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Iron in PDB 2pmz: Archaeal Rna Polymerase From Sulfolobus Solfataricus

Enzymatic activity of Archaeal Rna Polymerase From Sulfolobus Solfataricus

All present enzymatic activity of Archaeal Rna Polymerase From Sulfolobus Solfataricus:
2.7.7.6;

Protein crystallography data

The structure of Archaeal Rna Polymerase From Sulfolobus Solfataricus, PDB code: 2pmz 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) 39.79 / 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 (%) 27.4 / 34.3

Other elements in 2pmz:

The structure of Archaeal Rna Polymerase From Sulfolobus Solfataricus also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 8 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Archaeal Rna Polymerase From Sulfolobus Solfataricus (pdb code 2pmz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Archaeal Rna Polymerase From Sulfolobus Solfataricus, PDB code: 2pmz:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 2pmz

Go back to Iron Binding Sites List in 2pmz
Iron binding site 1 out of 6 in the Archaeal Rna Polymerase From Sulfolobus Solfataricus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Archaeal Rna Polymerase From Sulfolobus Solfataricus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1001

b:80.5
occ:1.00
 FE1 D:F3S1001 0.0 80.5 1.0
S2 D:F3S1001 2.2 80.7 1.0
S1 D:F3S1001 2.3 80.8 1.0
S3 D:F3S1001 2.3 80.7 1.0
SG D:CYS209 2.5 86.6 1.0
FE3 D:F3S1001 2.7 79.7 1.0
FE4 D:F3S1001 2.8 80.3 1.0
CB D:CYS209 2.8 87.6 1.0
N D:CYS209 3.3 79.7 1.0
CA D:CYS209 3.7 79.7 1.0
S4 D:F3S1001 3.9 79.5 1.0
N D:GLU208 4.1 0.1 1.0
SG D:CYS183 4.1 0.1 1.0
CD1 D:ILE219 4.1 0.1 1.0
CB D:CYS183 4.2 0.3 1.0
N D:GLU207 4.2 0.1 1.0
CA D:GLU207 4.3 0.9 1.0
C D:GLU207 4.4 0.8 1.0
C D:GLU208 4.5 0.1 1.0
SG D:CYS206 4.7 98.8 1.0
CB D:CYS206 4.7 99.0 1.0
SG D:CYS203 4.7 72.3 1.0
CA D:GLU208 4.7 0.1 1.0
CA D:CYS183 4.8 99.6 1.0
C D:CYS209 4.8 80.0 1.0
CB D:GLU208 4.9 0.9 1.0
N D:LEU210 4.9 0.2 1.0

Iron binding site 2 out of 6 in 2pmz

Go back to Iron Binding Sites List in 2pmz
Iron binding site 2 out of 6 in the Archaeal Rna Polymerase From Sulfolobus Solfataricus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Archaeal Rna Polymerase From Sulfolobus Solfataricus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1001

b:79.7
occ:1.00
 FE3 D:F3S1001 0.0 79.7 1.0
S4 D:F3S1001 2.2 79.5 1.0
S1 D:F3S1001 2.2 80.8 1.0
S3 D:F3S1001 2.3 80.7 1.0
SG D:CYS203 2.4 72.3 1.0
FE1 D:F3S1001 2.7 80.5 1.0
FE4 D:F3S1001 2.7 80.3 1.0
CB D:CYS203 3.2 72.3 1.0
SG D:CYS183 3.7 0.1 1.0
S2 D:F3S1001 3.8 80.7 1.0
CD1 D:ILE219 3.9 0.1 1.0
CA D:CYS203 4.1 0.9 1.0
CG2 D:VAL187 4.2 1.0 1.0
SG D:CYS209 4.4 86.6 1.0
CG1 D:VAL187 4.4 0.1 1.0
CB D:VAL187 4.4 0.9 1.0
N D:THR204 4.6 0.0 1.0
CB D:CYS183 4.8 0.3 1.0
C D:CYS203 4.9 0.6 1.0

Iron binding site 3 out of 6 in 2pmz

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Iron binding site 3 out of 6 in the Archaeal Rna Polymerase From Sulfolobus Solfataricus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Archaeal Rna Polymerase From Sulfolobus Solfataricus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1001

b:80.3
occ:1.00
 FE4 D:F3S1001 0.0 80.3 1.0
S3 D:F3S1001 2.1 80.7 1.0
S2 D:F3S1001 2.3 80.7 1.0
S4 D:F3S1001 2.3 79.5 1.0
FE3 D:F3S1001 2.7 79.7 1.0
FE1 D:F3S1001 2.8 80.5 1.0
CB D:CYS206 2.8 99.0 1.0
SG D:CYS206 3.2 98.8 1.0
SG D:CYS203 3.7 72.3 1.0
SG D:CYS183 3.9 0.1 1.0
S1 D:F3S1001 3.9 80.8 1.0
O D:THR204 3.9 1.0 1.0
N D:GLU207 4.0 0.1 1.0
CA D:CYS206 4.2 0.8 1.0
N D:THR204 4.5 0.0 1.0
O D:LEU205 4.5 0.7 1.0
C D:CYS206 4.7 0.8 1.0
CB D:CYS203 4.8 72.3 1.0
N D:CYS206 4.8 0.8 1.0
C D:THR204 4.8 0.3 1.0
CB D:CYS183 4.8 0.3 1.0
N D:GLU208 4.8 0.1 1.0
C D:LEU205 4.9 0.8 1.0
CA D:CYS203 4.9 0.9 1.0

Iron binding site 4 out of 6 in 2pmz

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Iron binding site 4 out of 6 in the Archaeal Rna Polymerase From Sulfolobus Solfataricus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Archaeal Rna Polymerase From Sulfolobus Solfataricus within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:1.0
occ:1.00
 FE1 S:F3S1001 0.0 1.0 1.0
S2 S:F3S1001 2.2 0.2 1.0
S1 S:F3S1001 2.3 0.9 1.0
S3 S:F3S1001 2.3 0.3 1.0
SG S:CYS209 2.4 68.8 1.0
FE3 S:F3S1001 2.7 0.6 1.0
CB S:CYS209 2.7 69.1 1.0
FE4 S:F3S1001 2.7 0.0 1.0
N S:CYS209 3.2 73.7 1.0
CA S:CYS209 3.6 73.8 1.0
S4 S:F3S1001 3.9 0.4 1.0
N S:GLU208 4.0 96.3 1.0
SG S:CYS183 4.1 0.7 1.0
CD1 S:ILE219 4.1 0.1 1.0
N S:GLU207 4.2 0.1 1.0
CB S:CYS183 4.2 0.7 1.0
CA S:GLU207 4.3 1.0 1.0
C S:GLU207 4.3 0.8 1.0
C S:GLU208 4.4 96.3 1.0
CA S:GLU208 4.7 96.2 1.0
SG S:CYS206 4.7 0.1 1.0
CB S:CYS206 4.7 0.2 1.0
C S:CYS209 4.8 74.1 1.0
SG S:CYS203 4.8 94.3 1.0
CA S:CYS183 4.8 0.5 1.0
CB S:GLU208 4.8 0.1 1.0
N S:LEU210 4.9 90.2 1.0

Iron binding site 5 out of 6 in 2pmz

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Iron binding site 5 out of 6 in the Archaeal Rna Polymerase From Sulfolobus Solfataricus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Archaeal Rna Polymerase From Sulfolobus Solfataricus within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:0.6
occ:1.00
 FE3 S:F3S1001 0.0 0.6 1.0
S4 S:F3S1001 2.2 0.4 1.0
S1 S:F3S1001 2.3 0.9 1.0
S3 S:F3S1001 2.3 0.3 1.0
SG S:CYS203 2.4 94.3 1.0
FE1 S:F3S1001 2.7 1.0 1.0
FE4 S:F3S1001 2.7 0.0 1.0
CB S:CYS203 3.3 94.2 1.0
SG S:CYS183 3.8 0.7 1.0
CD1 S:ILE219 3.8 0.1 1.0
S2 S:F3S1001 3.8 0.2 1.0
CA S:CYS203 4.2 0.6 1.0
SG S:CYS209 4.3 68.8 1.0
CG2 S:VAL187 4.3 0.6 1.0
CG1 S:VAL187 4.5 0.7 1.0
CB S:VAL187 4.5 0.6 1.0
N S:THR204 4.7 0.7 1.0
CB S:CYS183 4.8 0.7 1.0
CB S:CYS209 4.9 69.1 1.0
C S:CYS203 5.0 0.2 1.0

Iron binding site 6 out of 6 in 2pmz

Go back to Iron Binding Sites List in 2pmz
Iron binding site 6 out of 6 in the Archaeal Rna Polymerase From Sulfolobus Solfataricus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Archaeal Rna Polymerase From Sulfolobus Solfataricus within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:0.0
occ:1.00
 FE4 S:F3S1001 0.0 0.0 1.0
S3 S:F3S1001 2.1 0.3 1.0
S2 S:F3S1001 2.3 0.2 1.0
S4 S:F3S1001 2.3 0.4 1.0
FE3 S:F3S1001 2.7 0.6 1.0
FE1 S:F3S1001 2.7 1.0 1.0
CB S:CYS206 2.8 0.2 1.0
SG S:CYS206 3.2 0.1 1.0
SG S:CYS203 3.8 94.3 1.0
SG S:CYS183 3.9 0.7 1.0
S1 S:F3S1001 3.9 0.9 1.0
O S:THR204 4.0 0.8 1.0
N S:GLU207 4.0 0.1 1.0
CA S:CYS206 4.2 87.1 1.0
O S:LEU205 4.5 0.9 1.0
N S:THR204 4.6 0.7 1.0
C S:CYS206 4.6 87.0 1.0
N S:GLU208 4.7 96.3 1.0
N S:CYS206 4.8 87.2 1.0
CB S:CYS183 4.8 0.7 1.0
CB S:CYS203 4.8 94.2 1.0
C S:THR204 4.8 0.8 1.0
C S:LEU205 4.9 0.1 1.0
SG S:CYS209 4.9 68.8 1.0
CA S:GLU207 5.0 1.0 1.0
CA S:CYS203 5.0 0.6 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 01:27:05 2024

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