Chemical elements
  Nickel
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    PDB 1a5n-1g2a
    PDB 1g3v-1mn0
    PDB 1mro-1s9b
    PDB 1scr-1xmk
    PDB 1xu1-2cg5
      1xu1
      1xu2
      1xx7
      1y1o
      1ynu
      1yq9
      1yqw
      1yrq
      1ysj
      1ziu
      1zle
      1znv
      1zqr
      1zrr
      1ztc
      1zvf
      1zx8
      260l
      2adw
      2afb
      2ai7
      2ai8
      2ai9
      2aia
      2aie
      2aj7
      2ap9
      2arp
      2atf
      2aw2
      2bdg
      2be6
      2bj1
      2bj7
      2bj8
      2bj9
      2bmo
      2bmq
      2bmr
      2c0n
      2c21
      2c2l
      2c5d
      2c7v
      2c9h
      2c9w
      2cad
      2caj
      2cfv
      2cg5
    PDB 2cqz-2jih
    PDB 2jk8-2v4b
    PDB 2vbq-3c2q
    PDB 3c6c-3h85
    PDB 3hdp-3kvb
    PDB 3l1m-3o00
    PDB 3o01-4ubp
    PDB 8icl-9ant

Nickel in the structure of Conserved Hypothetical Protein From Pyrococcus Furiosus Pfu- 403030-001 (pdb 1xx7)






The binding sites of Nickel atom in the structure of Conserved Hypothetical Protein From Pyrococcus Furiosus Pfu- 403030-001 (pdb code 1xx7). This binding sites where shown with 5.0 Angstroms radius around Nickel atom.
The 1xx7 structure was solved by L.CHEN, W.TEMPEL, J.HABEL, W.ZHOU, D.NGUYEN, S.-H.CHANG, D.LEE, L.-L.C.KELLEY, B.D.DILLARD, Z.-J.LIU, S.BRIDGER, J.C.ENEH, R.C.HOPKINS, F.E.JENNEY JR, H.-S.LEE, T.LI, F.L.POOLE II, C.SHAH, F.J.SUGAR, M.W.W.ADAMS, W.B.ARENDALL III, J.S.RICHARDSON, D.C.RICHARDSON, J.P.ROSE, B.-C.WANG, SOUTHEAST COLLABORATORYFOR STRUCTURAL GENOMICS (SECSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)83.3-2.3
Space groupP212121
a (A)98.073
b (A)111.335
c (A)125.984
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)20
Rfree (%)24.6


Nickel Binding Sites:

Nickel binding site 1 out of 6 in 1xx7


Nickel binding site 1 out of 6 in 1xx7
Click to enlarge
stereopicture of Nickel binding site 1 out of 6 in 1xx7
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 1xx7. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Arg16, A: His33, A: Val37, A: His67, A: Asp68, A: Tyr109, A: Asp124, A: Unx2019, A: Hoh1038,

conact list:


AtomAtomDistance (A)
NiNH2 A:Arg164.34
NiNE2 A:His332.23
NiND1 A:His334.36
NiCD2 A:His333.06
NiCE1 A:His333.32
NiCG A:His334.27
NiCG2 A:Val374.66
NiNE2 A:His672.32
NiND1 A:His674.40
NiCD2 A:His673.23
NiCE1 A:His673.32
NiCG A:His674.39
NiCB A:Asp684.29
NiOD2 A:Asp682.14
NiOD1 A:Asp683.31
NiCG A:Asp683.01
NiOH A:Tyr1094.27
NiCB A:Asp1244.28
NiOD2 A:Asp1243.48
NiOD1 A:Asp1242.02
NiCG A:Asp1243.04
NiUNK A:Unx20193.85
NiO A:Hoh10383.91

interactive model:


Nickel binding site 2 out of 6 in 1xx7


Nickel binding site 2 out of 6 in 1xx7
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stereopicture of Nickel binding site 2 out of 6 in 1xx7
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 1xx7. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: Arg16, B: His33, B: Val37, B: His67, B: Asp68, B: Tyr109, B: Asp124, B: Hoh1040, B: Hoh1041,

conact list:


AtomAtomDistance (A)
NiNH2 B:Arg164.23
NiNE2 B:His332.19
NiND1 B:His334.31
NiCD2 B:His333.11
NiCE1 B:His333.21
NiCG B:His334.29
NiCG2 B:Val374.62
NiNE2 B:His672.35
NiND1 B:His674.42
NiCD2 B:His673.12
NiCE1 B:His673.42
NiCG B:His674.31
NiCB B:Asp684.37
NiOD2 B:Asp682.23
NiOD1 B:Asp683.35
NiCG B:Asp683.08
NiOH B:Tyr1094.52
NiCB B:Asp1244.21
NiOD2 B:Asp1243.49
NiOD1 B:Asp1241.96
NiCG B:Asp1243.01
NiCA B:Asp1244.90
NiO B:Hoh10404.23
NiO B:Hoh10413.96

interactive model:


Nickel binding site 3 out of 6 in 1xx7


Nickel binding site 3 out of 6 in 1xx7
Click to enlarge
stereopicture of Nickel binding site 3 out of 6 in 1xx7
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Nickel in the PDB 1xx7. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: C: Arg16, C: His33, C: Val37, C: His67, C: Asp68, C: Tyr109, C: Asp124, C: Hoh1042, C: Hoh1043,

conact list:


AtomAtomDistance (A)
NiNH2 C:Arg164.15
NiNE2 C:His332.32
NiND1 C:His334.45
NiCD2 C:His333.11
NiCE1 C:His333.42
NiCG C:His334.33
NiCG2 C:Val374.75
NiNE2 C:His672.42
NiND1 C:His674.48
NiCD2 C:His673.17
NiCE1 C:His673.48
NiCG C:His674.37
NiCB C:Asp684.19
NiOD2 C:Asp682.15
NiOD1 C:Asp683.22
NiCG C:Asp682.94
NiOH C:Tyr1094.42
NiCB C:Asp1244.35
NiOD2 C:Asp1243.68
NiOD1 C:Asp1242.02
NiCG C:Asp1243.15
NiO C:Hoh10424.41
NiO C:Hoh10433.92

interactive model:


Nickel binding site 4 out of 6 in 1xx7


Nickel binding site 4 out of 6 in 1xx7
Click to enlarge
stereopicture of Nickel binding site 4 out of 6 in 1xx7
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Nickel in the PDB 1xx7. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: D: Arg16, D: His33, D: Val37, D: His67, D: Asp68, D: Tyr109, D: Asp124, D: Hoh1052,

conact list:


AtomAtomDistance (A)
NiNH2 D:Arg164.24
NiNE2 D:His332.25
NiND1 D:His334.35
NiCD2 D:His333.14
NiCE1 D:His333.28
NiCG D:His334.32
NiCG2 D:Val374.70
NiNE2 D:His672.51
NiND1 D:His674.61
NiCD2 D:His673.25
NiCE1 D:His673.60
NiCG D:His674.48
NiCB D:Asp684.29
NiOD2 D:Asp682.23
NiOD1 D:Asp683.22
NiCG D:Asp682.99
NiOH D:Tyr1094.22
NiCB D:Asp1244.37
NiOD2 D:Asp1243.39
NiOD1 D:Asp1242.16
NiCG D:Asp1243.09
NiO D:Hoh10523.95

interactive model:


Nickel binding site 5 out of 6 in 1xx7


Nickel binding site 5 out of 6 in 1xx7
Click to enlarge
stereopicture of Nickel binding site 5 out of 6 in 1xx7
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Nickel in the PDB 1xx7. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: E: Arg16, E: His33, E: Val37, E: His67, E: Asp68, E: Tyr109, E: Asp124, E: Hoh1050,

conact list:


AtomAtomDistance (A)
NiNH2 E:Arg164.27
NiNE2 E:His332.17
NiND1 E:His334.30
NiCD2 E:His333.03
NiCE1 E:His333.23
NiCG E:His334.24
NiCG2 E:Val374.70
NiNE2 E:His672.29
NiND1 E:His674.35
NiCD2 E:His673.16
NiCE1 E:His673.30
NiCG E:His674.31
NiCB E:Asp684.35
NiOD2 E:Asp682.29
NiOD1 E:Asp683.45
NiCG E:Asp683.13
NiOH E:Tyr1094.43
NiCB E:Asp1244.34
NiOD2 E:Asp1243.64
NiOD1 E:Asp1242.03
NiCG E:Asp1243.14
NiCA E:Asp1244.90
NiO E:Hoh10504.12

interactive model:


Nickel binding site 6 out of 6 in 1xx7


Nickel binding site 6 out of 6 in 1xx7
Click to enlarge
stereopicture of Nickel binding site 6 out of 6 in 1xx7
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Nickel in the PDB 1xx7. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: F: Arg16, F: His33, F: Val37, F: His67, F: Asp68, F: Tyr109, F: Asp124, F: Hoh1051,

conact list:


AtomAtomDistance (A)
NiNH2 F:Arg164.24
NiNE2 F:His332.18
NiND1 F:His334.30
NiCD2 F:His333.08
NiCE1 F:His333.22
NiCG F:His334.27
NiCG2 F:Val374.73
NiNE2 F:His672.46
NiND1 F:His674.52
NiCD2 F:His673.23
NiCE1 F:His673.51
NiCG F:His674.42
NiCB F:Asp684.28
NiOD2 F:Asp682.21
NiOD1 F:Asp683.27
NiCG F:Asp683.00
NiOH F:Tyr1094.37
NiCB F:Asp1244.34
NiOD2 F:Asp1243.41
NiOD1 F:Asp1242.09
NiCG F:Asp1243.06
NiO F:Hoh10513.97

interactive model:




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