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      3ow2
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      3oyo
      3p0q
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      3p2y
      3p3e
      3p3q
      3p7z
      3p8n
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      3pa8
      3pak
      3paq
      3pbx
      3pc4
      3peb
      3pfv
      3pio
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      3pj0
      3ply
      3pm8
      3pml
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      3pnc
      3pnx
      3pru
      3pvz
      3pzj
      3q2i
      3q3u
      3q94
      3q9b
      3q9c
      3q9e
      3q9f
      3qae
      3qau
      3qf9
      3qfh
      3qhx
      3qi6
      3qlj
      3qoo
      3qsr
      3qst
      3qto
      3qtv
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Sodium in the structure of Crystal Structure of A Polymerase Lambda Variant With A Dgtp Analog Opposite A Templating T (pdb 3pml)






The binding sites of Sodium atom in the structure of Crystal Structure of A Polymerase Lambda Variant With A Dgtp Analog Opposite A Templating T (pdb code 3pml). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 3pml structure was solved by K.BEBENEK, L.C.PEDERSEN, T.A.KUNKEL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)25.0-2.6
Space groupP21212
a (A)97.038
b (A)191.570
c (A)59.084
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)23.3
Rfree (%)27.1


Sodium Binding Sites:

Sodium binding site 1 out of 3 in 3pml


Sodium binding site 1 out of 3 in 3pml
Click to enlarge
stereopicture of Sodium binding site 1 out of 3 in 3pml
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3pml. 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: Ser339, A: Asn340, A: Ile341, A: Trp342, A: Gly343, A: Ala344, A: Gly345, H: Dt4, H: Da5, A: Hoh61, H: Hoh19, H: Hoh29, H: Hoh78,

conact list:


AtomAtomDistance (A)
NaO A:Ser3392.37
NaCB A:Ser3394.74
NaC A:Ser3393.36
NaCA A:Ser3394.17
NaO A:Asn3404.33
NaN A:Asn3404.23
NaC A:Asn3404.03
NaCA A:Asn3404.33
NaO A:Ile3412.76
NaN A:Ile3414.09
NaC A:Ile3413.54
NaCA A:Ile3414.50
NaN A:Trp3424.12
NaC A:Trp3424.54
NaCA A:Trp3424.05
NaN A:Gly3434.30
NaO A:Ala3442.67
NaN A:Ala3444.16
NaC A:Ala3443.79
NaCB A:Ala3444.90
NaCA A:Ala3444.50
NaN A:Gly3454.79
NaCA A:Gly3454.95
NaO3' H:Dt44.62
NaOP1 H:Da52.54
NaP H:Da53.55
NaOP2 H:Da53.68
NaO5' H:Da54.72
NaO A:Hoh613.77
NaO H:Hoh193.39
NaO H:Hoh292.45
NaO H:Hoh784.92

interactive model:


Sodium binding site 2 out of 3 in 3pml


Sodium binding site 2 out of 3 in 3pml
Click to enlarge
stereopicture of Sodium binding site 2 out of 3 in 3pml
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3pml. 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: B: Ser339, B: Asn340, B: Ile341, B: Trp342, B: Gly343, B: Ala344, B: Gly345, F: Dt4, F: Da5, B: Hoh15, B: Hoh111,

conact list:


AtomAtomDistance (A)
NaO B:Ser3392.29
NaCB B:Ser3394.53
NaC B:Ser3393.40
NaCA B:Ser3394.13
NaO B:Asn3404.91
NaN B:Asn3404.40
NaC B:Asn3404.41
NaCA B:Asn3404.58
NaO B:Ile3413.13
NaN B:Ile3414.28
NaC B:Ile3413.88
NaCA B:Ile3414.78
NaN B:Trp3424.43
NaC B:Trp3424.78
NaCA B:Trp3424.32
NaN B:Gly3434.34
NaO B:Ala3442.83
NaN B:Ala3444.31
NaC B:Ala3443.87
NaCA B:Ala3444.62
NaN B:Gly3454.79
NaCA B:Gly3454.91
NaO3' F:Dt44.71
NaOP1 F:Da52.54
NaP F:Da53.43
NaOP2 F:Da53.46
NaO5' F:Da54.38
NaO B:Hoh152.23
NaO B:Hoh1113.55

interactive model:


Sodium binding site 3 out of 3 in 3pml


Sodium binding site 3 out of 3 in 3pml
Click to enlarge
stereopicture of Sodium binding site 3 out of 3 in 3pml
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3pml. 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: B: Ala299, B: Cys300, B: Ser301, B: Ile302, B: Pro303, B: Gly304, B: Ile305, B: Gly306, G: Dc2, G: Dc3, B: Hoh135,

conact list:


AtomAtomDistance (A)
NaO B:Ala2994.88
NaO B:Cys3002.27
NaC B:Cys3003.46
NaCA B:Cys3004.31
NaO B:Ser3014.30
NaN B:Ser3014.40
NaC B:Ser3014.03
NaCA B:Ser3014.46
NaO B:Ile3022.84
NaN B:Ile3024.02
NaC B:Ile3023.50
NaCA B:Ile3024.37
NaN B:Pro3034.04
NaC B:Pro3034.82
NaCA B:Pro3034.12
NaN B:Gly3044.59
NaO B:Ile3052.73
NaN B:Ile3054.37
NaC B:Ile3053.91
NaCA B:Ile3054.64
NaN B:Gly3064.93
NaO3' G:Dc24.83
NaOP1 G:Dc32.81
NaP G:Dc33.84
NaOP2 G:Dc33.94
NaO5' G:Dc34.98
NaO B:Hoh1352.08

interactive model:




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