Research Article
Modeling Cu(II) Binding to Peptides Using the Extensible Systematic Force Field
(a) Ligand-copper distances (in Å) for different geometries of the copper ion. |
| Distances for: | C ion | C ion | Cu024 | Cu025 | Cu026 |
| Cu–His16 (N2) | 3.51 | 2.36 | 2.39 | 2.91 | 2.90 | Cu–Wtr366 (O1) | 2.44 | 3.75 | 2.13 | 2.7 | 2.63 | Cu–Gln13 (O1) | 2.54 | 3.74 | 2.19 | 2.71 | 2.68 | Cu–His9 (N2) | 2.85 | 2.34 | 2.41 | 2.94 | 3.08 | Cu–His23 (N1) | 3.86 | 4.69 | 2.45 | 3.05 | 2.94 | Cu–Ser22 (O) | 2.49 | 2.17 | 2.20 | 2.69 | 2.72 | His16 (N2)–Wtr366 (O) | 4.89 | 3.93 | 3.16 | 5.6 | 4.88 | His9 (N2)–His16 (N2) | 6.11 | 4.46 | 4.67 | 5.73 | 5.85 | Gln13 (O1)–Ser22 (O1) | 4.83 | 5.09 | 4.27 | 5.20 | 5.32 | His9 (N1)–Gln 13 (O1) | 4.44 | 4.89 | 3.97 | 4.53 | 4.44 | His23 (N1)–Ser22 (O1) | 3.07 | 7.04 | 3.13 | 2.96 | 3.14 | Ser22 (O1)–Wtr366 (O) | 4.36 | 4.45 | 3.06 | 4.27 | 4.18 | His23 (N1)–Wtr366 (O1) | 6.08 | 7.86 | 4.44 | 5.58 | 5.54 | His23 (N1)–Gln13 (O1) | 5.69 | 6.37 | 3.10 | 4.41 | 4.34 | His16 (N2)–Ser22 (O) | 4.16 | 2.94 | 3.07 | 3.36 | 3.8 | His9 (N1)–Wtr366 (O) | 3.98 | 5.32 | 3.14 | 4.15 | 3.61 | His9 (N1)–Ser22 (O) | 3.93 | 3.70 | 3.19 | 4.45 | 4.39 | His9 (N2)–His23 (N1) | 3.26 | 4.11 | 4.29 | 4.81 | 4.83 | His23 (N1)–His16 (N2) | 5.72 | 4.92 | 2.30 | 2.53 | 2.62 | Gln13 (O1)–Wtr366 (O) | 3.09 | 7.26 | 3.01 | 3.50 | 3.68 | His16 (N2)–Gln13 (O1) | 3.17 | 5.13 | 2.73 | 3.33 | 3.41 |
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(b) Ligand-copper angles for different geometries of the copper ion1. |
| Angles (in for: | C ion | C ion | Cu024 | Cu025 | Cu026 |
| N16–Cu–O366 | 109.29 | 76.32 | 84.36 | 108.41 | 124.13 | N16–Cu–N9 | 147.48 | 143.12 | 154.01 | 156.76 | 156.46 | N9–Cu–O13 | 65.25 | 111.3 | 118.96 | 106.37 | 100.33 | O13–Cu–O366 | 76.52 | 41.17 | 88.33 | 80.71 | 87.64 | N23–Cu–N9 | 55.67 | 63.04 | 95.74 | 107.51 | 106.28 | N23–Cu–N16 | 101.63 | 83.38 | 71.96 | 50.44 | 53.45 | N23–Cu–O13 | 51.21 | 99.28 | 54.11 | 100.31 | 66.69 | N23–Cu–O366 | 148.79 | 140.31 | 148.08 | 156.41 | 169.19 | O22–Cu–O366 | 124.45 | 122.43 | 90.12 | 105.02 | 102.62 | O22–Cu–N16 | 85.89 | 80.87 | 84.36 | 90.97 | 85.04 | O22–Cu–O13 | 97.62 | 136.03 | 153.41 | 148.27 | 160.31 | O22–Cu–N9 | 94.59 | 111.10 | 87.45 | 104.26 | 98.24 | N23–Cu–O22 | 52.65 | 86.66 | 131.33 | 62.16 | 67.21 | N9–Cu–O366 | 97.21 | 119.77 | 87.35 | 94.59 | 78.11 | N16–Cu–O13 | 82.45 | 74.71 | 74.16 | 73.57 | 75.31 |
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1Refer to Table 3(a) for the exact ligand atoms for column 1.
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