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Sodium in the structure of Crystal Structure of the GLUR6 Ligand Binding Domain Dimer K665R I749L Q753K Mutant With Glutamate and Nacl At 1.5 Angstrom Resolution (pdb 3g3h)






The binding sites of Sodium atom in the structure of Crystal Structure of the GLUR6 Ligand Binding Domain Dimer K665R I749L Q753K Mutant With Glutamate and Nacl At 1.5 Angstrom Resolution (pdb code 3g3h). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 3g3h structure was solved by C.CHAUDHRY, M.L.MAYER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)29.5-1.5
Space groupP1211
a (A)51.136
b (A)113.499
c (A)52.163
alpha (°)90.00
beta (°)115.14
gamma (°)90.00
Rfactor (%)14.7
Rfree (%)17.6


Sodium Binding Sites:

Sodium binding site 1 out of 3 in 3g3h


Sodium binding site 1 out of 3 in 3g3h
Click to enlarge
stereopicture of Sodium binding site 1 out of 3 in 3g3h
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3g3h. 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: Glu97, A: Lys98, A: Val99, A: Ile100, A: Asp101, A: Phe102, A: Met223, A: Arg228, B: Leu233, A: Hoh345, A: Hoh532, A: Hoh642, B: Hoh480, B: Hoh505, B: Hoh634,

conact list:


AtomAtomDistance (A)
NaHB2 A:Glu974.79
NaOE1 A:Glu974.53
NaHG3 A:Glu972.77
NaCB A:Glu974.12
NaHB3 A:Glu974.70
NaOE2 A:Glu972.47
NaCD A:Glu973.35
NaC A:Glu973.35
NaCG A:Glu973.45
NaCA A:Glu973.70
NaHG2 A:Glu974.24
NaO A:Glu972.38
NaHA A:Glu973.22
NaN A:Lys984.55
NaCA A:Lys984.99
NaHA A:Lys984.72
NaH A:Val994.99
NaN A:Ile1004.59
NaC A:Ile1003.43
NaCA A:Ile1004.64
NaO A:Ile1002.43
NaH A:Ile1004.30
NaHB2 A:Asp1014.88
NaN A:Asp1013.90
NaCB A:Asp1014.13
NaHB3 A:Asp1014.61
NaHA A:Asp1012.74
NaHA A:Asp1012.71
NaOD2 A:Asp1014.56
NaH A:Asp1014.71
NaOD1 A:Asp1012.41
NaC A:Asp1014.77
NaC A:Asp1014.68
NaCG A:Asp1013.54
NaCA A:Asp1013.58
NaN A:Phe1024.81
NaHD2 A:Phe1024.80
NaH A:Phe1024.24
NaHG3 A:Met2234.61
NaHE3 A:Met2233.01
NaHE3 A:Met2233.37
NaSD A:Met2233.73
NaCE A:Met2233.67
NaCE A:Met2233.37
NaHE1 A:Met2233.93
NaHE1 A:Met2233.47
NaHE2 A:Met2234.50
NaHE2 A:Met2232.77
NaHE A:Arg2284.95
NaHH12 A:Arg2284.21
NaNH1 A:Arg2284.16
NaHH11 A:Arg2284.01
NaCZ A:Arg2284.77
NaHD21 B:Leu2334.81
NaO A:Hoh3452.32
NaO A:Hoh5324.56
NaO A:Hoh6423.37
NaO B:Hoh4803.97
NaO B:Hoh5053.97
NaO B:Hoh6344.80

interactive model:


Sodium binding site 2 out of 3 in 3g3h


Sodium binding site 2 out of 3 in 3g3h
Click to enlarge
stereopicture of Sodium binding site 2 out of 3 in 3g3h
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3g3h. 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: Ile11, A: Leu12, A: Glu13, A: Gly59, A: Ser173, A: Hoh292, A: Hoh319, A: Hoh445, A: Hoh458, A: Hoh483, A: Hoh620, A: Hoh705,

conact list:


AtomAtomDistance (A)
NaHG13 A:Ile113.58
NaCB A:Ile114.84
NaHG12 A:Ile112.83
NaCD1 A:Ile114.17
NaC A:Ile114.77
NaCG1 A:Ile113.59
NaHD11 A:Ile113.73
NaHG23 A:Ile114.88
NaHD13 A:Ile114.49
NaHD12 A:Ile115.00
NaHB2 A:Leu123.17
NaN A:Leu123.88
NaCB A:Leu124.00
NaHB3 A:Leu124.45
NaC A:Leu123.79
NaCA A:Leu124.09
NaO A:Leu122.80
NaHG A:Leu125.00
NaH A:Leu123.49
NaHD12 A:Leu124.87
NaHB2 A:Glu134.85
NaN A:Glu135.00
NaO A:Gly594.85
NaHB2 A:Ser1734.23
NaCB A:Ser1734.60
NaHB3 A:Ser1734.02
NaO A:Hoh2923.16
NaO A:Hoh3194.84
NaO A:Hoh4453.08
NaO A:Hoh4584.32
NaO A:Hoh4832.99
NaO A:Hoh6203.79
NaO A:Hoh7052.49

interactive model:


Sodium binding site 3 out of 3 in 3g3h


Sodium binding site 3 out of 3 in 3g3h
Click to enlarge
stereopicture of Sodium binding site 3 out of 3 in 3g3h
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3g3h. 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: Leu233, B: Glu97, B: Lys98, B: Ile100, B: Asp101, B: Phe102, B: Met223, B: Arg228, A: Hoh378, A: Hoh490, A: Hoh710, B: Hoh510, B: Hoh685,

conact list:


AtomAtomDistance (A)
NaHD21 A:Leu2334.81
NaHB2 B:Glu974.86
NaOE1 B:Glu974.66
NaHG3 B:Glu972.92
NaCB B:Glu974.22
NaHB3 B:Glu974.85
NaOE2 B:Glu972.55
NaCD B:Glu973.48
NaC B:Glu973.38
NaCG B:Glu973.58
NaCA B:Glu973.74
NaHG2 B:Glu974.40
NaO B:Glu972.41
NaHA B:Glu973.27
NaN B:Lys984.58
NaC B:Lys984.99
NaHA B:Lys984.72
NaN B:Ile1004.54
NaC B:Ile1003.34
NaCA B:Ile1004.56
NaO B:Ile1002.35
NaHA B:Ile1004.92
NaH B:Ile1004.29
NaHB2 B:Asp1014.79
NaN B:Asp1013.83
NaN B:Asp1013.81
NaCB B:Asp1014.06
NaHB3 B:Asp1014.57
NaHA B:Asp1012.66
NaHA B:Asp1012.63
NaOD2 B:Asp1014.50
NaH B:Asp1014.65
NaH B:Asp1014.61
NaOD1 B:Asp1012.36
NaC B:Asp1014.70
NaC B:Asp1014.63
NaCG B:Asp1013.47
NaCA B:Asp1013.50
NaN B:Phe1024.75
NaHD2 B:Phe1024.95
NaH B:Phe1024.18
NaHG3 B:Met2234.70
NaHE3 B:Met2233.37
NaHE3 B:Met2234.49
NaSD B:Met2234.91
NaSD B:Met2233.79
NaCE B:Met2233.28
NaCE B:Met2233.66
NaHA B:Met2234.92
NaHA B:Met2234.91
NaHE1 B:Met2233.33
NaHE1 B:Met2232.97
NaHE2 B:Met2232.66
NaHE2 B:Met2233.90
NaHH22 B:Arg2283.83
NaHH21 B:Arg2284.75
NaHH12 B:Arg2284.34
NaNH2 B:Arg2284.37
NaNH1 B:Arg2284.82
NaCZ B:Arg2284.92
NaO A:Hoh3784.05
NaO A:Hoh4904.28
NaO A:Hoh7104.75
NaO B:Hoh5102.40
NaO B:Hoh6853.36

interactive model:




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