The binding sites of Sodium atom in the structure of Crystal Structure Of A Plig-Ec Mutant, A Periplasmic Lysozyme Inhibitor of G-Type Lysozyme From Escherichia Coli (pdb code 4dxz). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 4dxz structure was solved by S.LEYSEN, S.VANHEUVERZWIJN, K.VAN ASTEN, L.VANDERKELEN, C.W.MICHIELS, S.V.STRELKOV, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
| Resolution (A) | 40.2-1.2 | | Space group | I41 | | a (A) | 80.316 | | b (A) | 80.316 | | c (A) | 31.098 | | alpha (°) | 90.00 | | beta (°) | 90.00 | | gamma (°) | 90.00 | | Rfactor (%) | 14.1 | | Rfree (%) | 17.1 |
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Sodium binding site 1 out of 3 in 4dxz
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 4dxz. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: His63, A: Val64, A: Ser65, A: Asp129, A: Ile130, A: Gln131, | conact list:
| Atom | Atom | Distance (A) | | Na | CB A:His63 | 4.36 | | Na | CB A:His63 | 4.32 | | Na | HB3 A:His63 | 4.03 | | Na | HB3 A:His63 | 3.75 | | Na | CD2 A:His63 | 3.04 | | Na | CD2 A:His63 | 4.19 | | Na | HD1 A:His63 | 4.89 | | Na | C A:His63 | 3.76 | | Na | CG A:His63 | 3.81 | | Na | CG A:His63 | 4.11 | | Na | CA A:His63 | 4.70 | | Na | CA A:His63 | 4.70 | | Na | HD2 A:His63 | 2.60 | | Na | HD2 A:His63 | 4.30 | | Na | O A:His63 | 3.13 | | Na | NE2 A:His63 | 3.66 | | Na | NE2 A:His63 | 4.66 | | Na | ND1 A:His63 | 4.67 | | Na | ND1 A:His63 | 4.55 | | Na | CE1 A:His63 | 4.59 | | Na | CE1 A:His63 | 4.86 | | Na | HE2 A:His63 | 3.75 | | Na | N A:Val64 | 4.22 | | Na | C A:Val64 | 4.13 | | Na | CA A:Val64 | 4.14 | | Na | O A:Val64 | 4.99 | | Na | HA A:Val64 | 3.60 | | Na | H A:Val64 | 4.89 | | Na | HB2 A:Ser65 | 3.47 | | Na | HB2 A:Ser65 | 4.93 | | Na | HB2 A:Ser65 | 3.49 | | Na | HG A:Ser65 | 3.69 | | Na | HG A:Ser65 | 3.51 | | Na | N A:Ser65 | 3.64 | | Na | CB A:Ser65 | 3.90 | | Na | CB A:Ser65 | 4.03 | | Na | CB A:Ser65 | 3.91 | | Na | HB3 A:Ser65 | 3.51 | | Na | HB3 A:Ser65 | 3.61 | | Na | HB3 A:Ser65 | 4.79 | | Na | H A:Ser65 | 3.20 | | Na | H A:Ser65 | 3.19 | | Na | H A:Ser65 | 3.20 | | Na | OG A:Ser65 | 3.58 | | Na | OG A:Ser65 | 3.44 | | Na | CA A:Ser65 | 4.41 | | Na | CA A:Ser65 | 4.46 | | Na | CA A:Ser65 | 4.42 | | Na | O A:Asp129 | 3.17 | | Na | HB2 A:Asp129 | 4.58 | | Na | CB A:Asp129 | 3.79 | | Na | HB3 A:Asp129 | 3.06 | | Na | OD2 A:Asp129 | 4.18 | | Na | OD1 A:Asp129 | 3.97 | | Na | C A:Asp129 | 3.78 | | Na | CG A:Asp129 | 3.77 | | Na | CA A:Asp129 | 4.44 | | Na | N A:Ile130 | 4.45 | | Na | C A:Ile130 | 4.63 | | Na | CA A:Ile130 | 4.68 | | Na | HA A:Ile130 | 4.28 | | Na | HB2 A:Gln131 | 3.32 | | Na | HB2 A:Gln131 | 3.41 | | Na | N A:Gln131 | 4.13 | | Na | OE1 A:Gln131 | 4.92 | | Na | OE1 A:Gln131 | 3.75 | | Na | HG3 A:Gln131 | 2.72 | | Na | CB A:Gln131 | 3.86 | | Na | CB A:Gln131 | 3.91 | | Na | HB3 A:Gln131 | 3.49 | | Na | HB3 A:Gln131 | 4.69 | | Na | CD A:Gln131 | 4.90 | | Na | CD A:Gln131 | 3.36 | | Na | CG A:Gln131 | 5.00 | | Na | CG A:Gln131 | 3.38 | | Na | CA A:Gln131 | 4.66 | | Na | CA A:Gln131 | 4.68 | | Na | HG2 A:Gln131 | 4.22 | | Na | NE2 A:Gln131 | 3.67 | | Na | HE22 A:Gln131 | 3.81 | | Na | H A:Gln131 | 3.79 | | Na | H A:Gln131 | 3.78 | | Na | HE21 A:Gln131 | 4.07 |
| interactive model:
| Sodium binding site 2 out of 3 in 4dxz
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 4dxz. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Tyr49, A: Thr51, A: Glu108, A: Arg110, A: Hoh319, A: Hoh477, A: Hoh498, | conact list:
| Atom | Atom | Distance (A) | | Na | CD1 A:Tyr49 | 4.95 | | Na | OH A:Tyr49 | 3.10 | | Na | HE1 A:Tyr49 | 2.96 | | Na | CZ A:Tyr49 | 3.85 | | Na | CE1 A:Tyr49 | 3.68 | | Na | CG2 A:Thr51 | 4.20 | | Na | HG21 A:Thr51 | 3.30 | | Na | HG21 A:Thr51 | 4.61 | | Na | HG1 A:Thr51 | 4.48 | | Na | HG22 A:Thr51 | 4.45 | | Na | HG23 A:Thr51 | 4.48 | | Na | OG1 A:Thr51 | 4.24 | | Na | OE1 A:Glu108 | 3.42 | | Na | OE2 A:Glu108 | 4.43 | | Na | CD A:Glu108 | 4.25 | | Na | HH22 A:Arg110 | 4.40 | | Na | HE A:Arg110 | 4.27 | | Na | HH21 A:Arg110 | 3.91 | | Na | NE A:Arg110 | 4.37 | | Na | NH2 A:Arg110 | 4.09 | | Na | HD3 A:Arg110 | 4.90 | | Na | CZ A:Arg110 | 4.32 | | Na | O A:Hoh319 | 4.92 | | Na | O A:Hoh477 | 3.70 | | Na | O A:Hoh498 | 3.33 |
| interactive model:
| Sodium binding site 3 out of 3 in 4dxz
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 4dxz. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Thr114, A: Arg115, A: Asn116, A: Asp117, A: Hoh366, A: Hoh488, | conact list:
| Atom | Atom | Distance (A) | | Na | HB A:Thr114 | 2.93 | | Na | CB A:Thr114 | 3.84 | | Na | CG2 A:Thr114 | 4.83 | | Na | C A:Thr114 | 4.36 | | Na | HG21 A:Thr114 | 4.76 | | Na | HG1 A:Thr114 | 4.08 | | Na | CA A:Thr114 | 4.58 | | Na | HG22 A:Thr114 | 4.99 | | Na | HA A:Thr114 | 4.61 | | Na | OG1 A:Thr114 | 4.15 | | Na | HB2 A:Arg115 | 3.04 | | Na | N A:Arg115 | 3.63 | | Na | HG3 A:Arg115 | 4.77 | | Na | CB A:Arg115 | 3.90 | | Na | HB3 A:Arg115 | 4.34 | | Na | C A:Arg115 | 4.11 | | Na | CG A:Arg115 | 4.94 | | Na | CA A:Arg115 | 4.07 | | Na | H A:Arg115 | 3.22 | | Na | HB2 A:Asn116 | 3.21 | | Na | HD21 A:Asn116 | 2.77 | | Na | N A:Asn116 | 3.25 | | Na | CB A:Asn116 | 3.66 | | Na | HB3 A:Asn116 | 4.57 | | Na | HA A:Asn116 | 4.41 | | Na | ND2 A:Asn116 | 2.41 | | Na | H A:Asn116 | 2.48 | | Na | OD1 A:Asn116 | 4.41 | | Na | CG A:Asn116 | 3.36 | | Na | CA A:Asn116 | 4.02 | | Na | H A:Asp117 | 4.95 | | Na | O A:Hoh366 | 4.56 | | Na | O A:Hoh488 | 2.90 |
| interactive model:
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