Sodium in the structure of Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem Complex (pdb 4euz)

The binding sites of Sodium atom in the structure of Crystal Structure of Serratia Fonticola Carbapenemase Sfc-1 S70A- Meropenem Complex (pdb code 4euz). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 4euz structure was solved by F.FONSECA, J.SPENCER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 22.4-1.1 Space group P212121 a (A) 59.060 b (A) 61.910 c (A) 79.010 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 11.5 Rfree (%) 13.8 Sodium Binding Sites: Sodium binding site 1 out of 7 in 4euz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 4euz. 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: Leu81, A: Ser84, A: Gln85, A: Leu91, A: Thr202, A: Glu203, A: Hoh668, A: Hoh750, A: Hoh759, A: Hoh775, A: Hoh836, A: Hoh844, conact list: Atom Atom Distance (A) Na O A:Leu81 4.53 Na CD2 A:Leu81 4.53 Na O A:Ser84 4.46 Na CB A:Ser84 3.85 Na OG A:Ser84 2.80 Na C A:Ser84 4.34 Na CA A:Ser84 4.77 Na N A:Gln85 4.48 Na CA A:Gln85 4.70 Na CD1 A:Leu91 3.90 Na CG A:Leu91 4.55 Na CG2 A:Thr202 4.58 Na OE1 A:Glu203 4.70 Na CB A:Glu203 4.84 Na OE2 A:Glu203 2.73 Na CD A:Glu203 3.53 Na CG A:Glu203 3.54 Na O A:Hoh668 4.63 Na O A:Hoh750 4.75 Na O A:Hoh759 4.28 Na O A:Hoh775 3.94 Na O A:Hoh836 3.08 Na O A:Hoh844 2.64 interactive model: Sodium binding site 2 out of 7 in 4euz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 4euz. 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: Arg43, A: Pro174, A: Gly175, A: Ser266, A: Hoh622, A: Hoh644, A: Hoh654, A: Hoh694, A: Hoh816, A: Hoh877, A: Hoh957, A: Hoh1024, A: Hoh1050, A: Hoh1073, conact list: Atom Atom Distance (A) Na CD A:Arg43 4.70 Na CZ A:Arg43 3.77 Na CZ A:Arg43 3.71 Na NE A:Arg43 4.07 Na NE A:Arg43 3.67 Na NH2 A:Arg43 3.23 Na NH2 A:Arg43 3.31 Na NH1 A:Arg43 4.51 Na NH1 A:Arg43 4.62 Na N A:Pro174 4.88 Na CB A:Pro174 3.69 Na C A:Pro174 4.55 Na CG A:Pro174 4.24 Na CA A:Pro174 3.75 Na N A:Gly175 4.33 Na OG A:Ser266 4.11 Na O A:Hoh622 4.78 Na O A:Hoh644 4.42 Na O A:Hoh654 3.55 Na O A:Hoh694 2.85 Na O A:Hoh816 2.19 Na O A:Hoh877 4.42 Na O A:Hoh957 3.89 Na O A:Hoh1024 4.76 Na O A:Hoh1050 3.92 Na O A:Hoh1073 4.57 interactive model: Sodium binding site 3 out of 7 in 4euz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 4euz. 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: Val108, A: Met117, A: Glu121, A: Leu122, A: Ala124, A: Ala125, A: Hoh689, A: Hoh702, A: Hoh714, A: Hoh857, A: Hoh938, A: Hoh985, A: Hoh1003, A: Hoh1019, A: Hoh1053, conact list: Atom Atom Distance (A) Na CG1 A:Val108 4.52 Na CE A:Met117 4.36 Na O A:Glu121 2.78 Na CB A:Glu121 3.99 Na C A:Glu121 3.57 Na CG A:Glu121 4.50 Na CA A:Glu121 3.65 Na N A:Leu122 4.83 Na O A:Ala124 4.95 Na N A:Ala124 4.90 Na C A:Ala124 4.16 Na CB A:Ala124 3.71 Na CA A:Ala124 4.45 Na N A:Ala125 3.60 Na CB A:Ala125 3.91 Na CA A:Ala125 4.03 Na O A:Hoh689 2.98 Na O A:Hoh702 4.61 Na O A:Hoh714 2.81 Na O A:Hoh857 4.66 Na O A:Hoh938 2.43 Na O A:Hoh985 2.58 Na O A:Hoh1003 4.64 Na O A:Hoh1019 4.61 Na O A:Hoh1053 4.39 interactive model: Sodium binding site 4 out of 7 in 4euz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 4euz. 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: Phe66, A: Pro67, A: Leu68, A: Arg164, A: Leu169, A: Ala172, A: Asp176, A: Arg178, A: Asp179, A: Thr180, A: Hoh610, A: Hoh637, A: Hoh639, A: Hoh643, A: Hoh664, conact list: Atom Atom Distance (A) Na C A:Phe66 4.96 Na N A:Pro67 4.20 Na CB A:Pro67 3.35 Na CD A:Pro67 4.51 Na C A:Pro67 4.72 Na CG A:Pro67 3.54 Na CA A:Pro67 3.50 Na N A:Leu68 4.85 Na NH2 A:Arg164 4.97 Na O A:Leu169 4.79 Na N A:Ala172 4.46 Na C A:Ala172 4.93 Na CA A:Ala172 4.23 Na O A:Asp176 3.88 Na C A:Asp176 4.95 Na O A:Arg178 2.72 Na N A:Arg178 4.96 Na C A:Arg178 3.94 Na O A:Asp179 3.34 Na N A:Asp179 4.69 Na CB A:Asp179 4.32 Na C A:Asp179 3.85 Na CA A:Asp179 4.46 Na N A:Thr180 4.43 Na CB A:Thr180 4.53 Na CG2 A:Thr180 3.25 Na CA A:Thr180 4.67 Na O A:Hoh610 3.90 Na O A:Hoh637 2.93 Na O A:Hoh639 4.20 Na O A:Hoh643 2.72 Na O A:Hoh664 1.60 interactive model: Sodium binding site 5 out of 7 in 4euz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 4euz. 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: Leu167, A: Glu168, A: Asn170, A: Ser171, A: Hoh726, A: Hoh768, A: Hoh948, A: Hoh977, A: Hoh986, A: Hoh1012, A: Hoh1037, A: Hoh1048, A: Hoh1059, A: Hoh1077, A: Hoh1084, conact list: Atom Atom Distance (A) Na O A:Leu167 3.22 Na CB A:Leu167 4.56 Na C A:Leu167 4.10 Na O A:Glu168 4.65 Na N A:Glu168 4.67 Na C A:Glu168 4.76 Na CA A:Glu168 4.43 Na O A:Asn170 4.71 Na N A:Asn170 4.69 Na CB A:Asn170 4.30 Na C A:Asn170 4.37 Na CA A:Asn170 4.67 Na N A:Ser171 4.36 Na CB A:Ser171 5.00 Na CA A:Ser171 4.64 Na O A:Hoh726 4.42 Na O A:Hoh768 4.02 Na O A:Hoh948 3.14 Na O A:Hoh977 2.25 Na O A:Hoh986 3.24 Na O A:Hoh1012 2.96 Na O A:Hoh1037 4.88 Na O A:Hoh1048 4.93 Na O A:Hoh1059 3.77 Na O A:Hoh1077 4.62 Na O A:Hoh1084 3.17 interactive model: Sodium binding site 6 out of 7 in 4euz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 4euz. 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: Gln24, A: Val28, A: Lys32, A: Hoh853, conact list: Atom Atom Distance (A) Na NE2 A:Gln24 4.76 Na CG1 A:Val28 4.63 Na CE A:Lys32 4.08 Na CE A:Lys32 3.91 Na NZ A:Lys32 3.70 Na NZ A:Lys32 3.66 Na O A:Hoh853 3.13 interactive model: Sodium binding site 7 out of 7 in 4euz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 4euz. 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: Ser275, A: Ala277, A: Val278, A: Hoh666, A: Hoh785, A: Hoh918, A: Hoh960, A: Hoh983, A: Hoh1080, conact list: Atom Atom Distance (A) Na CB A:Ser275 3.40 Na OG A:Ser275 2.61 Na CA A:Ser275 4.50 Na CB A:Ala277 4.30 Na N A:Val278 4.72 Na CG2 A:Val278 4.05 Na O A:Hoh666 4.38 Na O A:Hoh785 4.63 Na O A:Hoh918 4.16 Na O A:Hoh960 3.95 Na O A:Hoh983 3.69 Na O A:Hoh1080 1.73 interactive model: