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Zinc in PDB 3h0m: 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: 3h0m 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) 39.37 / 2.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 128.248, 129.856, 155.069, 90.01, 89.96, 90.11
R / Rfree (%) 25.4 / 30.5

Other elements in 3h0m:

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

Magnesium (Mg) 7 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Trna-Dependent Amidotransferase Gatcab From Aquifex Aeolicus (pdb code 3h0m). 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: 3h0m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3h0m

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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:49.5
occ:1.00
 SG B:CYS27 2.1 52.2 1.0
SG B:CYS25 2.3 44.1 1.0
CB B:CYS40 2.5 46.8 1.0
SG B:CYS43 2.6 43.0 1.0
SG B:CYS40 2.7 48.4 1.0
CB B:CYS27 3.2 49.7 1.0
CB B:CYS25 3.3 44.6 1.0
CB B:CYS43 3.5 43.8 1.0
CA B:CYS40 3.6 46.4 1.0
N B:CYS40 3.7 47.1 1.0
N B:CYS27 4.0 48.4 1.0
C B:VAL39 4.1 47.6 1.0
N B:CYS43 4.1 44.5 1.0
CA B:CYS27 4.2 49.1 1.0
CA B:CYS43 4.4 44.0 1.0
CD B:LYS22 4.5 41.6 1.0
CE B:LYS22 4.6 43.6 1.0
CA B:CYS25 4.6 45.2 1.0
O B:VAL39 4.6 47.8 1.0
CA B:VAL39 4.6 47.7 1.0
C B:CYS25 4.6 45.6 1.0
C B:CYS40 4.7 46.1 1.0
N B:GLY26 4.7 46.6 1.0
NZ B:LYS22 4.8 43.8 1.0
CB B:VAL42 4.8 44.8 1.0
O B:ASN38 5.0 48.8 1.0

Zinc binding site 2 out of 8 in 3h0m

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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:59.4
occ:1.00
 SG E:CYS43 2.1 43.2 1.0
SG E:CYS27 2.3 51.8 1.0
SG E:CYS40 2.3 49.1 1.0
SG E:CYS25 2.3 46.4 1.0
CB E:CYS25 3.3 45.4 1.0
CB E:CYS40 3.3 46.7 1.0
CB E:CYS43 3.3 43.8 1.0
CB E:CYS27 3.4 49.4 1.0
N E:CYS40 3.6 47.2 1.0
N E:CYS43 3.6 44.6 1.0
CA E:CYS40 3.9 46.5 1.0
CA E:CYS43 4.1 44.1 1.0
C E:VAL39 4.2 47.7 1.0
N E:CYS27 4.2 48.7 1.0
C E:CYS40 4.4 46.3 1.0
CD E:LYS22 4.4 43.2 1.0
CA E:CYS27 4.4 49.2 1.0
O E:CYS40 4.4 45.8 1.0
CB E:VAL42 4.5 45.4 1.0
CA E:VAL39 4.5 47.9 1.0
CA E:CYS25 4.6 45.5 1.0
NZ E:LYS22 4.7 44.0 1.0
C E:VAL42 4.8 45.0 1.0
C E:CYS25 4.8 46.0 1.0
O E:VAL39 4.9 48.0 1.0
N E:VAL42 5.0 44.9 1.0
CA E:VAL42 5.0 44.8 1.0

Zinc binding site 3 out of 8 in 3h0m

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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:51.1
occ:1.00
 SG H:CYS43 2.1 41.7 1.0
SG H:CYS27 2.3 49.2 1.0
SG H:CYS25 2.4 44.4 1.0
SG H:CYS40 2.4 43.8 1.0
CB H:CYS43 3.3 43.7 1.0
CB H:CYS27 3.3 48.6 1.0
CB H:CYS25 3.4 44.8 1.0
CB H:CYS40 3.4 45.4 1.0
N H:CYS40 3.6 47.1 1.0
N H:CYS43 3.7 44.5 1.0
CA H:CYS40 4.0 46.0 1.0
CA H:CYS43 4.1 44.0 1.0
C H:VAL39 4.2 47.5 1.0
N H:CYS27 4.2 48.5 1.0
CE H:LYS22 4.3 44.0 1.0
CD H:LYS22 4.4 43.1 1.0
CA H:CYS27 4.4 49.0 1.0
C H:CYS40 4.5 45.8 1.0
O H:CYS40 4.5 45.5 1.0
CA H:VAL39 4.6 47.8 1.0
NZ H:LYS22 4.7 43.1 1.0
CA H:CYS25 4.7 45.1 1.0
CB H:VAL42 4.8 45.2 1.0
O H:VAL39 4.8 48.1 1.0
C H:VAL42 4.8 45.0 1.0
O H:ASN38 4.9 48.7 1.0
C H:CYS25 4.9 45.5 1.0

Zinc binding site 4 out of 8 in 3h0m

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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:46.4
occ:1.00
 SG K:CYS27 2.1 45.6 1.0
SG K:CYS25 2.2 42.9 1.0
SG K:CYS40 2.4 41.4 1.0
SG K:CYS43 2.4 41.4 1.0
CB K:CYS27 3.2 48.3 1.0
CB K:CYS25 3.3 44.2 1.0
CB K:CYS40 3.3 44.9 1.0
CB K:CYS43 3.5 43.5 1.0
N K:CYS40 3.8 47.0 1.0
N K:CYS27 3.9 48.6 1.0
N K:CYS43 4.0 44.4 1.0
CA K:CYS40 4.0 45.9 1.0
CA K:CYS27 4.1 48.9 1.0
CA K:CYS43 4.3 44.0 1.0
C K:VAL39 4.3 47.5 1.0
CD K:LYS22 4.4 38.8 1.0
CE K:LYS22 4.5 40.7 1.0
CA K:CYS25 4.5 45.0 1.0
C K:CYS40 4.5 45.9 1.0
C K:CYS25 4.6 45.6 1.0
N K:GLY26 4.6 46.5 1.0
O K:CYS40 4.6 45.7 1.0
CA K:VAL39 4.8 47.4 1.0
CB K:VAL42 4.8 44.9 1.0
NZ K:LYS22 4.9 39.9 1.0
O K:ASN38 4.9 48.8 1.0
O K:VAL39 4.9 47.9 1.0

Zinc binding site 5 out of 8 in 3h0m

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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:47.7
occ:1.00
 SG N:CYS25 2.2 44.7 1.0
SG N:CYS27 2.2 47.8 1.0
SG N:CYS43 2.2 41.1 1.0
SG N:CYS40 2.5 45.1 1.0
CB N:CYS25 3.2 44.5 1.0
CB N:CYS27 3.2 49.0 1.0
CB N:CYS40 3.4 46.3 1.0
CB N:CYS43 3.4 43.4 1.0
N N:CYS40 3.8 46.9 1.0
N N:CYS43 3.8 44.4 1.0
CA N:CYS40 4.0 46.0 1.0
N N:CYS27 4.1 48.6 1.0
CA N:CYS43 4.2 43.9 1.0
CA N:CYS27 4.3 48.9 1.0
CD N:LYS22 4.3 42.1 1.0
C N:VAL39 4.3 47.6 1.0
C N:CYS40 4.5 45.9 1.0
CA N:CYS25 4.6 45.2 1.0
O N:CYS40 4.6 45.5 1.0
NZ N:LYS22 4.6 40.6 1.0
CA N:VAL39 4.7 47.8 1.0
C N:CYS25 4.7 45.6 1.0
CB N:VAL42 4.8 45.2 1.0
N N:GLY26 4.8 46.6 1.0
O N:VAL39 4.9 48.0 1.0
CE N:LYS22 4.9 42.3 1.0
C N:VAL42 5.0 45.0 1.0
O N:ASN38 5.0 48.9 1.0

Zinc binding site 6 out of 8 in 3h0m

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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:44.9
occ:1.00
 SG Q:CYS25 2.0 40.1 1.0
SG Q:CYS27 2.1 47.2 1.0
SG Q:CYS40 2.5 41.1 1.0
SG Q:CYS43 2.5 42.4 1.0
CB Q:CYS25 3.2 44.6 1.0
CB Q:CYS27 3.3 48.4 1.0
CB Q:CYS40 3.3 45.3 1.0
CB Q:CYS43 3.5 43.5 1.0
N Q:CYS27 3.8 48.6 1.0
N Q:CYS40 3.9 47.1 1.0
N Q:CYS43 4.0 44.3 1.0
CA Q:CYS40 4.1 45.8 1.0
CA Q:CYS27 4.2 48.9 1.0
CD Q:LYS22 4.3 40.9 1.0
CA Q:CYS43 4.4 44.1 1.0
C Q:VAL39 4.4 47.5 1.0
CE Q:LYS22 4.4 40.6 1.0
CA Q:CYS25 4.4 45.0 1.0
C Q:CYS25 4.5 45.6 1.0
N Q:GLY26 4.5 46.7 1.0
C Q:CYS40 4.6 45.9 1.0
O Q:CYS40 4.7 45.8 1.0
NZ Q:LYS22 4.8 37.7 1.0
CB Q:VAL42 4.8 45.2 1.0
CA Q:VAL39 4.8 47.6 1.0
O Q:CYS25 5.0 45.8 1.0
O Q:ASN38 5.0 48.8 1.0

Zinc binding site 7 out of 8 in 3h0m

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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:49.1
occ:1.00
 SG T:CYS43 2.1 43.8 1.0
SG T:CYS27 2.2 52.5 1.0
SG T:CYS40 2.3 47.2 1.0
SG T:CYS25 2.4 46.3 1.0
CB T:CYS43 3.2 44.4 1.0
CB T:CYS40 3.3 46.4 1.0
CB T:CYS27 3.4 49.5 1.0
CB T:CYS25 3.5 45.3 1.0
N T:CYS40 3.5 47.3 1.0
N T:CYS43 3.8 44.6 1.0
CA T:CYS40 3.8 46.4 1.0
CA T:CYS43 4.1 44.3 1.0
C T:VAL39 4.1 47.7 1.0
CD T:LYS22 4.3 41.5 1.0
C T:CYS40 4.3 46.2 1.0
N T:CYS27 4.3 48.8 1.0
O T:CYS40 4.3 45.9 1.0
CA T:CYS27 4.4 49.3 1.0
CA T:VAL39 4.5 47.9 1.0
CB T:VAL42 4.6 45.0 1.0
NZ T:LYS22 4.7 44.1 1.0
CA T:CYS25 4.8 45.4 1.0
O T:VAL39 4.8 47.9 1.0
CE T:LYS22 4.9 45.1 1.0
C T:VAL42 4.9 45.0 1.0
C T:CYS25 4.9 45.7 1.0

Zinc binding site 8 out of 8 in 3h0m

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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:50.6
occ:1.00
 SG W:CYS27 2.0 48.0 1.0
SG W:CYS40 2.1 44.7 1.0
SG W:CYS25 2.3 43.5 1.0
SG W:CYS43 2.3 42.4 1.0
CB W:CYS40 3.2 46.7 1.0
CB W:CYS27 3.2 48.8 1.0
CB W:CYS25 3.3 44.8 1.0
CB W:CYS43 3.5 43.5 1.0
N W:CYS40 3.8 47.1 1.0
N W:CYS27 3.9 48.5 1.0
CA W:CYS40 4.0 46.1 1.0
N W:CYS43 4.0 44.3 1.0
CA W:CYS27 4.2 48.9 1.0
C W:VAL39 4.3 47.6 1.0
CA W:CYS43 4.4 44.2 1.0
CD W:LYS22 4.5 42.9 1.0
C W:CYS40 4.5 46.1 1.0
CA W:CYS25 4.6 45.2 1.0
C W:CYS25 4.6 45.6 1.0
O W:CYS40 4.7 45.9 1.0
N W:GLY26 4.7 46.7 1.0
CA W:VAL39 4.7 47.7 1.0
CB W:VAL42 4.7 44.6 1.0
CE W:LYS22 4.7 44.0 1.0
O W:VAL39 4.8 48.0 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 14:07:47 2024

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