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Zinc in PDB 3ld0: Crystal Structure of B.Licheniformis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions

Protein crystallography data

The structure of Crystal Structure of B.Licheniformis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions, PDB code: 3ld0 was solved by M.B.Shevtsov, Y.Chen, M.N.Isupov, P.Gollnick, A.A.Antson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.27 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 118.544, 99.865, 123.178, 90.00, 117.61, 90.00
R / Rfree (%) 19.4 / 25.9

Other elements in 3ld0:

The structure of Crystal Structure of B.Licheniformis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions also contains other interesting chemical elements:

Magnesium (Mg) 16 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of B.Licheniformis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions (pdb code 3ld0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 48 binding sites of Zinc where determined in the Crystal Structure of B.Licheniformis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions, PDB code: 3ld0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 48 in 3ld0

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Zinc binding site 1 out of 48 in the Crystal Structure of B.Licheniformis 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.Licheniformis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn60

b:15.0
occ:1.00
 SG A:CYS26 2.3 18.8 1.0
SG A:CYS12 2.3 14.1 1.0
SG A:CYS15 2.3 18.1 1.0
SG A:CYS29 2.4 17.1 1.0
CB A:CYS26 3.1 19.6 1.0
CB A:CYS12 3.2 16.8 1.0
CB A:CYS29 3.4 19.6 1.0
CB A:CYS15 3.4 18.9 1.0
N A:CYS15 3.7 21.4 1.0
N A:CYS29 3.9 21.3 1.0
CA A:CYS15 4.2 20.0 1.0
CA A:CYS29 4.2 20.9 1.0
CB A:ASN14 4.4 26.2 1.0
CA A:GLY19 4.4 21.8 1.0
CA A:CYS26 4.5 20.2 1.0
CA A:CYS12 4.6 17.9 1.0
CA A:GLY33 4.6 16.6 1.0
C A:ASN14 4.7 23.6 1.0
CB A:LYS28 4.7 25.0 1.0
C A:LYS28 4.7 24.2 1.0
N A:GLY19 4.7 24.4 1.0
N A:GLY33 4.8 19.6 1.0
CA A:ASN14 4.9 25.2 1.0
N A:ASN14 4.9 25.3 1.0
C A:CYS26 4.9 21.3 1.0
C A:GLY19 4.9 21.5 1.0
O A:CYS26 4.9 20.4 1.0
ND2 A:ASN14 4.9 21.7 1.0
C A:CYS12 5.0 20.8 1.0
N A:LYS28 5.0 24.8 1.0

Zinc binding site 2 out of 48 in 3ld0

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Zinc binding site 2 out of 48 in the Crystal Structure of B.Licheniformis 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.Licheniformis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn160

b:14.4
occ:1.00
 SG B:CYS112 2.3 15.6 1.0
SG B:CYS126 2.3 15.2 1.0
SG B:CYS115 2.3 16.6 1.0
SG B:CYS129 2.4 16.6 1.0
CB B:CYS112 3.2 15.7 1.0
CB B:CYS126 3.2 17.8 1.0
CB B:CYS129 3.3 16.7 1.0
CB B:CYS115 3.4 21.0 1.0
N B:CYS115 3.8 23.1 1.0
N B:CYS129 3.8 19.5 1.0
CA B:CYS129 4.2 18.4 1.0
CA B:CYS115 4.2 21.2 1.0
CB B:ASN114 4.3 25.1 1.0
CA B:GLY119 4.4 20.0 1.0
CA B:CYS126 4.6 17.9 1.0
CA B:CYS112 4.6 17.3 1.0
CB B:LYS128 4.6 26.2 1.0
C B:LYS128 4.6 23.8 1.0
N B:GLY119 4.6 20.6 1.0
CA B:GLY133 4.7 19.5 1.0
C B:ASN114 4.7 24.1 1.0
O B:CYS126 4.8 18.2 1.0
C B:CYS126 4.8 20.8 1.0
N B:LYS128 4.9 26.2 1.0
N B:GLY133 4.9 20.8 1.0
N B:ASN114 4.9 23.8 1.0
CA B:ASN114 4.9 23.6 1.0
CA B:LYS128 4.9 27.1 1.0
ND2 B:ASN114 5.0 25.8 1.0
C B:GLY119 5.0 21.7 1.0
C B:CYS112 5.0 19.1 1.0
C B:CYS115 5.0 21.9 1.0

Zinc binding site 3 out of 48 in 3ld0

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Zinc binding site 3 out of 48 in the Crystal Structure of B.Licheniformis 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.Licheniformis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn260

b:21.8
occ:1.00
 SG C:CYS215 2.3 17.7 1.0
SG C:CYS212 2.3 24.6 1.0
SG C:CYS229 2.3 17.3 1.0
SG C:CYS226 2.3 24.3 1.0
CB C:CYS226 3.2 24.4 1.0
CB C:CYS212 3.2 24.0 1.0
CB C:CYS215 3.3 28.6 1.0
CB C:CYS229 3.3 19.1 1.0
N C:CYS215 3.8 33.2 1.0
N C:CYS229 3.8 20.3 1.0
CA C:CYS215 4.1 29.7 1.0
CA C:CYS229 4.2 20.0 1.0
CA C:GLY219 4.5 23.8 1.0
CB C:ASN214 4.6 36.5 1.0
CA C:GLY233 4.6 23.6 1.0
CA C:CYS226 4.6 23.8 1.0
CA C:CYS212 4.6 25.8 1.0
C C:LYS228 4.7 23.4 1.0
C C:ASN214 4.7 34.5 1.0
CB C:LYS228 4.8 24.4 1.0
N C:GLY233 4.8 23.5 1.0
N C:GLY219 4.8 25.4 1.0
O C:CYS226 4.9 23.5 1.0
C C:CYS226 4.9 24.0 1.0
C C:GLY233 4.9 22.6 1.0
N C:ASN214 4.9 35.8 1.0
CA C:ASN214 5.0 35.9 1.0
N C:LYS228 5.0 25.9 1.0

Zinc binding site 4 out of 48 in 3ld0

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Zinc binding site 4 out of 48 in the Crystal Structure of B.Licheniformis 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.Licheniformis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn60

b:12.9
occ:1.00
 SG D:CYS12 2.3 14.4 1.0
SG D:CYS26 2.3 14.1 1.0
SG D:CYS29 2.3 13.2 1.0
SG D:CYS15 2.4 12.1 1.0
CB D:CYS12 3.2 15.1 1.0
CB D:CYS26 3.2 13.8 1.0
CB D:CYS29 3.4 20.3 1.0
CB D:CYS15 3.4 16.1 1.0
N D:CYS15 3.8 16.9 1.0
N D:CYS29 3.9 22.7 1.0
CA D:CYS15 4.2 16.8 1.0
CA D:CYS29 4.2 21.6 1.0
CB D:ASN14 4.5 21.3 1.0
CA D:GLY19 4.5 14.6 1.0
CA D:CYS12 4.6 14.3 1.0
CA D:GLY33 4.6 16.3 1.0
CA D:CYS26 4.6 14.8 1.0
CB D:LYS28 4.6 23.0 1.0
C D:LYS28 4.6 23.7 1.0
C D:ASN14 4.7 20.6 1.0
N D:GLY19 4.7 16.0 1.0
N D:GLY33 4.8 16.9 1.0
ND2 D:ASN14 4.9 34.4 1.0
N D:ASN14 4.9 20.9 1.0
O D:CYS26 4.9 15.5 1.0
C D:CYS26 4.9 15.6 1.0
C D:CYS12 4.9 18.1 1.0
N D:LYS28 4.9 21.4 1.0
CA D:ASN14 4.9 21.9 1.0
C D:GLY19 4.9 16.8 1.0
CA D:LYS28 4.9 22.4 1.0
C D:GLY33 5.0 17.1 1.0
O D:CYS12 5.0 15.8 1.0

Zinc binding site 5 out of 48 in 3ld0

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Zinc binding site 5 out of 48 in the Crystal Structure of B.Licheniformis 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.Licheniformis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn160

b:14.2
occ:1.00
 SG E:CYS112 2.3 13.1 1.0
SG E:CYS126 2.3 12.9 1.0
SG E:CYS115 2.3 14.1 1.0
SG E:CYS129 2.4 13.2 1.0
CB E:CYS126 3.2 12.2 1.0
CB E:CYS112 3.2 15.2 1.0
CB E:CYS115 3.4 20.7 1.0
CB E:CYS129 3.4 12.7 1.0
N E:CYS115 3.8 20.7 1.0
N E:CYS129 3.9 17.4 1.0
CA E:CYS115 4.2 20.3 1.0
CA E:CYS129 4.2 15.8 1.0
CB E:ASN114 4.4 24.7 1.0
CA E:GLY119 4.5 15.2 1.0
CB E:LYS128 4.5 17.3 1.0
CA E:CYS126 4.6 13.1 1.0
CA E:CYS112 4.6 15.4 1.0
C E:ASN114 4.6 24.5 1.0
CA E:GLY133 4.7 14.2 1.0
C E:LYS128 4.7 19.3 1.0
N E:GLY119 4.7 18.0 1.0
N E:GLY133 4.8 12.6 1.0
ND2 E:ASN114 4.8 30.1 1.0
CA E:ASN114 4.9 23.6 1.0
N E:ASN114 4.9 23.6 1.0
C E:CYS126 4.9 14.2 1.0
O E:CYS126 4.9 13.2 1.0
C E:CYS112 4.9 18.9 1.0
C E:GLY119 5.0 18.6 1.0
C E:GLY133 5.0 13.7 1.0
N E:LYS128 5.0 17.6 1.0
CA E:LYS128 5.0 19.9 1.0

Zinc binding site 6 out of 48 in 3ld0

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Zinc binding site 6 out of 48 in the Crystal Structure of B.Licheniformis 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.Licheniformis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn260

b:18.4
occ:1.00
 SG F:CYS226 2.3 23.5 1.0
SG F:CYS212 2.3 14.9 1.0
SG F:CYS229 2.3 17.6 1.0
SG F:CYS215 2.3 19.2 1.0
CB F:CYS212 3.2 20.4 1.0
CB F:CYS226 3.2 22.3 1.0
CB F:CYS229 3.3 15.6 1.0
CB F:CYS215 3.4 23.4 1.0
N F:CYS215 3.8 26.1 1.0
N F:CYS229 3.8 20.8 1.0
CA F:CYS229 4.2 19.0 1.0
CA F:CYS215 4.2 23.9 1.0
CA F:GLY219 4.4 28.2 1.0
CB F:ASN214 4.6 26.2 0.5
CA F:CYS226 4.6 22.6 1.0
CA F:CYS212 4.6 20.1 1.0
CB F:ASN214 4.7 27.3 0.5
C F:LYS228 4.7 23.1 1.0
CB F:LYS228 4.7 26.2 1.0
CA F:GLY233 4.7 18.9 1.0
N F:GLY219 4.7 28.6 1.0
N F:GLY233 4.8 21.8 1.0
ND2 F:ASN214 4.8 20.2 0.5
C F:ASN214 4.9 26.1 1.0
O F:CYS226 4.9 20.4 1.0
C F:CYS226 4.9 21.0 1.0
N F:LYS228 4.9 22.3 1.0
O F:CYS212 5.0 18.9 1.0
C F:GLY219 5.0 28.7 1.0
C F:CYS212 5.0 21.6 1.0
CA F:LYS228 5.0 24.6 1.0
C F:CYS229 5.0 19.6 1.0

Zinc binding site 7 out of 48 in 3ld0

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Zinc binding site 7 out of 48 in the Crystal Structure of B.Licheniformis 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.Licheniformis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn60

b:16.2
occ:1.00
 SG G:CYS12 2.3 15.7 1.0
SG G:CYS26 2.3 17.2 1.0
SG G:CYS15 2.3 18.1 1.0
SG G:CYS29 2.3 15.9 1.0
CB G:CYS26 3.2 17.2 1.0
CB G:CYS12 3.2 16.0 1.0
CB G:CYS29 3.4 13.9 1.0
CB G:CYS15 3.4 23.1 1.0
N G:CYS15 3.8 25.3 1.0
N G:CYS29 3.8 16.8 1.0
CA G:CYS15 4.2 25.1 1.0
CA G:CYS29 4.2 15.7 1.0
CB G:ASN14 4.5 28.0 1.0
CA G:CYS26 4.6 17.7 1.0
CA G:GLY19 4.6 21.1 1.0
CA G:CYS12 4.6 17.1 1.0
CB G:LYS28 4.6 22.2 1.0
CA G:GLY33 4.7 17.0 1.0
C G:LYS28 4.7 19.4 1.0
N G:GLY19 4.7 22.1 1.0
C G:ASN14 4.7 25.5 1.0
O G:CYS26 4.9 19.0 1.0
C G:CYS12 4.9 21.5 1.0
N G:ASN14 4.9 27.0 1.0
C G:CYS26 4.9 19.2 1.0
N G:GLY33 4.9 15.2 1.0
O G:CYS12 4.9 22.2 1.0
CA G:ASN14 4.9 27.0 1.0
N G:LYS28 4.9 20.2 1.0
CA G:LYS28 5.0 21.1 1.0
C G:GLY19 5.0 20.7 1.0

Zinc binding site 8 out of 48 in 3ld0

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Zinc binding site 8 out of 48 in the Crystal Structure of B.Licheniformis 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.Licheniformis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn160

b:14.8
occ:1.00
 SG H:CYS112 2.3 15.1 1.0
SG H:CYS126 2.3 15.4 1.0
SG H:CYS115 2.3 13.1 1.0
SG H:CYS129 2.4 16.8 1.0
CB H:CYS126 3.2 17.3 1.0
CB H:CYS112 3.2 14.8 1.0
CB H:CYS115 3.3 15.3 1.0
CB H:CYS129 3.3 17.2 1.0
N H:CYS115 3.8 19.3 1.0
N H:CYS129 3.8 20.4 1.0
CA H:CYS115 4.2 17.1 1.0
CA H:CYS129 4.2 19.6 1.0
CB H:ASN114 4.4 20.6 0.5
CA H:GLY119 4.5 18.7 1.0
CB H:LYS128 4.5 21.9 1.0
CA H:CYS126 4.5 17.8 1.0
CB H:ASN114 4.6 21.8 0.5
C H:LYS128 4.6 21.2 1.0
CA H:CYS112 4.6 16.2 1.0
CA H:GLY133 4.7 17.2 1.0
O H:CYS126 4.7 20.2 1.0
ND2 H:ASN114 4.7 15.3 0.5
C H:ASN114 4.7 19.7 1.0
N H:GLY119 4.8 17.7 1.0
C H:CYS126 4.8 19.5 1.0
N H:GLY133 4.8 16.3 1.0
N H:LYS128 4.9 20.3 1.0
CA H:LYS128 4.9 21.2 1.0
C H:GLY119 4.9 18.7 1.0
CA H:ASN114 5.0 19.6 0.5
N H:ASN114 5.0 21.4 1.0
C H:CYS112 5.0 18.7 1.0
CA H:ASN114 5.0 20.3 0.5

Zinc binding site 9 out of 48 in 3ld0

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Zinc binding site 9 out of 48 in the Crystal Structure of B.Licheniformis 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.Licheniformis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn260

b:20.6
occ:1.00
 SG I:CYS215 2.3 17.9 1.0
SG I:CYS226 2.3 25.6 1.0
SG I:CYS229 2.3 18.6 1.0
SG I:CYS212 2.3 22.5 1.0
CB I:CYS212 3.3 23.5 1.0
CB I:CYS226 3.3 24.3 1.0
CB I:CYS229 3.3 22.3 1.0
CB I:CYS215 3.3 28.2 1.0
N I:CYS215 3.8 29.6 1.0
N I:CYS229 3.8 21.2 1.0
CA I:CYS215 4.2 28.5 1.0
CA I:CYS229 4.2 21.1 1.0
CB I:LYS228 4.6 27.0 1.0
CA I:GLY219 4.6 34.0 1.0
CA I:CYS226 4.6 24.5 1.0
C I:LYS228 4.6 23.4 1.0
CA I:CYS212 4.7 24.5 1.0
CA I:GLY233 4.7 20.4 1.0
CB I:ASN214 4.7 31.9 1.0
C I:ASN214 4.7 30.7 1.0
O I:CYS226 4.8 27.1 1.0
C I:CYS226 4.8 25.5 1.0
N I:GLY233 4.8 19.1 1.0
N I:LYS228 4.8 26.3 1.0
N I:GLY219 4.9 33.4 1.0
CA I:LYS228 4.9 25.0 1.0
C I:CYS212 5.0 24.6 1.0

Zinc binding site 10 out of 48 in 3ld0

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Zinc binding site 10 out of 48 in the Crystal Structure of B.Licheniformis 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.Licheniformis Anti-Trap Protein, An Antagonist of Trap-Rna Interactions within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn60

b:47.0
occ:1.00
 SG J:CYS15 2.3 41.8 1.0
SG J:CYS29 2.3 46.1 1.0
SG J:CYS26 2.3 46.2 1.0
SG J:CYS12 2.3 45.8 1.0
CB J:CYS26 3.3 46.6 1.0
CB J:CYS12 3.3 46.9 1.0
CB J:CYS29 3.3 47.5 1.0
CB J:CYS15 3.4 50.2 1.0
N J:CYS29 3.7 48.3 1.0
N J:CYS15 3.8 52.3 1.0
CA J:CYS29 4.1 48.0 1.0
CB J:ASN14 4.2 53.0 1.0
CA J:CYS15 4.2 50.7 1.0
CB J:LYS28 4.3 49.8 1.0
C J:LYS28 4.5 49.1 1.0
CA J:GLY19 4.5 53.6 1.0
C J:ASN14 4.6 52.4 1.0
CA J:CYS26 4.7 46.7 1.0
CA J:GLY33 4.7 40.7 1.0
ND2 J:ASN14 4.7 54.9 1.0
CG J:ASN14 4.7 54.7 1.0
CA J:CYS12 4.8 46.1 1.0
CA J:LYS28 4.8 49.7 1.0
O J:CYS26 4.8 47.2 1.0
CA J:ASN14 4.8 52.8 1.0
N J:LYS28 4.8 49.6 1.0
C J:CYS26 4.8 47.3 1.0
N J:ASN14 4.9 52.9 1.0
N J:GLY19 4.9 54.5 1.0
N J:GLY33 4.9 43.3 1.0
CG J:LYS28 4.9 52.4 1.0
C J:CYS29 4.9 48.5 1.0
C J:GLY33 5.0 39.4 1.0

Reference:

M.B.Shevtsov, Y.Chen, M.N.Isupov, A.Leech, P.Gollnick, A.A.Antson. Bacillus Licheniformis Anti-Trap Can Assemble Into Two Types of Dodecameric Particles with the Same Symmetry But Inverted Orientation of Trimers. J.Struct.Biol. V. 170 127 2010.
ISSN: ISSN 1047-8477
PubMed: 20138150
DOI: 10.1016/J.JSB.2010.01.013
Page generated: Sat Oct 26 08:29:00 2024

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