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 group | P1 | 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 |
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Zinc Binding Sites:Zinc binding site 1 out of 8 in 3h0l
|  Click to enlarge |  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:
Atom | Atom | Distance (A) | Zn | CE B:Lys22 | 4.66 | Zn | CD B:Lys22 | 4.42 | Zn | NZ B:Lys22 | 4.34 | Zn | CB B:Cys25 | 3.25 | Zn | SG B:Cys25 | 2.24 | Zn | C B:Cys25 | 4.84 | Zn | CA B:Cys25 | 4.60 | Zn | N B:Gly26 | 4.84 | Zn | N B:Cys27 | 4.23 | Zn | CB B:Cys27 | 3.39 | Zn | SG B:Cys27 | 2.36 | Zn | CA B:Cys27 | 4.44 | Zn | O B:Val39 | 4.62 | Zn | C B:Val39 | 4.10 | Zn | CA B:Val39 | 4.44 | Zn | O B:Cys40 | 4.77 | Zn | N B:Cys40 | 3.84 | Zn | CB B:Cys40 | 2.11 | Zn | SG B:Cys40 | 2.94 | Zn | C B:Cys40 | 4.42 | Zn | CA B:Cys40 | 3.50 | Zn | N B:Val42 | 4.93 | Zn | CB B:Val42 | 4.66 | Zn | C B:Val42 | 4.87 | Zn | N B:Cys43 | 3.74 | Zn | CB B:Cys43 | 3.25 | Zn | SG B:Cys43 | 2.39 | Zn | CA B:Cys43 | 4.11 |
| interactive model:
| Zinc binding site 2 out of 8 in 3h0l
|  Click to enlarge |  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:
Atom | Atom | Distance (A) | Zn | CD E:Lys22 | 4.31 | Zn | NZ E:Lys22 | 4.79 | Zn | CB E:Cys25 | 3.15 | Zn | SG E:Cys25 | 2.21 | Zn | C E:Cys25 | 4.62 | Zn | CA E:Cys25 | 4.47 | Zn | N E:Gly26 | 4.65 | Zn | N E:Cys27 | 3.99 | Zn | CB E:Cys27 | 3.31 | Zn | SG E:Cys27 | 2.15 | Zn | CA E:Cys27 | 4.24 | Zn | O E:Val39 | 4.88 | Zn | C E:Val39 | 4.27 | Zn | CA E:Val39 | 4.66 | Zn | O E:Cys40 | 4.61 | Zn | N E:Cys40 | 3.74 | Zn | CB E:Cys40 | 3.24 | Zn | SG E:Cys40 | 2.26 | Zn | C E:Cys40 | 4.49 | Zn | CA E:Cys40 | 3.96 | Zn | CB E:Val42 | 4.63 | Zn | C E:Val42 | 4.98 | Zn | N E:Cys43 | 3.87 | Zn | CB E:Cys43 | 3.44 | Zn | SG E:Cys43 | 2.45 | Zn | CA E:Cys43 | 4.29 |
| interactive model:
| Zinc binding site 3 out of 8 in 3h0l
|  Click to enlarge |  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:
Atom | Atom | Distance (A) | Zn | CE H:Lys22 | 4.53 | Zn | CD H:Lys22 | 4.27 | Zn | NZ H:Lys22 | 4.68 | Zn | CB H:Cys25 | 3.23 | Zn | SG H:Cys25 | 2.17 | Zn | C H:Cys25 | 4.83 | Zn | CA H:Cys25 | 4.61 | Zn | N H:Gly26 | 4.81 | Zn | N H:Cys27 | 4.15 | Zn | CB H:Cys27 | 3.26 | Zn | SG H:Cys27 | 2.30 | Zn | CA H:Cys27 | 4.31 | Zn | O H:Asn38 | 4.78 | Zn | O H:Val39 | 4.79 | Zn | N H:Val39 | 4.99 | Zn | C H:Val39 | 4.14 | Zn | CA H:Val39 | 4.48 | Zn | O H:Cys40 | 4.45 | Zn | N H:Cys40 | 3.64 | Zn | CB H:Cys40 | 3.37 | Zn | SG H:Cys40 | 2.40 | Zn | C H:Cys40 | 4.49 | Zn | CA H:Cys40 | 3.99 | Zn | CB H:Val42 | 4.86 | Zn | C H:Val42 | 4.96 | Zn | N H:Cys43 | 3.81 | Zn | CB H:Cys43 | 3.26 | Zn | SG H:Cys43 | 2.39 | Zn | CA H:Cys43 | 4.15 |
| interactive model:
| Zinc binding site 4 out of 8 in 3h0l
|  Click to enlarge |  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:
Atom | Atom | Distance (A) | Zn | CE K:Lys22 | 4.85 | Zn | CD K:Lys22 | 4.36 | Zn | NZ K:Lys22 | 4.82 | Zn | CB K:Cys25 | 3.14 | Zn | SG K:Cys25 | 2.02 | Zn | C K:Cys25 | 4.68 | Zn | CA K:Cys25 | 4.48 | Zn | N K:Gly26 | 4.65 | Zn | N K:Cys27 | 4.02 | Zn | CB K:Cys27 | 3.31 | Zn | SG K:Cys27 | 2.20 | Zn | CA K:Cys27 | 4.26 | Zn | O K:Asn38 | 4.86 | Zn | O K:Val39 | 4.86 | Zn | C K:Val39 | 4.25 | Zn | CA K:Val39 | 4.64 | Zn | O K:Cys40 | 4.59 | Zn | N K:Cys40 | 3.71 | Zn | CB K:Cys40 | 3.17 | Zn | SG K:Cys40 | 2.10 | Zn | C K:Cys40 | 4.48 | Zn | CA K:Cys40 | 3.95 | Zn | CB K:Val42 | 4.74 | Zn | C K:Val42 | 4.99 | Zn | N K:Cys43 | 3.86 | Zn | CB K:Cys43 | 3.33 | Zn | SG K:Cys43 | 2.41 | Zn | CA K:Cys43 | 4.22 |
| interactive model:
| Zinc binding site 5 out of 8 in 3h0l
|  Click to enlarge |  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:
Atom | Atom | Distance (A) | Zn | CE N:Lys22 | 4.96 | Zn | CD N:Lys22 | 4.25 | Zn | NZ N:Lys22 | 4.58 | Zn | CB N:Cys25 | 3.17 | Zn | SG N:Cys25 | 2.12 | Zn | C N:Cys25 | 4.81 | Zn | CA N:Cys25 | 4.54 | Zn | N N:Gly26 | 4.84 | Zn | N N:Cys27 | 4.22 | Zn | CB N:Cys27 | 3.40 | Zn | SG N:Cys27 | 2.34 | Zn | CA N:Cys27 | 4.42 | Zn | O N:Asn38 | 4.92 | Zn | O N:Val39 | 4.84 | Zn | C N:Val39 | 4.21 | Zn | CA N:Val39 | 4.58 | Zn | O N:Cys40 | 4.44 | Zn | N N:Cys40 | 3.69 | Zn | CB N:Cys40 | 3.31 | Zn | SG N:Cys40 | 2.30 | Zn | C N:Cys40 | 4.43 | Zn | CA N:Cys40 | 3.97 | Zn | N N:Val42 | 4.96 | Zn | CB N:Val42 | 4.65 | Zn | C N:Val42 | 4.81 | Zn | N N:Cys43 | 3.65 | Zn | CB N:Cys43 | 3.16 | Zn | SG N:Cys43 | 2.26 | Zn | CA N:Cys43 | 4.01 |
| interactive model:
| Zinc binding site 6 out of 8 in 3h0l
|  Click to enlarge |  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:
Atom | Atom | Distance (A) | Zn | CE Q:Lys22 | 4.88 | Zn | CD Q:Lys22 | 4.34 | Zn | NZ Q:Lys22 | 4.73 | Zn | CB Q:Cys25 | 3.15 | Zn | SG Q:Cys25 | 2.07 | Zn | C Q:Cys25 | 4.72 | Zn | CA Q:Cys25 | 4.50 | Zn | N Q:Gly26 | 4.72 | Zn | N Q:Cys27 | 4.12 | Zn | CB Q:Cys27 | 3.40 | Zn | SG Q:Cys27 | 2.35 | Zn | CA Q:Cys27 | 4.37 | Zn | O Q:Asn38 | 4.86 | Zn | O Q:Val39 | 4.83 | Zn | C Q:Val39 | 4.20 | Zn | CA Q:Val39 | 4.57 | Zn | O Q:Cys40 | 4.45 | Zn | N Q:Cys40 | 3.67 | Zn | CB Q:Cys40 | 3.13 | Zn | SG Q:Cys40 | 2.15 | Zn | C Q:Cys40 | 4.43 | Zn | CA Q:Cys40 | 3.92 | Zn | N Q:Val42 | 4.98 | Zn | CB Q:Val42 | 4.79 | Zn | C Q:Val42 | 4.92 | Zn | N Q:Cys43 | 3.77 | Zn | CB Q:Cys43 | 3.18 | Zn | SG Q:Cys43 | 2.33 | Zn | CA Q:Cys43 | 4.10 |
| interactive model:
| Zinc binding site 7 out of 8 in 3h0l
|  Click to enlarge |  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:
Atom | Atom | Distance (A) | Zn | CE T:Lys22 | 4.84 | Zn | CD T:Lys22 | 4.17 | Zn | NZ T:Lys22 | 4.81 | Zn | CB T:Cys25 | 3.25 | Zn | SG T:Cys25 | 2.19 | Zn | C T:Cys25 | 4.74 | Zn | CA T:Cys25 | 4.57 | Zn | N T:Gly26 | 4.69 | Zn | N T:Cys27 | 4.03 | Zn | CB T:Cys27 | 3.26 | Zn | SG T:Cys27 | 2.16 | Zn | CA T:Cys27 | 4.24 | Zn | O T:Asn38 | 4.93 | Zn | O T:Val39 | 4.77 | Zn | C T:Val39 | 4.19 | Zn | CA T:Val39 | 4.60 | Zn | O T:Cys40 | 4.55 | Zn | N T:Cys40 | 3.68 | Zn | CB T:Cys40 | 3.16 | Zn | SG T:Cys40 | 2.18 | Zn | C T:Cys40 | 4.45 | Zn | CA T:Cys40 | 3.92 | Zn | CB T:Val42 | 4.74 | Zn | C T:Val42 | 4.99 | Zn | N T:Cys43 | 3.88 | Zn | CB T:Cys43 | 3.44 | Zn | SG T:Cys43 | 2.44 | Zn | CA T:Cys43 | 4.29 |
| interactive model:
| Zinc binding site 8 out of 8 in 3h0l
|  Click to enlarge |  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:
Atom | Atom | Distance (A) | Zn | CE W:Lys22 | 4.72 | Zn | CD W:Lys22 | 4.37 | Zn | NZ W:Lys22 | 4.86 | Zn | CB W:Cys25 | 3.13 | Zn | SG W:Cys25 | 2.17 | Zn | C W:Cys25 | 4.65 | Zn | CA W:Cys25 | 4.46 | Zn | N W:Gly26 | 4.64 | Zn | N W:Cys27 | 4.04 | Zn | CB W:Cys27 | 3.33 | Zn | SG W:Cys27 | 2.21 | Zn | CA W:Cys27 | 4.29 | Zn | O W:Val39 | 4.89 | Zn | C W:Val39 | 4.27 | Zn | CA W:Val39 | 4.63 | Zn | O W:Cys40 | 4.55 | Zn | N W:Cys40 | 3.75 | Zn | CB W:Cys40 | 3.22 | Zn | SG W:Cys40 | 2.09 | Zn | C W:Cys40 | 4.49 | Zn | CA W:Cys40 | 3.98 | Zn | N W:Val42 | 4.97 | Zn | CB W:Val42 | 4.57 | Zn | C W:Val42 | 4.95 | Zn | N W:Cys43 | 3.90 | Zn | CB W:Cys43 | 3.45 | Zn | SG W:Cys43 | 2.37 | Zn | CA W:Cys43 | 4.31 |
| interactive model:
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