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    PDB 2vpb-2vyo
    PDB 2vz5-2wey
    PDB 2wfq-2wx0
    PDB 2wx1-2xam
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    PDB 2yte-2z30
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      3ls1
      3ls6
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      3lvr
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      3lwq
      3lwr
      3lwu
      3lwv
      3lx3
      3lxe
      3lxg
      3ly0
      3ly2
      3lyr
      3lze
      3lzn
      3m0a
      3m0d
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      3m15
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    PDB 3m1v-3mek
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    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 Of Metallo Peptidase From Rhodobacter Sphaeroides Liganded With Phosphinate Mimic of Dipeptide L- Ala-D-Ala (pdb 3ly0)






The binding sites of Zinc atom in the structure of Crystal Structure Of Metallo Peptidase From Rhodobacter Sphaeroides Liganded With Phosphinate Mimic of Dipeptide L- Ala-D-Ala (pdb code 3ly0). This binding sites where shown with 5.0 Angstroms radius around Zinc atom.
The 3ly0 structure was solved by A.A.FEDOROV, E.V.FEDOROV, J.CUMMINGS, F.M.RAUSHEL, S.K.BURLEY, S.C.ALMO, NEW YORK SGX RESEARCH CENTER FOR STRUCTURALGENOMICS (NYSGXRC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)33.1-1.4
Space groupP1
a (A)46.649
b (A)50.325
c (A)81.436
alpha (°)83.65
beta (°)73.64
gamma (°)67.65
Rfactor (%)16.9
Rfree (%)19.2


Zinc Binding Sites:

Zinc binding site 1 out of 4 in 3ly0


Zinc binding site 1 out of 4 in 3ly0
Click to enlarge
stereopicture of Zinc binding site 1 out of 4 in 3ly0
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3ly0. 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: His11, A: Asp13, A: Ala54, A: Tyr56, A: Glu137, A: His231, A: Asp304, A: Ly0363, A: Zn365, A: Hoh453,

conact list:


AtomAtomDistance (A)
ZnNE2 A:His112.23
ZnND1 A:His114.30
ZnCD2 A:His113.26
ZnCE1 A:His113.15
ZnCG A:His114.39
ZnCB A:Asp134.07
ZnOD2 A:Asp132.22
ZnOD1 A:Asp132.26
ZnCG A:Asp132.55
ZnCA A:Asp134.89
ZnCB A:Ala544.30
ZnCB A:Tyr564.71
ZnCG A:Tyr564.90
ZnOE1 A:Glu1372.14
ZnCB A:Glu1374.86
ZnOE2 A:Glu1373.21
ZnCD A:Glu1373.03
ZnCG A:Glu1374.45
ZnNE2 A:His2314.46
ZnOD1 A:Asp3043.84
ZnN1 A:Ly03632.33
ZnP A:Ly03633.20
ZnO32 A:Ly03633.90
ZnC4 A:Ly03634.76
ZnC1 A:Ly03634.56
ZnO31 A:Ly03632.21
ZnC2 A:Ly03633.14
ZnZN A:Zn3653.68
ZnO A:Hoh4534.93

interactive model:


Zinc binding site 2 out of 4 in 3ly0


Zinc binding site 2 out of 4 in 3ly0
Click to enlarge
stereopicture of Zinc binding site 2 out of 4 in 3ly0
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3ly0. 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: His11, A: Glu137, A: Trp164, A: His210, A: His231, A: Arg242, A: Asp304, A: Ly0363, A: Zn364,

conact list:


AtomAtomDistance (A)
ZnNE2 A:His113.98
ZnCD2 A:His114.57
ZnCE1 A:His114.43
ZnOE1 A:Glu1373.80
ZnOE2 A:Glu1372.10
ZnCD A:Glu1373.26
ZnCG A:Glu1374.46
ZnCD1 A:Trp1644.24
ZnNE1 A:Trp1644.13
ZnNE2 A:His2102.20
ZnND1 A:His2104.30
ZnCD2 A:His2103.17
ZnCE1 A:His2103.18
ZnCG A:His2104.32
ZnNE2 A:His2312.24
ZnND1 A:His2314.35
ZnCD2 A:His2313.18
ZnCE1 A:His2313.25
ZnCG A:His2314.35
ZnCZ A:Arg2424.67
ZnNE A:Arg2424.75
ZnNH2 A:Arg2423.79
ZnOD2 A:Asp3044.44
ZnOD1 A:Asp3044.37
ZnCG A:Asp3044.80
ZnN1 A:Ly03634.35
ZnC6 A:Ly03633.17
ZnO62 A:Ly03632.24
ZnC5 A:Ly03634.07
ZnP A:Ly03632.77
ZnO32 A:Ly03632.22
ZnO61 A:Ly03633.90
ZnC4 A:Ly03633.90
ZnO31 A:Ly03632.36
ZnC2 A:Ly03634.27
ZnZN A:Zn3643.68

interactive model:


Zinc binding site 3 out of 4 in 3ly0


Zinc binding site 3 out of 4 in 3ly0
Click to enlarge
stereopicture of Zinc binding site 3 out of 4 in 3ly0
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 3ly0. 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: His11, B: Asp13, B: Ala54, B: Tyr56, B: Glu137, B: His231, B: Asp304, B: Ly0363, B: Zn365, B: Hoh393,

conact list:


AtomAtomDistance (A)
ZnNE2 B:His112.21
ZnND1 B:His114.27
ZnCD2 B:His113.27
ZnCE1 B:His113.11
ZnCG B:His114.37
ZnCB B:Asp134.09
ZnOD2 B:Asp132.25
ZnOD1 B:Asp132.27
ZnCG B:Asp132.58
ZnCA B:Asp134.91
ZnCB B:Ala544.32
ZnCB B:Tyr564.67
ZnCG B:Tyr564.88
ZnOE1 B:Glu1372.13
ZnCB B:Glu1374.83
ZnOE2 B:Glu1373.19
ZnCD B:Glu1373.01
ZnCG B:Glu1374.42
ZnNE2 B:His2314.45
ZnOD1 B:Asp3043.85
ZnN1 B:Ly03632.33
ZnP B:Ly03633.19
ZnO32 B:Ly03633.93
ZnC4 B:Ly03634.76
ZnC1 B:Ly03634.58
ZnO31 B:Ly03632.25
ZnC2 B:Ly03633.15
ZnZN B:Zn3653.69
ZnO B:Hoh3934.89

interactive model:


Zinc binding site 4 out of 4 in 3ly0


Zinc binding site 4 out of 4 in 3ly0
Click to enlarge
stereopicture of Zinc binding site 4 out of 4 in 3ly0
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 3ly0. 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: His11, B: Glu137, B: Trp164, B: His210, B: His231, B: Arg242, B: Asp304, B: Ly0363, B: Zn364,

conact list:


AtomAtomDistance (A)
ZnNE2 B:His114.01
ZnCD2 B:His114.61
ZnCE1 B:His114.43
ZnOE1 B:Glu1373.83
ZnOE2 B:Glu1372.11
ZnCD B:Glu1373.28
ZnCG B:Glu1374.46
ZnCD1 B:Trp1644.25
ZnNE1 B:Trp1644.12
ZnNE2 B:His2102.16
ZnND1 B:His2104.25
ZnCD2 B:His2103.14
ZnCE1 B:His2103.13
ZnCG B:His2104.28
ZnNE2 B:His2312.23
ZnND1 B:His2314.34
ZnCD2 B:His2313.17
ZnCE1 B:His2313.23
ZnCG B:His2314.34
ZnCZ B:Arg2424.69
ZnNE B:Arg2424.77
ZnNH2 B:Arg2423.82
ZnOD2 B:Asp3044.42
ZnOD1 B:Asp3044.41
ZnCG B:Asp3044.82
ZnN1 B:Ly03634.34
ZnC6 B:Ly03633.18
ZnO62 B:Ly03632.27
ZnC5 B:Ly03634.03
ZnP B:Ly03632.78
ZnO32 B:Ly03632.27
ZnO61 B:Ly03633.91
ZnC4 B:Ly03633.88
ZnO31 B:Ly03632.33
ZnC2 B:Ly03634.30
ZnZN B:Zn3643.69

interactive model:




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