Table 1.
Interactions between Smon0123 and unsaturated GAG disaccharides
| van der Waals (C-C distance <4.5 Å) | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Smon0123 (N-18/C-5)/C∆0S | Smon0123 (N-18/C-5)/C∆4S | Smon0123 (N-18/C-5)/C∆6S | ||||||||||||
| Sugar | Atom | Protein/Water | Atom | Distance | Sugar | Atom | Protein/Water | Atom | Distance | Sugar | Atom | Protein/Water | Atom | Distance |
| ΔGlcUA | C1 | Trp284 | CE2 | 4.31 | ΔGlcUA | C1 | Trp284 | CD2 | 4.22 | ΔGlcUA | C1 | Trp284 | CD2 | 4.06 |
| C1 | Trp284 | CE3 | 3.93 | C1 | Trp284 | CE3 | 4.00 | C1 | Trp284 | CE3 | 3.91 | |||
| C1 | Trp284 | CZ2 | 4.31 | C1 | Trp284 | CE2 | 4.39 | C1 | Trp284 | CE2 | 4.29 | |||
| C1 | Trp284 | CZ3 | 3.89 | C1 | Trp284 | CZ3 | 3.94 | C1 | Trp284 | CZ3 | 3.90 | |||
| C1 | Trp284 | CH2 | 4.10 | C1 | Trp284 | CH2 | 4.12 | C1 | Trp284 | CH2 | 4.13 | |||
| C1 | Trp284 | CD2 | 4.13 | C1 | Trp284 | CZ2 | 4.36 | C1 | Trp284 | CZ2 | 4.33 | |||
| C3 | Trp284 | CE3 | 4.27 | C3 | Trp284 | CE3 | 4.20 | C1 | Leu389 | CD2 | 4.21 | |||
| C3 | Trp284 | CZ3 | 4.14 | C3 | Trp284 | CZ3 | 4.05 | C2 | Leu389 | CD2 | 4.09 | |||
| C3 | Arg322 | CZ | 4.37 | C3 | Arg322 | CZ | 4.38 | C3 | Trp284 | CZ3 | 4.14 | |||
| C3 | Glu410 | CD2 | 4.05 | C3 | Glu410 | CD | 4.09 | C3 | Trp284 | CE3 | 4.30 | |||
| C4 | Trp284 | CE3 | 3.81 | C4 | Trp284 | CE3 | 3.86 | C3 | Glu410 | CD | 4.05 | |||
| C4 | Trp284 | CZ3 | 4.17 | C4 | Trp284 | CZ3 | 4.18 | C4 | Trp284 | CE3 | 3.78 | |||
| C4 | Leu389 | CD2 | 4.34 | C4 | Leu389 | CD2 | 4.28 | C4 | Trp284 | CZ3 | 4.14 | |||
| C4 | Glu410 | CD | 3.91 | C4 | Glu410 | CD | 3.88 | C4 | Leu389 | CD2 | 4.13 | |||
| C5 | Trp284 | CE3 | 3.58 | C5 | Trp284 | CB | 4.24 | C4 | Glu410 | CD | 3.90 | |||
| C5 | Trp284 | CZ3 | 4.22 | C5 | Trp284 | CG | 4.25 | C5 | Trp284 | CB | 4.09 | |||
| C5 | Trp284 | CB | 4.14 | C5 | Trp284 | CD2 | 3.93 | C5 | Trp284 | CG | 4.16 | |||
| C5 | Trp284 | CG | 4.19 | C5 | Trp284 | CE3 | 3.58 | C5 | Trp284 | CD2 | 3.91 | |||
| C5 | Trp284 | CD2 | 3.91 | C5 | Trp284 | CZ3 | 4.19 | C5 | Trp284 | CE3 | 3.60 | |||
| C5 | Leu389 | CD2 | 3.70 | C5 | Leu389 | CD2 | 3.71 | C5 | Trp284 | CZ3 | 4.25 | |||
| C6 | Trp284 | CE3 | 4.00 | C6 | Trp284 | CB | 3.43 | C5 | Leu389 | CD2 | 3.50 | |||
| C6 | Trp284 | CB | 3.36 | C6 | Trp284 | CG | 3.87 | C6 | Trp284 | CG | 3.88 | |||
| C6 | Trp284 | CG | 3.87 | C6 | Trp284 | CD2 | 4.01 | C6 | Trp284 | CD2 | 4.10 | |||
| C6 | Trp284 | CD2 | 4.07 | C6 | Trp284 | CE3 | 3.91 | C6 | Trp284 | CE3 | 4.04 | |||
| C6 | Ser287 | CB | 3.70 | C6 | Ser287 | CB | 3.66 | C6 | Trp284 | CB | 3.32 | |||
| C6 | Leu389 | CD2 | 3.79 | C6 | Leu389 | CD2 | 3.70 | C6 | Ser287 | CA | 4.38 | |||
| C6 | Trp413 | CH2 | 4.38 | GalNAc4S | C1 | Leu326 | CD2 | 4.18 | C6 | Ser287 | CB | 3.62 | ||
| GalNAc | C1 | His36 | CE1 | 4.29 | C2 | His36 | CE1 | 4.38 | C6 | Leu389 | CD2 | 3.69 | ||
| C1 | Leu326 | CD2 | 4.20 | C3 | Trp284 | CE2 | 4.10 | GalNAc6S | C1 | His36 | CE1 | 4.34 | ||
| C2 | His36 | CE1 | 3.95 | C3 | Trp284 | CH2 | 4.36 | C1 | Leu37 | CD2 | 4.39 | |||
| C3 | Trp284 | CE2 | 4.02 | C3 | Trp284 | CZ2 | 3.97 | C1 | Leu326 | CD2 | 4.06 | |||
| C3 | Trp284 | CZ2 | 3.90 | C4 | Trp284 | CD1 | 4.39 | C2 | His36 | CE1 | 4.35 | |||
| C3 | Trp284 | CH2 | 4.31 | C4 | Trp284 | CE2 | 4.08 | C3 | Trp284 | CE2 | 3.97 | |||
| C4 | Trp284 | CE2 | 3.96 | C4 | Trp284 | CZ2 | 4.40 | C3 | Trp284 | CZ2 | 3.89 | |||
| C4 | Trp284 | CZ2 | 4.31 | C5 | Trp284 | CD1 | 4.22 | C3 | Trp284 | CH2 | 4.31 | |||
| C4 | Trp284 | CD1 | 4.25 | C5 | Trp284 | CE2 | 3.99 | C4 | Trp284 | CD1 | 4.06 | |||
| C5 | Trp284 | CE2 | 4.06 | C5 | Trp284 | CZ2 | 4.28 | C4 | Trp284 | CD2 | 4.26 | |||
| C5 | Trp284 | CZ2 | 4.35 | C6 | Leu37 | CD2 | 4.22 | C4 | Trp284 | CE2 | 3.80 | |||
| C5 | Trp284 | CD1 | 4.25 | C6 | Arg204 | CZ | 4.30 | C4 | Trp284 | CZ2 | 4.20 | |||
| C6 | Leu37 | CD2 | 4.23 | C6 | Trp284 | CD1 | 4.24 | C5 | Trp284 | CD1 | 4.08 | |||
| C6 | Arg204 | CZ | 4.24 | C7 | His36 | CE1 | 4.02 | C5 | Trp284 | CE2 | 3.92 | |||
| C6 | Trp284 | CD1 | 4.21 | C7 | Tyr146 | CE1 | 4.28 | C5 | Trp284 | CZ2 | 4.25 | |||
| C7 | His36 | CE1 | 3.95 | C7 | Tyr146 | CZ | 4.29 | C6 | Arg204 | CZ | 4.34 | |||
| C7 | Tyr146 | CZ | 4.35 | C7 | Leu326 | CD2 | 4.31 | C6 | Trp284 | CD1 | 3.96 | |||
| C7 | Tyr146 | CE1 | 4.31 | C8 | Tyr146 | CE1 | 3.57 | C7 | His36 | CE1 | 3.88 | |||
| C7 | Leu326 | CD2 | 4.21 | C8 | Tyr146 | CZ | 3.62 | C7 | Tyr146 | CE1 | 4.32 | |||
| C8 | Tyr146 | CZ | 3.76 | C8 | Leu326 | CD2 | 4.17 | C7 | Tyr146 | CZ | 4.33 | |||
| C8 | Tyr146 | CE1 | 3.70 | C8 | Arg400 | CG | 4.20 | C7 | Leu326 | CD2 | 4.22 | |||
| C8 | Leu326 | CD2 | 4.00 | C8 | Tyr146 | CE1 | 3.73 | |||||||
| C8 | Arg400 | CG | 4.05 | C8 | Tyr146 | CZ | 3.76 | |||||||
| C8 | Leu326 | CD2 | 4.00 | |||||||||||
| C8 | Arg400 | CB | 4.30 | |||||||||||
| C8 | Arg400 | CG | 3.93 | |||||||||||
| Hydrogen bonds (<3.3 Å) | ||||||||||||||
| Smon0123 (N-18/C-5)/C∆0S | Smon0123 (N-18/C-5)/C∆4S | Smon0123 (N-18/C-5)/C∆6S | ||||||||||||
| Sugar | Atom | Protein/Water | Atom | Distance | Sugar | Atom | Protein/Water | Atom | Distance | Sugar | Atom | Protein/Water | Atom | Distance |
| ΔGlcA | O2 | Gln405 | NE2 | 2.86 | ΔGlcA | O2 | Gln405 | NE2 | 2.85 | ΔGlcA | O2 | Gln405 | NE2 | 2.99 |
| O3 | Tyr409 | OH | 2.73 | O3 | Tyr409 | OH | 2.87 | O3 | Glu410 | OE2 | 2.68 | |||
| O3 | Glu410 | OE2 | 2.68 | O3 | Glu410 | OE2 | 2.69 | O3 | Tyr409 | OH | 2.68 | |||
| O6A | Ser287 | N | 2.97 | O6A | Ser287 | N | 2.99 | O6A | Ser287 | N | 2.87 | |||
| O2 | water80 | 2.74 | O2 | water4 | 2.73 | O2 | water770 | 2.74 | ||||||
| O6A | water52 | 2.74 | O6A | water6 | 2.81 | O6A | water757 | 2.78 | ||||||
| O6B | water143 | 2.69 | GalNAc4S | O1S | Arg393 | NE | 2.72 | O6B | water767 | 2.55 | ||||
| GalNAc | O3 | Arg393 | NH2 | 2.91 | O1S | Arg393 | NH2 | 3.00 | GalNAc6S | O3 | Arg393 | NH2 | 2.96 | |
| O6 | Lys210 | NZ | 2.85 | O2S | Arg204 | NH1 | 3.10 | O3S | Arg204 | O | 3.2 | |||
| O7 | His36 | NE2 | 2.83 | O2S | Arg204 | NH2 | 2.83 | O7 | His36 | NE2 | 2.81 | |||
| O7 | Arg393 | NH2 | 3.10 | O3S | Arg204 | NH1 | 3.17 | N | Tyr146 | OH | 2.86 | |||
| N2 | Tyr146 | OH | 2.92 | O3 | Arg393 | NH2 | 2.91 | O1S | water766 | 3.17 | ||||
| O1 | water72 | 2.58 | O6 | Lys210 | NZ | 2.8 | O2S | water795 | 2.49 | |||||
| O4 | water143 | 2.69 | O7 | His36 | NE2 | 2.88 | O4 | water767 | 2.67 | |||||
| O6 | water55 | 2.69 | O7 | Arg393 | NH2 | 3.08 | O7 | water770 | 2.95 | |||||
| O6 | water621 | 2.57 | N | Tyr146 | OH | 2.88 | ||||||||
| O7 | water80 | 2.94 | O1S | water56 | 2.8 | |||||||||
| O7 | water1090 | 2.98 | O6 | water301 | 2.67 | |||||||||
| O6 | water324 | 2.64 | ||||||||||||
| O7 | water4 | 2.87 | ||||||||||||
| O7 | water543 | 2.98 | ||||||||||||