Chemical elements
  Sodium
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    PDB 131d-1bli
    PDB 1bph-1d10
    PDB 1d11-1ej2
    PDB 1eja-1gb5
    PDB 1gb6-1goh
    PDB 1gq2-1ikp
    PDB 1ikq-1jz1
    PDB 1jz2-1kvs
    PDB 1kvt-1me8
    PDB 1mg2-1nsz
    PDB 1nta-1oyt
    PDB 1p0s-1qjs
    PDB 1qnj-1s5d
    PDB 1s5e-1tjp
    PDB 1tk6-1uxt
    PDB 1uxu-1vzq
    PDB 1w15-1xc6
    PDB 1xcu-1yf1
    PDB 1ygg-1zko
    PDB 1zkp-2afh
    PDB 2agv-2bhc
    PDB 2bhp-2cc6
    PDB 2cc7-2dec
    PDB 2deg-2ein
    PDB 2eit-2fjb
    PDB 2fld-2gg8
    PDB 2gg9-2h9j
    PDB 2h9k-2ien
    PDB 2ieo-2jih
    PDB 2jin-2omd
      2jin
      2jja
      2jjz
      2jkh
      2jlm
      2jln
      2jlo
      2mat
      2meb
      2med
      2mee
      2mef
      2meg
      2meh
      2mei
      2nmx
      2nmy
      2nn1
      2nnk
      2nqd
      2nql
      2nrv
      2nw6
      2nwh
      2nwx
      2nxb
      2nz2
      2o0r
      2o11
      2o12
      2o34
      2o4f
      2o5w
      2o8m
      2o9j
      2o9s
      2oaj
      2obv
      2occ
      2ody
      2ofi
      2og5
      2oga
      2oge
      2ogg
      2oj0
      2ok7
      2okq
      2oln
      2omd
    PDB 2omg-2p77
    PDB 2p78-2q68
    PDB 2q69-2qz7
    PDB 2qzi-2v35
    PDB 2v3h-2vwo
    PDB 2vx4-2wig
    PDB 2wij-2x1z
    PDB 2x20-2xmk
    PDB 2xmm-2zfq
    PDB 2zfr-3a6s
    PDB 3a6t-3b1e
    PDB 3b2n-3bos
    PDB 3bov-3ccr
    PDB 3ccs-3d7r
    PDB 3d97-3e3y
    PDB 3e40-3erp
    PDB 3euw-3fgw
    PDB 3fh4-3g3r
    PDB 3g3s-3gxw
    PDB 3gyz-3hwt
    PDB 3hww-3ijp
    PDB 3imm-3k0g
    PDB 3k13-3l7x
    PDB 3l88-3max
    PDB 3mbb-3mr1
    PDB 3mty-3nu3
    PDB 3nu4-3ot1
    PDB 3ow2-3qwc
    PDB 3qx5-3tfr
    PDB 3tfs-3v6o
    PDB 3v72-4ag2
    PDB 4aga-4eae
    PDB 4ecn-4g8t
    PDB 4gdt-8icw
    PDB 8icx-9icy

Sodium in the structure of Crystal Structure of 3-Methyladenine Dna Glycosylase I (Tag) Bound to Dna/3MA (pdb 2ofi)






The binding sites of Sodium atom in the structure of Crystal Structure of 3-Methyladenine Dna Glycosylase I (Tag) Bound to Dna/3MA (pdb code 2ofi). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 2ofi structure was solved by A.H.METZ, T.HOLLIS, B.F.EICHMAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)50.0-1.9
Space groupP63
a (A)101.963
b (A)101.963
c (A)55.461
alpha (°)90.00
beta (°)90.00
gamma (°)120.00
Rfactor (%)17.6
Rfree (%)19.8


Sodium Binding Sites:

Sodium binding site 1 out of 1 in 2ofi


Sodium binding site 1 out of 1 in 2ofi
Click to enlarge
stereopicture of Sodium binding site 1 out of 1 in 2ofi
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2ofi. 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: Trp117, A: Ser118, A: Phe119, A: Val120, A: Asp121, A: Gly122, A: Hoh416, A: Hoh417, A: Hoh418, A: Hoh419,

conact list:


AtomAtomDistance (A)
NaCB A:Trp1174.46
NaC A:Trp1173.39
NaCE3 A:Trp1174.78
NaCA A:Trp1174.41
NaO A:Trp1172.25
NaO A:Ser1184.69
NaN A:Ser1184.19
NaC A:Ser1184.44
NaCA A:Ser1184.15
NaN A:Phe1194.97
NaO A:Val1202.25
NaN A:Val1204.13
NaCB A:Val1204.53
NaCG2 A:Val1204.15
NaC A:Val1203.35
NaCG1 A:Val1204.82
NaCA A:Val1204.14
NaN A:Asp1214.33
NaC A:Asp1214.86
NaCA A:Asp1214.54
NaO A:Gly1224.70
NaN A:Gly1224.28
NaO A:Hoh4164.72
NaO A:Hoh4172.83
NaO A:Hoh4182.14
NaO A:Hoh4192.57

interactive model:




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