Iron in PDB 36rp: Cryo-Em Structure of Sulfolobus Acidocaldarius Rna Polymerase Without Stalk (No RPO4/RPO7)
Enzymatic activity of Cryo-Em Structure of Sulfolobus Acidocaldarius Rna Polymerase Without Stalk (No RPO4/RPO7)
All present enzymatic activity of Cryo-Em Structure of Sulfolobus Acidocaldarius Rna Polymerase Without Stalk (No RPO4/RPO7):
2.7.7.6;
Other elements in 36rp:
The structure of Cryo-Em Structure of Sulfolobus Acidocaldarius Rna Polymerase Without Stalk (No RPO4/RPO7) also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Cryo-Em Structure of Sulfolobus Acidocaldarius Rna Polymerase Without Stalk (No RPO4/RPO7)
(pdb code 36rp). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Cryo-Em Structure of Sulfolobus Acidocaldarius Rna Polymerase Without Stalk (No RPO4/RPO7), PDB code: 36rp:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 36rp
Go back to
Iron Binding Sites List in 36rp
Iron binding site 1 out
of 4 in the Cryo-Em Structure of Sulfolobus Acidocaldarius Rna Polymerase Without Stalk (No RPO4/RPO7)
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Cryo-Em Structure of Sulfolobus Acidocaldarius Rna Polymerase Without Stalk (No RPO4/RPO7) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1001
b:531.0
occ:1.00
|
FE1
|
D:SF41001
|
0.0
|
531.0
|
1.0
|
|
SG
|
D:CYS206
|
2.3
|
531.0
|
1.0
|
|
S2
|
D:SF41001
|
2.3
|
531.0
|
1.0
|
|
S4
|
D:SF41001
|
2.3
|
531.0
|
1.0
|
|
S3
|
D:SF41001
|
2.3
|
531.0
|
1.0
|
|
FE4
|
D:SF41001
|
2.7
|
531.0
|
1.0
|
|
FE3
|
D:SF41001
|
2.7
|
531.0
|
1.0
|
|
FE2
|
D:SF41001
|
2.7
|
531.0
|
1.0
|
|
CD
|
D:PRO184
|
3.2
|
531.0
|
1.0
|
|
SG
|
D:CYS183
|
3.9
|
531.0
|
1.0
|
|
S1
|
D:SF41001
|
3.9
|
531.0
|
1.0
|
|
SG
|
D:CYS209
|
3.9
|
531.0
|
1.0
|
|
CG
|
D:PRO184
|
3.9
|
531.0
|
1.0
|
|
SG
|
D:CYS203
|
3.9
|
410.7
|
1.0
|
|
CB
|
D:CYS206
|
4.0
|
531.0
|
1.0
|
|
CG1
|
D:ILE204
|
4.2
|
370.4
|
1.0
|
|
N
|
D:PRO184
|
4.2
|
531.0
|
1.0
|
|
CA
|
D:CYS183
|
4.4
|
531.0
|
1.0
|
|
N
|
D:CYS206
|
4.5
|
531.0
|
1.0
|
|
N
|
D:ILE204
|
4.5
|
370.4
|
1.0
|
|
N
|
D:GLU207
|
4.6
|
351.8
|
1.0
|
|
CB
|
D:CYS183
|
4.7
|
531.0
|
1.0
|
|
CB
|
D:PRO184
|
4.7
|
531.0
|
1.0
|
|
CA
|
D:CYS203
|
4.7
|
410.7
|
1.0
|
|
CD1
|
D:ILE204
|
4.7
|
370.4
|
1.0
|
|
CB
|
D:CYS203
|
4.7
|
410.7
|
1.0
|
|
CA
|
D:CYS206
|
4.7
|
531.0
|
1.0
|
|
C
|
D:CYS183
|
4.8
|
531.0
|
1.0
|
|
N
|
D:GLU208
|
4.9
|
408.3
|
1.0
|
|
N
|
D:GLU185
|
5.0
|
477.4
|
1.0
|
|
Iron binding site 2 out
of 4 in 36rp
Go back to
Iron Binding Sites List in 36rp
Iron binding site 2 out
of 4 in the Cryo-Em Structure of Sulfolobus Acidocaldarius Rna Polymerase Without Stalk (No RPO4/RPO7)
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Cryo-Em Structure of Sulfolobus Acidocaldarius Rna Polymerase Without Stalk (No RPO4/RPO7) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1001
b:531.0
occ:1.00
|
FE2
|
D:SF41001
|
0.0
|
531.0
|
1.0
|
|
SG
|
D:CYS183
|
2.1
|
531.0
|
1.0
|
|
SG
|
D:CYS209
|
2.2
|
531.0
|
1.0
|
|
S1
|
D:SF41001
|
2.3
|
531.0
|
1.0
|
|
S4
|
D:SF41001
|
2.3
|
531.0
|
1.0
|
|
S3
|
D:SF41001
|
2.3
|
531.0
|
1.0
|
|
CB
|
D:CYS183
|
2.6
|
531.0
|
1.0
|
|
FE3
|
D:SF41001
|
2.7
|
531.0
|
1.0
|
|
FE4
|
D:SF41001
|
2.7
|
531.0
|
1.0
|
|
FE1
|
D:SF41001
|
2.7
|
531.0
|
1.0
|
|
CA
|
D:CYS183
|
3.2
|
531.0
|
1.0
|
|
S2
|
D:SF41001
|
3.9
|
531.0
|
1.0
|
|
CE2
|
D:PHE188
|
3.9
|
452.7
|
1.0
|
|
CB
|
D:CYS209
|
3.9
|
531.0
|
1.0
|
|
CD
|
D:PRO184
|
4.1
|
531.0
|
1.0
|
|
C
|
D:CYS183
|
4.2
|
531.0
|
1.0
|
|
CB
|
D:VAL187
|
4.2
|
531.0
|
1.0
|
|
CG2
|
D:VAL187
|
4.2
|
531.0
|
1.0
|
|
N
|
D:CYS183
|
4.3
|
531.0
|
1.0
|
|
CD2
|
D:PHE188
|
4.3
|
452.7
|
1.0
|
|
N
|
D:PRO184
|
4.3
|
531.0
|
1.0
|
|
SG
|
D:CYS203
|
4.5
|
410.7
|
1.0
|
|
SG
|
D:CYS206
|
4.8
|
531.0
|
1.0
|
|
O
|
D:ALA179
|
4.8
|
531.0
|
1.0
|
|
CB
|
D:CYS203
|
4.8
|
410.7
|
1.0
|
|
N
|
D:GLU185
|
4.9
|
477.4
|
1.0
|
|
N
|
D:CYS209
|
4.9
|
531.0
|
1.0
|
|
CG1
|
D:VAL187
|
4.9
|
531.0
|
1.0
|
|
CA
|
D:CYS209
|
5.0
|
531.0
|
1.0
|
|
Iron binding site 3 out
of 4 in 36rp
Go back to
Iron Binding Sites List in 36rp
Iron binding site 3 out
of 4 in the Cryo-Em Structure of Sulfolobus Acidocaldarius Rna Polymerase Without Stalk (No RPO4/RPO7)
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Cryo-Em Structure of Sulfolobus Acidocaldarius Rna Polymerase Without Stalk (No RPO4/RPO7) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1001
b:531.0
occ:1.00
|
FE3
|
D:SF41001
|
0.0
|
531.0
|
1.0
|
|
S4
|
D:SF41001
|
2.3
|
531.0
|
1.0
|
|
S1
|
D:SF41001
|
2.3
|
531.0
|
1.0
|
|
S2
|
D:SF41001
|
2.3
|
531.0
|
1.0
|
|
SG
|
D:CYS209
|
2.6
|
531.0
|
1.0
|
|
FE2
|
D:SF41001
|
2.7
|
531.0
|
1.0
|
|
FE1
|
D:SF41001
|
2.7
|
531.0
|
1.0
|
|
FE4
|
D:SF41001
|
2.7
|
531.0
|
1.0
|
|
SG
|
D:CYS203
|
3.0
|
410.7
|
1.0
|
|
CD1
|
D:ILE219
|
3.1
|
385.1
|
1.0
|
|
CB
|
D:CYS209
|
3.5
|
531.0
|
1.0
|
|
SG
|
D:CYS206
|
3.8
|
531.0
|
1.0
|
|
S3
|
D:SF41001
|
3.9
|
531.0
|
1.0
|
|
N
|
D:CYS209
|
3.9
|
531.0
|
1.0
|
|
N
|
D:GLU207
|
3.9
|
351.8
|
1.0
|
|
CG1
|
D:ILE219
|
4.0
|
385.1
|
1.0
|
|
CA
|
D:GLU207
|
4.1
|
351.8
|
1.0
|
|
N
|
D:GLU208
|
4.2
|
408.3
|
1.0
|
|
CA
|
D:CYS209
|
4.3
|
531.0
|
1.0
|
|
CB
|
D:CYS203
|
4.3
|
410.7
|
1.0
|
|
CG2
|
D:ILE219
|
4.5
|
385.1
|
1.0
|
|
C
|
D:GLU207
|
4.6
|
351.8
|
1.0
|
|
SG
|
D:CYS183
|
4.7
|
531.0
|
1.0
|
|
N
|
D:CYS206
|
4.9
|
531.0
|
1.0
|
|
CB
|
D:ILE219
|
4.9
|
385.1
|
1.0
|
|
C
|
D:CYS206
|
4.9
|
531.0
|
1.0
|
|
C
|
D:GLU208
|
4.9
|
408.3
|
1.0
|
|
CE2
|
D:PHE188
|
5.0
|
452.7
|
1.0
|
|
Iron binding site 4 out
of 4 in 36rp
Go back to
Iron Binding Sites List in 36rp
Iron binding site 4 out
of 4 in the Cryo-Em Structure of Sulfolobus Acidocaldarius Rna Polymerase Without Stalk (No RPO4/RPO7)
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Cryo-Em Structure of Sulfolobus Acidocaldarius Rna Polymerase Without Stalk (No RPO4/RPO7) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1001
b:531.0
occ:1.00
|
FE4
|
D:SF41001
|
0.0
|
531.0
|
1.0
|
|
SG
|
D:CYS203
|
2.1
|
410.7
|
1.0
|
|
CB
|
D:CYS203
|
2.2
|
410.7
|
1.0
|
|
S3
|
D:SF41001
|
2.3
|
531.0
|
1.0
|
|
S1
|
D:SF41001
|
2.3
|
531.0
|
1.0
|
|
S2
|
D:SF41001
|
2.3
|
531.0
|
1.0
|
|
CA
|
D:CYS203
|
2.6
|
410.7
|
1.0
|
|
FE2
|
D:SF41001
|
2.7
|
531.0
|
1.0
|
|
FE1
|
D:SF41001
|
2.7
|
531.0
|
1.0
|
|
FE3
|
D:SF41001
|
2.7
|
531.0
|
1.0
|
|
CG2
|
D:VAL187
|
3.4
|
531.0
|
1.0
|
|
C
|
D:CYS203
|
3.6
|
410.7
|
1.0
|
|
SG
|
D:CYS183
|
3.7
|
531.0
|
1.0
|
|
N
|
D:CYS203
|
3.8
|
410.7
|
1.0
|
|
N
|
D:ILE204
|
3.8
|
370.4
|
1.0
|
|
S4
|
D:SF41001
|
3.9
|
531.0
|
1.0
|
|
CB
|
D:VAL187
|
4.0
|
531.0
|
1.0
|
|
CG1
|
D:VAL187
|
4.3
|
531.0
|
1.0
|
|
SG
|
D:CYS209
|
4.3
|
531.0
|
1.0
|
|
O
|
D:CYS203
|
4.6
|
410.7
|
1.0
|
|
SG
|
D:CYS206
|
4.6
|
531.0
|
1.0
|
|
CG2
|
D:VAL170
|
4.7
|
402.6
|
1.0
|
|
C
|
D:SER202
|
4.7
|
454.1
|
1.0
|
|
N
|
D:LEU205
|
4.8
|
197.3
|
1.0
|
|
O
|
D:SER202
|
4.8
|
454.1
|
1.0
|
|
Reference:
G.N.R.Fordjour,
K.Murakami,
J.-P.Armache,
K.S.Murakami.
Clamp Conformational Flexibility and Dynamics in Archaeal and Eukaryotic Rna Polymerases Revealed By Cryo-Em To Be Published.
Page generated: Sun Oct 4 10:38:54 2026
|