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Zinc in PDB 3lcz: B.Licheniformis Anti-Trap Can Assemble Into Two Types of Dodecameric Particles with the Same Symmetry But Inverted Orientation of Trimers

Protein crystallography data

The structure of B.Licheniformis Anti-Trap Can Assemble Into Two Types of Dodecameric Particles with the Same Symmetry But Inverted Orientation of Trimers, PDB code: 3lcz 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) 28.76 / 2.06
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 108.076, 108.076, 49.370, 90.00, 90.00, 120.00
R / Rfree (%) 21.3 / 28.6

Zinc Binding Sites:

The binding sites of Zinc atom in the B.Licheniformis Anti-Trap Can Assemble Into Two Types of Dodecameric Particles with the Same Symmetry But Inverted Orientation of Trimers (pdb code 3lcz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the B.Licheniformis Anti-Trap Can Assemble Into Two Types of Dodecameric Particles with the Same Symmetry But Inverted Orientation of Trimers, PDB code: 3lcz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3lcz

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Zinc binding site 1 out of 4 in the B.Licheniformis Anti-Trap Can Assemble Into Two Types of Dodecameric Particles with the Same Symmetry But Inverted Orientation of Trimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of B.Licheniformis Anti-Trap Can Assemble Into Two Types of Dodecameric Particles with the Same Symmetry But Inverted Orientation of Trimers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn54

b:54.5
occ:1.00
SG A:CYS12 2.3 44.6 1.0
SG A:CYS29 2.3 42.3 1.0
SG A:CYS15 2.3 48.8 1.0
SG A:CYS26 2.3 47.5 1.0
CB A:CYS12 3.1 41.8 1.0
CB A:CYS26 3.1 42.5 1.0
CB A:CYS29 3.3 45.7 1.0
CB A:CYS15 3.3 56.4 1.0
N A:CYS29 3.7 46.6 1.0
N A:CYS15 3.7 52.7 1.0
CA A:CYS29 4.1 46.3 1.0
CA A:CYS15 4.2 57.3 1.0
CA A:GLY33 4.5 46.6 1.0
CB A:ASN14 4.5 54.5 1.0
CA A:CYS26 4.5 43.6 1.0
CA A:CYS12 4.5 39.8 1.0
CB A:LYS28 4.5 51.8 1.0
C A:LYS28 4.5 48.7 1.0
O A:HOH55 4.6 58.7 1.0
C A:ASN14 4.6 58.4 1.0
CA A:GLY19 4.6 47.1 1.0
N A:GLY33 4.7 49.6 1.0
O A:CYS26 4.7 47.0 1.0
C A:CYS26 4.8 45.5 1.0
N A:ASN14 4.8 56.1 1.0
CA A:ASN14 4.8 59.0 1.0
N A:GLY19 4.8 48.9 1.0
CA A:LYS28 4.9 51.0 1.0
N A:LYS28 4.9 52.2 1.0
C A:GLY33 4.9 47.4 1.0
C A:CYS12 4.9 47.5 1.0

Zinc binding site 2 out of 4 in 3lcz

Go back to Zinc Binding Sites List in 3lcz
Zinc binding site 2 out of 4 in the B.Licheniformis Anti-Trap Can Assemble Into Two Types of Dodecameric Particles with the Same Symmetry But Inverted Orientation of Trimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of B.Licheniformis Anti-Trap Can Assemble Into Two Types of Dodecameric Particles with the Same Symmetry But Inverted Orientation of Trimers within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn54

b:78.7
occ:1.00
SG B:CYS12 2.3 71.1 1.0
SG B:CYS29 2.3 65.5 1.0
SG B:CYS26 2.3 63.3 1.0
SG B:CYS15 2.3 71.6 1.0
CB B:CYS12 2.9 62.1 1.0
CB B:CYS26 3.2 71.9 1.0
CB B:CYS29 3.2 72.9 1.0
CB B:CYS15 3.3 77.8 1.0
N B:CYS15 3.6 78.5 1.0
CA B:GLY19 3.7 78.3 0.0
N B:CYS29 3.9 74.2 1.0
CA B:CYS15 4.1 79.7 1.0
CA B:CYS29 4.1 73.3 1.0
N B:GLY19 4.3 79.2 1.0
CA B:CYS12 4.3 62.0 1.0
CB B:ASN14 4.4 78.4 1.0
CA B:GLY33 4.4 68.6 1.0
C B:GLY19 4.5 80.4 0.0
C B:ASN14 4.5 81.3 1.0
CB B:LYS28 4.6 72.3 1.0
N B:ASN14 4.6 77.7 1.0
C B:CYS12 4.6 67.5 1.0
CA B:CYS26 4.6 75.3 1.0
O B:CYS12 4.7 64.9 1.0
C B:LYS28 4.7 71.2 1.0
CA B:ASN14 4.7 80.8 1.0
N B:GLY33 4.7 67.9 1.0
C B:GLY33 4.8 62.8 1.0
N B:ASN16 4.8 78.5 1.0
C B:CYS15 4.8 79.0 1.0
N B:ARG20 5.0 82.8 0.0

Zinc binding site 3 out of 4 in 3lcz

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Zinc binding site 3 out of 4 in the B.Licheniformis Anti-Trap Can Assemble Into Two Types of Dodecameric Particles with the Same Symmetry But Inverted Orientation of Trimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of B.Licheniformis Anti-Trap Can Assemble Into Two Types of Dodecameric Particles with the Same Symmetry But Inverted Orientation of Trimers within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn54

b:0.3
occ:1.00
SG C:CYS26 2.3 0.6 1.0
SG C:CYS12 2.3 80.8 1.0
SG C:CYS29 2.4 99.0 1.0
SG C:CYS15 2.4 0.7 1.0
CB C:CYS12 3.2 84.0 1.0
CB C:CYS15 3.4 0.5 1.0
CB C:CYS29 3.4 94.1 1.0
CB C:CYS26 3.5 0.0 1.0
N C:CYS29 3.7 91.0 1.0
N C:CYS15 4.0 98.1 1.0
CA C:CYS29 4.2 91.0 1.0
CA C:CYS15 4.3 0.0 1.0
CB C:LYS28 4.3 88.8 0.0
C C:ASN14 4.4 97.7 1.0
CB C:ASN14 4.5 93.1 1.0
CA C:GLY33 4.6 87.2 1.0
C C:LYS28 4.6 88.1 1.0
CA C:CYS12 4.6 83.8 1.0
CA C:LYS28 4.8 88.4 1.0
CA C:ASN14 4.8 94.8 1.0
N C:LYS28 4.8 92.2 1.0
CA C:CYS26 4.8 0.6 1.0
N C:ASN14 4.9 90.6 1.0
CA C:GLY19 4.9 0.1 0.0
C C:CYS12 5.0 86.1 1.0
ND2 C:ASN14 5.0 0.5 1.0

Zinc binding site 4 out of 4 in 3lcz

Go back to Zinc Binding Sites List in 3lcz
Zinc binding site 4 out of 4 in the B.Licheniformis Anti-Trap Can Assemble Into Two Types of Dodecameric Particles with the Same Symmetry But Inverted Orientation of Trimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of B.Licheniformis Anti-Trap Can Assemble Into Two Types of Dodecameric Particles with the Same Symmetry But Inverted Orientation of Trimers within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn54

b:65.1
occ:1.00
SG D:CYS26 2.3 52.2 1.0
SG D:CYS29 2.3 54.4 1.0
SG D:CYS12 2.3 54.8 1.0
SG D:CYS15 2.3 49.0 1.0
CB D:CYS12 3.1 45.5 1.0
CB D:CYS29 3.2 55.2 1.0
CB D:CYS26 3.2 57.0 1.0
CB D:CYS15 3.4 44.8 1.0
N D:CYS29 3.6 66.0 1.0
N D:CYS15 3.8 52.9 1.0
CA D:CYS29 4.0 63.9 1.0
CA D:CYS15 4.2 48.0 1.0
CB D:ASN14 4.4 51.8 1.0
CA D:CYS12 4.5 50.2 1.0
C D:LYS28 4.5 68.3 1.0
CA D:CYS26 4.6 55.7 1.0
CA D:GLY33 4.6 54.0 1.0
CA D:GLY19 4.6 58.4 1.0
CB D:LYS28 4.7 69.8 1.0
C D:ASN14 4.7 52.7 1.0
N D:GLY19 4.7 53.9 1.0
N D:GLY33 4.7 58.2 1.0
C D:CYS29 4.8 65.8 1.0
N D:LYS28 4.8 69.2 1.0
C D:CYS26 4.8 60.6 1.0
C D:CYS12 4.9 50.0 1.0
CA D:LYS28 4.9 70.8 1.0
CA D:ASN14 4.9 49.9 1.0
C D:GLY33 4.9 49.1 1.0
O D:CYS26 4.9 62.0 1.0
N D:ASN14 4.9 50.0 1.0
O D:CYS12 4.9 48.3 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: Wed Dec 16 04:32:05 2020

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