Iron in PDB 3hkz: The X-Ray Crystal Structure of Rna Polymerase From Archaea
Enzymatic activity of The X-Ray Crystal Structure of Rna Polymerase From Archaea
All present enzymatic activity of The X-Ray Crystal Structure of Rna Polymerase From Archaea:
2.7.7.6;
Protein crystallography data
The structure of The X-Ray Crystal Structure of Rna Polymerase From Archaea, PDB code: 3hkz
was solved by
K.S.Murakami,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.00 /
3.40
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
125.820,
201.235,
196.050,
90.00,
100.92,
90.00
|
R / Rfree (%)
|
26.5 /
34.1
|
Other elements in 3hkz:
The structure of The X-Ray Crystal Structure of Rna Polymerase From Archaea also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the The X-Ray Crystal Structure of Rna Polymerase From Archaea
(pdb code 3hkz). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
The X-Ray Crystal Structure of Rna Polymerase From Archaea, PDB code: 3hkz:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 3hkz
Go back to
Iron Binding Sites List in 3hkz
Iron binding site 1 out
of 6 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of The X-Ray Crystal Structure of Rna Polymerase From Archaea within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1001
b:81.5
occ:1.00
|
FE1
|
D:F3S1001
|
0.0
|
81.5
|
1.0
|
S1
|
D:F3S1001
|
2.2
|
84.0
|
1.0
|
S3
|
D:F3S1001
|
2.2
|
82.9
|
1.0
|
S2
|
D:F3S1001
|
2.2
|
79.1
|
1.0
|
SG
|
D:CYS209
|
2.3
|
95.4
|
1.0
|
FE3
|
D:F3S1001
|
2.3
|
82.9
|
1.0
|
FE4
|
D:F3S1001
|
2.9
|
80.8
|
1.0
|
CB
|
D:CYS209
|
3.3
|
96.9
|
1.0
|
CD1
|
D:ILE219
|
3.9
|
0.3
|
1.0
|
S4
|
D:F3S1001
|
4.1
|
82.6
|
1.0
|
N
|
D:CYS209
|
4.1
|
97.4
|
1.0
|
SG
|
D:CYS183
|
4.2
|
93.9
|
1.0
|
SG
|
D:CYS203
|
4.2
|
98.2
|
1.0
|
CA
|
D:CYS209
|
4.4
|
97.1
|
1.0
|
N
|
D:GLU207
|
4.5
|
98.9
|
1.0
|
CB
|
D:CYS183
|
4.5
|
94.4
|
1.0
|
CB
|
D:CYS206
|
4.6
|
99.4
|
1.0
|
CA
|
D:GLU207
|
4.8
|
98.7
|
1.0
|
N
|
D:GLU208
|
4.8
|
98.3
|
1.0
|
SG
|
D:CYS206
|
5.0
|
99.2
|
1.0
|
|
Iron binding site 2 out
of 6 in 3hkz
Go back to
Iron Binding Sites List in 3hkz
Iron binding site 2 out
of 6 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of The X-Ray Crystal Structure of Rna Polymerase From Archaea within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1001
b:82.9
occ:1.00
|
FE3
|
D:F3S1001
|
0.0
|
82.9
|
1.0
|
S4
|
D:F3S1001
|
2.2
|
82.6
|
1.0
|
S1
|
D:F3S1001
|
2.2
|
84.0
|
1.0
|
S3
|
D:F3S1001
|
2.2
|
82.9
|
1.0
|
FE1
|
D:F3S1001
|
2.3
|
81.5
|
1.0
|
FE4
|
D:F3S1001
|
2.4
|
80.8
|
1.0
|
S2
|
D:F3S1001
|
2.6
|
79.1
|
1.0
|
CB
|
D:CYS206
|
2.8
|
99.4
|
1.0
|
SG
|
D:CYS206
|
3.1
|
99.2
|
1.0
|
SG
|
D:CYS183
|
3.7
|
93.9
|
1.0
|
N
|
D:GLU207
|
4.0
|
98.9
|
1.0
|
SG
|
D:CYS203
|
4.0
|
98.2
|
1.0
|
CA
|
D:CYS206
|
4.2
|
99.4
|
1.0
|
SG
|
D:CYS209
|
4.3
|
95.4
|
1.0
|
O
|
D:LEU205
|
4.5
|
0.1
|
1.0
|
CB
|
D:CYS183
|
4.5
|
94.4
|
1.0
|
C
|
D:CYS206
|
4.6
|
99.3
|
1.0
|
O
|
D:THR204
|
4.7
|
0.1
|
1.0
|
N
|
D:GLU208
|
4.8
|
98.3
|
1.0
|
N
|
D:CYS206
|
4.8
|
99.7
|
1.0
|
C
|
D:LEU205
|
4.9
|
0.1
|
1.0
|
N
|
D:THR204
|
4.9
|
99.7
|
1.0
|
CA
|
D:GLU207
|
4.9
|
98.7
|
1.0
|
|
Iron binding site 3 out
of 6 in 3hkz
Go back to
Iron Binding Sites List in 3hkz
Iron binding site 3 out
of 6 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of The X-Ray Crystal Structure of Rna Polymerase From Archaea within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1001
b:80.8
occ:1.00
|
FE4
|
D:F3S1001
|
0.0
|
80.8
|
1.0
|
SG
|
D:CYS203
|
1.9
|
98.2
|
1.0
|
S4
|
D:F3S1001
|
2.2
|
82.6
|
1.0
|
S3
|
D:F3S1001
|
2.2
|
82.9
|
1.0
|
S2
|
D:F3S1001
|
2.2
|
79.1
|
1.0
|
FE3
|
D:F3S1001
|
2.4
|
82.9
|
1.0
|
CB
|
D:CYS203
|
2.7
|
99.5
|
1.0
|
FE1
|
D:F3S1001
|
2.9
|
81.5
|
1.0
|
CA
|
D:CYS203
|
3.3
|
99.7
|
1.0
|
N
|
D:THR204
|
3.8
|
99.7
|
1.0
|
C
|
D:CYS203
|
4.0
|
99.7
|
1.0
|
SG
|
D:CYS183
|
4.0
|
93.9
|
1.0
|
CG2
|
D:VAL187
|
4.2
|
0.6
|
1.0
|
S1
|
D:F3S1001
|
4.3
|
84.0
|
1.0
|
N
|
D:CYS203
|
4.5
|
0.2
|
1.0
|
CB
|
D:CYS206
|
4.6
|
99.4
|
1.0
|
CB
|
D:VAL187
|
4.9
|
0.2
|
1.0
|
O
|
D:THR204
|
4.9
|
0.1
|
1.0
|
CG1
|
D:VAL187
|
5.0
|
0.7
|
1.0
|
CA
|
D:THR204
|
5.0
|
99.9
|
1.0
|
|
Iron binding site 4 out
of 6 in 3hkz
Go back to
Iron Binding Sites List in 3hkz
Iron binding site 4 out
of 6 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of The X-Ray Crystal Structure of Rna Polymerase From Archaea within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Fe1001
b:0.3
occ:1.00
|
FE1
|
O:F3S1001
|
0.0
|
0.3
|
1.0
|
SG
|
O:CYS209
|
1.7
|
95.6
|
1.0
|
S2
|
O:F3S1001
|
2.2
|
0.0
|
1.0
|
S3
|
O:F3S1001
|
2.2
|
0.7
|
1.0
|
S1
|
O:F3S1001
|
2.2
|
0.6
|
1.0
|
FE4
|
O:F3S1001
|
2.5
|
0.8
|
1.0
|
FE3
|
O:F3S1001
|
2.9
|
0.6
|
1.0
|
CB
|
O:CYS209
|
2.9
|
96.9
|
1.0
|
CD1
|
O:ILE219
|
3.6
|
0.4
|
1.0
|
N
|
O:CYS209
|
3.7
|
97.4
|
1.0
|
CA
|
O:CYS209
|
3.9
|
97.1
|
1.0
|
N
|
O:GLU207
|
4.1
|
99.0
|
1.0
|
CA
|
O:GLU207
|
4.3
|
98.6
|
1.0
|
S4
|
O:F3S1001
|
4.3
|
0.2
|
1.0
|
N
|
O:GLU208
|
4.4
|
98.2
|
1.0
|
C
|
O:GLU207
|
4.5
|
98.6
|
1.0
|
N
|
O:LEU210
|
4.6
|
97.8
|
1.0
|
CB
|
O:CYS206
|
4.7
|
99.4
|
1.0
|
SG
|
O:CYS203
|
4.8
|
98.4
|
1.0
|
C
|
O:CYS209
|
4.8
|
97.3
|
1.0
|
SG
|
O:CYS183
|
4.9
|
93.9
|
1.0
|
C
|
O:GLU208
|
4.9
|
97.7
|
1.0
|
O
|
O:LEU205
|
4.9
|
0.1
|
1.0
|
CB
|
O:CYS183
|
5.0
|
94.5
|
1.0
|
CG1
|
O:ILE219
|
5.0
|
0.2
|
1.0
|
|
Iron binding site 5 out
of 6 in 3hkz
Go back to
Iron Binding Sites List in 3hkz
Iron binding site 5 out
of 6 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of The X-Ray Crystal Structure of Rna Polymerase From Archaea within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Fe1001
b:0.6
occ:1.00
|
FE3
|
O:F3S1001
|
0.0
|
0.6
|
1.0
|
FE4
|
O:F3S1001
|
2.2
|
0.8
|
1.0
|
S4
|
O:F3S1001
|
2.2
|
0.2
|
1.0
|
S3
|
O:F3S1001
|
2.2
|
0.7
|
1.0
|
S1
|
O:F3S1001
|
2.2
|
0.6
|
1.0
|
SG
|
O:CYS203
|
2.6
|
98.4
|
1.0
|
FE1
|
O:F3S1001
|
2.9
|
0.3
|
1.0
|
CB
|
O:CYS203
|
3.3
|
99.5
|
1.0
|
SG
|
O:CYS183
|
3.7
|
93.9
|
1.0
|
S2
|
O:F3S1001
|
4.0
|
0.0
|
1.0
|
CA
|
O:CYS203
|
4.0
|
99.8
|
1.0
|
CG2
|
O:VAL187
|
4.2
|
0.6
|
1.0
|
SG
|
O:CYS209
|
4.5
|
95.6
|
1.0
|
N
|
O:THR204
|
4.6
|
99.8
|
1.0
|
CB
|
O:VAL187
|
4.6
|
0.3
|
1.0
|
CG1
|
O:VAL187
|
4.7
|
0.7
|
1.0
|
C
|
O:CYS203
|
4.8
|
99.7
|
1.0
|
CB
|
O:CYS183
|
4.8
|
94.5
|
1.0
|
CB
|
O:CYS206
|
4.8
|
99.4
|
1.0
|
CD1
|
O:ILE219
|
5.0
|
0.4
|
1.0
|
|
Iron binding site 6 out
of 6 in 3hkz
Go back to
Iron Binding Sites List in 3hkz
Iron binding site 6 out
of 6 in the The X-Ray Crystal Structure of Rna Polymerase From Archaea
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of The X-Ray Crystal Structure of Rna Polymerase From Archaea within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Fe1001
b:0.8
occ:1.00
|
FE4
|
O:F3S1001
|
0.0
|
0.8
|
1.0
|
FE3
|
O:F3S1001
|
2.2
|
0.6
|
1.0
|
S4
|
O:F3S1001
|
2.2
|
0.2
|
1.0
|
S2
|
O:F3S1001
|
2.2
|
0.0
|
1.0
|
S3
|
O:F3S1001
|
2.2
|
0.7
|
1.0
|
FE1
|
O:F3S1001
|
2.5
|
0.3
|
1.0
|
S1
|
O:F3S1001
|
2.7
|
0.6
|
1.0
|
CB
|
O:CYS206
|
3.0
|
99.4
|
1.0
|
SG
|
O:CYS206
|
3.3
|
99.0
|
1.0
|
SG
|
O:CYS183
|
3.8
|
93.9
|
1.0
|
N
|
O:GLU207
|
4.0
|
99.0
|
1.0
|
SG
|
O:CYS209
|
4.1
|
95.6
|
1.0
|
SG
|
O:CYS203
|
4.1
|
98.4
|
1.0
|
CA
|
O:CYS206
|
4.4
|
99.5
|
1.0
|
CB
|
O:CYS183
|
4.5
|
94.5
|
1.0
|
O
|
O:LEU205
|
4.5
|
0.1
|
1.0
|
C
|
O:CYS206
|
4.7
|
99.3
|
1.0
|
N
|
O:GLU208
|
4.8
|
98.2
|
1.0
|
O
|
O:THR204
|
4.9
|
0.2
|
1.0
|
CA
|
O:GLU207
|
4.9
|
98.6
|
1.0
|
N
|
O:CYS206
|
5.0
|
99.8
|
1.0
|
C
|
O:LEU205
|
5.0
|
0.2
|
1.0
|
|
Reference:
A.Hirata,
B.J.Klein,
K.S.Murakami.
The X-Ray Crystal Structure of Rna Polymerase From Archaea. Nature V. 451 851 2008.
ISSN: ISSN 0028-0836
PubMed: 18235446
DOI: 10.1038/NATURE06530
Page generated: Sun Aug 4 11:31:42 2024
|