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Zinc in PDB 2bx9: Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions

Protein crystallography data

The structure of Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions, PDB code: 2bx9 was solved by M.B.Shevtsov, Y.Chen, P.Gollnick, A.A.Antson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 51.552, 60.125, 60.348, 113.99, 101.37, 100.50
R / Rfree (%) 19.2 / 29.6

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions (pdb code 2bx9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions, PDB code: 2bx9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 2bx9

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Zinc binding site 1 out of 12 in the Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions


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 B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1054

b:66.6
occ:1.00
 SG A:CYS29 2.3 76.5 1.0
SG A:CYS15 2.3 74.8 1.0
SG A:CYS26 2.3 71.5 1.0
SG A:CYS12 2.3 65.6 1.0
CB A:CYS12 3.2 65.7 1.0
CB A:CYS29 3.3 68.6 1.0
CB A:CYS26 3.3 78.9 1.0
CB A:CYS15 3.4 75.7 1.0
N A:CYS29 3.6 70.0 1.0
N A:CYS15 3.7 72.8 1.0
CA A:CYS29 4.0 71.1 1.0
CA A:CYS15 4.2 77.8 1.0
CB A:ALA28 4.2 66.2 1.0
CA A:GLY33 4.4 74.2 1.0
CB A:LYS14 4.4 70.0 1.0
C A:ALA28 4.6 70.9 1.0
CA A:CYS12 4.6 64.6 1.0
N A:GLY33 4.7 76.2 1.0
CA A:CYS26 4.7 83.1 1.0
CA A:GLY19 4.7 84.7 0.0
C A:LYS14 4.8 75.4 1.0
CA A:ALA28 4.8 70.9 1.0
C A:GLY33 4.8 71.6 1.0
C A:CYS29 4.8 77.3 1.0
N A:ALA28 4.8 75.6 1.0
CA A:LYS14 5.0 73.0 1.0
CG A:LYS14 5.0 76.3 1.0
C A:CYS26 5.0 83.3 1.0
N A:LYS14 5.0 70.5 1.0

Zinc binding site 2 out of 12 in 2bx9

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Zinc binding site 2 out of 12 in the Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions


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 B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1054

b:99.5
occ:1.00
 SG B:CYS15 2.3 0.7 1.0
SG B:CYS29 2.3 99.0 1.0
SG B:CYS26 2.3 0.4 1.0
SG B:CYS12 2.4 90.5 1.0
CB B:CYS29 3.3 91.9 1.0
CB B:CYS15 3.3 0.5 1.0
CB B:CYS26 3.3 0.8 1.0
CB B:CYS12 3.5 86.0 1.0
N B:CYS29 3.8 96.2 1.0
N B:CYS15 4.1 0.1 1.0
CA B:CYS29 4.2 94.9 1.0
CA B:GLY33 4.2 96.1 1.0
N B:GLY33 4.3 98.7 1.0
CA B:CYS15 4.3 0.1 1.0
CA B:GLY19 4.6 0.7 0.0
CA B:CYS26 4.7 0.8 1.0
N B:GLY19 4.7 0.2 1.0
CB B:ALA28 4.8 99.2 1.0
O B:CYS26 4.8 0.2 1.0
C B:GLY33 4.8 89.8 1.0
C B:CYS26 4.9 0.7 1.0
C B:ALA28 4.9 97.5 0.0
C B:CYS29 4.9 0.1 1.0
CA B:CYS12 4.9 81.9 1.0
CG B:LYS14 5.0 0.5 1.0
CB B:LYS14 5.0 0.9 1.0

Zinc binding site 3 out of 12 in 2bx9

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Zinc binding site 3 out of 12 in the Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions


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 B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1054

b:0.4
occ:1.00
 SG C:CYS12 2.3 0.6 1.0
SG C:CYS29 2.3 0.9 1.0
SG C:CYS15 2.3 0.8 1.0
SG C:CYS26 2.3 0.4 1.0
CB C:CYS12 3.2 99.4 1.0
CB C:CYS15 3.3 0.6 1.0
CB C:CYS26 3.3 0.9 1.0
CB C:CYS29 3.4 0.8 1.0
N C:CYS29 3.6 0.6 1.0
N C:CYS15 3.9 0.8 1.0
CA C:CYS29 4.1 0.3 1.0
CA C:CYS15 4.2 0.5 1.0
CB C:ALA28 4.4 0.5 1.0
CA C:GLY33 4.6 0.2 1.0
CB C:LYS14 4.6 0.5 1.0
CA C:CYS12 4.6 99.5 1.0
C C:LYS14 4.6 1.0 1.0
CA C:CYS26 4.7 0.9 1.0
C C:ALA28 4.7 0.9 1.0
N C:GLY33 4.8 0.9 1.0
O C:CYS12 4.9 0.9 1.0
C C:GLY33 4.9 96.3 1.0
C C:CYS12 4.9 0.1 1.0
CA C:ALA28 4.9 0.9 1.0
O C:CYS26 4.9 0.2 1.0
C C:CYS29 4.9 0.7 1.0
C C:CYS26 5.0 0.2 1.0
N C:ALA28 5.0 0.3 1.0
CA C:LYS14 5.0 0.9 1.0
N C:LYS14 5.0 0.9 1.0

Zinc binding site 4 out of 12 in 2bx9

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Zinc binding site 4 out of 12 in the Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions


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 B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1054

b:68.5
occ:1.00
 SG D:CYS29 2.3 65.0 1.0
SG D:CYS15 2.3 68.1 1.0
SG D:CYS26 2.3 75.9 1.0
SG D:CYS12 2.3 68.3 1.0
CB D:CYS26 3.2 75.1 1.0
CB D:CYS29 3.3 64.1 1.0
CB D:CYS12 3.3 63.9 1.0
CB D:CYS15 3.3 73.1 1.0
N D:CYS29 3.9 71.2 1.0
N D:CYS15 3.9 76.6 1.0
CA D:CYS29 4.2 67.6 1.0
CA D:CYS15 4.2 76.7 1.0
CA D:GLY33 4.2 58.6 1.0
N D:GLY33 4.4 58.2 1.0
CB D:LYS14 4.5 81.1 1.0
CB D:ALA28 4.5 78.4 1.0
CA D:CYS26 4.6 77.9 1.0
O D:CYS26 4.6 75.7 1.0
C D:CYS26 4.7 78.9 1.0
C D:ALA28 4.8 75.1 1.0
C D:GLY33 4.8 58.6 1.0
CA D:CYS12 4.8 64.9 1.0
N D:ALA28 4.9 82.6 1.0
C D:LYS14 4.9 82.4 1.0
CA D:GLY19 5.0 65.4 1.0
C D:CYS15 5.0 75.9 1.0
CA D:ALA28 5.0 79.8 1.0
N D:VAL34 5.0 59.1 1.0

Zinc binding site 5 out of 12 in 2bx9

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Zinc binding site 5 out of 12 in the Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1054

b:69.6
occ:1.00
 SG E:CYS15 2.3 67.7 1.0
SG E:CYS26 2.3 68.7 1.0
SG E:CYS29 2.3 67.4 1.0
SG E:CYS12 2.4 71.3 1.0
CB E:CYS15 3.3 75.5 1.0
CB E:CYS26 3.3 74.3 1.0
CB E:CYS29 3.4 64.0 1.0
CB E:CYS12 3.4 66.6 1.0
N E:CYS15 3.7 75.1 1.0
N E:CYS29 3.7 68.9 1.0
CA E:CYS15 4.1 77.3 1.0
CA E:CYS29 4.2 67.5 1.0
CB E:ALA28 4.2 70.1 1.0
CB E:LYS14 4.4 73.7 1.0
CA E:GLY33 4.5 70.4 1.0
CA E:CYS26 4.7 78.1 1.0
C E:ALA28 4.7 70.5 1.0
C E:LYS14 4.7 78.6 1.0
N E:ALA28 4.8 73.2 1.0
CA E:CYS12 4.8 67.2 1.0
CA E:GLY19 4.8 80.1 1.0
CA E:ALA28 4.8 71.1 1.0
N E:GLY33 4.8 71.7 1.0
C E:CYS26 4.9 77.5 1.0
CA E:LYS14 4.9 77.0 1.0
C E:GLY33 4.9 68.8 1.0
C E:CYS29 4.9 72.2 1.0
C E:CYS15 5.0 80.5 1.0
N E:LYS14 5.0 75.9 1.0

Zinc binding site 6 out of 12 in 2bx9

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Zinc binding site 6 out of 12 in the Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1054

b:68.4
occ:1.00
 SG F:CYS12 2.3 64.0 1.0
SG F:CYS26 2.3 75.3 1.0
SG F:CYS15 2.3 71.0 1.0
SG F:CYS29 2.3 67.9 1.0
CB F:CYS12 3.2 63.8 1.0
CB F:CYS26 3.2 79.3 1.0
CB F:CYS15 3.3 75.7 1.0
CB F:CYS29 3.4 66.5 1.0
N F:CYS15 3.6 74.8 1.0
N F:CYS29 3.9 73.2 1.0
CA F:CYS15 4.1 76.0 1.0
CA F:CYS29 4.3 70.7 1.0
CB F:LYS14 4.4 77.8 1.0
CA F:CYS12 4.5 63.5 1.0
CA F:CYS26 4.6 84.4 1.0
O F:CYS12 4.6 69.8 1.0
C F:LYS14 4.6 78.3 1.0
C F:CYS12 4.7 67.0 1.0
CB F:ALA28 4.7 78.1 1.0
CA F:GLY33 4.7 70.4 1.0
O F:CYS26 4.7 84.2 1.0
N F:LYS14 4.8 73.5 1.0
C F:CYS26 4.8 85.0 1.0
CA F:LYS14 4.8 77.5 1.0
C F:CYS15 4.9 76.0 1.0
CA F:GLY19 4.9 81.6 1.0
N F:GLY19 4.9 80.7 1.0
N F:SER30 4.9 81.2 1.0
N F:ALA28 5.0 82.6 1.0

Zinc binding site 7 out of 12 in 2bx9

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Zinc binding site 7 out of 12 in the Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1054

b:82.5
occ:1.00
 SG G:CYS26 2.3 93.8 1.0
SG G:CYS29 2.3 77.1 1.0
SG G:CYS15 2.3 71.4 1.0
SG G:CYS12 2.3 81.4 1.0
CB G:CYS26 3.3 91.9 1.0
CB G:CYS29 3.3 79.3 1.0
CB G:CYS12 3.3 71.1 1.0
CB G:CYS15 3.4 79.8 1.0
N G:CYS29 3.6 91.0 1.0
N G:CYS15 3.9 83.5 1.0
CA G:CYS29 4.1 85.9 1.0
CB G:ALA28 4.2 99.3 1.0
CA G:CYS15 4.2 81.5 1.0
CA G:GLY33 4.6 66.5 1.0
C G:ALA28 4.6 97.2 1.0
CA G:CYS26 4.7 99.1 1.0
CB G:LYS14 4.7 96.1 1.0
N G:GLY33 4.7 70.8 1.0
CA G:CYS12 4.7 69.3 1.0
O G:CYS26 4.7 0.6 1.0
CA G:ALA28 4.8 0.1 1.0
CA G:GLY19 4.8 76.4 1.0
N G:ALA28 4.9 0.7 1.0
C G:LYS14 4.9 90.9 1.0
C G:CYS26 4.9 0.8 1.0
C G:GLY33 4.9 65.1 1.0
C G:CYS29 5.0 89.7 1.0
N G:GLY19 5.0 73.7 1.0

Zinc binding site 8 out of 12 in 2bx9

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Zinc binding site 8 out of 12 in the Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1054

b:85.5
occ:1.00
 SG H:CYS12 2.3 78.9 1.0
SG H:CYS29 2.3 77.1 1.0
SG H:CYS26 2.3 83.8 1.0
SG H:CYS15 2.3 83.3 1.0
CB H:CYS12 3.2 75.3 1.0
CB H:CYS26 3.3 91.8 1.0
CB H:CYS15 3.3 87.3 1.0
CB H:CYS29 3.5 79.9 1.0
N H:CYS15 3.8 84.3 1.0
CA H:CYS15 4.1 86.7 1.0
N H:CYS29 4.2 85.9 1.0
CA H:GLY19 4.2 91.7 1.0
N H:GLY19 4.4 90.5 1.0
CA H:CYS29 4.5 82.8 1.0
O H:CYS12 4.5 80.2 1.0
CB H:LYS14 4.5 87.6 1.0
CA H:CYS26 4.5 95.7 1.0
O H:CYS26 4.5 94.4 1.0
CA H:CYS12 4.5 74.8 1.0
C H:CYS26 4.6 95.8 1.0
C H:LYS14 4.7 87.1 1.0
C H:CYS12 4.7 77.2 1.0
C H:GLY19 4.7 95.8 1.0
CA H:GLY33 4.7 81.4 1.0
C H:ALA28 4.8 86.0 1.0
CB H:ALA28 4.9 90.1 1.0
N H:LYS14 4.9 83.6 1.0
CA H:LYS14 4.9 86.5 1.0
N H:ALA28 5.0 92.2 1.0
C H:CYS15 5.0 86.9 1.0

Zinc binding site 9 out of 12 in 2bx9

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Zinc binding site 9 out of 12 in the Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1054

b:63.2
occ:1.00
 SG I:CYS26 2.3 69.1 1.0
SG I:CYS15 2.3 63.3 1.0
SG I:CYS12 2.3 66.0 1.0
SG I:CYS29 2.3 63.4 1.0
CB I:CYS12 3.2 63.2 1.0
CB I:CYS15 3.2 65.9 1.0
CB I:CYS26 3.2 66.2 1.0
CB I:CYS29 3.5 61.4 1.0
N I:CYS29 3.7 66.5 1.0
N I:CYS15 4.0 69.7 1.0
CA I:CYS15 4.2 69.8 1.0
CA I:CYS29 4.2 65.0 1.0
CB I:ALA28 4.4 69.1 1.0
CA I:CYS12 4.5 63.3 1.0
CA I:CYS26 4.6 69.6 1.0
O I:CYS12 4.7 69.2 1.0
CA I:GLY33 4.7 66.8 1.0
C I:ALA28 4.7 69.0 1.0
C I:CYS12 4.7 66.4 1.0
N I:SER30 4.8 69.5 1.0
O I:CYS26 4.8 70.7 1.0
C I:CYS26 4.8 70.8 1.0
N I:ALA28 4.9 72.3 1.0
C I:CYS29 4.9 68.4 1.0
CA I:ALA28 4.9 71.0 1.0
C I:LYS14 4.9 74.5 1.0
CA I:GLY19 5.0 70.7 1.0

Zinc binding site 10 out of 12 in 2bx9

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Zinc binding site 10 out of 12 in the Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of B.Subtilis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1054

b:93.5
occ:1.00
 SG J:CYS15 2.3 95.9 1.0
SG J:CYS26 2.3 98.0 1.0
SG J:CYS29 2.3 0.5 1.0
SG J:CYS12 2.3 90.2 1.0
CB J:CYS26 3.2 0.5 1.0
CB J:CYS15 3.3 0.6 1.0
CB J:CYS29 3.3 90.8 1.0
CB J:CYS12 3.4 88.5 1.0
N J:CYS29 3.6 94.1 1.0
N J:CYS15 3.6 0.3 1.0
CA J:CYS15 4.1 0.3 1.0
CA J:CYS29 4.1 92.5 1.0
CB J:LYS14 4.2 0.1 1.0
CB J:ALA28 4.3 97.8 1.0
C J:LYS14 4.5 0.7 1.0
CA J:GLY33 4.6 93.9 1.0
CA J:CYS26 4.6 0.5 1.0
C J:ALA28 4.7 95.3 1.0
CA J:LYS14 4.7 0.3 1.0
CG J:LYS14 4.7 0.7 0.0
N J:LYS14 4.8 98.6 1.0
CA J:CYS12 4.8 86.3 1.0
CA J:ALA28 4.8 98.7 1.0
N J:ALA28 4.8 0.6 1.0
O J:ALA18 4.9 0.1 1.0
N J:GLY33 4.9 95.7 1.0
C J:CYS29 4.9 97.1 1.0
C J:CYS26 4.9 0.3 1.0
O J:CYS26 4.9 0.8 1.0
C J:CYS15 5.0 0.0 1.0

Reference:

M.B.Shevtsov, Y.Chen, P.Gollnick, A.A.Antson. Crystal Structure of Bacillus Subtilis Anti-Trap Protein, An Antagonist of Trap/Rna Interaction. Proc.Natl.Acad.Sci.Usa V. 102 17600 2005.
ISSN: ISSN 0027-8424
PubMed: 16306262
DOI: 10.1073/PNAS.0508728102
Page generated: Wed Oct 16 22:07:57 2024

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