Zinc in PDB 3h0l: Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus

The structure of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus, PDB code: 3h0l was solved by J.Wu, W.Bu, K.Sheppard, M.Kitabatake, D.Soll, J.L.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.50 / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	127.482, 131.012, 154.668, 90.02, 90.00, 89.91
R / Rfree (%)	24 / 27.3

The structure of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

The binding sites of Zinc atom in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus (pdb code 3h0l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus, PDB code: 3h0l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:37.3 occ:1.00 CB B:CYS40 2.1 38.9 1.0 SG B:CYS25 2.2 34.1 1.0 SG B:CYS27 2.4 45.9 1.0 SG B:CYS43 2.4 32.3 1.0 SG B:CYS40 2.9 39.7 1.0 CB B:CYS25 3.3 35.7 1.0 CB B:CYS43 3.3 34.8 1.0 CB B:CYS27 3.4 42.5 1.0 CA B:CYS40 3.5 38.2 1.0 N B:CYS43 3.7 36.2 1.0 N B:CYS40 3.8 39.0 1.0 C B:VAL39 4.1 39.3 1.0 CA B:CYS43 4.1 35.4 1.0 N B:CYS27 4.2 40.9 1.0 NZ B:LYS22 4.3 34.4 1.0 C B:CYS40 4.4 38.1 1.0 CD B:LYS22 4.4 32.2 1.0 CA B:VAL39 4.4 39.4 1.0 CA B:CYS27 4.4 41.8 1.0 CA B:CYS25 4.6 36.6 1.0 O B:VAL39 4.6 39.6 1.0 CB B:VAL42 4.7 36.8 1.0 CE B:LYS22 4.7 34.4 1.0 O B:CYS40 4.8 37.7 1.0 C B:CYS25 4.8 37.2 1.0 N B:GLY26 4.8 38.5 1.0 C B:VAL42 4.9 36.8 1.0 N B:VAL42 4.9 37.0 1.0

Zinc binding site 2 out of 8 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn902 b:40.5 occ:1.00 SG E:CYS27 2.1 44.0 1.0 SG E:CYS25 2.2 37.1 1.0 SG E:CYS40 2.3 40.9 1.0 SG E:CYS43 2.5 33.4 1.0 CB E:CYS25 3.2 36.4 1.0 CB E:CYS40 3.2 38.7 1.0 CB E:CYS27 3.3 42.0 1.0 CB E:CYS43 3.4 35.1 1.0 N E:CYS40 3.7 39.0 1.0 N E:CYS43 3.9 36.3 1.0 CA E:CYS40 4.0 38.4 1.0 N E:CYS27 4.0 41.2 1.0 CA E:CYS27 4.2 41.9 1.0 C E:VAL39 4.3 39.5 1.0 CA E:CYS43 4.3 35.5 1.0 CD E:LYS22 4.3 33.4 1.0 CA E:CYS25 4.5 36.9 1.0 C E:CYS40 4.5 38.2 1.0 O E:CYS40 4.6 37.8 1.0 C E:CYS25 4.6 37.6 1.0 CB E:VAL42 4.6 37.4 1.0 N E:GLY26 4.6 38.6 1.0 CA E:VAL39 4.7 39.5 1.0 NZ E:LYS22 4.8 35.2 1.0 O E:VAL39 4.9 39.8 1.0 C E:VAL42 5.0 36.9 1.0

Zinc binding site 3 out of 8 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn903 b:33.2 occ:1.00 SG H:CYS25 2.2 35.2 1.0 SG H:CYS27 2.3 42.5 1.0 SG H:CYS43 2.4 31.3 1.0 SG H:CYS40 2.4 36.1 1.0 CB H:CYS25 3.2 36.3 1.0 CB H:CYS43 3.3 34.9 1.0 CB H:CYS27 3.3 41.6 1.0 CB H:CYS40 3.4 37.4 1.0 N H:CYS40 3.6 38.9 1.0 N H:CYS43 3.8 36.2 1.0 CA H:CYS40 4.0 37.9 1.0 C H:VAL39 4.1 39.3 1.0 N H:CYS27 4.1 41.0 1.0 CA H:CYS43 4.2 35.4 1.0 CD H:LYS22 4.3 32.5 1.0 CA H:CYS27 4.3 41.7 1.0 O H:CYS40 4.5 37.5 1.0 CA H:VAL39 4.5 39.4 1.0 C H:CYS40 4.5 37.8 1.0 CE H:LYS22 4.5 35.1 1.0 CA H:CYS25 4.6 36.6 1.0 NZ H:LYS22 4.7 34.3 1.0 O H:ASN38 4.8 40.1 1.0 O H:VAL39 4.8 39.7 1.0 N H:GLY26 4.8 38.5 1.0 C H:CYS25 4.8 37.1 1.0 CB H:VAL42 4.9 37.1 1.0 C H:VAL42 5.0 36.9 1.0 N H:VAL39 5.0 39.9 1.0

Zinc binding site 4 out of 8 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn904 b:29.6 occ:1.00 SG K:CYS25 2.0 33.5 1.0 SG K:CYS40 2.1 32.8 1.0 SG K:CYS27 2.2 38.6 1.0 SG K:CYS43 2.4 30.5 1.0 CB K:CYS25 3.1 35.8 1.0 CB K:CYS40 3.2 36.9 1.0 CB K:CYS27 3.3 41.3 1.0 CB K:CYS43 3.3 34.7 1.0 N K:CYS40 3.7 38.9 1.0 N K:CYS43 3.9 36.0 1.0 CA K:CYS40 3.9 37.7 1.0 N K:CYS27 4.0 41.1 1.0 CA K:CYS43 4.2 35.4 1.0 C K:VAL39 4.3 39.2 1.0 CA K:CYS27 4.3 41.6 1.0 CD K:LYS22 4.4 28.8 1.0 C K:CYS40 4.5 37.8 1.0 CA K:CYS25 4.5 36.4 1.0 O K:CYS40 4.6 37.6 1.0 CA K:VAL39 4.6 39.1 1.0 N K:GLY26 4.7 38.4 1.0 C K:CYS25 4.7 37.3 1.0 CB K:VAL42 4.7 36.7 1.0 NZ K:LYS22 4.8 31.0 1.0 CE K:LYS22 4.9 31.6 1.0 O K:ASN38 4.9 40.3 1.0 O K:VAL39 4.9 39.6 1.0 C K:VAL42 5.0 36.7 1.0

Zinc binding site 5 out of 8 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn905 b:36.5 occ:1.00 SG N:CYS25 2.1 35.8 1.0 SG N:CYS43 2.3 32.5 1.0 SG N:CYS40 2.3 37.3 1.0 SG N:CYS27 2.3 39.7 1.0 CB N:CYS43 3.2 34.5 1.0 CB N:CYS25 3.2 35.9 1.0 CB N:CYS40 3.3 38.0 1.0 CB N:CYS27 3.4 41.7 1.0 N N:CYS43 3.7 36.0 1.0 N N:CYS40 3.7 38.8 1.0 CA N:CYS40 4.0 37.9 1.0 CA N:CYS43 4.0 35.4 1.0 C N:VAL39 4.2 39.3 1.0 N N:CYS27 4.2 41.1 1.0 CD N:LYS22 4.3 33.3 1.0 CA N:CYS27 4.4 41.5 1.0 C N:CYS40 4.4 37.9 1.0 O N:CYS40 4.4 37.4 1.0 CA N:CYS25 4.5 36.6 1.0 NZ N:LYS22 4.6 32.1 1.0 CA N:VAL39 4.6 39.4 1.0 CB N:VAL42 4.6 37.2 1.0 C N:CYS25 4.8 37.3 1.0 C N:VAL42 4.8 36.9 1.0 N N:GLY26 4.8 38.5 1.0 O N:VAL39 4.8 39.7 1.0 O N:ASN38 4.9 40.3 1.0 N N:VAL42 5.0 36.9 1.0 CE N:LYS22 5.0 33.2 1.0

Zinc binding site 6 out of 8 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ Q:Zn906 b:30.9 occ:1.00 SG Q:CYS25 2.1 30.6 1.0 SG Q:CYS40 2.1 32.3 1.0 SG Q:CYS43 2.3 33.5 1.0 SG Q:CYS27 2.4 40.9 1.0 CB Q:CYS40 3.1 37.1 1.0 CB Q:CYS25 3.2 36.0 1.0 CB Q:CYS43 3.2 34.6 1.0 CB Q:CYS27 3.4 41.5 1.0 N Q:CYS40 3.7 38.9 1.0 N Q:CYS43 3.8 36.0 1.0 CA Q:CYS40 3.9 37.7 1.0 CA Q:CYS43 4.1 35.5 1.0 N Q:CYS27 4.1 41.1 1.0 C Q:VAL39 4.2 39.2 1.0 CD Q:LYS22 4.3 28.0 1.0 CA Q:CYS27 4.4 41.6 1.0 C Q:CYS40 4.4 37.8 1.0 O Q:CYS40 4.4 37.6 1.0 CA Q:CYS25 4.5 36.4 1.0 CA Q:VAL39 4.6 39.2 1.0 C Q:CYS25 4.7 37.3 1.0 N Q:GLY26 4.7 38.5 1.0 NZ Q:LYS22 4.7 27.3 1.0 CB Q:VAL42 4.8 37.1 1.0 O Q:VAL39 4.8 39.8 1.0 O Q:ASN38 4.9 40.1 1.0 CE Q:LYS22 4.9 30.6 1.0 C Q:VAL42 4.9 36.8 1.0 N Q:VAL42 5.0 36.7 1.0

Zinc binding site 7 out of 8 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ T:Zn907 b:37.6 occ:1.00 SG T:CYS27 2.2 45.2 1.0 SG T:CYS40 2.2 38.5 1.0 SG T:CYS25 2.2 37.2 1.0 SG T:CYS43 2.4 33.2 1.0 CB T:CYS40 3.2 38.3 1.0 CB T:CYS25 3.3 36.7 1.0 CB T:CYS27 3.3 42.2 1.0 CB T:CYS43 3.4 35.9 1.0 N T:CYS40 3.7 39.2 1.0 N T:CYS43 3.9 36.3 1.0 CA T:CYS40 3.9 38.3 1.0 N T:CYS27 4.0 41.3 1.0 CD T:LYS22 4.2 32.9 1.0 C T:VAL39 4.2 39.5 1.0 CA T:CYS27 4.2 41.9 1.0 CA T:CYS43 4.3 35.7 1.0 C T:CYS40 4.5 38.1 1.0 O T:CYS40 4.5 37.9 1.0 CA T:CYS25 4.6 36.8 1.0 CA T:VAL39 4.6 39.5 1.0 N T:GLY26 4.7 38.5 1.0 C T:CYS25 4.7 37.4 1.0 CB T:VAL42 4.7 36.9 1.0 O T:VAL39 4.8 39.7 1.0 NZ T:LYS22 4.8 35.9 1.0 CE T:LYS22 4.8 36.6 1.0 O T:ASN38 4.9 40.3 1.0 C T:VAL42 5.0 36.9 1.0

Zinc binding site 8 out of 8 in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ W:Zn908 b:33.1 occ:1.00 SG W:CYS40 2.1 36.3 1.0 SG W:CYS25 2.2 34.5 1.0 SG W:CYS27 2.2 41.3 1.0 SG W:CYS43 2.4 32.7 1.0 CB W:CYS25 3.1 36.2 1.0 CB W:CYS40 3.2 38.5 1.0 CB W:CYS27 3.3 41.6 1.0 CB W:CYS43 3.4 34.9 1.0 N W:CYS40 3.7 39.0 1.0 N W:CYS43 3.9 36.1 1.0 CA W:CYS40 4.0 38.0 1.0 N W:CYS27 4.0 41.0 1.0 C W:VAL39 4.3 39.3 1.0 CA W:CYS27 4.3 41.6 1.0 CA W:CYS43 4.3 35.6 1.0 CD W:LYS22 4.4 33.7 1.0 CA W:CYS25 4.5 36.6 1.0 C W:CYS40 4.5 38.0 1.0 O W:CYS40 4.6 37.8 1.0 CB W:VAL42 4.6 36.8 1.0 CA W:VAL39 4.6 39.4 1.0 N W:GLY26 4.6 38.5 1.0 C W:CYS25 4.7 37.3 1.0 CE W:LYS22 4.7 35.1 1.0 NZ W:LYS22 4.9 35.8 1.0 O W:VAL39 4.9 39.6 1.0 C W:VAL42 5.0 36.8 1.0 N W:VAL42 5.0 37.1 1.0

J.Wu, W.Bu, K.Sheppard, M.Kitabatake, S.T.Kwon, D.Soll, J.L.Smith. Insights Into Trna-Dependent Amidotransferase Evolution and Catalysis From the Structure of the Aquifex Aeolicus Enzyme J.Mol.Biol. V. 391 703 2009.
ISSN: ISSN 0022-2836
PubMed: 19520089
DOI: 10.1016/J.JMB.2009.06.014