Magnesium in the structure of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex With Iptg (pdb 3dyo)
The binding sites of Magnesium atom in the structure of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex With Iptg (pdb code 3dyo). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3dyo structure was solved by D.H.JUERS, R.E.HUBER, B.W.MATTHEWS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 30.0-1.8 | Space group | P212121 | a (A) | 152.010 | b (A) | 162.520 | c (A) | 204.010 | alpha (°) | 90.00 | beta (°) | 90.00 | gamma (°) | 90.00 | Rfactor (%) | n/a | Rfree (%) | n/a |
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Magnesium Binding Sites:Magnesium binding site 1 out of 14 in 3dyo
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3dyo. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asn102, A: Val103, A: Asp199, A: Gln200, A: Asp201, A: Glu416, A: Asn418, A: Asn460, A: Glu461, A: Ipt2001, A: Hoh4001, A: Hoh4013, A: Hoh4077, A: Hoh4153, | conact list:
Atom | Atom | Distance (A) | Mg | O A:Asn102 | 4.56 | Mg | OD1 A:Asn102 | 4.17 | Mg | CG2 A:Val103 | 4.73 | Mg | O A:Asp199 | 4.20 | Mg | C A:Gln200 | 4.88 | Mg | CA A:Gln200 | 4.95 | Mg | N A:Asp201 | 4.13 | Mg | CB A:Asp201 | 4.15 | Mg | CA A:Asp201 | 4.70 | Mg | OE1 A:Glu416 | 3.48 | Mg | OE2 A:Glu416 | 2.04 | Mg | CD A:Glu416 | 3.11 | Mg | CG A:Glu416 | 4.34 | Mg | CB A:Asn418 | 3.59 | Mg | ND2 A:Asn418 | 4.25 | Mg | OD1 A:Asn418 | 2.00 | Mg | CG A:Asn418 | 3.08 | Mg | ND2 A:Asn460 | 4.27 | Mg | OE1 A:Glu461 | 2.13 | Mg | CB A:Glu461 | 4.12 | Mg | OE2 A:Glu461 | 3.89 | Mg | CD A:Glu461 | 3.09 | Mg | CG A:Glu461 | 4.09 | Mg | O3 A:Ipt2001 | 4.84 | Mg | C2 A:Ipt2001 | 4.80 | Mg | O4 A:Ipt2001 | 4.38 | Mg | O A:Hoh4001 | 4.23 | Mg | O A:Hoh4013 | 2.03 | Mg | O A:Hoh4077 | 2.11 | Mg | O A:Hoh4153 | 2.10 |
| interactive model:
| Magnesium binding site 2 out of 14 in 3dyo
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3dyo. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp15, A: Trp16, A: Glu17, A: Asn18, A: Pro19, A: Gly20, A: Val21, A: Thr22, A: Tyr161, A: Gln163, A: Asp193, | conact list:
Atom | Atom | Distance (A) | Mg | O A:Asp15 | 2.27 | Mg | C A:Asp15 | 3.46 | Mg | CA A:Asp15 | 4.61 | Mg | N A:Trp16 | 4.23 | Mg | C A:Trp16 | 4.34 | Mg | CA A:Trp16 | 4.22 | Mg | O A:Trp16 | 4.86 | Mg | N A:Glu17 | 4.43 | Mg | C A:Glu17 | 4.70 | Mg | O A:Asn18 | 1.95 | Mg | N A:Asn18 | 3.46 | Mg | CB A:Asn18 | 4.03 | Mg | C A:Asn18 | 2.93 | Mg | CG A:Asn18 | 4.90 | Mg | CA A:Asn18 | 3.65 | Mg | N A:Pro19 | 3.85 | Mg | C A:Pro19 | 4.68 | Mg | CA A:Pro19 | 4.13 | Mg | N A:Gly20 | 4.82 | Mg | O A:Val21 | 2.29 | Mg | N A:Val21 | 4.16 | Mg | CB A:Val21 | 4.22 | Mg | C A:Val21 | 3.43 | Mg | CG1 A:Val21 | 4.74 | Mg | CA A:Val21 | 4.21 | Mg | N A:Thr22 | 4.43 | Mg | CA A:Thr22 | 4.61 | Mg | CE2 A:Tyr161 | 4.61 | Mg | CZ A:Tyr161 | 4.92 | Mg | OH A:Tyr161 | 4.14 | Mg | NE2 A:Gln163 | 3.48 | Mg | OE1 A:Gln163 | 2.33 | Mg | CD A:Gln163 | 3.22 | Mg | CG A:Gln163 | 4.55 | Mg | CB A:Asp193 | 4.43 | Mg | OD2 A:Asp193 | 2.34 | Mg | OD1 A:Asp193 | 2.88 | Mg | CG A:Asp193 | 2.96 |
| interactive model:
| Magnesium binding site 3 out of 14 in 3dyo
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3dyo. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His622, A: Gln718, A: Gln719, A: Thr911, A: Hoh4079, A: Hoh4238, A: Hoh4252, A: Hoh4262, A: Hoh4277, A: Hoh4366, A: Hoh4408, A: Hoh4573, A: Hoh4621, A: Hoh4724, A: Hoh4799, | conact list:
Atom | Atom | Distance (A) | Mg | NE2 A:His622 | 4.32 | Mg | CE1 A:His622 | 4.88 | Mg | NE2 A:Gln718 | 3.53 | Mg | OE1 A:Gln718 | 2.25 | Mg | CD A:Gln718 | 3.22 | Mg | CG A:Gln718 | 4.62 | Mg | O A:Gln719 | 4.22 | Mg | N A:Gln719 | 4.44 | Mg | O A:Thr911 | 4.28 | Mg | O A:Hoh4079 | 4.87 | Mg | O A:Hoh4238 | 4.74 | Mg | O A:Hoh4252 | 4.56 | Mg | O A:Hoh4262 | 2.33 | Mg | O A:Hoh4277 | 4.06 | Mg | O A:Hoh4366 | 2.32 | Mg | O A:Hoh4408 | 3.97 | Mg | O A:Hoh4573 | 2.57 | Mg | O A:Hoh4621 | 2.24 | Mg | O A:Hoh4724 | 4.25 | Mg | O A:Hoh4799 | 4.62 |
| interactive model:
| Magnesium binding site 4 out of 14 in 3dyo
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3dyo. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asn232, A: Ser236, A: Arg237, C: Asn232, C: Ser236, C: Arg237, A: Hoh4759, A: Hoh4791, A: Hoh4794, C: Hoh4007, C: Hoh4008, C: Hoh4883, C: Hoh4884, C: Hoh4888, | conact list:
Atom | Atom | Distance (A) | Mg | ND2 A:Asn232 | 4.88 | Mg | OG A:Ser236 | 4.17 | Mg | CD A:Arg237 | 4.76 | Mg | CG A:Arg237 | 4.91 | Mg | ND2 C:Asn232 | 4.85 | Mg | OG C:Ser236 | 4.19 | Mg | CD C:Arg237 | 4.68 | Mg | CG C:Arg237 | 4.86 | Mg | O A:Hoh4759 | 4.63 | Mg | O A:Hoh4791 | 2.47 | Mg | O A:Hoh4794 | 2.20 | Mg | O C:Hoh4007 | 2.14 | Mg | O C:Hoh4008 | 4.57 | Mg | O C:Hoh4883 | 2.19 | Mg | O C:Hoh4884 | 2.06 | Mg | O C:Hoh4888 | 2.20 |
| interactive model:
| Magnesium binding site 5 out of 14 in 3dyo
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 3dyo. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asn102, B: Val103, B: Asp199, B: Gln200, B: Asp201, B: Glu416, B: Asn418, B: Asn460, B: Glu461, B: Ipt2001, B: Hoh4025, B: Hoh4038, B: Hoh4102, B: Hoh4179, B: Hoh4315, | conact list:
Atom | Atom | Distance (A) | Mg | O B:Asn102 | 4.64 | Mg | OD1 B:Asn102 | 4.17 | Mg | CG2 B:Val103 | 4.76 | Mg | O B:Asp199 | 4.33 | Mg | C B:Gln200 | 4.94 | Mg | CA B:Gln200 | 4.93 | Mg | N B:Asp201 | 4.18 | Mg | CB B:Asp201 | 4.22 | Mg | CA B:Asp201 | 4.76 | Mg | OE1 B:Glu416 | 3.62 | Mg | OE2 B:Glu416 | 2.09 | Mg | CD B:Glu416 | 3.20 | Mg | CG B:Glu416 | 4.37 | Mg | CB B:Asn418 | 3.55 | Mg | ND2 B:Asn418 | 4.33 | Mg | OD1 B:Asn418 | 2.04 | Mg | CG B:Asn418 | 3.11 | Mg | ND2 B:Asn460 | 4.21 | Mg | OE1 B:Glu461 | 2.00 | Mg | CB B:Glu461 | 4.02 | Mg | OE2 B:Glu461 | 3.88 | Mg | CD B:Glu461 | 3.07 | Mg | CG B:Glu461 | 4.08 | Mg | O3 B:Ipt2001 | 4.71 | Mg | C2 B:Ipt2001 | 4.81 | Mg | O4 B:Ipt2001 | 4.46 | Mg | O B:Hoh4025 | 4.20 | Mg | O B:Hoh4038 | 2.21 | Mg | O B:Hoh4102 | 2.12 | Mg | O B:Hoh4179 | 2.20 | Mg | O B:Hoh4315 | 4.53 |
| interactive model:
| Magnesium binding site 6 out of 14 in 3dyo
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 3dyo. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asp15, B: Trp16, B: Glu17, B: Asn18, B: Pro19, B: Val21, B: Thr22, B: Tyr161, B: Gln163, B: Asp193, | conact list:
Atom | Atom | Distance (A) | Mg | O B:Asp15 | 2.28 | Mg | C B:Asp15 | 3.45 | Mg | CA B:Asp15 | 4.58 | Mg | N B:Trp16 | 4.17 | Mg | C B:Trp16 | 4.27 | Mg | CA B:Trp16 | 4.01 | Mg | O B:Trp16 | 4.84 | Mg | N B:Glu17 | 4.41 | Mg | C B:Glu17 | 4.83 | Mg | O B:Asn18 | 2.28 | Mg | N B:Asn18 | 3.64 | Mg | CB B:Asn18 | 4.30 | Mg | C B:Asn18 | 3.21 | Mg | CA B:Asn18 | 3.90 | Mg | N B:Pro19 | 4.16 | Mg | C B:Pro19 | 4.85 | Mg | CA B:Pro19 | 4.46 | Mg | O B:Val21 | 2.25 | Mg | N B:Val21 | 4.14 | Mg | CB B:Val21 | 4.32 | Mg | C B:Val21 | 3.41 | Mg | CG1 B:Val21 | 4.89 | Mg | CA B:Val21 | 4.16 | Mg | N B:Thr22 | 4.46 | Mg | CA B:Thr22 | 4.64 | Mg | CE2 B:Tyr161 | 4.31 | Mg | CZ B:Tyr161 | 4.60 | Mg | OH B:Tyr161 | 3.97 | Mg | NE2 B:Gln163 | 3.32 | Mg | OE1 B:Gln163 | 2.40 | Mg | CD B:Gln163 | 3.19 | Mg | CG B:Gln163 | 4.59 | Mg | CB B:Asp193 | 4.43 | Mg | OD2 B:Asp193 | 2.38 | Mg | OD1 B:Asp193 | 2.86 | Mg | CG B:Asp193 | 2.97 |
| interactive model:
| Magnesium binding site 7 out of 14 in 3dyo
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 3dyo. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Glu369, B: Hoh4824, B: Hoh4937, B: Hoh4958, B: Hoh4966, B: Hoh4967, B: Hoh4968, B: Hoh4969, B: Hoh4986, | conact list:
Atom | Atom | Distance (A) | Mg | OE1 B:Glu369 | 3.81 | Mg | OE2 B:Glu369 | 4.07 | Mg | CD B:Glu369 | 4.38 | Mg | O B:Hoh4824 | 2.11 | Mg | O B:Hoh4937 | 4.40 | Mg | O B:Hoh4958 | 4.16 | Mg | O B:Hoh4966 | 2.01 | Mg | O B:Hoh4967 | 1.94 | Mg | O B:Hoh4968 | 2.33 | Mg | O B:Hoh4969 | 2.29 | Mg | O B:Hoh4986 | 2.07 |
| interactive model:
| Magnesium binding site 8 out of 14 in 3dyo
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Magnesium in the PDB 3dyo. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asn232, B: Ser236, B: Arg237, D: Asn232, D: Ser236, D: Arg237, B: Hoh4888, B: Hoh4889, B: Hoh4906, D: Hoh4017, D: Hoh4019, D: Hoh4848, D: Hoh4849, D: Hoh4852, D: Hoh4864, | conact list:
Atom | Atom | Distance (A) | Mg | ND2 B:Asn232 | 4.73 | Mg | OG B:Ser236 | 4.18 | Mg | CD B:Arg237 | 4.37 | Mg | CG B:Arg237 | 4.84 | Mg | ND2 D:Asn232 | 4.82 | Mg | OG D:Ser236 | 4.15 | Mg | CD D:Arg237 | 4.99 | Mg | CG D:Arg237 | 4.96 | Mg | O B:Hoh4888 | 2.50 | Mg | O B:Hoh4889 | 2.16 | Mg | O B:Hoh4906 | 3.94 | Mg | O D:Hoh4017 | 4.40 | Mg | O D:Hoh4019 | 4.52 | Mg | O D:Hoh4848 | 2.33 | Mg | O D:Hoh4849 | 2.13 | Mg | O D:Hoh4852 | 2.23 | Mg | O D:Hoh4864 | 3.86 |
| interactive model:
| Magnesium binding site 9 out of 14 in 3dyo
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Magnesium in the PDB 3dyo. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Asn102, C: Val103, C: Asp199, C: Gln200, C: Asp201, C: Glu416, C: Asn418, C: Asn460, C: Glu461, C: Ipt2001, C: Hoh4025, C: Hoh4038, C: Hoh4102, C: Hoh4180, C: Hoh4318, | conact list:
Atom | Atom | Distance (A) | Mg | O C:Asn102 | 4.60 | Mg | OD1 C:Asn102 | 4.16 | Mg | CG2 C:Val103 | 4.83 | Mg | O C:Asp199 | 4.23 | Mg | C C:Gln200 | 4.88 | Mg | CA C:Gln200 | 4.83 | Mg | N C:Asp201 | 4.22 | Mg | CB C:Asp201 | 4.11 | Mg | CA C:Asp201 | 4.76 | Mg | OE1 C:Glu416 | 3.67 | Mg | OE2 C:Glu416 | 2.11 | Mg | CD C:Glu416 | 3.24 | Mg | CG C:Glu416 | 4.41 | Mg | CB C:Asn418 | 3.59 | Mg | ND2 C:Asn418 | 4.31 | Mg | OD1 C:Asn418 | 2.08 | Mg | CG C:Asn418 | 3.13 | Mg | ND2 C:Asn460 | 4.32 | Mg | OE1 C:Glu461 | 2.06 | Mg | CB C:Glu461 | 4.05 | Mg | OE2 C:Glu461 | 3.88 | Mg | CD C:Glu461 | 3.10 | Mg | CG C:Glu461 | 4.14 | Mg | O3 C:Ipt2001 | 4.85 | Mg | C2 C:Ipt2001 | 4.88 | Mg | O4 C:Ipt2001 | 4.42 | Mg | O C:Hoh4025 | 4.17 | Mg | O C:Hoh4038 | 2.19 | Mg | O C:Hoh4102 | 2.09 | Mg | O C:Hoh4180 | 2.13 | Mg | O C:Hoh4318 | 4.60 |
| interactive model:
| Magnesium binding site 10 out of 14 in 3dyo
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Magnesium in the PDB 3dyo. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Asp15, C: Trp16, C: Glu17, C: Asn18, C: Pro19, C: Val21, C: Thr22, C: Tyr161, C: Gln163, C: Asp193, | conact list:
Atom | Atom | Distance (A) | Mg | O C:Asp15 | 2.38 | Mg | CB C:Asp15 | 4.93 | Mg | C C:Asp15 | 3.57 | Mg | CA C:Asp15 | 4.61 | Mg | N C:Trp16 | 4.31 | Mg | C C:Trp16 | 4.28 | Mg | CA C:Trp16 | 4.05 | Mg | O C:Trp16 | 4.86 | Mg | N C:Glu17 | 4.52 | Mg | C C:Glu17 | 4.92 | Mg | O C:Asn18 | 2.44 | Mg | N C:Asn18 | 3.74 | Mg | CB C:Asn18 | 4.41 | Mg | C C:Asn18 | 3.32 | Mg | CA C:Asn18 | 4.04 | Mg | N C:Pro19 | 4.21 | Mg | C C:Pro19 | 4.87 | Mg | CA C:Pro19 | 4.37 | Mg | O C:Val21 | 2.23 | Mg | N C:Val21 | 4.22 | Mg | CB C:Val21 | 4.17 | Mg | C C:Val21 | 3.38 | Mg | CG1 C:Val21 | 4.69 | Mg | CA C:Val21 | 4.14 | Mg | N C:Thr22 | 4.36 | Mg | CA C:Thr22 | 4.44 | Mg | CE2 C:Tyr161 | 4.38 | Mg | CZ C:Tyr161 | 4.71 | Mg | OH C:Tyr161 | 4.08 | Mg | NE2 C:Gln163 | 3.47 | Mg | OE1 C:Gln163 | 2.35 | Mg | CD C:Gln163 | 3.17 | Mg | CG C:Gln163 | 4.46 | Mg | CB C:Asp193 | 4.56 | Mg | OD2 C:Asp193 | 2.46 | Mg | OD1 C:Asp193 | 3.06 | Mg | CG C:Asp193 | 3.12 |
| interactive model:
| Magnesium binding site 11 out of 14 in 3dyo
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Magnesium in the PDB 3dyo. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: His622, C: Gln718, C: Gln719, C: Thr911, C: Dms8427, C: Hoh4104, C: Hoh4266, C: Hoh4280, C: Hoh4290, C: Hoh4305, C: Hoh4399, C: Hoh4446, C: Hoh4463, C: Hoh4632, C: Hoh4692, | conact list:
Atom | Atom | Distance (A) | Mg | NE2 C:His622 | 4.00 | Mg | CE1 C:His622 | 4.60 | Mg | NE2 C:Gln718 | 3.64 | Mg | OE1 C:Gln718 | 2.22 | Mg | CD C:Gln718 | 3.26 | Mg | CG C:Gln718 | 4.61 | Mg | O C:Gln719 | 4.74 | Mg | N C:Gln719 | 4.74 | Mg | O C:Thr911 | 4.03 | Mg | C C:Thr911 | 4.96 | Mg | C2 C:Dms8427 | 3.84 | Mg | O C:Hoh4104 | 4.51 | Mg | O C:Hoh4266 | 4.95 | Mg | O C:Hoh4280 | 4.68 | Mg | O C:Hoh4290 | 1.98 | Mg | O C:Hoh4305 | 4.41 | Mg | O C:Hoh4399 | 2.42 | Mg | O C:Hoh4446 | 4.43 | Mg | O C:Hoh4463 | 2.26 | Mg | O C:Hoh4632 | 2.24 | Mg | O C:Hoh4692 | 2.96 |
| interactive model:
| Magnesium binding site 12 out of 14 in 3dyo
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Magnesium in the PDB 3dyo. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Asn102, D: Val103, D: Asp199, D: Gln200, D: Asp201, D: Glu416, D: Asn418, D: Asn460, D: Glu461, D: Ipt2001, D: Hoh4032, D: Hoh4045, D: Hoh4109, D: Hoh4184, D: Hoh4322, | conact list:
Atom | Atom | Distance (A) | Mg | O D:Asn102 | 4.64 | Mg | OD1 D:Asn102 | 4.21 | Mg | CG2 D:Val103 | 4.79 | Mg | O D:Asp199 | 4.26 | Mg | C D:Gln200 | 4.87 | Mg | CA D:Gln200 | 4.91 | Mg | N D:Asp201 | 4.20 | Mg | CB D:Asp201 | 4.11 | Mg | CA D:Asp201 | 4.75 | Mg | OE1 D:Glu416 | 3.46 | Mg | OE2 D:Glu416 | 2.06 | Mg | CD D:Glu416 | 3.11 | Mg | CG D:Glu416 | 4.37 | Mg | CB D:Asn418 | 3.50 | Mg | ND2 D:Asn418 | 4.34 | Mg | OD1 D:Asn418 | 2.01 | Mg | CG D:Asn418 | 3.08 | Mg | ND2 D:Asn460 | 4.27 | Mg | OE1 D:Glu461 | 2.09 | Mg | CB D:Glu461 | 4.03 | Mg | OE2 D:Glu461 | 3.81 | Mg | CD D:Glu461 | 3.04 | Mg | CG D:Glu461 | 4.08 | Mg | O3 D:Ipt2001 | 4.75 | Mg | C2 D:Ipt2001 | 4.73 | Mg | O4 D:Ipt2001 | 4.44 | Mg | O D:Hoh4032 | 4.07 | Mg | O D:Hoh4045 | 2.17 | Mg | O D:Hoh4109 | 2.04 | Mg | O D:Hoh4184 | 2.20 | Mg | O D:Hoh4322 | 4.12 |
| interactive model:
| Magnesium binding site 13 out of 14 in 3dyo
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Magnesium in the PDB 3dyo. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Asp15, D: Trp16, D: Glu17, D: Asn18, D: Pro19, D: Gly20, D: Val21, D: Thr22, D: Tyr161, D: Gln163, D: Asp193, | conact list:
Atom | Atom | Distance (A) | Mg | O D:Asp15 | 2.33 | Mg | C D:Asp15 | 3.51 | Mg | CA D:Asp15 | 4.62 | Mg | N D:Trp16 | 4.23 | Mg | C D:Trp16 | 4.26 | Mg | CA D:Trp16 | 4.11 | Mg | O D:Trp16 | 4.82 | Mg | N D:Glu17 | 4.33 | Mg | C D:Glu17 | 4.81 | Mg | O D:Asn18 | 2.14 | Mg | N D:Asn18 | 3.63 | Mg | CB D:Asn18 | 4.22 | Mg | C D:Asn18 | 3.09 | Mg | CA D:Asn18 | 3.83 | Mg | N D:Pro19 | 3.97 | Mg | C D:Pro19 | 4.71 | Mg | CA D:Pro19 | 4.14 | Mg | N D:Gly20 | 4.84 | Mg | O D:Val21 | 2.39 | Mg | N D:Val21 | 4.26 | Mg | CB D:Val21 | 4.32 | Mg | C D:Val21 | 3.54 | Mg | CG1 D:Val21 | 4.80 | Mg | CA D:Val21 | 4.25 | Mg | N D:Thr22 | 4.55 | Mg | CA D:Thr22 | 4.65 | Mg | CE2 D:Tyr161 | 4.46 | Mg | CZ D:Tyr161 | 4.76 | Mg | OH D:Tyr161 | 4.07 | Mg | NE2 D:Gln163 | 3.41 | Mg | OE1 D:Gln163 | 2.43 | Mg | CD D:Gln163 | 3.22 | Mg | CG D:Gln163 | 4.56 | Mg | N D:Asp193 | 4.99 | Mg | CB D:Asp193 | 4.31 | Mg | OD2 D:Asp193 | 2.38 | Mg | OD1 D:Asp193 | 2.74 | Mg | CG D:Asp193 | 2.87 |
| interactive model:
| Magnesium binding site 14 out of 14 in 3dyo
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Magnesium in the PDB 3dyo. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: His622, D: Gln718, D: Gln719, D: Thr911, D: Hoh4111, D: Hoh4284, D: Hoh4294, D: Hoh4309, D: Hoh4401, D: Hoh4447, D: Hoh4625, D: Hoh4674, D: Hoh4780, D: Hoh4837, D: Hoh4860, | conact list:
Atom | Atom | Distance (A) | Mg | NE2 D:His622 | 3.93 | Mg | CE1 D:His622 | 4.55 | Mg | NE2 D:Gln718 | 3.62 | Mg | OE1 D:Gln718 | 2.36 | Mg | CD D:Gln718 | 3.30 | Mg | CG D:Gln718 | 4.67 | Mg | CA D:Gln718 | 4.91 | Mg | O D:Gln719 | 4.68 | Mg | N D:Gln719 | 4.58 | Mg | O D:Thr911 | 3.89 | Mg | C D:Thr911 | 4.83 | Mg | O D:Hoh4111 | 4.69 | Mg | O D:Hoh4284 | 4.47 | Mg | O D:Hoh4294 | 2.14 | Mg | O D:Hoh4309 | 4.68 | Mg | O D:Hoh4401 | 2.59 | Mg | O D:Hoh4447 | 4.15 | Mg | O D:Hoh4625 | 2.58 | Mg | O D:Hoh4674 | 2.25 | Mg | O D:Hoh4780 | 4.27 | Mg | O D:Hoh4837 | 4.69 | Mg | O D:Hoh4860 | 4.93 |
| interactive model:
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