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Zinc in PDB 3trz: Mouse LIN28A in Complex with Let-7D Microrna Pre-Element

Protein crystallography data

The structure of Mouse LIN28A in Complex with Let-7D Microrna Pre-Element, PDB code: 3trz was solved by Y.Nam, P.Sliz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.66 / 2.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 143.820, 143.820, 177.720, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 21

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Mouse LIN28A in Complex with Let-7D Microrna Pre-Element (pdb code 3trz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Mouse LIN28A in Complex with Let-7D Microrna Pre-Element, PDB code: 3trz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 3trz

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Zinc binding site 1 out of 12 in the Mouse LIN28A in Complex with Let-7D Microrna Pre-Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mouse LIN28A in Complex with Let-7D Microrna Pre-Element within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:71.4
occ:1.00
NE2 A:HIS147 2.1 74.5 1.0
SG A:CYS142 2.2 63.5 1.0
SG A:CYS152 2.2 67.6 1.0
SG A:CYS139 2.4 69.9 1.0
CE1 A:HIS147 3.0 74.1 1.0
CD2 A:HIS147 3.1 77.6 1.0
CB A:CYS139 3.1 65.8 1.0
CB A:CYS152 3.2 67.3 1.0
CB A:CYS142 3.3 57.5 1.0
N A:CYS142 3.7 56.5 1.0
CA A:CYS152 4.0 70.5 1.0
CA A:CYS142 4.1 56.1 1.0
ND1 A:HIS147 4.2 77.6 1.0
CG A:HIS147 4.2 78.3 1.0
CB A:ASN141 4.4 58.4 1.0
C A:ASN141 4.6 59.3 1.0
CA A:CYS139 4.6 65.2 1.0
CA A:ASN141 4.8 59.5 1.0
C A:CYS142 4.9 61.8 1.0
N A:GLY144 4.9 68.0 1.0
N A:ASN141 4.9 61.1 1.0
N A:GLY143 4.9 59.8 1.0
ND2 A:ASN141 4.9 55.7 1.0
N A:CYS152 4.9 74.5 1.0
CD1 A:LEU154 5.0 62.2 1.0

Zinc binding site 2 out of 12 in 3trz

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Zinc binding site 2 out of 12 in the Mouse LIN28A in Complex with Let-7D Microrna Pre-Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mouse LIN28A in Complex with Let-7D Microrna Pre-Element within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:52.4
occ:1.00
NE2 A:HIS169 2.0 58.2 1.0
SG A:CYS161 2.2 49.5 1.0
SG A:CYS164 2.3 57.6 1.0
SG A:CYS174 2.4 62.2 1.0
CD2 A:HIS169 2.9 58.7 1.0
CE1 A:HIS169 3.0 57.9 1.0
CB A:CYS174 3.1 59.2 1.0
CB A:CYS161 3.1 44.6 1.0
CB A:CYS164 3.5 53.2 1.0
N A:CYS164 3.8 55.1 1.0
CA A:CYS174 3.8 59.4 1.0
CG A:HIS169 4.1 57.2 1.0
ND1 A:HIS169 4.1 58.9 1.0
CA A:CYS164 4.2 52.5 1.0
CA A:CYS161 4.5 44.9 1.0
CB A:PHE163 4.5 59.8 1.0
CD A:PRO175 4.5 63.2 1.0
CB A:SER166 4.6 52.2 1.0
C A:CYS174 4.7 65.6 1.0
C A:PHE163 4.8 60.7 1.0
C A:CYS164 4.8 54.2 1.0
N A:CYS174 4.9 59.7 1.0
N A:PRO175 4.9 62.5 1.0

Zinc binding site 3 out of 12 in 3trz

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Zinc binding site 3 out of 12 in the Mouse LIN28A in Complex with Let-7D Microrna Pre-Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mouse LIN28A in Complex with Let-7D Microrna Pre-Element within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:69.3
occ:1.00
NE2 B:HIS147 2.1 93.1 1.0
SG B:CYS142 2.2 64.1 1.0
SG B:CYS152 2.2 76.8 1.0
SG B:CYS139 2.4 73.3 1.0
CE1 B:HIS147 3.0 93.0 1.0
CB B:CYS152 3.1 76.0 1.0
CD2 B:HIS147 3.1 95.9 1.0
CB B:CYS139 3.2 69.9 1.0
CB B:CYS142 3.3 58.1 1.0
N B:CYS142 3.8 57.6 1.0
CA B:CYS152 3.9 79.3 1.0
CA B:CYS142 4.1 56.6 1.0
ND1 B:HIS147 4.2 96.0 1.0
CG B:HIS147 4.2 95.7 1.0
CB B:ASN141 4.5 56.9 1.0
C B:ASN141 4.6 62.1 1.0
CA B:CYS139 4.7 69.9 1.0
C B:CYS142 4.9 61.7 1.0
N B:CYS152 4.9 83.6 1.0
N B:GLY144 4.9 66.4 1.0
C B:CYS152 4.9 80.9 1.0
CA B:ASN141 4.9 59.0 1.0
CD1 B:LEU154 4.9 64.1 1.0
N B:GLY143 5.0 59.0 1.0
ND2 B:ASN141 5.0 67.5 1.0

Zinc binding site 4 out of 12 in 3trz

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Zinc binding site 4 out of 12 in the Mouse LIN28A in Complex with Let-7D Microrna Pre-Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mouse LIN28A in Complex with Let-7D Microrna Pre-Element within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:52.3
occ:1.00
NE2 B:HIS169 2.0 56.1 1.0
SG B:CYS164 2.2 53.1 1.0
SG B:CYS174 2.3 63.0 1.0
SG B:CYS161 2.3 53.3 1.0
CD2 B:HIS169 3.0 57.1 1.0
CE1 B:HIS169 3.0 56.1 1.0
CB B:CYS174 3.1 60.2 1.0
CB B:CYS161 3.2 48.2 1.0
CB B:CYS164 3.4 49.2 1.0
N B:CYS164 3.8 49.6 1.0
CA B:CYS174 3.9 61.4 1.0
CG B:HIS169 4.1 56.2 1.0
ND1 B:HIS169 4.1 57.7 1.0
CA B:CYS164 4.1 48.3 1.0
CD B:PRO175 4.5 67.3 1.0
CB B:PHE163 4.6 51.7 1.0
CB B:SER166 4.6 55.1 1.0
CA B:CYS161 4.6 47.7 1.0
C B:CYS174 4.7 68.5 1.0
C B:PHE163 4.8 53.4 1.0
C B:CYS164 4.8 54.0 1.0
N B:PRO175 4.9 66.8 1.0
N B:CYS174 4.9 62.6 1.0
N B:GLN165 5.0 49.7 1.0
N B:SER166 5.0 49.8 1.0

Zinc binding site 5 out of 12 in 3trz

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Zinc binding site 5 out of 12 in the Mouse LIN28A in Complex with Let-7D Microrna Pre-Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Mouse LIN28A in Complex with Let-7D Microrna Pre-Element within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1

b:72.0
occ:1.00
NE2 C:HIS147 2.1 79.5 1.0
SG C:CYS142 2.2 69.3 1.0
SG C:CYS152 2.3 76.0 1.0
SG C:CYS139 2.3 72.0 1.0
CE1 C:HIS147 3.0 79.0 1.0
CD2 C:HIS147 3.1 82.9 1.0
CB C:CYS139 3.1 68.9 1.0
CB C:CYS152 3.2 76.0 1.0
CB C:CYS142 3.3 63.4 1.0
N C:CYS142 3.7 63.0 1.0
CA C:CYS152 3.9 79.2 1.0
CA C:CYS142 4.1 62.0 1.0
ND1 C:HIS147 4.1 82.8 1.0
CG C:HIS147 4.2 83.2 1.0
CB C:ASN141 4.4 63.8 1.0
CA C:CYS139 4.6 69.6 1.0
C C:ASN141 4.6 66.2 1.0
C C:CYS142 4.8 67.7 1.0
CA C:ASN141 4.9 63.4 1.0
N C:GLY144 4.9 77.8 1.0
N C:CYS152 4.9 83.2 1.0
N C:GLY143 4.9 66.8 1.0
N C:ASN141 4.9 64.0 1.0
ND2 C:ASN141 5.0 70.5 1.0
C C:CYS152 5.0 83.6 1.0

Zinc binding site 6 out of 12 in 3trz

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Zinc binding site 6 out of 12 in the Mouse LIN28A in Complex with Let-7D Microrna Pre-Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Mouse LIN28A in Complex with Let-7D Microrna Pre-Element within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2

b:64.2
occ:1.00
NE2 C:HIS169 1.9 67.8 1.0
SG C:CYS164 2.3 61.8 1.0
SG C:CYS174 2.3 75.2 1.0
SG C:CYS161 2.3 58.1 1.0
CD2 C:HIS169 2.9 69.0 1.0
CE1 C:HIS169 3.0 67.0 1.0
CB C:CYS174 3.1 72.7 1.0
CB C:CYS161 3.2 52.4 1.0
CB C:CYS164 3.5 57.9 1.0
N C:CYS164 3.8 60.7 1.0
CA C:CYS174 3.8 73.3 1.0
CG C:HIS169 4.0 68.3 1.0
ND1 C:HIS169 4.1 68.7 1.0
CA C:CYS164 4.2 57.9 1.0
CD C:PRO175 4.5 77.7 1.0
CB C:PHE163 4.6 64.4 1.0
CB C:SER166 4.6 59.5 1.0
CA C:CYS161 4.6 52.2 1.0
C C:CYS174 4.7 80.5 1.0
C C:PHE163 4.8 65.8 1.0
C C:CYS164 4.8 62.0 1.0
N C:PRO175 4.9 77.4 1.0
N C:CYS174 4.9 73.6 1.0

Zinc binding site 7 out of 12 in 3trz

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Zinc binding site 7 out of 12 in the Mouse LIN28A in Complex with Let-7D Microrna Pre-Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Mouse LIN28A in Complex with Let-7D Microrna Pre-Element within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1

b:69.8
occ:1.00
NE2 D:HIS147 2.1 83.2 1.0
SG D:CYS142 2.2 61.5 1.0
SG D:CYS139 2.3 70.7 1.0
SG D:CYS152 2.3 71.1 1.0
CB D:CYS152 3.0 70.7 1.0
CE1 D:HIS147 3.1 83.0 1.0
CD2 D:HIS147 3.1 86.1 1.0
CB D:CYS139 3.2 67.2 1.0
CB D:CYS142 3.3 55.6 1.0
N D:CYS142 3.7 56.0 1.0
CA D:CYS152 3.8 74.1 1.0
CA D:CYS142 4.1 54.3 1.0
ND1 D:HIS147 4.2 86.2 1.0
CG D:HIS147 4.2 86.4 1.0
CB D:ASN141 4.4 58.1 1.0
C D:ASN141 4.6 61.2 1.0
CA D:CYS139 4.6 67.3 1.0
CA D:ASN141 4.8 60.6 1.0
C D:CYS152 4.8 77.2 1.0
N D:CYS152 4.9 78.6 1.0
C D:CYS142 4.9 60.5 1.0
N D:ASN141 4.9 63.8 1.0
ND2 D:ASN141 4.9 73.7 1.0
N D:GLY144 4.9 63.7 1.0
N D:GLY143 5.0 57.2 1.0

Zinc binding site 8 out of 12 in 3trz

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Zinc binding site 8 out of 12 in the Mouse LIN28A in Complex with Let-7D Microrna Pre-Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Mouse LIN28A in Complex with Let-7D Microrna Pre-Element within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2

b:54.6
occ:1.00
NE2 D:HIS169 2.0 61.4 1.0
SG D:CYS164 2.2 53.0 1.0
SG D:CYS174 2.2 62.0 1.0
SG D:CYS161 2.3 54.8 1.0
CD2 D:HIS169 3.0 62.5 1.0
CE1 D:HIS169 3.0 61.5 1.0
CB D:CYS174 3.1 59.7 1.0
CB D:CYS161 3.2 49.8 1.0
CB D:CYS164 3.4 48.9 1.0
CA D:CYS174 3.8 61.5 1.0
N D:CYS164 3.8 49.8 1.0
CG D:HIS169 4.1 61.1 1.0
CA D:CYS164 4.1 48.1 1.0
ND1 D:HIS169 4.1 63.0 1.0
CD D:PRO175 4.5 66.5 1.0
CB D:SER166 4.6 58.0 1.0
CA D:CYS161 4.6 49.8 1.0
C D:CYS174 4.7 68.8 1.0
CB D:PHE163 4.7 54.8 1.0
C D:CYS164 4.8 51.7 1.0
C D:PHE163 4.8 54.5 1.0
N D:PRO175 4.9 66.4 1.0
N D:CYS174 4.9 63.1 1.0
N D:SER166 5.0 50.7 1.0
N D:GLN165 5.0 47.3 1.0

Zinc binding site 9 out of 12 in 3trz

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Zinc binding site 9 out of 12 in the Mouse LIN28A in Complex with Let-7D Microrna Pre-Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Mouse LIN28A in Complex with Let-7D Microrna Pre-Element within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1

b:71.3
occ:1.00
NE2 E:HIS147 2.0 84.3 1.0
SG E:CYS142 2.2 62.7 1.0
SG E:CYS152 2.2 73.0 1.0
SG E:CYS139 2.4 68.1 1.0
CE1 E:HIS147 3.0 83.8 1.0
CD2 E:HIS147 3.1 87.0 1.0
CB E:CYS139 3.2 65.1 1.0
CB E:CYS152 3.2 72.7 1.0
CB E:CYS142 3.3 57.5 1.0
N E:CYS142 3.8 60.1 1.0
CA E:CYS152 4.0 75.2 1.0
ND1 E:HIS147 4.1 86.5 1.0
CA E:CYS142 4.1 57.6 1.0
CG E:HIS147 4.2 86.4 1.0
CB E:ASN141 4.5 62.5 1.0
CA E:CYS139 4.6 66.2 1.0
C E:ASN141 4.7 64.7 1.0
N E:GLY144 4.9 71.2 1.0
C E:CYS142 4.9 62.3 1.0
N E:CYS152 4.9 78.7 1.0
N E:GLY143 4.9 60.9 1.0
CA E:ASN141 4.9 62.8 1.0
CD1 E:LEU154 5.0 67.8 1.0
C E:CYS152 5.0 79.1 1.0
ND2 E:ASN141 5.0 60.5 1.0

Zinc binding site 10 out of 12 in 3trz

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Zinc binding site 10 out of 12 in the Mouse LIN28A in Complex with Let-7D Microrna Pre-Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Mouse LIN28A in Complex with Let-7D Microrna Pre-Element within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn2

b:64.5
occ:1.00
NE2 E:HIS169 2.0 64.1 1.0
SG E:CYS161 2.2 57.2 1.0
SG E:CYS174 2.2 71.2 1.0
SG E:CYS164 2.3 63.4 1.0
CD2 E:HIS169 2.9 65.2 1.0
CB E:CYS161 3.0 52.0 1.0
CE1 E:HIS169 3.0 63.7 1.0
CB E:CYS174 3.1 68.7 1.0
CB E:CYS164 3.4 59.4 1.0
N E:CYS164 3.8 60.5 1.0
CA E:CYS174 3.8 69.7 1.0
CG E:HIS169 4.0 64.5 1.0
ND1 E:HIS169 4.1 65.4 1.0
CA E:CYS164 4.1 58.7 1.0
CA E:CYS161 4.5 51.8 1.0
CD E:PRO175 4.6 75.3 1.0
CB E:SER166 4.6 63.0 1.0
CB E:PHE163 4.7 62.7 1.0
C E:CYS164 4.7 61.9 1.0
C E:CYS174 4.8 76.7 1.0
C E:PHE163 4.8 64.9 1.0
N E:CYS174 4.9 70.8 1.0
N E:SER166 4.9 58.0 1.0
N E:GLN165 4.9 57.4 1.0
C E:CYS161 4.9 56.8 1.0
N E:PRO175 5.0 74.9 1.0

Reference:

Y.Nam, C.Chen, R.I.Gregory, J.J.Chou, P.Sliz. Molecular Basis For Interaction of Let-7 Micrornas with LIN28. Cell(Cambridge,Mass.) V. 147 1080 2011.
ISSN: ISSN 0092-8674
PubMed: 22078496
DOI: 10.1016/J.CELL.2011.10.020
Page generated: Wed Dec 16 04:52:37 2020

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