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Iron in PDB 4ayb: Rnap at 3.2ANG

Enzymatic activity of Rnap at 3.2ANG

All present enzymatic activity of Rnap at 3.2ANG:
2.7.7.6;

Protein crystallography data

The structure of Rnap at 3.2ANG, PDB code: 4ayb was solved by M.N.Wojtas, M.Mogni, O.Millet, 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) 40.10 / 3.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 195.725, 212.415, 128.757, 90.00, 90.00, 90.00
R / Rfree (%) 24.3 / 30.1

Other elements in 4ayb:

The structure of Rnap at 3.2ANG also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 10 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Rnap at 3.2ANG (pdb code 4ayb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Rnap at 3.2ANG, PDB code: 4ayb:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 4ayb

Go back to Iron Binding Sites List in 4ayb
Iron binding site 1 out of 3 in the Rnap at 3.2ANG


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Rnap at 3.2ANG within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1264

b:81.4
occ:1.00
FE1 D:SF41264 0.0 81.4 1.0
SG D:CYS209 2.3 69.3 1.0
S3 D:SF41264 2.3 81.4 1.0
S4 D:SF41264 2.3 81.4 1.0
S2 D:SF41264 2.3 81.4 1.0
FE3 D:SF41264 2.7 81.4 1.0
FE2 D:SF41264 2.7 81.4 1.0
H D:CYS209 3.1 81.4 1.0
HB3 D:CYS209 3.2 81.4 1.0
CB D:CYS209 3.4 71.5 1.0
HE2 D:PHE188 3.6 81.4 1.0
SG D:CYS183 3.8 77.8 1.0
S1 D:SF41264 3.9 81.4 1.0
HB2 D:CYS183 3.9 81.4 1.0
N D:CYS209 3.9 80.9 1.0
HG D:CYS183 3.9 81.4 1.0
SG D:CYS206 3.9 0.6 1.0
H D:GLU207 4.0 81.4 1.0
HG12 D:ILE219 4.0 81.4 1.0
H D:GLU208 4.0 81.4 1.0
HB2 D:CYS209 4.1 81.4 1.0
HB3 D:CYS206 4.1 81.4 1.0
CA D:CYS209 4.3 83.5 1.0
CE2 D:PHE188 4.3 87.4 1.0
HD12 D:ILE219 4.3 81.4 1.0
CB D:CYS183 4.4 79.7 1.0
HB2 D:GLU208 4.4 81.4 1.0
HA D:CYS183 4.4 81.4 1.0
HA D:GLU207 4.4 81.4 1.0
N D:GLU208 4.5 96.1 1.0
HZ D:PHE188 4.6 81.4 1.0
N D:GLU207 4.6 88.1 1.0
SG D:CYS203 4.6 62.5 1.0
CB D:CYS206 4.7 99.8 1.0
HD2 D:PRO184 4.7 81.4 1.0
CG1 D:ILE219 4.7 74.6 1.0
HG13 D:ILE219 4.8 81.4 1.0
CZ D:PHE188 4.8 88.0 1.0
H D:LEU210 4.8 81.4 1.0
HA D:CYS209 4.9 81.4 1.0
CA D:GLU207 4.9 89.0 1.0
CA D:CYS183 5.0 66.8 1.0
CD1 D:ILE219 5.0 76.3 1.0
HB D:VAL187 5.0 81.4 1.0

Iron binding site 2 out of 3 in 4ayb

Go back to Iron Binding Sites List in 4ayb
Iron binding site 2 out of 3 in the Rnap at 3.2ANG


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Rnap at 3.2ANG within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1264

b:81.4
occ:1.00
FE2 D:SF41264 0.0 81.4 1.0
S4 D:SF41264 2.3 81.4 1.0
S3 D:SF41264 2.3 81.4 1.0
S1 D:SF41264 2.3 81.4 1.0
SG D:CYS203 2.3 62.5 1.0
HG22 D:VAL187 2.7 81.4 1.0
FE3 D:SF41264 2.7 81.4 1.0
FE1 D:SF41264 2.7 81.4 1.0
HB2 D:CYS203 3.1 81.4 1.0
CB D:CYS203 3.3 63.7 1.0
HG D:CYS183 3.4 81.4 1.0
HA D:CYS203 3.4 81.4 1.0
CG2 D:VAL187 3.5 72.1 1.0
HB D:VAL187 3.7 81.4 1.0
HG21 D:VAL187 3.7 81.4 1.0
HG12 D:VAL187 3.8 81.4 1.0
SG D:CYS183 3.8 77.8 1.0
S2 D:SF41264 3.9 81.4 1.0
H D:THR204 3.9 81.4 1.0
CA D:CYS203 3.9 72.9 1.0
CB D:VAL187 4.1 74.8 1.0
HB3 D:CYS203 4.1 81.4 1.0
HG22 D:VAL170 4.2 81.4 1.0
HG23 D:VAL187 4.2 81.4 1.0
HG12 D:ILE219 4.3 81.4 1.0
HB3 D:CYS206 4.3 81.4 1.0
HG23 D:VAL170 4.3 81.4 1.0
HG13 D:ILE219 4.4 81.4 1.0
CG1 D:VAL187 4.4 76.1 1.0
SG D:CYS209 4.5 69.3 1.0
N D:THR204 4.6 80.4 1.0
CG2 D:VAL170 4.7 0.1 1.0
HE2 D:PHE188 4.8 81.4 1.0
CG1 D:ILE219 4.8 74.6 1.0
C D:CYS203 4.8 70.5 1.0
HB2 D:GLU185 4.9 81.4 1.0
H D:GLU207 5.0 81.4 1.0
SG D:CYS206 5.0 0.6 1.0
CB D:CYS206 5.0 99.8 1.0
N D:CYS203 5.0 74.3 1.0
HZ D:PHE188 5.0 81.4 1.0

Iron binding site 3 out of 3 in 4ayb

Go back to Iron Binding Sites List in 4ayb
Iron binding site 3 out of 3 in the Rnap at 3.2ANG


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Rnap at 3.2ANG within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1264

b:81.4
occ:1.00
FE3 D:SF41264 0.0 81.4 1.0
HB3 D:CYS206 2.1 81.4 1.0
S4 D:SF41264 2.3 81.4 1.0
S1 D:SF41264 2.3 81.4 1.0
S2 D:SF41264 2.3 81.4 1.0
SG D:CYS206 2.3 0.6 1.0
CB D:CYS206 2.5 99.8 1.0
FE2 D:SF41264 2.7 81.4 1.0
FE1 D:SF41264 2.7 81.4 1.0
HB2 D:CYS206 2.7 81.4 1.0
H D:GLU207 3.3 81.4 1.0
HD2 D:PRO184 3.7 81.4 1.0
H D:THR204 3.7 81.4 1.0
S3 D:SF41264 3.9 81.4 1.0
SG D:CYS183 3.9 77.8 1.0
SG D:CYS203 3.9 62.5 1.0
CA D:CYS206 4.0 90.6 1.0
N D:GLU207 4.0 88.1 1.0
H D:GLU208 4.1 81.4 1.0
HA D:CYS203 4.2 81.4 1.0
HG D:CYS183 4.3 81.4 1.0
O D:LEU205 4.4 97.0 1.0
C D:CYS206 4.5 91.2 1.0
HG2 D:GLU185 4.5 81.4 1.0
N D:THR204 4.5 80.4 1.0
HA D:CYS206 4.5 81.4 1.0
CD D:PRO184 4.6 69.8 1.0
OG1 D:THR204 4.6 77.8 1.0
HA D:CYS183 4.6 81.4 1.0
HB2 D:GLU208 4.6 81.4 1.0
HG22 D:VAL187 4.7 81.4 1.0
HG2 D:PRO184 4.7 81.4 1.0
O D:THR204 4.7 78.9 1.0
N D:CYS206 4.7 89.5 1.0
SG D:CYS209 4.7 69.3 1.0
H D:CYS209 4.8 81.4 1.0
C D:LEU205 4.8 95.4 1.0
HG3 D:GLU185 4.8 81.4 1.0
HD3 D:PRO184 4.9 81.4 1.0
N D:GLU208 4.9 96.1 1.0
HB2 D:GLU185 4.9 81.4 1.0
HA D:GLU207 5.0 81.4 1.0

Reference:

M.N.Wojtas, M.Mogni, O.Millet, S.D.Bell, N.G.A.Abrescia. Structural and Functional Analyses of the Interaction of Archaeal Rna Polymerase with Dna. Nucleic Acids Res. V. 40 9941 2012.
ISSN: ISSN 0305-1048
PubMed: 22848102
DOI: 10.1093/NAR/GKS692
Page generated: Sun Aug 4 23:48:36 2024

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