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Iron in PDB 2waq: The Complete Structure of the Archaeal 13-Subunit Dna-Directed Rna Polymerase

Protein crystallography data

The structure of The Complete Structure of the Archaeal 13-Subunit Dna-Directed Rna Polymerase, PDB code: 2waq was solved by Y.Korkhin, U.M.Unligil, O.Littlefield, P.J.Nelson, D.I.Stuart, P.B.Sigler, 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) 42.78 / 3.35
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 193.501, 212.620, 128.998, 90.00, 90.00, 90.00
R / Rfree (%) 27.1 / 34.1

Other elements in 2waq:

The structure of The Complete Structure of the Archaeal 13-Subunit Dna-Directed Rna Polymerase also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 9 atoms

Iron Binding Sites:

The binding sites of Iron atom in the The Complete Structure of the Archaeal 13-Subunit Dna-Directed Rna Polymerase (pdb code 2waq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the The Complete Structure of the Archaeal 13-Subunit Dna-Directed Rna Polymerase, PDB code: 2waq:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 2waq

Go back to Iron Binding Sites List in 2waq
Iron binding site 1 out of 3 in the The Complete Structure of the Archaeal 13-Subunit Dna-Directed Rna Polymerase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Complete Structure of the Archaeal 13-Subunit Dna-Directed Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1001

b:68.0
occ:1.00
FE1 D:F3S1001 0.0 68.0 1.0
S3 D:F3S1001 2.1 68.0 1.0
S2 D:F3S1001 2.2 68.0 1.0
SG D:CYS209 2.2 92.7 1.0
S1 D:F3S1001 2.2 68.0 1.0
FE4 D:F3S1001 2.5 68.0 1.0
FE3 D:F3S1001 2.5 68.0 1.0
CB D:CYS209 3.4 93.0 1.0
S4 D:F3S1001 3.6 68.0 1.0
CD1 D:ILE219 4.0 89.2 1.0
N D:CYS209 4.2 91.4 1.0
CE1 D:PHE188 4.4 99.5 1.0
CA D:CYS209 4.5 92.3 1.0
SG D:CYS206 4.5 77.2 1.0
SG D:CYS203 4.5 81.5 1.0
N D:GLU207 4.6 81.9 1.0
CG1 D:ILE219 4.8 90.0 1.0
CA D:GLU207 4.8 82.0 1.0
CD1 D:PHE188 4.9 99.8 1.0
CB D:CYS206 4.9 77.0 1.0
SG D:CYS183 4.9 88.3 1.0
N D:GLU208 5.0 86.2 1.0

Iron binding site 2 out of 3 in 2waq

Go back to Iron Binding Sites List in 2waq
Iron binding site 2 out of 3 in the The Complete Structure of the Archaeal 13-Subunit Dna-Directed Rna Polymerase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Complete Structure of the Archaeal 13-Subunit Dna-Directed Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1001

b:68.0
occ:1.00
FE3 D:F3S1001 0.0 68.0 1.0
S3 D:F3S1001 2.1 68.0 1.0
S4 D:F3S1001 2.2 68.0 1.0
S1 D:F3S1001 2.2 68.0 1.0
SG D:CYS203 2.3 81.5 1.0
FE4 D:F3S1001 2.5 68.0 1.0
FE1 D:F3S1001 2.5 68.0 1.0
CB D:CYS203 3.3 82.3 1.0
S2 D:F3S1001 3.5 68.0 1.0
CA D:CYS203 3.8 81.9 1.0
N D:THR204 4.1 77.2 1.0
CG2 D:VAL187 4.4 90.7 1.0
C D:CYS203 4.5 81.0 1.0
SG D:CYS209 4.6 92.7 1.0
CB D:VAL187 4.7 91.4 1.0
CB D:CYS206 4.8 77.0 1.0
SG D:CYS183 4.9 88.3 1.0
CG2 D:VAL170 4.9 97.2 1.0
CD1 D:ILE219 4.9 89.2 1.0
N D:CYS203 5.0 82.7 1.0
O D:LEU205 5.0 75.4 1.0
CG1 D:VAL187 5.0 92.0 1.0

Iron binding site 3 out of 3 in 2waq

Go back to Iron Binding Sites List in 2waq
Iron binding site 3 out of 3 in the The Complete Structure of the Archaeal 13-Subunit Dna-Directed Rna Polymerase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Complete Structure of the Archaeal 13-Subunit Dna-Directed Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1001

b:68.0
occ:1.00
FE4 D:F3S1001 0.0 68.0 1.0
S3 D:F3S1001 2.1 68.0 1.0
S2 D:F3S1001 2.2 68.0 1.0
S4 D:F3S1001 2.2 68.0 1.0
FE1 D:F3S1001 2.5 68.0 1.0
FE3 D:F3S1001 2.5 68.0 1.0
SG D:CYS206 2.6 77.2 1.0
CB D:CYS206 2.8 77.0 1.0
S1 D:F3S1001 3.5 68.0 1.0
N D:GLU207 4.0 81.9 1.0
CA D:CYS206 4.2 76.2 1.0
CD D:PRO184 4.3 83.1 1.0
O D:LEU205 4.4 75.4 1.0
SG D:CYS209 4.4 92.7 1.0
SG D:CYS203 4.5 81.5 1.0
C D:CYS206 4.5 76.1 1.0
SG D:CYS183 4.6 88.3 1.0
N D:GLU208 4.8 86.2 1.0
N D:CYS206 4.8 76.1 1.0
OG1 D:THR204 4.8 75.5 1.0
C D:LEU205 4.9 74.9 1.0
CA D:GLU207 4.9 82.0 1.0
N D:THR204 5.0 77.2 1.0

Reference:

Y.Korkhin, U.M.Unligil, O.Littlefield, P.J.Nelson, D.I.Stuart, P.B.Sigler, S.D.Bell, N.G.Abrescia. Evolution of Complex Rna Polymerases: the Complete Archaeal Rna Polymerase Structure. Plos Biol. V. 7 00102 2009.
ISSN: ESSN 1545-7885
PubMed: 19419240
DOI: 10.1371/JOURNAL.PBIO.1000102
Page generated: Sun Dec 13 14:55:17 2020

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