
|
4.7
|
24.9
|
1.0
|
N
|
C:ALA113
|
4.7
|
27.4
|
1.0
|
CG1
|
C:ILE112
|
4.8
|
33.9
|
1.0
|
CG1
|
C:ILE93
|
4.9
|
30.9
|
1.0
|
CD
|
A:GLU8
|
4.9
|
26.4
|
1.0
|
CD
|
C:ARG94
|
5.0
|
29.1
|
1.0
|
|
Iron binding site 3 out
of 8 in 6y45
Go back to
Iron Binding Sites List in 6y45
Iron binding site 3 out
of 8 in the Crystal Structure of the H33A Variant of Rsrr
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of the H33A Variant of Rsrr within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:29.1
occ:1.00
|
FE1
|
B:FES201
|
0.0
|
29.1
|
1.0
|
OE2
|
B:GLU8
|
2.0
|
27.8
|
1.0
|
S2
|
B:FES201
|
2.2
|
29.4
|
1.0
|
S1
|
B:FES201
|
2.3
|
27.4
|
1.0
|
SG
|
D:CYS90
|
2.4
|
32.2
|
1.0
|
FE2
|
B:FES201
|
2.7
|
28.5
|
1.0
|
CD
|
B:GLU8
|
3.0
|
27.6
|
1.0
|
CB
|
D:CYS90
|
3.4
|
32.3
|
1.0
|
CG
|
B:GLU8
|
3.5
|
24.6
|
1.0
|
CA
|
D:CYS90
|
3.8
|
30.5
|
1.0
|
N
|
D:GLU92
|
3.8
|
26.4
|
1.0
|
N
|
D:THR91
|
4.0
|
29.2
|
1.0
|
OE1
|
B:GLU8
|
4.1
|
28.9
|
1.0
|
NE2
|
B:HIS12
|
4.2
|
28.0
|
1.0
|
CA
|
D:GLU92
|
4.2
|
30.6
|
1.0
|
C
|
D:CYS90
|
4.3
|
30.1
|
1.0
|
CB
|
D:CYS110
|
4.4
|
29.2
|
1.0
|
N
|
D:ILE93
|
4.4
|
29.3
|
1.0
|
SG
|
D:CYS110
|
4.6
|
29.1
|
1.0
|
CG1
|
D:ILE93
|
4.7
|
32.8
|
1.0
|
O
|
D:HOH574
|
4.8
|
34.1
|
1.0
|
C
|
D:THR91
|
4.8
|
29.6
|
1.0
|
CB
|
D:ALA113
|
4.8
|
32.9
|
1.0
|
CD2
|
B:HIS12
|
4.8
|
27.7
|
1.0
|
C
|
D:GLU92
|
4.8
|
30.6
|
1.0
|
CZ
|
D:PHE88
|
4.9
|
27.1
|
1.0
|
CB
|
B:GLU8
|
4.9
|
26.8
|
1.0
|
CE2
|
D:PHE88
|
5.0
|
30.6
|
1.0
|
|
Iron binding site 4 out
of 8 in 6y45
Go back to
Iron Binding Sites List in 6y45
Iron binding site 4 out
of 8 in the Crystal Structure of the H33A Variant of Rsrr
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of the H33A Variant of Rsrr within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:28.5
occ:1.00
|
FE2
|
B:FES201
|
0.0
|
28.5
|
1.0
|
NE2
|
B:HIS12
|
2.1
|
28.0
|
1.0
|
S1
|
B:FES201
|
2.3
|
27.4
|
1.0
|
SG
|
D:CYS110
|
2.3
|
29.1
|
1.0
|
S2
|
B:FES201
|
2.3
|
29.4
|
1.0
|
FE1
|
B:FES201
|
2.7
|
29.1
|
1.0
|
CE1
|
B:HIS12
|
3.0
|
35.3
|
1.0
|
CB
|
D:CYS110
|
3.1
|
29.2
|
1.0
|
CD2
|
B:HIS12
|
3.2
|
27.7
|
1.0
|
CB
|
D:ILE112
|
4.1
|
32.1
|
1.0
|
ND1
|
B:HIS12
|
4.1
|
32.0
|
1.0
|
OE2
|
B:GLU8
|
4.2
|
27.8
|
1.0
|
CG
|
B:HIS12
|
4.3
|
28.3
|
1.0
|
SG
|
D:CYS90
|
4.5
|
32.2
|
1.0
|
CD1
|
D:ILE112
|
4.5
|
36.6
|
1.0
|
CA
|
D:CYS110
|
4.6
|
31.4
|
1.0
|
CG2
|
D:ILE112
|
4.6
|
33.1
|
1.0
|
N
|
D:ALA113
|
4.7
|
28.6
|
1.0
|
CG
|
B:GLU8
|
4.7
|
24.6
|
1.0
|
CG1
|
D:ILE112
|
4.7
|
37.0
|
1.0
|
CG1
|
D:ILE93
|
4.9
|
32.8
|
1.0
|
CD
|
B:GLU8
|
5.0
|
27.6
|
1.0
|
N
|
D:ILE112
|
5.0
|
30.3
|
1.0
|
CA
|
D:ILE112
|
5.0
|
29.4
|
1.0
|
|
Iron binding site 5 out
of 8 in 6y45
Go back to
Iron Binding Sites List in 6y45
Iron binding site 5 out
of 8 in the Crystal Structure of the H33A Variant of Rsrr
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of the H33A Variant of Rsrr within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:28.9
occ:1.00
|
FE1
|
C:FES201
|
0.0
|
28.9
|
1.0
|
OE2
|
C:GLU8
|
1.9
|
25.7
|
1.0
|
S2
|
C:FES201
|
2.2
|
28.6
|
1.0
|
S1
|
C:FES201
|
2.3
|
27.7
|
1.0
|
SG
|
A:CYS90
|
2.3
|
31.2
|
1.0
|
FE2
|
C:FES201
|
2.7
|
27.8
|
1.0
|
CD
|
C:GLU8
|
3.0
|
27.6
|
1.0
|
CB
|
A:CYS90
|
3.4
|
31.6
|
1.0
|
CG
|
C:GLU8
|
3.5
|
24.4
|
1.0
|
N
|
A:GLU92
|
3.8
|
26.7
|
1.0
|
CA
|
A:CYS90
|
3.8
|
29.5
|
1.0
|
N
|
A:THR91
|
4.0
|
30.8
|
1.0
|
OE1
|
C:GLU8
|
4.1
|
28.7
|
1.0
|
NE2
|
C:HIS12
|
4.2
|
27.9
|
1.0
|
CA
|
A:GLU92
|
4.2
|
28.8
|
1.0
|
C
|
A:CYS90
|
4.3
|
31.9
|
1.0
|
N
|
A:ILE93
|
4.3
|
29.6
|
1.0
|
CB
|
A:CYS110
|
4.4
|
29.1
|
1.0
|
SG
|
A:CYS110
|
4.6
|
29.3
|
1.0
|
CG1
|
A:ILE93
|
4.6
|
31.9
|
1.0
|
C
|
A:GLU92
|
4.8
|
30.2
|
1.0
|
C
|
A:THR91
|
4.8
|
28.7
|
1.0
|
CB
|
A:ALA113
|
4.8
|
31.4
|
1.0
|
CD2
|
C:HIS12
|
4.8
|
25.6
|
1.0
|
O
|
A:HOH370
|
4.8
|
36.3
|
1.0
|
CB
|
C:GLU8
|
4.9
|
25.6
|
1.0
|
CZ
|
A:PHE88
|
5.0
|
28.9
|
1.0
|
|
Iron binding site 6 out
of 8 in 6y45
Go back to
Iron Binding Sites List in 6y45
Iron binding site 6 out
of 8 in the Crystal Structure of the H33A Variant of Rsrr
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of the H33A Variant of Rsrr within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:27.8
occ:1.00
|
FE2
|
C:FES201
|
0.0
|
27.8
|
1.0
|
NE2
|
C:HIS12
|
2.1
|
27.9
|
1.0
|
S1
|
C:FES201
|
2.3
|
27.7
|
1.0
|
SG
|
A:CYS110
|
2.3
|
29.3
|
1.0
|
S2
|
C:FES201
|
2.3
|
28.6
|
1.0
|
FE1
|
C:FES201
|
2.7
|
28.9
|
1.0
|
CE1
|
C:HIS12
|
3.0
|
31.1
|
1.0
|
CB
|
A:CYS110
|
3.1
|
29.1
|
1.0
|
CD2
|
C:HIS12
|
3.2
|
25.6
|
1.0
|
CB
|
A:ILE112
|
4.1
|
30.1
|
1.0
|
ND1
|
C:HIS12
|
4.2
|
28.2
|
1.0
|
OE2
|
C:GLU8
|
4.2
|
25.7
|
1.0
|
CG
|
C:HIS12
|
4.3
|
27.6
|
1.0
|
SG
|
A:CYS90
|
4.5
|
31.2
|
1.0
|
CA
|
A:CYS110
|
4.5
|
30.3
|
1.0
|
CD1
|
A:ILE112
|
4.6
|
34.5
|
1.0
|
CG2
|
A:ILE112
|
4.6
|
34.3
|
1.0
|
N
|
A:ALA113
|
4.7
|
27.9
|
1.0
|
CG
|
C:GLU8
|
4.7
|
24.4
|
1.0
|
CG1
|
A:ILE112
|
4.7
|
33.8
|
1.0
|
CD
|
A:ARG94
|
4.9
|
32.1
|
1.0
|
CD
|
C:GLU8
|
4.9
|
27.6
|
1.0
|
CG1
|
A:ILE93
|
4.9
|
31.9
|
1.0
|
N
|
A:ILE112
|
4.9
|
30.4
|
1.0
|
CA
|
A:ILE112
|
5.0
|
30.6
|
1.0
|
CB
|
A:ARG94
|
5.0
|
27.4
|
1.0
|
|
Iron binding site 7 out
of 8 in 6y45
Go back to
Iron Binding Sites List in 6y45
Iron binding site 7 out
of 8 in the Crystal Structure of the H33A Variant of Rsrr
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Crystal Structure of the H33A Variant of Rsrr within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe402
b:33.7
occ:1.00
|
FE1
|
D:FES402
|
0.0
|
33.7
|
1.0
|
OE2
|
D:GLU8
|
2.0
|
32.3
|
1.0
|
S2
|
D:FES402
|
2.2
|
31.8
|
1.0
|
S1
|
D:FES402
|
2.2
|
35.2
|
1.0
|
SG
|
B:CYS90
|
2.4
|
37.3
|
1.0
|
FE2
|
D:FES402
|
2.6
|
32.8
|
1.0
|
CD
|
D:GLU8
|
3.1
|
36.5
|
1.0
|
CB
|
B:CYS90
|
3.4
|
33.2
|
1.0
|
CG
|
D:GLU8
|
3.6
|
32.0
|
1.0
|
CA
|
B:CYS90
|
3.8
|
35.0
|
1.0
|
N
|
B:GLU92
|
3.8
|
33.7
|
1.0
|
N
|
B:THR91
|
4.1
|
35.0
|
1.0
|
OE1
|
D:GLU8
|
4.2
|
36.6
|
1.0
|
NE2
|
D:HIS12
|
4.2
|
31.5
|
1.0
|
CA
|
B:GLU92
|
4.2
|
35.9
|
1.0
|
C
|
B:CYS90
|
4.3
|
37.2
|
1.0
|
N
|
B:ILE93
|
4.3
|
32.0
|
1.0
|
CB
|
B:CYS110
|
4.4
|
37.3
|
1.0
|
SG
|
B:CYS110
|
4.6
|
35.1
|
1.0
|
CG1
|
B:ILE93
|
4.7
|
35.3
|
1.0
|
O
|
B:HOH365
|
4.8
|
43.3
|
1.0
|
CB
|
B:ALA113
|
4.8
|
36.8
|
1.0
|
CD2
|
D:HIS12
|
4.8
|
28.7
|
1.0
|
C
|
B:GLU92
|
4.8
|
36.5
|
1.0
|
C
|
B:THR91
|
4.8
|
37.6
|
1.0
|
CB
|
D:GLU8
|
4.9
|
30.2
|
1.0
|
CZ
|
B:PHE88
|
4.9
|
33.9
|
1.0
|
|
Iron binding site 8 out
of 8 in 6y45
Go back to
Iron Binding Sites List in 6y45
Iron binding site 8 out
of 8 in the Crystal Structure of the H33A Variant of Rsrr
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Crystal Structure of the H33A Variant of Rsrr within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe402
b:32.8
occ:1.00
|
FE2
|
D:FES402
|
0.0
|
32.8
|
1.0
|
NE2
|
D:HIS12
|
2.1
|
31.5
|
1.0
|
S1
|
D:FES402
|
2.3
|
35.2
|
1.0
|
S2
|
D:FES402
|
2.3
|
31.8
|
1.0
|
SG
|
B:CYS110
|
2.3
|
35.1
|
1.0
|
FE1
|
D:FES402
|
2.6
|
33.7
|
1.0
|
CE1
|
D:HIS12
|
3.0
|
34.1
|
1.0
|
CB
|
B:CYS110
|
3.1
|
37.3
|
1.0
|
CD2
|
D:HIS12
|
3.2
|
28.7
|
1.0
|
CB
|
B:ILE112
|
4.1
|
36.6
|
1.0
|
ND1
|
D:HIS12
|
4.2
|
33.1
|
1.0
|
OE2
|
D:GLU8
|
4.2
|
32.3
|
1.0
|
CG
|
D:HIS12
|
4.3
|
31.6
|
1.0
|
SG
|
B:CYS90
|
4.5
|
37.3
|
1.0
|
CA
|
B:CYS110
|
4.6
|
35.1
|
1.0
|
CD1
|
B:ILE112
|
4.6
|
37.4
|
1.0
|
CG2
|
B:ILE112
|
4.6
|
41.1
|
1.0
|
N
|
B:ALA113
|
4.6
|
30.5
|
1.0
|
CG
|
D:GLU8
|
4.8
|
32.0
|
1.0
|
CG1
|
B:ILE112
|
4.8
|
39.7
|
1.0
|
CD
|
B:ARG94
|
4.9
|
35.0
|
1.0
|
CG1
|
B:ILE93
|
4.9
|
35.3
|
1.0
|
CB
|
B:ARG94
|
5.0
|
35.1
|
1.0
|
CD
|
D:GLU8
|
5.0
|
36.5
|
1.0
|
CA
|
B:ILE112
|
5.0
|
33.3
|
1.0
|
|
Reference:
J.C.Crack,
P.Amara,
A.Volbeda,
J.M.Mouesca,
R.Rohac,
M.T.Pellicer Martinez,
C.Y.Huang,
O.Gigarel,
C.Rinaldi,
N.E.Le Brun,
J.C.Fontecilla-Camps.
Electron and Proton Transfers Modulate Dna Binding By the Transcription Regulator Rsrr. J.Am.Chem.Soc. 2020.
ISSN: ESSN 1520-5126
PubMed: 32078310
DOI: 10.1021/JACS.9B12250
Page generated: Wed Aug 7 15:51:25 2024
|