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Zinc in PDB 3h0r: Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus

Protein crystallography data

The structure of Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus, PDB code: 3h0r 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) 48.97 / 3.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 127.377, 130.411, 153.973, 89.89, 90.21, 89.95
R / Rfree (%) 26.3 / 30.6

Other elements in 3h0r:

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

Manganese (Mn) 16 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus (pdb code 3h0r). 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: 3h0r:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3h0r

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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:57.1
occ:1.00
 SG B:CYS25 2.3 46.7 1.0
SG B:CYS43 2.4 45.1 1.0
CB B:CYS40 2.6 48.5 1.0
SG B:CYS27 2.6 50.4 1.0
CB B:CYS43 3.2 45.5 1.0
CB B:CYS27 3.3 50.3 1.0
CB B:CYS25 3.4 46.0 1.0
SG B:CYS40 3.6 49.2 1.0
N B:CYS43 3.7 46.1 1.0
CA B:CYS40 3.8 48.4 1.0
N B:CYS40 3.9 49.0 1.0
C B:VAL39 4.0 49.2 1.0
CA B:CYS43 4.1 45.5 1.0
CD B:LYS22 4.2 45.5 1.0
N B:CYS27 4.2 49.6 1.0
CE B:LYS22 4.3 46.4 1.0
CA B:CYS27 4.4 50.4 1.0
O B:VAL39 4.4 49.0 1.0
CA B:VAL39 4.5 49.5 1.0
NZ B:LYS22 4.6 45.9 1.0
C B:CYS40 4.7 47.9 1.0
CB B:VAL42 4.7 46.4 1.0
CA B:CYS25 4.7 46.6 1.0
C B:CYS25 4.8 47.1 1.0
C B:VAL42 4.9 46.2 1.0
O B:CYS40 4.9 48.1 1.0

Zinc binding site 2 out of 8 in 3h0r

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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:59.9
occ:1.00
 SG E:CYS27 2.3 51.5 1.0
SG E:CYS25 2.4 48.1 1.0
SG E:CYS40 2.4 51.2 1.0
SG E:CYS43 2.6 43.8 1.0
CB E:CYS43 3.2 45.6 1.0
CB E:CYS27 3.3 51.3 1.0
CB E:CYS40 3.3 48.8 1.0
CB E:CYS25 3.5 47.6 1.0
N E:CYS40 3.6 49.4 1.0
N E:CYS43 3.8 46.2 1.0
CA E:CYS40 3.9 49.0 1.0
CA E:CYS43 4.1 45.6 1.0
CD E:LYS22 4.2 45.5 1.0
O E:CYS40 4.3 48.7 1.0
C E:VAL39 4.3 50.1 1.0
C E:CYS40 4.3 48.6 1.0
N E:CYS27 4.4 50.7 1.0
CA E:CYS27 4.4 51.5 1.0
CA E:VAL39 4.5 50.5 1.0
CB E:VAL42 4.6 46.9 1.0
NZ E:LYS22 4.7 45.4 1.0
CA E:CYS25 4.8 48.1 1.0
CE E:LYS22 4.8 46.5 1.0
C E:VAL42 4.9 46.5 1.0
C E:CYS25 4.9 48.5 1.0
N E:VAL42 4.9 46.7 1.0
O E:ASN38 5.0 50.9 1.0

Zinc binding site 3 out of 8 in 3h0r

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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:53.5
occ:1.00
 SG H:CYS25 2.2 45.0 1.0
SG H:CYS27 2.3 50.0 1.0
SG H:CYS40 2.3 45.4 1.0
SG H:CYS43 2.4 43.3 1.0
CB H:CYS25 3.2 45.3 1.0
CB H:CYS27 3.3 49.6 1.0
CB H:CYS40 3.3 46.4 1.0
CB H:CYS43 3.5 44.8 1.0
N H:CYS40 3.8 48.0 1.0
N H:CYS43 4.0 45.4 1.0
CA H:CYS40 4.1 46.7 1.0
N H:CYS27 4.2 49.4 1.0
CD H:LYS22 4.3 45.0 1.0
C H:VAL39 4.3 48.8 1.0
CA H:CYS27 4.3 50.0 1.0
CA H:CYS43 4.4 44.9 1.0
O H:CYS40 4.5 45.4 1.0
C H:CYS40 4.5 46.1 1.0
CA H:CYS25 4.5 45.5 1.0
CA H:VAL39 4.6 49.2 1.0
CE H:LYS22 4.6 45.1 1.0
C H:CYS25 4.7 46.2 1.0
N H:GLY26 4.8 46.9 1.0
CB H:VAL42 4.8 46.1 1.0
NZ H:LYS22 4.9 44.3 1.0
O H:VAL39 4.9 49.6 1.0

Zinc binding site 4 out of 8 in 3h0r

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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:50.8
occ:1.00
 SG K:CYS43 2.2 43.7 1.0
SG K:CYS25 2.3 43.9 1.0
SG K:CYS27 2.3 47.7 1.0
SG K:CYS40 2.4 43.5 1.0
CB K:CYS43 3.3 44.8 1.0
CB K:CYS27 3.3 49.7 1.0
CB K:CYS40 3.4 45.9 1.0
CB K:CYS25 3.4 45.1 1.0
N K:CYS40 3.5 47.6 1.0
N K:CYS43 3.8 45.0 1.0
CA K:CYS40 3.9 46.1 1.0
CD K:LYS22 4.1 42.4 1.0
C K:VAL39 4.1 48.5 1.0
CA K:CYS43 4.1 44.6 1.0
N K:CYS27 4.2 49.3 1.0
O K:CYS40 4.3 46.0 1.0
C K:CYS40 4.4 46.1 1.0
CA K:CYS27 4.4 49.6 1.0
CA K:VAL39 4.4 48.6 1.0
NZ K:LYS22 4.6 41.9 1.0
CE K:LYS22 4.7 43.5 1.0
CB K:VAL42 4.8 45.5 1.0
CA K:CYS25 4.8 45.5 1.0
O K:VAL39 4.9 48.6 1.0
N K:GLY26 4.9 46.9 1.0
O K:ASN38 4.9 50.6 1.0
C K:VAL42 4.9 45.4 1.0
C K:CYS25 5.0 46.2 1.0

Zinc binding site 5 out of 8 in 3h0r

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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:53.0
occ:1.00
 SG N:CYS25 2.2 45.0 1.0
SG N:CYS27 2.3 48.4 1.0
SG N:CYS43 2.3 42.8 1.0
SG N:CYS40 2.4 46.4 1.0
CB N:CYS27 3.2 49.9 1.0
CB N:CYS25 3.3 45.1 1.0
CB N:CYS40 3.4 47.0 1.0
CB N:CYS43 3.5 44.5 1.0
N N:CYS40 3.7 48.2 1.0
N N:CYS43 3.9 44.9 1.0
CA N:CYS40 4.1 47.0 1.0
N N:CYS27 4.1 49.8 1.0
CD N:LYS22 4.2 44.0 1.0
C N:VAL39 4.3 49.0 1.0
CA N:CYS43 4.3 44.5 1.0
CA N:CYS27 4.3 50.1 1.0
O N:CYS40 4.6 46.1 1.0
CA N:CYS25 4.6 45.9 1.0
CA N:VAL39 4.6 49.3 1.0
C N:CYS40 4.6 46.6 1.0
CE N:LYS22 4.6 45.4 1.0
NZ N:LYS22 4.7 42.0 1.0
C N:CYS25 4.8 46.2 1.0
CB N:VAL42 4.8 46.0 1.0
O N:ASN38 4.8 49.5 1.0
N N:GLY26 4.9 47.4 1.0
O N:VAL39 5.0 49.6 1.0

Zinc binding site 6 out of 8 in 3h0r

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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:51.6
occ:1.00
 SG Q:CYS25 2.2 43.8 1.0
SG Q:CYS43 2.3 43.0 1.0
SG Q:CYS27 2.4 47.4 1.0
SG Q:CYS40 2.4 45.4 1.0
CB Q:CYS25 3.3 46.2 1.0
CB Q:CYS43 3.3 44.9 1.0
CB Q:CYS40 3.4 46.2 1.0
CB Q:CYS27 3.4 49.4 1.0
N Q:CYS40 3.7 47.3 1.0
N Q:CYS43 3.8 44.8 1.0
CA Q:CYS40 4.0 46.5 1.0
N Q:CYS27 4.1 48.9 1.0
CA Q:CYS43 4.2 44.9 1.0
CD Q:LYS22 4.2 44.0 1.0
C Q:VAL39 4.4 47.9 1.0
O Q:CYS40 4.4 46.4 1.0
CA Q:CYS27 4.4 49.1 1.0
C Q:CYS40 4.4 46.2 1.0
CA Q:CYS25 4.6 46.1 1.0
CB Q:VAL42 4.6 45.7 1.0
N Q:GLY26 4.7 47.5 1.0
NZ Q:LYS22 4.7 41.5 1.0
CE Q:LYS22 4.7 43.5 1.0
CA Q:VAL39 4.8 48.2 1.0
C Q:CYS25 4.8 46.8 1.0
C Q:VAL42 5.0 45.5 1.0

Zinc binding site 7 out of 8 in 3h0r

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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:55.3
occ:1.00
 SG T:CYS43 2.2 46.6 1.0
SG T:CYS27 2.3 51.6 1.0
SG T:CYS25 2.4 47.8 1.0
SG T:CYS40 2.5 49.8 1.0
CB T:CYS27 3.1 50.9 1.0
CB T:CYS43 3.2 46.3 1.0
N T:CYS40 3.3 49.5 1.0
CB T:CYS40 3.4 48.4 1.0
CB T:CYS25 3.6 47.2 1.0
N T:CYS43 3.8 46.4 1.0
CA T:CYS40 3.8 48.7 1.0
C T:VAL39 3.9 49.9 1.0
CD T:LYS22 3.9 46.2 1.0
CA T:CYS43 4.1 46.4 1.0
CA T:VAL39 4.1 50.4 1.0
O T:CYS40 4.2 48.2 1.0
C T:CYS40 4.3 48.2 1.0
CA T:CYS27 4.4 51.2 1.0
NZ T:LYS22 4.4 46.1 1.0
N T:CYS27 4.4 50.8 1.0
CE T:LYS22 4.6 46.8 1.0
O T:ASN38 4.8 51.3 1.0
O T:VAL39 4.8 50.1 1.0
N T:VAL39 4.8 51.0 1.0
CA T:CYS25 4.9 47.6 1.0
C T:VAL42 5.0 46.7 1.0

Zinc binding site 8 out of 8 in 3h0r

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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:55.5
occ:1.00
 SG W:CYS25 2.2 47.0 1.0
SG W:CYS27 2.3 49.7 1.0
SG W:CYS43 2.4 45.2 1.0
SG W:CYS40 2.4 46.9 1.0
CB W:CYS25 3.2 46.5 1.0
CB W:CYS27 3.2 50.5 1.0
CB W:CYS43 3.3 45.0 1.0
CB W:CYS40 3.4 48.2 1.0
N W:CYS40 3.7 49.0 1.0
N W:CYS43 3.8 45.1 1.0
CA W:CYS40 4.0 47.8 1.0
N W:CYS27 4.0 49.9 1.0
CA W:CYS43 4.2 45.3 1.0
CA W:CYS27 4.2 50.6 1.0
C W:VAL39 4.2 49.5 1.0
O W:CYS40 4.3 47.8 1.0
CD W:LYS22 4.4 45.5 1.0
C W:CYS40 4.4 47.6 1.0
CA W:CYS25 4.5 46.9 1.0
CA W:VAL39 4.6 50.0 1.0
C W:CYS25 4.6 47.4 1.0
NZ W:LYS22 4.7 44.5 1.0
N W:GLY26 4.7 48.2 1.0
CB W:VAL42 4.8 45.9 1.0
CE W:LYS22 4.9 47.1 1.0
N W:VAL42 4.9 46.2 1.0
C W:VAL42 4.9 45.8 1.0
O W:VAL39 4.9 49.4 1.0

Reference:

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
Page generated: Thu Oct 24 14:10:28 2024

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