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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:

Magnesium (Mg) 2 atoms
Zinc (Zn) 10 atoms

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

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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

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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

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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

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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

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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

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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: Tue Aug 5 01:59:49 2025

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