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Iron in PDB 2wb1: 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: 2wb1 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) 30.20 / 3.52
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 196.095, 211.871, 238.905, 90.00, 90.00, 90.00
R / Rfree (%) 33.3 / 38.4

Other elements in 2wb1:

The structure of The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase 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 Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase (pdb code 2wb1). 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 Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase, PDB code: 2wb1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 2wb1

Go back to Iron Binding Sites List in 2wb1
Iron binding site 1 out of 6 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:Fe1265

b:88.3
occ:1.00
FE1 D:F3S1265 0.0 88.3 1.0
S3 D:F3S1265 2.1 88.3 1.0
S2 D:F3S1265 2.2 88.3 1.0
SG D:CYS209 2.2 0.5 1.0
S1 D:F3S1265 2.2 88.3 1.0
FE4 D:F3S1265 2.5 88.3 1.0
FE3 D:F3S1265 2.5 88.3 1.0
S4 D:F3S1265 3.6 88.3 1.0
CB D:CYS209 3.6 0.4 1.0
CD1 D:ILE219 3.7 0.2 1.0
N D:CYS209 4.2 0.4 1.0
N D:GLU207 4.4 95.8 1.0
CE1 D:PHE188 4.5 0.3 1.0
SG D:CYS203 4.5 0.7 1.0
SG D:CYS206 4.5 96.9 1.0
CA D:CYS209 4.5 0.6 1.0
N D:GLU208 4.6 98.0 1.0
CA D:GLU207 4.6 96.6 1.0
CG1 D:ILE219 4.6 0.3 1.0
SG D:CYS183 4.9 0.3 1.0
C D:GLU207 4.9 97.5 1.0

Iron binding site 2 out of 6 in 2wb1

Go back to Iron Binding Sites List in 2wb1
Iron binding site 2 out of 6 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:Fe1265

b:88.3
occ:1.00
FE3 D:F3S1265 0.0 88.3 1.0
S3 D:F3S1265 2.1 88.3 1.0
S1 D:F3S1265 2.2 88.3 1.0
S4 D:F3S1265 2.2 88.3 1.0
SG D:CYS203 2.2 0.7 1.0
FE4 D:F3S1265 2.5 88.3 1.0
FE1 D:F3S1265 2.5 88.3 1.0
CB D:CYS203 3.2 0.1 1.0
S2 D:F3S1265 3.5 88.3 1.0
CA D:CYS203 3.7 0.0 1.0
N D:THR204 3.9 97.7 1.0
CG2 D:VAL187 4.3 0.8 1.0
C D:CYS203 4.3 99.0 1.0
O D:THR204 4.7 96.1 1.0
SG D:CYS209 4.7 0.5 1.0
CD1 D:ILE219 4.7 0.2 1.0
O D:LEU205 4.8 95.0 1.0
SG D:CYS183 4.9 0.3 1.0
CB D:VAL187 4.9 0.8 1.0
CB D:CYS206 4.9 95.3 1.0
OG1 D:THR204 4.9 95.4 1.0
C D:THR204 5.0 95.1 1.0
N D:CYS203 5.0 0.3 1.0
CA D:THR204 5.0 95.8 1.0

Iron binding site 3 out of 6 in 2wb1

Go back to Iron Binding Sites List in 2wb1
Iron binding site 3 out of 6 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:Fe1265

b:88.3
occ:1.00
FE4 D:F3S1265 0.0 88.3 1.0
S3 D:F3S1265 2.1 88.3 1.0
S4 D:F3S1265 2.2 88.3 1.0
S2 D:F3S1265 2.2 88.3 1.0
FE3 D:F3S1265 2.5 88.3 1.0
FE1 D:F3S1265 2.5 88.3 1.0
SG D:CYS206 2.7 96.9 1.0
CB D:CYS206 3.0 95.3 1.0
S1 D:F3S1265 3.5 88.3 1.0
CD D:PRO184 3.9 0.8 1.0
N D:GLU207 4.0 95.8 1.0
CA D:CYS206 4.3 93.7 1.0
OG1 D:THR204 4.3 95.4 1.0
O D:LEU205 4.4 95.0 1.0
SG D:CYS183 4.5 0.3 1.0
SG D:CYS209 4.5 0.5 1.0
SG D:CYS203 4.5 0.7 1.0
C D:CYS206 4.5 94.2 1.0
CG D:PRO184 4.6 98.9 1.0
N D:GLU208 4.6 98.0 1.0
N D:THR204 4.8 97.7 1.0
CA D:GLU207 4.9 96.6 1.0
C D:LEU205 4.9 93.7 1.0
N D:CYS206 4.9 92.9 1.0

Iron binding site 4 out of 6 in 2wb1

Go back to Iron Binding Sites List in 2wb1
Iron binding site 4 out of 6 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 4 of The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1265

b:86.5
occ:1.00
FE1 S:F3S1265 0.0 86.5 1.0
S3 S:F3S1265 2.1 86.5 1.0
SG S:CYS209 2.2 99.8 1.0
S2 S:F3S1265 2.2 86.5 1.0
S1 S:F3S1265 2.2 86.5 1.0
FE4 S:F3S1265 2.5 86.5 1.0
FE3 S:F3S1265 2.5 86.5 1.0
CB S:CYS209 3.6 0.7 1.0
S4 S:F3S1265 3.6 86.5 1.0
CD1 S:ILE219 3.8 97.8 1.0
N S:CYS209 4.1 98.5 1.0
N S:GLU207 4.4 92.2 1.0
SG S:CYS206 4.5 93.1 1.0
CA S:CYS209 4.5 0.8 1.0
N S:GLU208 4.5 94.2 1.0
CE1 S:PHE188 4.5 0.9 1.0
CA S:GLU207 4.6 93.0 1.0
SG S:CYS203 4.6 97.6 1.0
CG1 S:ILE219 4.7 99.1 1.0
C S:GLU207 4.9 93.8 1.0
SG S:CYS183 4.9 0.7 1.0
CB S:CYS206 5.0 91.6 1.0

Iron binding site 5 out of 6 in 2wb1

Go back to Iron Binding Sites List in 2wb1
Iron binding site 5 out of 6 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 5 of The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1265

b:86.5
occ:1.00
FE3 S:F3S1265 0.0 86.5 1.0
S3 S:F3S1265 2.1 86.5 1.0
S1 S:F3S1265 2.2 86.5 1.0
S4 S:F3S1265 2.2 86.5 1.0
SG S:CYS203 2.3 97.6 1.0
FE4 S:F3S1265 2.5 86.5 1.0
FE1 S:F3S1265 2.5 86.5 1.0
CB S:CYS203 3.3 99.0 1.0
S2 S:F3S1265 3.6 86.5 1.0
CA S:CYS203 3.7 97.9 1.0
N S:THR204 3.9 94.5 1.0
CG2 S:VAL187 4.2 0.6 1.0
C S:CYS203 4.3 95.9 1.0
SG S:CYS209 4.6 99.8 1.0
CD1 S:ILE219 4.7 97.8 1.0
SG S:CYS183 4.8 0.7 1.0
CB S:VAL187 4.8 0.6 1.0
O S:THR204 4.8 92.8 1.0
O S:LEU205 4.9 91.5 1.0
OG1 S:THR204 4.9 92.0 1.0
N S:CYS203 5.0 99.2 1.0
CB S:CYS206 5.0 91.6 1.0

Iron binding site 6 out of 6 in 2wb1

Go back to Iron Binding Sites List in 2wb1
Iron binding site 6 out of 6 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 6 of The Complete Structure of the Archaeal 13-Subunit Dna- Directed Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1265

b:86.5
occ:1.00
FE4 S:F3S1265 0.0 86.5 1.0
S3 S:F3S1265 2.1 86.5 1.0
S2 S:F3S1265 2.2 86.5 1.0
S4 S:F3S1265 2.2 86.5 1.0
FE1 S:F3S1265 2.5 86.5 1.0
FE3 S:F3S1265 2.5 86.5 1.0
SG S:CYS206 2.7 93.1 1.0
CB S:CYS206 2.8 91.6 1.0
S1 S:F3S1265 3.5 86.5 1.0
N S:GLU207 3.7 92.2 1.0
CA S:CYS206 4.0 90.0 1.0
O S:LEU205 4.2 91.5 1.0
OG1 S:THR204 4.2 92.0 1.0
CD S:PRO184 4.2 97.0 1.0
C S:CYS206 4.3 90.6 1.0
SG S:CYS203 4.5 97.6 1.0
SG S:CYS209 4.5 99.8 1.0
N S:GLU208 4.5 94.2 1.0
C S:LEU205 4.6 90.2 1.0
N S:CYS206 4.6 89.4 1.0
N S:THR204 4.7 94.5 1.0
CA S:GLU207 4.7 93.0 1.0
CG S:PRO184 4.8 95.0 1.0
SG S:CYS183 4.8 0.7 1.0

Reference:

Y.Korkhin, U.M.Unligil, O.Littlefield, P.J.Nelson, D.I.Stuart, P.B.Sigler, S.D.Bell, N.G.A.Abrescia. Evolution of Complex Rna Polymerase: the Complete Archaeal Rna Polymerase Structure Plos Biol. V. 7 E102 2009.
ISSN: ISSN 1544-9173
PubMed: 19419240
DOI: 10.1371/JOURNAL.PBIO.1000102
Page generated: Sun Dec 13 14:55:23 2020

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