Chemical elements
  Cobalt
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    PDB 1a0c-1epy
    PDB 1et4-1k7y
      1et4
      1f69
      1f78
      1f79
      1f7h
      1f7i
      1fa6
      1fd5
      1fdg
      1fe2
      1fn1
      1fn2
      1fof
      1fqr
      1fsq
      1fx7
      1g16
      1g5l
      1g64
      1gid
      1gj2
      1gqi
      1gqj
      1gqk
      1gql
      1gwm
      1h0n
      1h0o
      1h41
      1hgw
      1hv9
      1i3a
      1i9c
      1iab
      1igx
      1igz
      1ih1
      1in4
      1in6
      1iqx
      1ire
      1iwb
      1iwp
      1ixj
      1j7k
      1jn1
      1jym
      1k1e
      1k2l
      1k7y
    PDB 1k98-1r6x
    PDB 1r8k-1v9b
    PDB 1vl3-212d
    PDB 222d-2eff
    PDB 2ehd-2j3z
    PDB 2j4j-2r1p
    PDB 2r2s-331d
    PDB 362d-3fqw
    PDB 3ft6-3igy
    PDB 3igz-3o0n
    PDB 3o0o-4req
    PDB 4xim-9icb

Cobalt in the structure of Crystals Of Peptide Deformylase From Plasmodium Falciparum With Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design (pdb 1jym)






The binding sites of Cobalt atom in the structure of Crystals Of Peptide Deformylase From Plasmodium Falciparum With Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design (pdb code 1jym). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom.
The 1jym structure was solved by A.KUMAR, K.T.NGUYEN, S.SRIVATHSAN, B.ORNSTEIN, S.TURLEY, I.HIRSH, D.PEI, W.G.J.HOL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)30.0-2.8
Space groupP41
a (A)121.263
b (A)121.263
c (A)177.272
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)23.1
Rfree (%)29.6


Cobalt Binding Sites:

Cobalt binding site 1 out of 10 in 1jym


Cobalt binding site 1 out of 10 in 1jym
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stereopicture of Cobalt binding site 1 out of 10 in 1jym
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 1jym. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Gln111, A: Gly154, A: Cys155, A: Leu156, A: His196, A: Glu197, A: His200, A: Hoh9319,

conact list:


AtomAtomDistance (A)
CoNE2 A:Gln1113.58
CoOE1 A:Gln1113.07
CoCD A:Gln1113.46
CoCG A:Gln1114.57
CoO A:Gly1544.70
CoCB A:Cys1553.46
CoSG A:Cys1552.25
CoC A:Cys1554.74
CoCA A:Cys1553.99
CoN A:Leu1564.49
CoNE2 A:His1962.00
CoND1 A:His1964.11
CoCD2 A:His1962.64
CoCE1 A:His1963.19
CoCG A:His1963.89
CoOE1 A:Glu1974.93
CoOE2 A:Glu1974.75
CoNE2 A:His2002.00
CoND1 A:His2004.10
CoCD2 A:His2002.91
CoCE1 A:His2003.05
CoCG A:His2004.08
CoO A:Hoh93192.10

interactive model:


Cobalt binding site 2 out of 10 in 1jym


Cobalt binding site 2 out of 10 in 1jym
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stereopicture of Cobalt binding site 2 out of 10 in 1jym
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 1jym. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: Gln111, B: Gly154, B: Cys155, B: Leu156, B: His196, B: Glu197, B: His200, B: Hoh9320,

conact list:


AtomAtomDistance (A)
CoNE2 B:Gln1114.33
CoOE1 B:Gln1113.14
CoCD B:Gln1113.99
CoO B:Gly1544.76
CoN B:Cys1554.93
CoCB B:Cys1552.84
CoSG B:Cys1552.28
CoC B:Cys1554.50
CoCA B:Cys1553.72
CoN B:Leu1564.51
CoNE2 B:His1962.00
CoND1 B:His1964.14
CoCD2 B:His1962.69
CoCE1 B:His1963.18
CoCG B:His1963.95
CoOE1 B:Glu1974.17
CoOE2 B:Glu1974.65
CoCD B:Glu1974.68
CoNE2 B:His2001.99
CoND1 B:His2004.09
CoCD2 B:His2002.96
CoCE1 B:His2002.99
CoCG B:His2004.11
CoO B:Hoh93202.11

interactive model:


Cobalt binding site 3 out of 10 in 1jym


Cobalt binding site 3 out of 10 in 1jym
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stereopicture of Cobalt binding site 3 out of 10 in 1jym
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 1jym. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: C: Gln111, C: Gly154, C: Cys155, C: Leu156, C: His196, C: Glu197, C: His200, C: Hoh2316, C: Hoh9321,

conact list:


AtomAtomDistance (A)
CoNE2 C:Gln1114.29
CoOE1 C:Gln1113.60
CoCD C:Gln1114.23
CoO C:Gly1544.72
CoN C:Cys1554.83
CoCB C:Cys1553.03
CoSG C:Cys1552.27
CoC C:Cys1554.31
CoCA C:Cys1553.60
CoN C:Leu1564.12
CoNE2 C:His1962.01
CoND1 C:His1964.14
CoCD2 C:His1962.64
CoCE1 C:His1963.21
CoCG C:His1963.91
CoOE1 C:Glu1974.66
CoOE2 C:Glu1974.22
CoCD C:Glu1974.79
CoNE2 C:His2002.02
CoND1 C:His2004.02
CoCD2 C:His2003.11
CoCE1 C:His2002.87
CoCG C:His2004.17
CoO C:Hoh23163.66
CoO C:Hoh93212.06

interactive model:


Cobalt binding site 4 out of 10 in 1jym


Cobalt binding site 4 out of 10 in 1jym
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stereopicture of Cobalt binding site 4 out of 10 in 1jym
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 1jym. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: D: Gln111, D: Gly154, D: Cys155, D: Leu156, D: His196, D: Glu197, D: His200, D: Hoh3308, D: Hoh9322,

conact list:


AtomAtomDistance (A)
CoNE2 D:Gln1114.10
CoOE1 D:Gln1113.42
CoCD D:Gln1114.07
CoO D:Gly1544.59
CoN D:Cys1554.66
CoCB D:Cys1552.74
CoSG D:Cys1552.26
CoC D:Cys1554.18
CoCA D:Cys1553.42
CoN D:Leu1564.18
CoNE2 D:His1962.00
CoND1 D:His1964.14
CoCD2 D:His1962.75
CoCE1 D:His1963.15
CoCG D:His1963.99
CoOE1 D:Glu1974.69
CoOE2 D:Glu1974.86
CoNE2 D:His2002.03
CoND1 D:His2004.01
CoCD2 D:His2002.88
CoCE1 D:His2003.02
CoCG D:His2003.99
CoO D:Hoh33084.96
CoO D:Hoh93222.03

interactive model:


Cobalt binding site 5 out of 10 in 1jym


Cobalt binding site 5 out of 10 in 1jym
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stereopicture of Cobalt binding site 5 out of 10 in 1jym
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cobalt in the PDB 1jym. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: E: Gln111, E: Gly154, E: Cys155, E: Leu156, E: His196, E: Glu197, E: His200, E: Hoh9323,

conact list:


AtomAtomDistance (A)
CoNE2 E:Gln1113.33
CoOE1 E:Gln1113.85
CoCD E:Gln1113.84
CoO E:Gly1544.77
CoCB E:Cys1553.43
CoSG E:Cys1552.24
CoC E:Cys1554.82
CoCA E:Cys1554.03
CoN E:Leu1564.69
CoNE2 E:His1962.00
CoND1 E:His1964.12
CoCD2 E:His1962.73
CoCE1 E:His1963.14
CoCG E:His1963.96
CoOE1 E:Glu1974.74
CoOE2 E:Glu1974.33
CoCD E:Glu1974.84
CoNE2 E:His2002.03
CoND1 E:His2004.06
CoCD2 E:His2003.12
CoCE1 E:His2002.90
CoCG E:His2004.20
CoO E:Hoh93232.09

interactive model:


Cobalt binding site 6 out of 10 in 1jym


Cobalt binding site 6 out of 10 in 1jym
Click to enlarge
stereopicture of Cobalt binding site 6 out of 10 in 1jym
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cobalt in the PDB 1jym. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: F: Gln111, F: Gly154, F: Cys155, F: Leu156, F: His196, F: Glu197, F: His200, F: Hoh5310, F: Hoh5314, F: Hoh9324,

conact list:


AtomAtomDistance (A)
CoNE2 F:Gln1114.08
CoOE1 F:Gln1113.25
CoCD F:Gln1113.91
CoO F:Gly1544.81
CoCB F:Cys1553.66
CoSG F:Cys1552.24
CoCA F:Cys1554.30
CoN F:Leu1564.94
CoNE2 F:His1961.99
CoND1 F:His1964.13
CoCD2 F:His1962.67
CoCE1 F:His1963.19
CoCG F:His1963.93
CoOE1 F:Glu1973.63
CoOE2 F:Glu1974.28
CoCD F:Glu1974.24
CoNE2 F:His2001.96
CoND1 F:His2004.10
CoCD2 F:His2002.66
CoCE1 F:His2003.15
CoCG F:His2003.91
CoO F:Hoh53103.76
CoO F:Hoh53144.70
CoO F:Hoh93242.14

interactive model:


Cobalt binding site 7 out of 10 in 1jym


Cobalt binding site 7 out of 10 in 1jym
Click to enlarge
stereopicture of Cobalt binding site 7 out of 10 in 1jym
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cobalt in the PDB 1jym. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: G: Gln111, G: Gly154, G: Cys155, G: Leu156, G: His196, G: Glu197, G: His200, G: Hoh6309, G: Hoh9325,

conact list:


AtomAtomDistance (A)
CoNE2 G:Gln1114.79
CoOE1 G:Gln1113.19
CoCD G:Gln1114.21
CoO G:Gly1544.69
CoCB G:Cys1553.05
CoSG G:Cys1552.25
CoC G:Cys1554.59
CoCA G:Cys1553.88
CoN G:Leu1564.67
CoNE2 G:His1961.99
CoND1 G:His1964.12
CoCD2 G:His1962.71
CoCE1 G:His1963.16
CoCG G:His1963.96
CoOE1 G:Glu1974.36
CoOE2 G:Glu1974.50
CoCD G:Glu1974.76
CoNE2 G:His2002.03
CoND1 G:His2004.06
CoCD2 G:His2003.04
CoCE1 G:His2002.95
CoCG G:His2004.14
CoO G:Hoh63093.28
CoO G:Hoh93252.06

interactive model:


Cobalt binding site 8 out of 10 in 1jym


Cobalt binding site 8 out of 10 in 1jym
Click to enlarge
stereopicture of Cobalt binding site 8 out of 10 in 1jym
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cobalt in the PDB 1jym. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: H: Gln111, H: Gly154, H: Cys155, H: Leu156, H: His196, H: Glu197, H: His200, H: Hoh7302, H: Hoh9326,

conact list:


AtomAtomDistance (A)
CoNE2 H:Gln1113.88
CoOE1 H:Gln1112.39
CoCD H:Gln1113.36
CoCG H:Gln1114.54
CoO H:Gly1545.00
CoCB H:Cys1553.72
CoSG H:Cys1552.23
CoC H:Cys1554.96
CoCA H:Cys1554.24
CoN H:Leu1564.57
CoNE2 H:His1962.00
CoND1 H:His1964.15
CoCD2 H:His1962.62
CoCE1 H:His1963.23
CoCG H:His1963.91
CoOE1 H:Glu1973.79
CoOE2 H:Glu1974.55
CoCD H:Glu1974.44
CoNE2 H:His2002.00
CoND1 H:His2003.98
CoCD2 H:His2002.68
CoCE1 H:His2003.08
CoCG H:His2003.83
CoO H:Hoh73024.77
CoO H:Hoh93262.11

interactive model:


Cobalt binding site 9 out of 10 in 1jym


Cobalt binding site 9 out of 10 in 1jym
Click to enlarge
stereopicture of Cobalt binding site 9 out of 10 in 1jym
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cobalt in the PDB 1jym. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: I: Gln111, I: Gly154, I: Cys155, I: Leu156, I: His196, I: Glu197, I: His200, I: Hoh9327,

conact list:


AtomAtomDistance (A)
CoNE2 I:Gln1114.05
CoOE1 I:Gln1112.57
CoCD I:Gln1113.57
CoCG I:Gln1114.78
CoO I:Gly1544.91
CoCB I:Cys1553.47
CoSG I:Cys1552.23
CoC I:Cys1554.75
CoCA I:Cys1554.04
CoN I:Leu1564.51
CoNE2 I:His1962.00
CoND1 I:His1964.13
CoCD2 I:His1962.62
CoCE1 I:His1963.21
CoCG I:His1963.90
CoOE1 I:Glu1974.47
CoOE2 I:Glu1974.60
CoCD I:Glu1974.80
CoNE2 I:His2002.00
CoND1 I:His2004.08
CoCD2 I:His2002.88
CoCE1 I:His2003.04
CoCG I:His2004.05
CoO I:Hoh93272.12

interactive model:


Cobalt binding site 10 out of 10 in 1jym


Cobalt binding site 10 out of 10 in 1jym
Click to enlarge
stereopicture of Cobalt binding site 10 out of 10 in 1jym
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Cobalt in the PDB 1jym. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: J: Gln111, J: Cys155, J: Leu156, J: His196, J: Glu197, J: His200, J: Hoh9328,

conact list:


AtomAtomDistance (A)
CoNE2 J:Gln1113.71
CoOE1 J:Gln1112.88
CoCD J:Gln1113.56
CoCG J:Gln1114.84
CoCB J:Cys1553.44
CoSG J:Cys1552.24
CoC J:Cys1554.84
CoCA J:Cys1554.21
CoN J:Leu1564.57
CoNE2 J:His1961.98
CoND1 J:His1964.12
CoCD2 J:His1962.68
CoCE1 J:His1963.16
CoCG J:His1963.93
CoOE1 J:Glu1974.03
CoOE2 J:Glu1974.32
CoCD J:Glu1974.44
CoNE2 J:His2002.01
CoND1 J:His2004.05
CoCD2 J:His2003.06
CoCE1 J:His2002.92
CoCG J:His2004.16
CoO J:Hoh93282.10

interactive model:




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