Chemical elements
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    PDB 12ca-1ai0
    PDB 1aiy-1b6z
    PDB 1b71-1bs8
    PDB 1bsk-1cao
    PDB 1caq-1ctt
    PDB 1ctu-1de6
    PDB 1def-1dy0
    PDB 1dy1-1ed6
    PDB 1ed8-1exk
    PDB 1eyf-1fj9
    PDB 1fjg-1g0e
    PDB 1g0f-1gkq
    PDB 1gkr-1ha5
    PDB 1hbm-1hso
    PDB 1hsz-1i6v
    PDB 1i73-1im5
    PDB 1iml-1jcv
    PDB 1jcz-1jy8
    PDB 1jyb-1kh4
    PDB 1kh5-1kys
    PDB 1kzo-1llm
    PDB 1llu-1m7j
    PDB 1m9j-1mwo
    PDB 1mwq-1ndv
    PDB 1ndw-1nyq
    PDB 1nyr-1os4
    PDB 1os9-1p9w
    PDB 1paa-1pud
    PDB 1pv8-1q9l
    PDB 1q9m-1qv6
    PDB 1qv7-1r6o
    PDB 1r79-1ro9
    PDB 1ror-1sfo
    PDB 1sg0-1t3k
    PDB 1t4k-1tkh
    PDB 1tkj-1u0l
    PDB 1u10-1ums
    PDB 1umt-1v67
    PDB 1v6g-1vrq
    PDB 1vs0-1wew
    PDB 1wfe-1wwf
    PDB 1wwg-1xb1
    PDB 1xb8-1xpz
    PDB 1xq0-1y5w
    PDB 1y5x-1ylk
    PDB 1ylo-1z8r
    PDB 1z93-1zkx
    PDB 1zl6-258l
    PDB 2a03-2afo
    PDB 2afs-2atq
    PDB 2au3-2bfz
    PDB 2bg2-2c3a
    PDB 2c4r-2cij
    PDB 2cim-2czr
    PDB 2d0w-2djw
    PDB 2dkc-2e1b
    PDB 2e1s-2eer
    PDB 2eex-2em4
    PDB 2em5-2eoj
    PDB 2eok-2erq
    PDB 2esf-2fa7
    PDB 2fac-2fpx
    PDB 2fqp-2g84
    PDB 2g87-2gvf
    PDB 2gvi-2han
    PDB 2hap-2huc
    PDB 2hue-2imc
    PDB 2imr-2j65
    PDB 2j6a-2jq5
    PDB 2jr7-2kfn
    PDB 2kft-2l75
    PDB 2lgv-2nx9
    PDB 2nxa-2oc8
    PDB 2occ-2osm
    PDB 2oso-2p53
    PDB 2p57-2pow
    PDB 2ppb-2q8j
    PDB 2qa1-2qp6
    PDB 2qpj-2r71
    PDB 2r74-2sod
    PDB 2srt-2v86
    PDB 2v87-2vp7
    PDB 2vpb-2vyo
    PDB 2vz5-2wey
    PDB 2wfq-2wx0
    PDB 2wx1-2xam
    PDB 2xan-2xr9
    PDB 2xrg-2ytd
    PDB 2yte-2z30
    PDB 2z3g-2zet
    PDB 2zh0-3a32
    PDB 3a36-3aoi
    PDB 3at1-3bk1
    PDB 3bk2-3byr
    PDB 3byw-3cia
    PDB 3ciz-3d08
    PDB 3d09-3dbu
    PDB 3dc3-3dp6
    PDB 3dpe-3e1w
    PDB 3e1z-3ebh
    PDB 3ebi-3epk
    PDB 3epl-3f28
      3epl
      3epm
      3epz
      3eql
      3eqn
      3eqo
      3eqt
      3ern
      3erp
      3erz
      3esj
      3esq
      3esr
      3esw
      3eu5
      3euv
      3ew8
      3ewc
      3ewd
      3ewf
      3ewj
      3ex8
      3exj
      3exl
      3eyd
      3eyl
      3eyv
      3eyw
      3eyx
      3eyy
      3ez5
      3ez8
      3ezp
      3ezt
      3f06
      3f07
      3f0d
      3f0e
      3f0f
      3f0g
      3f0r
      3f15
      3f16
      3f17
      3f18
      3f19
      3f1a
      3f1e
      3f1g
      3f28
    PDB 3f2b-3fhe
    PDB 3fhp-3ful
    PDB 3fum-3g9y
    PDB 3ga3-3gpu
    PDB 3gpx-3h2w
    PDB 3h3e-3hfy
    PDB 3hgz-3hsn
    PDB 3hso-3i8v
    PDB 3i9b-3ij6
    PDB 3ijf-3ixe
    PDB 3iz0-3k34
    PDB 3k35-3kiy
    PDB 3kj1-3kvt
    PDB 3kwa-3lat
    PDB 3lcn-3lrr
    PDB 3ls1-3m1n
    PDB 3m1v-3mek
    PDB 3men-3mru
    PDB 3ms0-3n63
    PDB 3n64-3nin
    PDB 3nis-3ny2
    PDB 3ny3-3ohc
    PDB 3ohd-3oyl
    PDB 3oym-3pih
    PDB 3pki-3r0d
    PDB 3rj7-3t74
    PDB 3t87-3u9g
    PDB 3ua7-3v24
    PDB 3v25-4agl
    PDB 4agm-4dih
    PDB 4dii-4efs
    PDB 4eg2-4fc8
    PDB 4fgm-6tli
    PDB 6tmn-9nse

Zinc in the structure of Crystal Structure Analysis of Human HDAC8 D101N Variant (pdb 3ezp)






The binding sites of Zinc atom in the structure of Crystal Structure Analysis of Human HDAC8 D101N Variant (pdb code 3ezp). This binding sites where shown with 5.0 Angstroms radius around Zinc atom.
The 3ezp structure was solved by D.P.DOWLING, S.L.GANTT, S.G.GATTIS, C.A.FIERKE, D.W.CHRISTIANON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)47.2-2.6
Space groupP1211
a (A)55.310
b (A)85.874
c (A)94.642
alpha (°)90.00
beta (°)93.60
gamma (°)90.00
Rfactor (%)22.5
Rfree (%)26.2


Zinc Binding Sites:

Zinc binding site 1 out of 2 in 3ezp


Zinc binding site 1 out of 2 in 3ezp
Click to enlarge		stereopicture of Zinc binding site 1 out of 2 in 3ezp
Click to enlarge		Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3ezp. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: His142, A: Asp178, A: Leu179, A: His180, A: Asp267, A: Gly304, A: Tyr306, A: B3n501,

conact list:


AtomAtomDistance (A)
ZnNE2 A:His1424.55
ZnCE1 A:His1424.91
ZnCB A:Asp1784.24
ZnOD2 A:Asp1781.85
ZnC A:Asp1784.84
ZnOD1 A:Asp1783.46
ZnCG A:Asp1782.97
ZnCA A:Asp1784.96
ZnN A:Leu1794.18
ZnCB A:Leu1794.42
ZnC A:Leu1794.60
ZnCA A:Leu1794.65
ZnNE2 A:His1804.13
ZnN A:His1803.80
ZnCB A:His1803.78
ZnND1 A:His1802.18
ZnCD2 A:His1804.32
ZnCE1 A:His1802.94
ZnCG A:His1803.30
ZnCA A:His1804.42
ZnCB A:Asp2674.28
ZnOD2 A:Asp2671.91
ZnOD1 A:Asp2673.28
ZnCG A:Asp2672.94
ZnN A:Gly3044.30
ZnCA A:Gly3043.96
ZnCE1 A:Tyr3064.69
ZnOH A:Tyr3064.54
ZnN3 A:B3n5012.97
ZnN3 A:B3n5012.92
ZnC1 A:B3n5012.92
ZnC1 A:B3n5012.93
ZnC6 A:B3n5014.77
ZnC6 A:B3n5014.79
ZnC5 A:B3n5014.36
ZnC5 A:B3n5014.37
ZnO2 A:B3n5012.23
ZnO2 A:B3n5012.32
ZnO4 A:B3n5012.35
ZnO4 A:B3n5012.29

interactive model:


Zinc binding site 2 out of 2 in 3ezp


Zinc binding site 2 out of 2 in 3ezp
Click to enlarge		stereopicture of Zinc binding site 2 out of 2 in 3ezp
Click to enlarge		Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3ezp. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: His142, B: Asp178, B: Leu179, B: His180, B: Asp267, B: Gly304, B: Tyr306, B: B3n500,

conact list:


AtomAtomDistance (A)
ZnNE2 B:His1424.53
ZnCE1 B:His1424.91
ZnCB B:Asp1784.23
ZnOD2 B:Asp1781.86
ZnC B:Asp1784.84
ZnOD1 B:Asp1783.57
ZnCG B:Asp1783.01
ZnCA B:Asp1784.96
ZnN B:Leu1794.14
ZnCB B:Leu1794.41
ZnC B:Leu1794.57
ZnCA B:Leu1794.62
ZnNE2 B:His1804.17
ZnN B:His1803.82
ZnCB B:His1803.78
ZnND1 B:His1802.22
ZnCD2 B:His1804.33
ZnCE1 B:His1803.01
ZnCG B:His1803.31
ZnCA B:His1804.43
ZnCB B:Asp2674.31
ZnOD2 B:Asp2671.92
ZnOD1 B:Asp2673.32
ZnCG B:Asp2672.97
ZnN B:Gly3044.35
ZnCA B:Gly3043.97
ZnCE1 B:Tyr3064.67
ZnOH B:Tyr3064.52
ZnN3 B:B3n5002.63
ZnN3 B:B3n5002.77
ZnC1 B:B3n5002.62
ZnC1 B:B3n5002.90
ZnC6 B:B3n5004.57
ZnC6 B:B3n5004.94
ZnC5 B:B3n5004.08
ZnC5 B:B3n5004.39
ZnO2 B:B3n5002.02
ZnO2 B:B3n5002.35
ZnO4 B:B3n5002.03
ZnO4 B:B3n5002.02

interactive model:
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