Iron in PDB 2y0s: Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group
Enzymatic activity of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group
All present enzymatic activity of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group:
2.7.7.6;
Protein crystallography data
The structure of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group, PDB code: 2y0s
was solved by
M.Wojtas,
B.Peralta,
M.Ondiviela,
M.Mogni,
S.D.Bell,
N.G.A.Abrescia,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.86 /
3.80
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
129.330,
195.909,
212.451,
90.00,
105.73,
90.00
|
R / Rfree (%)
|
30 /
35.4
|
Other elements in 2y0s:
The structure of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group
(pdb code 2y0s). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group, PDB code: 2y0s:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 2y0s
Go back to
Iron Binding Sites List in 2y0s
Iron binding site 1 out
of 6 in the Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group
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 Sulfolobus Shibatae Rna Polymerase in P21 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1001
b:0.6
occ:1.00
|
FE1
|
D:F3S1001
|
0.0
|
0.6
|
1.0
|
SG
|
D:CYS209
|
1.9
|
81.8
|
1.0
|
S3
|
D:F3S1001
|
2.1
|
0.2
|
1.0
|
S2
|
D:F3S1001
|
2.2
|
0.4
|
1.0
|
S1
|
D:F3S1001
|
2.2
|
0.6
|
1.0
|
FE4
|
D:F3S1001
|
2.5
|
0.5
|
1.0
|
FE3
|
D:F3S1001
|
2.5
|
0.8
|
1.0
|
CD1
|
D:ILE219
|
3.3
|
0.9
|
1.0
|
CB
|
D:CYS209
|
3.4
|
92.6
|
1.0
|
S4
|
D:F3S1001
|
3.6
|
0.2
|
1.0
|
SG
|
D:CYS203
|
3.8
|
72.1
|
1.0
|
SG
|
D:CYS206
|
4.2
|
73.8
|
1.0
|
N
|
D:CYS209
|
4.5
|
74.7
|
1.0
|
CG1
|
D:ILE219
|
4.6
|
0.9
|
1.0
|
CE2
|
D:PHE188
|
4.6
|
93.4
|
1.0
|
N
|
D:GLU207
|
4.6
|
89.8
|
1.0
|
CA
|
D:CYS209
|
4.6
|
87.9
|
1.0
|
CB
|
D:CYS206
|
4.7
|
71.8
|
1.0
|
SG
|
D:CYS183
|
4.7
|
75.2
|
1.0
|
CB
|
D:CYS203
|
5.0
|
74.5
|
1.0
|
CA
|
D:GLU207
|
5.0
|
98.1
|
1.0
|
|
Iron binding site 2 out
of 6 in 2y0s
Go back to
Iron Binding Sites List in 2y0s
Iron binding site 2 out
of 6 in the Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group
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 Sulfolobus Shibatae Rna Polymerase in P21 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1001
b:0.8
occ:1.00
|
FE3
|
D:F3S1001
|
0.0
|
0.8
|
1.0
|
SG
|
D:CYS203
|
1.9
|
72.1
|
1.0
|
S3
|
D:F3S1001
|
2.1
|
0.2
|
1.0
|
S4
|
D:F3S1001
|
2.2
|
0.2
|
1.0
|
S1
|
D:F3S1001
|
2.2
|
0.6
|
1.0
|
FE4
|
D:F3S1001
|
2.5
|
0.5
|
1.0
|
FE1
|
D:F3S1001
|
2.5
|
0.6
|
1.0
|
CB
|
D:CYS203
|
3.0
|
74.5
|
1.0
|
N
|
D:THR204
|
3.2
|
74.7
|
1.0
|
CA
|
D:CYS203
|
3.2
|
76.8
|
1.0
|
S2
|
D:F3S1001
|
3.5
|
0.4
|
1.0
|
C
|
D:CYS203
|
3.7
|
72.8
|
1.0
|
CB
|
D:CYS206
|
4.2
|
71.8
|
1.0
|
CD1
|
D:ILE219
|
4.3
|
0.9
|
1.0
|
SG
|
D:CYS209
|
4.3
|
81.8
|
1.0
|
CA
|
D:THR204
|
4.4
|
74.3
|
1.0
|
O
|
D:THR204
|
4.4
|
72.9
|
1.0
|
C
|
D:THR204
|
4.4
|
72.2
|
1.0
|
OG1
|
D:THR204
|
4.5
|
72.4
|
1.0
|
SG
|
D:CYS206
|
4.5
|
73.8
|
1.0
|
N
|
D:CYS203
|
4.5
|
75.2
|
1.0
|
O
|
D:LEU205
|
4.6
|
0.2
|
1.0
|
O
|
D:CYS203
|
4.9
|
77.4
|
1.0
|
CG2
|
D:VAL187
|
4.9
|
78.2
|
1.0
|
SG
|
D:CYS183
|
5.0
|
75.2
|
1.0
|
|
Iron binding site 3 out
of 6 in 2y0s
Go back to
Iron Binding Sites List in 2y0s
Iron binding site 3 out
of 6 in the Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group
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 Sulfolobus Shibatae Rna Polymerase in P21 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1001
b:0.5
occ:1.00
|
FE4
|
D:F3S1001
|
0.0
|
0.5
|
1.0
|
SG
|
D:CYS206
|
2.0
|
73.8
|
1.0
|
S3
|
D:F3S1001
|
2.1
|
0.2
|
1.0
|
S2
|
D:F3S1001
|
2.2
|
0.4
|
1.0
|
S4
|
D:F3S1001
|
2.2
|
0.2
|
1.0
|
CB
|
D:CYS206
|
2.5
|
71.8
|
1.0
|
FE1
|
D:F3S1001
|
2.5
|
0.6
|
1.0
|
FE3
|
D:F3S1001
|
2.5
|
0.8
|
1.0
|
S1
|
D:F3S1001
|
3.5
|
0.6
|
1.0
|
SG
|
D:CYS209
|
3.7
|
81.8
|
1.0
|
N
|
D:GLU207
|
3.7
|
89.8
|
1.0
|
CA
|
D:CYS206
|
3.8
|
75.3
|
1.0
|
C
|
D:CYS206
|
4.2
|
77.4
|
1.0
|
O
|
D:LEU205
|
4.2
|
0.2
|
1.0
|
CD
|
D:PRO184
|
4.4
|
77.5
|
1.0
|
SG
|
D:CYS203
|
4.4
|
72.1
|
1.0
|
OG1
|
D:THR204
|
4.5
|
72.4
|
1.0
|
N
|
D:CYS206
|
4.6
|
70.6
|
1.0
|
N
|
D:GLU208
|
4.6
|
90.5
|
1.0
|
C
|
D:LEU205
|
4.7
|
0.2
|
1.0
|
SG
|
D:CYS183
|
4.7
|
75.2
|
1.0
|
CA
|
D:GLU207
|
4.7
|
98.1
|
1.0
|
N
|
D:THR204
|
4.8
|
74.7
|
1.0
|
CD1
|
D:ILE219
|
5.0
|
0.9
|
1.0
|
CB
|
D:CYS209
|
5.0
|
92.6
|
1.0
|
|
Iron binding site 4 out
of 6 in 2y0s
Go back to
Iron Binding Sites List in 2y0s
Iron binding site 4 out
of 6 in the Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group
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 Sulfolobus Shibatae Rna Polymerase in P21 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe1001
b:0.2
occ:1.00
|
FE1
|
S:F3S1001
|
0.0
|
0.2
|
1.0
|
SG
|
S:CYS209
|
1.8
|
99.2
|
1.0
|
S3
|
S:F3S1001
|
2.1
|
0.6
|
1.0
|
S2
|
S:F3S1001
|
2.2
|
0.9
|
1.0
|
S1
|
S:F3S1001
|
2.2
|
0.6
|
1.0
|
FE4
|
S:F3S1001
|
2.5
|
0.8
|
1.0
|
FE3
|
S:F3S1001
|
2.5
|
0.3
|
1.0
|
CD1
|
S:ILE219
|
3.3
|
0.5
|
1.0
|
CB
|
S:CYS209
|
3.4
|
0.9
|
1.0
|
S4
|
S:F3S1001
|
3.6
|
0.6
|
1.0
|
SG
|
S:CYS203
|
3.7
|
89.8
|
1.0
|
SG
|
S:CYS206
|
4.0
|
87.7
|
1.0
|
N
|
S:CYS209
|
4.5
|
86.1
|
1.0
|
CA
|
S:CYS209
|
4.6
|
95.2
|
1.0
|
CG1
|
S:ILE219
|
4.6
|
0.1
|
1.0
|
N
|
S:GLU207
|
4.6
|
0.1
|
1.0
|
CE2
|
S:PHE188
|
4.6
|
0.0
|
1.0
|
CB
|
S:CYS206
|
4.7
|
87.1
|
1.0
|
SG
|
S:CYS183
|
4.8
|
0.4
|
1.0
|
CB
|
S:CYS203
|
4.9
|
90.8
|
1.0
|
CA
|
S:GLU207
|
5.0
|
0.8
|
1.0
|
|
Iron binding site 5 out
of 6 in 2y0s
Go back to
Iron Binding Sites List in 2y0s
Iron binding site 5 out
of 6 in the Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group
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 Sulfolobus Shibatae Rna Polymerase in P21 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe1001
b:0.3
occ:1.00
|
FE3
|
S:F3S1001
|
0.0
|
0.3
|
1.0
|
SG
|
S:CYS203
|
1.8
|
89.8
|
1.0
|
S3
|
S:F3S1001
|
2.1
|
0.6
|
1.0
|
S4
|
S:F3S1001
|
2.2
|
0.6
|
1.0
|
S1
|
S:F3S1001
|
2.2
|
0.6
|
1.0
|
FE4
|
S:F3S1001
|
2.5
|
0.8
|
1.0
|
FE1
|
S:F3S1001
|
2.5
|
0.2
|
1.0
|
CB
|
S:CYS203
|
2.9
|
90.8
|
1.0
|
N
|
S:THR204
|
3.2
|
89.9
|
1.0
|
CA
|
S:CYS203
|
3.2
|
90.6
|
1.0
|
S2
|
S:F3S1001
|
3.5
|
0.9
|
1.0
|
C
|
S:CYS203
|
3.7
|
90.0
|
1.0
|
CB
|
S:CYS206
|
4.2
|
87.1
|
1.0
|
SG
|
S:CYS209
|
4.2
|
99.2
|
1.0
|
CD1
|
S:ILE219
|
4.3
|
0.5
|
1.0
|
SG
|
S:CYS206
|
4.3
|
87.7
|
1.0
|
CA
|
S:THR204
|
4.3
|
88.5
|
1.0
|
O
|
S:THR204
|
4.4
|
88.3
|
1.0
|
C
|
S:THR204
|
4.4
|
87.9
|
1.0
|
OG1
|
S:THR204
|
4.5
|
88.9
|
1.0
|
N
|
S:CYS203
|
4.5
|
92.7
|
1.0
|
O
|
S:LEU205
|
4.6
|
0.3
|
1.0
|
O
|
S:CYS203
|
4.9
|
90.4
|
1.0
|
CG2
|
S:VAL187
|
4.9
|
0.3
|
1.0
|
|
Iron binding site 6 out
of 6 in 2y0s
Go back to
Iron Binding Sites List in 2y0s
Iron binding site 6 out
of 6 in the Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group
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 Sulfolobus Shibatae Rna Polymerase in P21 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe1001
b:0.8
occ:1.00
|
FE4
|
S:F3S1001
|
0.0
|
0.8
|
1.0
|
SG
|
S:CYS206
|
1.9
|
87.7
|
1.0
|
S3
|
S:F3S1001
|
2.1
|
0.6
|
1.0
|
S2
|
S:F3S1001
|
2.2
|
0.9
|
1.0
|
S4
|
S:F3S1001
|
2.2
|
0.6
|
1.0
|
CB
|
S:CYS206
|
2.5
|
87.1
|
1.0
|
FE1
|
S:F3S1001
|
2.5
|
0.2
|
1.0
|
FE3
|
S:F3S1001
|
2.5
|
0.3
|
1.0
|
S1
|
S:F3S1001
|
3.5
|
0.6
|
1.0
|
SG
|
S:CYS209
|
3.5
|
99.2
|
1.0
|
N
|
S:GLU207
|
3.7
|
0.1
|
1.0
|
CA
|
S:CYS206
|
3.8
|
85.9
|
1.0
|
C
|
S:CYS206
|
4.2
|
85.8
|
1.0
|
O
|
S:LEU205
|
4.2
|
0.3
|
1.0
|
SG
|
S:CYS203
|
4.3
|
89.8
|
1.0
|
CD
|
S:PRO184
|
4.4
|
0.2
|
1.0
|
OG1
|
S:THR204
|
4.5
|
88.9
|
1.0
|
N
|
S:CYS206
|
4.6
|
85.9
|
1.0
|
N
|
S:GLU208
|
4.6
|
95.3
|
1.0
|
C
|
S:LEU205
|
4.7
|
0.1
|
1.0
|
CA
|
S:GLU207
|
4.7
|
0.8
|
1.0
|
N
|
S:THR204
|
4.8
|
89.9
|
1.0
|
SG
|
S:CYS183
|
4.8
|
0.4
|
1.0
|
CD1
|
S:ILE219
|
5.0
|
0.5
|
1.0
|
|
Reference:
M.Wojtas,
B.Peralta,
M.Ondiviela,
M.Mogni,
S.D.Bell,
N.G.Abrescia.
Archaeal Rna Polymerase: the Influence of the Protruding Stalk in Crystal Packing and Preliminary Biophysical Analysis of the RPO13 Subunit. Biochem. Soc. Trans. V. 39 25 2011.
ISSN: ISSN 1470-8752
PubMed: 21265742
DOI: 10.1042/BST0390025
Page generated: Sun Aug 4 05:04:12 2024
|