Chemical elements
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    PDB 2zh0-3a32
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      3gpx
      3gpy
      3gq3
      3gq4
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      3gtk
      3gtl
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      3gto
      3gtp
      3gtq
      3gtt
      3gtv
      3guc
      3gug
      3guw
      3gv4
      3gwt
      3gyy
      3gz0
      3gze
      3gzk
      3gzn
      3gzo
      3gzu
      3h03
      3h0g
      3h0l
      3h0m
      3h0n
      3h0r
      3h15
      3h1k
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      3h1w
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      3h2p
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    PDB 3h3e-3hfy
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    PDB 3kwa-3lat
    PDB 3lcn-3lrr
    PDB 3ls1-3m1n
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    PDB 3v25-4agl
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    PDB 4eg2-4fc8
    PDB 4fgm-6tli
    PDB 6tmn-9nse

Zinc in the structure of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus (pdb 3h0l)






The binding sites of Zinc atom in the structure of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus (pdb code 3h0l). This binding sites where shown with 5.0 Angstroms radius around Zinc atom.
The 3h0l structure was solved by J.WU, W.BU, K.SHEPPARD, M.KITABATAKE, D.SOLL, J.L.SMITH, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)40.5-2.3
Space groupP1
a (A)127.482
b (A)131.012
c (A)154.668
alpha (°)90.02
beta (°)90.00
gamma (°)89.91
Rfactor (%)24
Rfree (%)27.3


Zinc Binding Sites:

Zinc binding site 1 out of 8 in 3h0l


Zinc binding site 1 out of 8 in 3h0l
Click to enlarge		stereopicture of Zinc binding site 1 out of 8 in 3h0l
Click to enlarge		Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3h0l. 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: Lys22, B: Cys25, B: Gly26, B: Cys27, B: Val39, B: Cys40, B: Val42, B: Cys43,

conact list:


AtomAtomDistance (A)
ZnCE B:Lys224.66
ZnCD B:Lys224.42
ZnNZ B:Lys224.34
ZnCB B:Cys253.25
ZnSG B:Cys252.24
ZnC B:Cys254.84
ZnCA B:Cys254.60
ZnN B:Gly264.84
ZnN B:Cys274.23
ZnCB B:Cys273.39
ZnSG B:Cys272.36
ZnCA B:Cys274.44
ZnO B:Val394.62
ZnC B:Val394.10
ZnCA B:Val394.44
ZnO B:Cys404.77
ZnN B:Cys403.84
ZnCB B:Cys402.11
ZnSG B:Cys402.94
ZnC B:Cys404.42
ZnCA B:Cys403.50
ZnN B:Val424.93
ZnCB B:Val424.66
ZnC B:Val424.87
ZnN B:Cys433.74
ZnCB B:Cys433.25
ZnSG B:Cys432.39
ZnCA B:Cys434.11

interactive model:


Zinc binding site 2 out of 8 in 3h0l


Zinc binding site 2 out of 8 in 3h0l
Click to enlarge		stereopicture of Zinc binding site 2 out of 8 in 3h0l
Click to enlarge		Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3h0l. 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: E: Lys22, E: Cys25, E: Gly26, E: Cys27, E: Val39, E: Cys40, E: Val42, E: Cys43,

conact list:


AtomAtomDistance (A)
ZnCD E:Lys224.31
ZnNZ E:Lys224.79
ZnCB E:Cys253.15
ZnSG E:Cys252.21
ZnC E:Cys254.62
ZnCA E:Cys254.47
ZnN E:Gly264.65
ZnN E:Cys273.99
ZnCB E:Cys273.31
ZnSG E:Cys272.15
ZnCA E:Cys274.24
ZnO E:Val394.88
ZnC E:Val394.27
ZnCA E:Val394.66
ZnO E:Cys404.61
ZnN E:Cys403.74
ZnCB E:Cys403.24
ZnSG E:Cys402.26
ZnC E:Cys404.49
ZnCA E:Cys403.96
ZnCB E:Val424.63
ZnC E:Val424.98
ZnN E:Cys433.87
ZnCB E:Cys433.44
ZnSG E:Cys432.45
ZnCA E:Cys434.29

interactive model:


Zinc binding site 3 out of 8 in 3h0l


Zinc binding site 3 out of 8 in 3h0l
Click to enlarge		stereopicture of Zinc binding site 3 out of 8 in 3h0l
Click to enlarge		Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 3h0l. 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: H: Lys22, H: Cys25, H: Gly26, H: Cys27, H: Asn38, H: Val39, H: Cys40, H: Val42, H: Cys43,

conact list:


AtomAtomDistance (A)
ZnCE H:Lys224.53
ZnCD H:Lys224.27
ZnNZ H:Lys224.68
ZnCB H:Cys253.23
ZnSG H:Cys252.17
ZnC H:Cys254.83
ZnCA H:Cys254.61
ZnN H:Gly264.81
ZnN H:Cys274.15
ZnCB H:Cys273.26
ZnSG H:Cys272.30
ZnCA H:Cys274.31
ZnO H:Asn384.78
ZnO H:Val394.79
ZnN H:Val394.99
ZnC H:Val394.14
ZnCA H:Val394.48
ZnO H:Cys404.45
ZnN H:Cys403.64
ZnCB H:Cys403.37
ZnSG H:Cys402.40
ZnC H:Cys404.49
ZnCA H:Cys403.99
ZnCB H:Val424.86
ZnC H:Val424.96
ZnN H:Cys433.81
ZnCB H:Cys433.26
ZnSG H:Cys432.39
ZnCA H:Cys434.15

interactive model:


Zinc binding site 4 out of 8 in 3h0l


Zinc binding site 4 out of 8 in 3h0l
Click to enlarge		stereopicture of Zinc binding site 4 out of 8 in 3h0l
Click to enlarge		Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 3h0l. 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: K: Lys22, K: Cys25, K: Gly26, K: Cys27, K: Asn38, K: Val39, K: Cys40, K: Val42, K: Cys43,

conact list:


AtomAtomDistance (A)
ZnCE K:Lys224.85
ZnCD K:Lys224.36
ZnNZ K:Lys224.82
ZnCB K:Cys253.14
ZnSG K:Cys252.02
ZnC K:Cys254.68
ZnCA K:Cys254.48
ZnN K:Gly264.65
ZnN K:Cys274.02
ZnCB K:Cys273.31
ZnSG K:Cys272.20
ZnCA K:Cys274.26
ZnO K:Asn384.86
ZnO K:Val394.86
ZnC K:Val394.25
ZnCA K:Val394.64
ZnO K:Cys404.59
ZnN K:Cys403.71
ZnCB K:Cys403.17
ZnSG K:Cys402.10
ZnC K:Cys404.48
ZnCA K:Cys403.95
ZnCB K:Val424.74
ZnC K:Val424.99
ZnN K:Cys433.86
ZnCB K:Cys433.33
ZnSG K:Cys432.41
ZnCA K:Cys434.22

interactive model:


Zinc binding site 5 out of 8 in 3h0l


Zinc binding site 5 out of 8 in 3h0l
Click to enlarge		stereopicture of Zinc binding site 5 out of 8 in 3h0l
Click to enlarge		Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 3h0l. 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: N: Lys22, N: Cys25, N: Gly26, N: Cys27, N: Asn38, N: Val39, N: Cys40, N: Val42, N: Cys43,

conact list:


AtomAtomDistance (A)
ZnCE N:Lys224.96
ZnCD N:Lys224.25
ZnNZ N:Lys224.58
ZnCB N:Cys253.17
ZnSG N:Cys252.12
ZnC N:Cys254.81
ZnCA N:Cys254.54
ZnN N:Gly264.84
ZnN N:Cys274.22
ZnCB N:Cys273.40
ZnSG N:Cys272.34
ZnCA N:Cys274.42
ZnO N:Asn384.92
ZnO N:Val394.84
ZnC N:Val394.21
ZnCA N:Val394.58
ZnO N:Cys404.44
ZnN N:Cys403.69
ZnCB N:Cys403.31
ZnSG N:Cys402.30
ZnC N:Cys404.43
ZnCA N:Cys403.97
ZnN N:Val424.96
ZnCB N:Val424.65
ZnC N:Val424.81
ZnN N:Cys433.65
ZnCB N:Cys433.16
ZnSG N:Cys432.26
ZnCA N:Cys434.01

interactive model:


Zinc binding site 6 out of 8 in 3h0l


Zinc binding site 6 out of 8 in 3h0l
Click to enlarge		stereopicture of Zinc binding site 6 out of 8 in 3h0l
Click to enlarge		Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 3h0l. 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: Q: Lys22, Q: Cys25, Q: Gly26, Q: Cys27, Q: Asn38, Q: Val39, Q: Cys40, Q: Val42, Q: Cys43,

conact list:


AtomAtomDistance (A)
ZnCE Q:Lys224.88
ZnCD Q:Lys224.34
ZnNZ Q:Lys224.73
ZnCB Q:Cys253.15
ZnSG Q:Cys252.07
ZnC Q:Cys254.72
ZnCA Q:Cys254.50
ZnN Q:Gly264.72
ZnN Q:Cys274.12
ZnCB Q:Cys273.40
ZnSG Q:Cys272.35
ZnCA Q:Cys274.37
ZnO Q:Asn384.86
ZnO Q:Val394.83
ZnC Q:Val394.20
ZnCA Q:Val394.57
ZnO Q:Cys404.45
ZnN Q:Cys403.67
ZnCB Q:Cys403.13
ZnSG Q:Cys402.15
ZnC Q:Cys404.43
ZnCA Q:Cys403.92
ZnN Q:Val424.98
ZnCB Q:Val424.79
ZnC Q:Val424.92
ZnN Q:Cys433.77
ZnCB Q:Cys433.18
ZnSG Q:Cys432.33
ZnCA Q:Cys434.10

interactive model:


Zinc binding site 7 out of 8 in 3h0l


Zinc binding site 7 out of 8 in 3h0l
Click to enlarge		stereopicture of Zinc binding site 7 out of 8 in 3h0l
Click to enlarge		Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 3h0l. 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: T: Lys22, T: Cys25, T: Gly26, T: Cys27, T: Asn38, T: Val39, T: Cys40, T: Val42, T: Cys43,

conact list:


AtomAtomDistance (A)
ZnCE T:Lys224.84
ZnCD T:Lys224.17
ZnNZ T:Lys224.81
ZnCB T:Cys253.25
ZnSG T:Cys252.19
ZnC T:Cys254.74
ZnCA T:Cys254.57
ZnN T:Gly264.69
ZnN T:Cys274.03
ZnCB T:Cys273.26
ZnSG T:Cys272.16
ZnCA T:Cys274.24
ZnO T:Asn384.93
ZnO T:Val394.77
ZnC T:Val394.19
ZnCA T:Val394.60
ZnO T:Cys404.55
ZnN T:Cys403.68
ZnCB T:Cys403.16
ZnSG T:Cys402.18
ZnC T:Cys404.45
ZnCA T:Cys403.92
ZnCB T:Val424.74
ZnC T:Val424.99
ZnN T:Cys433.88
ZnCB T:Cys433.44
ZnSG T:Cys432.44
ZnCA T:Cys434.29

interactive model:


Zinc binding site 8 out of 8 in 3h0l


Zinc binding site 8 out of 8 in 3h0l
Click to enlarge		stereopicture of Zinc binding site 8 out of 8 in 3h0l
Click to enlarge		Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Zinc in the PDB 3h0l. 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: W: Lys22, W: Cys25, W: Gly26, W: Cys27, W: Val39, W: Cys40, W: Val42, W: Cys43,

conact list:


AtomAtomDistance (A)
ZnCE W:Lys224.72
ZnCD W:Lys224.37
ZnNZ W:Lys224.86
ZnCB W:Cys253.13
ZnSG W:Cys252.17
ZnC W:Cys254.65
ZnCA W:Cys254.46
ZnN W:Gly264.64
ZnN W:Cys274.04
ZnCB W:Cys273.33
ZnSG W:Cys272.21
ZnCA W:Cys274.29
ZnO W:Val394.89
ZnC W:Val394.27
ZnCA W:Val394.63
ZnO W:Cys404.55
ZnN W:Cys403.75
ZnCB W:Cys403.22
ZnSG W:Cys402.09
ZnC W:Cys404.49
ZnCA W:Cys403.98
ZnN W:Val424.97
ZnCB W:Val424.57
ZnC W:Val424.95
ZnN W:Cys433.90
ZnCB W:Cys433.45
ZnSG W:Cys432.37
ZnCA W:Cys434.31

interactive model:
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