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Zinc in PDB 2i13: Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets

Protein crystallography data

The structure of Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets, PDB code: 2i13 was solved by N.C.Horton, D.J.Segal, M.Bhakta, J.W.Crotty, C.F.Barbas Iii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.96
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 41.586, 72.054, 74.212, 75.53, 83.80, 72.67
R / Rfree (%) 20.3 / 24.9

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets (pdb code 2i13). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets, PDB code: 2i13:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 2i13

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Zinc binding site 1 out of 11 in the Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:96.2
occ:1.00
NE2 A:HIS44 1.7 86.5 1.0
CE1 A:HIS44 2.5 87.1 1.0
NE2 A:HIS40 2.6 95.8 1.0
CD2 A:HIS40 2.8 94.9 1.0
CD2 A:HIS44 2.9 87.7 1.0
ND1 A:HIS44 3.7 87.7 1.0
CE1 A:HIS40 3.8 95.8 1.0
CG A:HIS44 3.9 88.6 1.0
CG A:HIS40 4.0 94.7 1.0
ND1 A:HIS40 4.5 95.6 1.0
NE2 A:GLN41 4.7 99.3 1.0
O A:HIS40 4.9 93.6 1.0

Zinc binding site 2 out of 11 in 2i13

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Zinc binding site 2 out of 11 in the Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:33.6
occ:1.00
NE2 A:HIS100 1.9 24.3 1.0
NE2 A:HIS96 2.2 22.0 1.0
SG A:CYS80 2.2 36.5 1.0
SG A:CYS83 2.3 31.1 1.0
CD2 A:HIS100 2.7 26.0 1.0
CD2 A:HIS96 2.9 24.5 1.0
CE1 A:HIS100 3.0 34.0 1.0
CE1 A:HIS96 3.2 30.2 1.0
CB A:CYS80 3.3 29.9 1.0
CB A:CYS83 3.3 31.0 1.0
N A:CYS83 3.6 33.0 1.0
CG A:HIS100 3.9 27.3 1.0
CA A:CYS83 4.0 28.3 1.0
ND1 A:HIS100 4.0 29.4 1.0
CG A:HIS96 4.1 24.0 1.0
ND1 A:HIS96 4.2 23.0 1.0
CB A:GLU82 4.4 39.7 1.0
C A:GLU82 4.5 35.2 1.0
CA A:CYS80 4.7 33.6 1.0
C A:CYS83 4.7 21.5 1.0
CA A:GLU82 4.8 36.1 1.0
CB A:LYS85 4.8 30.0 1.0
N A:GLY84 4.8 24.6 1.0
N A:GLU82 4.9 33.3 1.0
N A:LYS85 4.9 24.6 1.0

Zinc binding site 3 out of 11 in 2i13

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Zinc binding site 3 out of 11 in the Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:36.4
occ:1.00
NE2 A:HIS128 2.1 34.5 1.0
NE2 A:HIS124 2.1 30.2 1.0
SG A:CYS108 2.2 32.0 1.0
SG A:CYS111 2.3 39.0 1.0
CD2 A:HIS124 2.8 28.4 1.0
CD2 A:HIS128 2.9 35.7 1.0
CE1 A:HIS128 3.2 39.6 1.0
CE1 A:HIS124 3.3 34.4 1.0
CB A:CYS108 3.3 21.9 1.0
CB A:CYS111 3.3 41.8 1.0
N A:CYS111 3.7 43.7 1.0
CA A:CYS111 4.1 41.8 1.0
CG A:HIS124 4.1 29.8 1.0
CG A:HIS128 4.1 37.3 1.0
ND1 A:HIS128 4.2 38.1 1.0
ND1 A:HIS124 4.3 30.9 1.0
CB A:GLU110 4.5 45.5 1.0
C A:GLU110 4.7 46.0 1.0
CA A:CYS108 4.7 32.2 1.0
C A:CYS111 4.8 41.3 1.0
CA A:GLU110 4.9 45.4 1.0
N A:GLY112 4.9 39.4 1.0
CB A:LYS113 5.0 41.4 1.0
N A:GLU110 5.0 44.4 1.0

Zinc binding site 4 out of 11 in 2i13

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Zinc binding site 4 out of 11 in the Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:41.4
occ:1.00
SG A:CYS136 2.0 36.8 1.0
NE2 A:HIS152 2.1 38.7 1.0
NE2 A:HIS156 2.2 40.4 1.0
SG A:CYS139 2.2 35.9 1.0
CD2 A:HIS152 2.9 37.0 1.0
CD2 A:HIS156 2.9 39.9 1.0
CB A:CYS136 3.1 30.4 1.0
CE1 A:HIS152 3.3 39.4 1.0
CB A:CYS139 3.3 43.6 1.0
CE1 A:HIS156 3.3 42.0 1.0
N A:CYS139 3.6 43.1 1.0
CA A:CYS139 4.0 40.9 1.0
CG A:HIS152 4.1 37.9 1.0
CG A:HIS156 4.2 42.2 1.0
ND1 A:HIS152 4.3 35.6 1.0
ND1 A:HIS156 4.3 40.4 1.0
CB A:GLU138 4.6 48.9 1.0
CA A:CYS136 4.6 33.5 1.0
C A:GLU138 4.6 47.4 1.0
C A:CYS139 4.7 39.4 1.0
N A:GLY140 4.8 39.3 1.0
CB A:LYS141 4.9 43.0 1.0
N A:LYS141 4.9 40.2 1.0
CA A:GLU138 4.9 46.1 1.0

Zinc binding site 5 out of 11 in 2i13

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Zinc binding site 5 out of 11 in the Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:63.1
occ:1.00
SG A:CYS167 2.1 59.6 1.0
NE2 A:HIS180 2.2 51.9 1.0
NE2 A:HIS184 2.2 67.5 1.0
SG A:CYS164 2.3 60.2 1.0
CD2 A:HIS180 2.8 52.4 1.0
CD2 A:HIS184 3.0 67.7 1.0
CB A:CYS167 3.1 62.3 1.0
CE1 A:HIS184 3.2 68.2 1.0
CB A:CYS164 3.3 62.5 1.0
CE1 A:HIS180 3.3 54.4 1.0
N A:CYS167 3.7 66.0 1.0
CA A:CYS167 3.9 63.9 1.0
CG A:HIS180 4.0 53.4 1.0
CG A:HIS184 4.2 67.3 1.0
ND1 A:HIS180 4.2 53.0 1.0
ND1 A:HIS184 4.3 67.1 1.0
C A:GLU166 4.5 68.9 1.0
CB A:GLU166 4.7 69.9 1.0
C A:CYS167 4.7 64.7 1.0
CA A:CYS164 4.7 61.5 1.0
N A:GLY168 4.7 64.4 1.0

Zinc binding site 6 out of 11 in 2i13

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Zinc binding site 6 out of 11 in the Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:49.7
occ:1.00
NE2 A:HIS72 2.1 37.1 1.0
SG A:CYS52 2.2 51.3 1.0
NE2 A:HIS68 2.2 46.8 1.0
SG A:CYS55 2.4 50.1 1.0
CD2 A:HIS72 2.8 38.5 1.0
CD2 A:HIS68 2.9 42.0 1.0
CE1 A:HIS72 3.2 37.4 1.0
CB A:CYS52 3.3 52.9 1.0
CE1 A:HIS68 3.4 45.6 1.0
CB A:CYS55 3.4 55.9 1.0
N A:CYS55 3.7 57.8 1.0
CG A:HIS72 4.0 37.3 1.0
CG A:HIS68 4.1 42.3 1.0
CA A:CYS55 4.1 54.9 1.0
ND1 A:HIS72 4.2 42.0 1.0
ND1 A:HIS68 4.3 40.9 1.0
CB A:GLU54 4.6 60.5 1.0
C A:GLU54 4.8 59.7 1.0
CA A:CYS52 4.8 57.4 1.0
N A:GLY56 4.8 52.9 1.0
C A:CYS55 4.9 51.5 1.0
CG A:GLU54 4.9 60.9 1.0

Zinc binding site 7 out of 11 in 2i13

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Zinc binding site 7 out of 11 in the Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn507

b:54.7
occ:1.00
NE2 B:HIS44 1.9 40.4 1.0
NE2 B:HIS40 2.2 58.2 1.0
SG B:CYS27 2.3 47.5 1.0
SG B:CYS24 2.4 51.9 1.0
CD2 B:HIS44 2.8 42.3 1.0
CD2 B:HIS40 2.9 56.3 1.0
CE1 B:HIS44 3.0 44.7 1.0
CB B:CYS27 3.3 50.2 1.0
CE1 B:HIS40 3.3 58.0 1.0
CB B:CYS24 3.4 54.9 1.0
N B:CYS27 3.6 54.0 1.0
CG B:HIS44 4.0 44.2 1.0
CA B:CYS27 4.0 50.9 1.0
ND1 B:HIS44 4.0 44.2 1.0
CG B:HIS40 4.1 56.1 1.0
ND1 B:HIS40 4.2 57.2 1.0
CB B:GLU26 4.4 65.1 1.0
C B:GLU26 4.6 59.0 1.0
C B:CYS27 4.7 45.9 1.0
N B:GLY28 4.8 47.0 1.0
CA B:CYS24 4.8 57.4 1.0
CA B:GLU26 4.9 60.9 1.0
CB B:LYS29 4.9 52.4 1.0
N B:LYS29 4.9 48.8 1.0
N B:GLU26 5.0 61.5 1.0

Zinc binding site 8 out of 11 in 2i13

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Zinc binding site 8 out of 11 in the Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn508

b:36.1
occ:1.00
SG B:CYS83 2.0 35.1 1.0
NE2 B:HIS96 2.1 28.8 1.0
SG B:CYS80 2.1 34.2 1.0
NE2 B:HIS100 2.2 28.1 1.0
CD2 B:HIS96 2.9 25.1 1.0
CD2 B:HIS100 3.0 29.5 1.0
CB B:CYS80 3.2 22.2 1.0
CB B:CYS83 3.2 40.0 1.0
CE1 B:HIS96 3.2 31.6 1.0
CE1 B:HIS100 3.3 33.8 1.0
N B:CYS83 3.6 36.0 1.0
CA B:CYS83 3.9 31.2 1.0
CG B:HIS96 4.1 26.5 1.0
CG B:HIS100 4.2 32.2 1.0
ND1 B:HIS96 4.3 28.6 1.0
ND1 B:HIS100 4.4 33.9 1.0
C B:GLU82 4.5 40.5 1.0
CB B:GLU82 4.6 40.5 1.0
CA B:CYS80 4.6 28.0 1.0
C B:CYS83 4.7 28.3 1.0
CB B:LYS85 4.7 34.2 1.0
N B:GLY84 4.8 31.3 1.0
CA B:GLU82 4.9 37.7 1.0
N B:LYS85 4.9 33.4 1.0
N B:GLU82 5.0 40.7 1.0
C B:CYS80 5.0 25.0 1.0

Zinc binding site 9 out of 11 in 2i13

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Zinc binding site 9 out of 11 in the Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn509

b:48.9
occ:1.00
SG B:CYS108 2.0 43.9 1.0
NE2 B:HIS128 2.1 66.4 1.0
NE2 B:HIS124 2.2 40.5 1.0
SG B:CYS111 2.3 51.8 1.0
CD2 B:HIS128 2.8 64.4 1.0
CD2 B:HIS124 2.8 38.6 1.0
CB B:CYS108 3.1 49.0 1.0
CB B:CYS111 3.3 55.5 1.0
CE1 B:HIS128 3.3 68.0 1.0
CE1 B:HIS124 3.4 43.2 1.0
N B:CYS111 3.7 57.1 1.0
CG B:HIS128 4.0 66.2 1.0
CA B:CYS111 4.0 54.0 1.0
CG B:HIS124 4.1 40.5 1.0
ND1 B:HIS128 4.2 67.5 1.0
ND1 B:HIS124 4.3 42.2 1.0
CA B:CYS108 4.6 51.5 1.0
C B:CYS111 4.7 54.2 1.0
C B:GLU110 4.8 59.7 1.0
CB B:GLU110 4.8 60.4 1.0
CB B:LYS113 4.9 45.6 1.0

Zinc binding site 10 out of 11 in 2i13

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Zinc binding site 10 out of 11 in the Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Aart, A Six Finger Zinc Finger Designed to Recognize Ann Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn510

b:56.4
occ:1.00
NE2 B:HIS156 2.1 59.8 1.0
SG B:CYS136 2.2 48.2 1.0
SG B:CYS139 2.2 52.0 1.0
NE2 B:HIS152 2.3 58.7 1.0
CD2 B:HIS152 2.9 58.9 1.0
CD2 B:HIS156 3.0 60.3 1.0
CE1 B:HIS156 3.1 61.3 1.0
CB B:CYS136 3.2 45.9 1.0
CB B:CYS139 3.3 51.2 1.0
CE1 B:HIS152 3.4 61.2 1.0
N B:CYS139 3.7 52.1 1.0
CA B:CYS139 4.1 51.8 1.0
CG B:HIS152 4.2 58.9 1.0
ND1 B:HIS156 4.2 60.4 1.0
CG B:HIS156 4.2 60.9 1.0
CB B:GLU138 4.3 61.8 1.0
ND1 B:HIS152 4.4 58.7 1.0
C B:GLU138 4.6 56.3 1.0
CA B:CYS136 4.7 47.5 1.0
C B:CYS139 4.7 50.9 1.0
N B:GLY140 4.8 49.4 1.0
CA B:GLU138 4.8 57.8 1.0
CB B:LYS141 4.9 47.0 1.0
N B:LYS141 4.9 46.9 1.0
N B:GLU138 5.0 56.3 1.0
C B:CYS136 5.0 50.2 1.0

Reference:

D.J.Segal, J.W.Crotty, M.S.Bhakta, C.F.Barbas, N.C.Horton. Structure of Aart, A Designed Six-Finger Zinc Finger Peptide, Bound to Dna. J.Mol.Biol. V. 363 405 2006.
ISSN: ISSN 0022-2836
PubMed: 16963084
DOI: 10.1016/J.JMB.2006.08.016
Page generated: Wed Dec 16 03:30:42 2020

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