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Zinc in PDB 2b3j: Crystal Structure of Staphylococcus Aureus Trna Adenosine Deaminase, Tada, in Complex with Rna

Protein crystallography data

The structure of Crystal Structure of Staphylococcus Aureus Trna Adenosine Deaminase, Tada, in Complex with Rna, PDB code: 2b3j was solved by H.C.Losey, A.J.Ruthenburg, G.L.Verdine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.055, 89.029, 119.133, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 24.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Staphylococcus Aureus Trna Adenosine Deaminase, Tada, in Complex with Rna (pdb code 2b3j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Staphylococcus Aureus Trna Adenosine Deaminase, Tada, in Complex with Rna, PDB code: 2b3j:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2b3j

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Zinc binding site 1 out of 4 in the Crystal Structure of Staphylococcus Aureus Trna Adenosine Deaminase, Tada, in Complex with Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Staphylococcus Aureus Trna Adenosine Deaminase, Tada, in Complex with Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:25.3
occ:1.00
O A:HOH2002 2.1 18.0 1.0
ND1 A:HIS53 2.2 25.8 1.0
SG A:CYS86 2.3 19.9 1.0
SG A:CYS83 2.4 22.7 1.0
CB A:CYS86 3.1 17.3 1.0
CE1 A:HIS53 3.1 27.0 1.0
CG A:HIS53 3.2 26.5 1.0
CB A:CYS83 3.5 21.5 1.0
CB A:HIS53 3.5 23.6 1.0
N A:CYS83 3.8 22.6 1.0
N A:CYS86 3.8 18.3 1.0
OE1 A:GLU55 3.9 23.6 1.0
C6 E:P5P34 4.0 25.5 1.0
N7 E:P5P34 4.0 29.5 1.0
C5 E:P5P34 4.1 28.0 1.0
CA A:CYS86 4.1 21.0 1.0
CD A:GLU55 4.1 27.1 1.0
CA A:CYS83 4.2 21.9 1.0
CE A:MET85 4.2 23.6 1.0
NE2 A:HIS53 4.3 27.5 1.0
CD2 A:HIS53 4.3 25.8 1.0
OE2 A:GLU55 4.4 24.1 1.0
C A:CYS83 4.7 21.8 1.0
CG A:GLU55 4.7 26.3 1.0
N1 E:P5P34 4.8 27.2 1.0
C A:PRO82 4.9 22.5 1.0
C8 E:P5P34 4.9 31.2 1.0
O A:CYS83 4.9 22.1 1.0
CB A:MET85 4.9 21.3 1.0
C A:MET85 5.0 20.8 1.0

Zinc binding site 2 out of 4 in 2b3j

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Zinc binding site 2 out of 4 in the Crystal Structure of Staphylococcus Aureus Trna Adenosine Deaminase, Tada, in Complex with Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Staphylococcus Aureus Trna Adenosine Deaminase, Tada, in Complex with Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2002

b:25.5
occ:1.00
O B:HOH2003 2.1 20.1 1.0
ND1 B:HIS53 2.2 25.3 1.0
SG B:CYS86 2.3 22.9 1.0
SG B:CYS83 2.4 23.2 1.0
CG B:HIS53 3.2 24.7 1.0
CB B:CYS86 3.2 20.8 1.0
CE1 B:HIS53 3.2 27.5 1.0
CB B:HIS53 3.4 25.1 1.0
CB B:CYS83 3.5 21.9 1.0
OE2 B:GLU55 3.6 30.8 1.0
N B:CYS83 3.8 22.0 1.0
N B:CYS86 3.9 22.4 1.0
N7 F:P5P34 3.9 27.4 1.0
C6 F:P5P34 4.0 28.1 1.0
C5 F:P5P34 4.0 29.0 1.0
CE B:MET85 4.1 22.8 1.0
CA B:CYS86 4.1 22.9 1.0
OE1 B:GLU55 4.2 26.6 1.0
CD B:GLU55 4.2 29.4 1.0
CA B:CYS83 4.2 22.6 1.0
NE2 B:HIS53 4.3 25.8 1.0
CD2 B:HIS53 4.3 24.9 1.0
C8 F:P5P34 4.8 28.3 1.0
C B:CYS83 4.8 23.1 1.0
O B:CYS83 4.9 22.1 1.0
CB B:MET85 4.9 24.0 1.0
C B:PRO82 4.9 24.7 1.0
N1 F:P5P34 4.9 28.8 1.0
C B:MET85 5.0 23.9 1.0
CA B:HIS53 5.0 25.1 1.0
C4 F:P5P34 5.0 28.4 1.0

Zinc binding site 3 out of 4 in 2b3j

Go back to Zinc Binding Sites List in 2b3j
Zinc binding site 3 out of 4 in the Crystal Structure of Staphylococcus Aureus Trna Adenosine Deaminase, Tada, in Complex with Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Staphylococcus Aureus Trna Adenosine Deaminase, Tada, in Complex with Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2003

b:23.6
occ:1.00
O C:HOH2004 2.0 17.7 1.0
ND1 C:HIS53 2.2 28.1 1.0
SG C:CYS83 2.4 22.1 1.0
SG C:CYS86 2.4 19.1 1.0
CB C:CYS86 3.2 18.9 1.0
CE1 C:HIS53 3.2 30.2 1.0
CG C:HIS53 3.2 26.7 1.0
CB C:CYS83 3.5 20.2 1.0
CB C:HIS53 3.5 22.4 1.0
N C:CYS86 3.8 18.7 1.0
OE2 C:GLU55 3.8 19.7 1.0
N C:CYS83 3.8 19.4 1.0
C6 G:P5P34 4.0 67.7 1.0
CE C:MET85 4.0 20.7 1.0
CA C:CYS86 4.1 18.5 1.0
O C:HOH2012 4.1 22.9 1.0
CA C:CYS83 4.2 20.6 1.0
OE1 C:GLU55 4.3 21.7 1.0
NE2 C:HIS53 4.3 30.1 1.0
CD C:GLU55 4.3 23.5 1.0
CD2 C:HIS53 4.4 28.0 1.0
N1 G:P5P34 4.4 70.0 1.0
C C:CYS83 4.8 20.3 1.0
CB C:MET85 4.8 21.8 1.0
C C:MET85 4.9 20.5 1.0
O C:CYS83 4.9 20.8 1.0
C C:PRO82 5.0 21.4 1.0

Zinc binding site 4 out of 4 in 2b3j

Go back to Zinc Binding Sites List in 2b3j
Zinc binding site 4 out of 4 in the Crystal Structure of Staphylococcus Aureus Trna Adenosine Deaminase, Tada, in Complex with Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Staphylococcus Aureus Trna Adenosine Deaminase, Tada, in Complex with Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2004

b:26.3
occ:1.00
O D:HOH2005 2.2 19.0 1.0
ND1 D:HIS53 2.2 19.6 1.0
SG D:CYS86 2.3 23.9 1.0
SG D:CYS83 2.4 23.0 1.0
CE1 D:HIS53 3.1 20.7 1.0
CG D:HIS53 3.1 20.0 1.0
CB D:CYS86 3.2 24.4 1.0
CB D:HIS53 3.4 21.9 1.0
CB D:CYS83 3.4 22.0 1.0
N D:CYS83 3.8 23.0 1.0
OE2 D:GLU55 3.8 28.5 1.0
N D:CYS86 3.8 19.5 1.0
C6 H:P5P34 4.0 28.1 1.0
N7 H:P5P34 4.1 30.1 1.0
C5 H:P5P34 4.1 28.8 1.0
CA D:CYS86 4.1 23.6 1.0
OE1 D:GLU55 4.1 27.9 1.0
CA D:CYS83 4.2 22.5 1.0
CE D:MET85 4.2 18.3 1.0
NE2 D:HIS53 4.3 22.6 1.0
CD D:GLU55 4.3 27.9 1.0
CD2 D:HIS53 4.3 19.6 1.0
C D:CYS83 4.8 21.9 1.0
N1 H:P5P34 4.8 25.1 1.0
C D:PRO82 4.9 24.5 1.0
C8 H:P5P34 4.9 32.5 1.0
CB D:MET85 4.9 19.3 1.0
O D:CYS83 4.9 22.1 1.0
C D:MET85 5.0 20.9 1.0
CA D:HIS53 5.0 22.9 1.0
C4 H:P5P34 5.0 30.3 1.0

Reference:

H.C.Losey, A.J.Ruthenburg, G.L.Verdine. Crystal Structure of Staphylococcus Aureus Trna Adenosine Deaminase Tada in Complex with Rna. Nat.Struct.Mol.Biol. V. 13 153 2006.
ISSN: ISSN 1545-9993
PubMed: 16415880
DOI: 10.1038/NSMB1047
Page generated: Wed Dec 16 03:18:01 2020

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