Iron in the structure of Rnap At 3.2ANG (pdb 4ayb)
The binding sites of Iron atom in the structure of Rnap At 3.2ANG (pdb code 4ayb). This binding sites where shown with 5.0 Angstroms radius around Iron atom.
The 4ayb structure was solved by M.N.WOJTAS, M.MOGNI, O.MILLET, S.D.BELL, N.G.A.ABRESCIA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
| Resolution (A) | 40.1-3.2 | | Space group | P21212 | | a (A) | 195.725 | | b (A) | 212.415 | | c (A) | 128.757 | | alpha (°) | 90.00 | | beta (°) | 90.00 | | gamma (°) | 90.00 | | Rfactor (%) | 24.25 | | Rfree (%) | 30.05 |
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Iron Binding Sites:Iron binding site 1 out of 3 in 4ayb
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 4ayb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: D: Cys183, D: Pro184, D: Val187, D: Phe188, D: Cys203, D: Cys206, D: Glu207, D: Glu208, D: Cys209, D: Leu210, D: Ile219, D: F3s1264, | conact list:
| Atom | Atom | Distance (A) | | Fe | HB2 D:Cys183 | 3.89 | | Fe | HG D:Cys183 | 3.94 | | Fe | CB D:Cys183 | 4.38 | | Fe | HA D:Cys183 | 4.41 | | Fe | SG D:Cys183 | 3.85 | | Fe | CA D:Cys183 | 4.96 | | Fe | HD2 D:Pro184 | 4.72 | | Fe | HB D:Val187 | 4.97 | | Fe | HE1 D:Phe188 | 3.60 | | Fe | CE2 D:Phe188 | 4.31 | | Fe | CZ D:Phe188 | 4.84 | | Fe | HZ D:Phe188 | 4.59 | | Fe | SG D:Cys203 | 4.63 | | Fe | CB D:Cys206 | 4.66 | | Fe | HB3 D:Cys206 | 4.13 | | Fe | SG D:Cys206 | 3.94 | | Fe | N D:Glu207 | 4.61 | | Fe | CA D:Glu207 | 4.91 | | Fe | HA D:Glu207 | 4.43 | | Fe | H D:Glu207 | 3.98 | | Fe | HB2 D:Glu208 | 4.38 | | Fe | N D:Glu208 | 4.52 | | Fe | H D:Glu208 | 4.04 | | Fe | HB2 D:Cys209 | 4.10 | | Fe | N D:Cys209 | 3.89 | | Fe | CB D:Cys209 | 3.38 | | Fe | HB3 D:Cys209 | 3.21 | | Fe | HA D:Cys209 | 4.88 | | Fe | SG D:Cys209 | 2.26 | | Fe | H D:Cys209 | 3.09 | | Fe | CA D:Cys209 | 4.27 | | Fe | H D:Leu210 | 4.85 | | Fe | HG13 D:Ile219 | 4.75 | | Fe | HG12 D:Ile219 | 4.01 | | Fe | CD1 D:Ile219 | 4.96 | | Fe | CG1 D:Ile219 | 4.73 | | Fe | HD12 D:Ile219 | 4.33 | | Fe | S1 D:F3s1264 | 2.29 | | Fe | FE1 D:F3s1264 | 0.00 | | Fe | FE3 D:F3s1264 | 2.70 | | Fe | S4 D:F3s1264 | 3.89 | | Fe | S2 D:F3s1264 | 2.28 | | Fe | FE4 D:F3s1264 | 2.70 | | Fe | S3 D:F3s1264 | 2.28 |
| interactive model:
| Iron binding site 2 out of 3 in 4ayb
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 4ayb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: D: Cys183, D: Pro184, D: Glu185, D: Val187, D: Cys203, D: Thr204, D: Leu205, D: Cys206, D: Glu207, D: Glu208, D: Cys209, D: F3s1264, | conact list:
| Atom | Atom | Distance (A) | | Fe | HG D:Cys183 | 4.29 | | Fe | HA D:Cys183 | 4.62 | | Fe | SG D:Cys183 | 3.88 | | Fe | CD D:Pro184 | 4.55 | | Fe | HD2 D:Pro184 | 3.65 | | Fe | HG2 D:Pro184 | 4.69 | | Fe | HD3 D:Pro184 | 4.85 | | Fe | HB2 D:Glu185 | 4.91 | | Fe | HG3 D:Glu185 | 4.84 | | Fe | HG2 D:Glu185 | 4.48 | | Fe | HG22 D:Val187 | 4.68 | | Fe | HA D:Cys203 | 4.23 | | Fe | SG D:Cys203 | 3.89 | | Fe | N D:Thr204 | 4.52 | | Fe | O D:Thr204 | 4.71 | | Fe | H D:Thr204 | 3.66 | | Fe | OG1 D:Thr204 | 4.58 | | Fe | C D:Leu205 | 4.81 | | Fe | O D:Leu205 | 4.40 | | Fe | HB2 D:Cys206 | 2.73 | | Fe | N D:Cys206 | 4.71 | | Fe | CB D:Cys206 | 2.52 | | Fe | HB3 D:Cys206 | 2.14 | | Fe | HA D:Cys206 | 4.53 | | Fe | SG D:Cys206 | 2.34 | | Fe | C D:Cys206 | 4.48 | | Fe | CA D:Cys206 | 3.99 | | Fe | N D:Glu207 | 4.02 | | Fe | HA D:Glu207 | 4.97 | | Fe | H D:Glu207 | 3.34 | | Fe | HB2 D:Glu208 | 4.62 | | Fe | N D:Glu208 | 4.90 | | Fe | H D:Glu208 | 4.11 | | Fe | SG D:Cys209 | 4.74 | | Fe | H D:Cys209 | 4.77 | | Fe | S1 D:F3s1264 | 2.28 | | Fe | FE1 D:F3s1264 | 2.70 | | Fe | FE3 D:F3s1264 | 0.00 | | Fe | S4 D:F3s1264 | 2.28 | | Fe | S2 D:F3s1264 | 3.87 | | Fe | FE4 D:F3s1264 | 2.70 | | Fe | S3 D:F3s1264 | 2.28 |
| interactive model:
| Iron binding site 3 out of 3 in 4ayb
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 4ayb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: D: Val170, D: Cys183, D: Glu185, D: Val187, D: Phe188, D: Cys203, D: Thr204, D: Cys206, D: Glu207, D: Cys209, D: Ile219, D: F3s1264, | conact list:
| Atom | Atom | Distance (A) | | Fe | CG2 D:Val170 | 4.71 | | Fe | HG22 D:Val170 | 4.16 | | Fe | HG23 D:Val170 | 4.34 | | Fe | HG D:Cys183 | 3.39 | | Fe | SG D:Cys183 | 3.81 | | Fe | HB2 D:Glu185 | 4.87 | | Fe | HB D:Val187 | 3.69 | | Fe | CB D:Val187 | 4.06 | | Fe | HG12 D:Val187 | 3.75 | | Fe | CG2 D:Val187 | 3.52 | | Fe | CG1 D:Val187 | 4.41 | | Fe | HG21 D:Val187 | 3.70 | | Fe | HG22 D:Val187 | 2.68 | | Fe | HG23 D:Val187 | 4.24 | | Fe | HE1 D:Phe188 | 4.80 | | Fe | HZ D:Phe188 | 5.00 | | Fe | HB2 D:Cys203 | 3.15 | | Fe | N D:Cys203 | 5.00 | | Fe | CB D:Cys203 | 3.29 | | Fe | HB3 D:Cys203 | 4.12 | | Fe | HA D:Cys203 | 3.43 | | Fe | SG D:Cys203 | 2.30 | | Fe | C D:Cys203 | 4.82 | | Fe | CA D:Cys203 | 3.93 | | Fe | N D:Thr204 | 4.59 | | Fe | H D:Thr204 | 3.93 | | Fe | CB D:Cys206 | 4.99 | | Fe | HB3 D:Cys206 | 4.29 | | Fe | SG D:Cys206 | 4.99 | | Fe | H D:Glu207 | 4.98 | | Fe | SG D:Cys209 | 4.50 | | Fe | HG13 D:Ile219 | 4.40 | | Fe | HG12 D:Ile219 | 4.28 | | Fe | CG1 D:Ile219 | 4.82 | | Fe | S1 D:F3s1264 | 3.91 | | Fe | FE1 D:F3s1264 | 2.70 | | Fe | FE3 D:F3s1264 | 2.70 | | Fe | S4 D:F3s1264 | 2.28 | | Fe | S2 D:F3s1264 | 2.28 | | Fe | FE4 D:F3s1264 | 0.00 | | Fe | S3 D:F3s1264 | 2.28 |
| interactive model:
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