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Zinc in PDB 5elh: Crystal Structure of Mouse Unkempt Zinc Fingers 1-3 (ZNF1-3), Bound to Rna

Protein crystallography data

The structure of Crystal Structure of Mouse Unkempt Zinc Fingers 1-3 (ZNF1-3), Bound to Rna, PDB code: 5elh was solved by M.Teplova, J.Murn, K.Zarnack, Y.Shi, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.94 / 1.80
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.194, 56.559, 131.025, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Mouse Unkempt Zinc Fingers 1-3 (ZNF1-3), Bound to Rna (pdb code 5elh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Mouse Unkempt Zinc Fingers 1-3 (ZNF1-3), Bound to Rna, PDB code: 5elh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5elh

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Zinc binding site 1 out of 6 in the Crystal Structure of Mouse Unkempt Zinc Fingers 1-3 (ZNF1-3), Bound to Rna


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 Mouse Unkempt Zinc Fingers 1-3 (ZNF1-3), Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:36.9
occ:1.00
NE2 A:HIS65 2.0 29.3 1.0
SG A:CYS45 2.3 30.2 1.0
SG A:CYS53 2.4 33.9 1.0
SG A:CYS61 2.4 27.8 1.0
CE1 A:HIS65 3.0 30.6 1.0
HB2 A:CYS45 3.0 43.5 1.0
HB2 A:CYS61 3.0 45.6 1.0
CD2 A:HIS65 3.1 27.9 1.0
HE1 A:HIS65 3.1 36.8 1.0
CB A:CYS45 3.2 36.3 1.0
CB A:CYS61 3.2 38.0 1.0
HB2 A:CYS53 3.2 43.1 1.0
HD2 A:HIS65 3.3 33.5 1.0
CB A:CYS53 3.4 35.9 1.0
HB2 A:PHE48 3.4 41.7 1.0
HB3 A:CYS45 3.4 43.5 1.0
HB3 A:CYS61 3.5 45.6 1.0
HB3 A:CYS53 3.7 43.1 1.0
HB2 A:HIS63 4.0 33.3 1.0
HB2 A:GLN55 4.1 55.1 1.0
ND1 A:HIS65 4.1 31.3 1.0
H A:PHE48 4.1 41.1 1.0
O A:HOH376 4.1 42.6 1.0
CG A:HIS65 4.2 28.5 1.0
HB2 A:LEU47 4.2 45.2 1.0
CB A:PHE48 4.3 34.8 1.0
HB3 A:PHE48 4.5 41.7 1.0
HE1 A:TYR59 4.5 50.0 1.0
H A:HIS63 4.6 28.2 1.0
CA A:CYS45 4.6 31.8 1.0
CA A:CYS61 4.6 38.7 1.0
N A:PHE48 4.6 34.2 1.0
HD2 A:HIS63 4.6 43.6 1.0
HA A:CYS61 4.7 46.4 1.0
H A:GLN55 4.7 45.0 1.0
CA A:CYS53 4.7 40.2 1.0
HA A:CYS45 4.7 38.1 1.0
HA A:CYS53 4.7 48.3 1.0
O A:HIS63 4.8 23.8 1.0
HD1 A:HIS65 4.9 37.5 1.0
CA A:PHE48 4.9 40.6 1.0
HA A:PHE48 5.0 48.7 1.0
O A:GLN55 5.0 47.4 1.0

Zinc binding site 2 out of 6 in 5elh

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Zinc binding site 2 out of 6 in the Crystal Structure of Mouse Unkempt Zinc Fingers 1-3 (ZNF1-3), Bound to Rna


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 Mouse Unkempt Zinc Fingers 1-3 (ZNF1-3), Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:27.1
occ:1.00
NE2 A:HIS110 2.1 13.9 1.0
SG A:CYS90 2.2 19.1 1.0
SG A:CYS106 2.3 19.2 1.0
SG A:CYS100 2.4 18.9 1.0
CD2 A:HIS110 3.0 17.9 1.0
HB2 A:CYS90 3.0 21.8 1.0
HD2 A:HIS110 3.1 21.5 1.0
CE1 A:HIS110 3.1 15.6 1.0
HB2 A:CYS106 3.1 22.6 1.0
CB A:CYS106 3.2 18.9 1.0
HB2 A:CYS100 3.2 23.8 1.0
CB A:CYS90 3.2 18.2 1.0
HB3 A:CYS106 3.2 22.6 1.0
HE1 A:HIS110 3.3 18.7 1.0
CB A:CYS100 3.3 19.8 1.0
HB3 A:CYS90 3.5 21.8 1.0
HB2 A:TYR93 3.6 23.6 1.0
HB3 A:CYS100 3.6 23.8 1.0
HB2 A:PHE108 4.1 21.7 1.0
HB2 A:LYS92 4.1 36.5 1.0
CG A:HIS110 4.1 13.9 1.0
ND1 A:HIS110 4.2 13.8 1.0
H A:TYR93 4.3 29.6 1.0
HB2 A:GLU102 4.3 36.4 1.0
O A:HOH355 4.4 31.0 1.0
CB A:TYR93 4.5 19.6 1.0
H A:PHE108 4.6 15.3 1.0
O A:PHE108 4.6 13.7 1.0
CA A:CYS106 4.6 15.8 1.0
HD2 A:PHE108 4.6 21.8 1.0
CA A:CYS90 4.6 18.2 1.0
H A:GLU102 4.6 30.0 1.0
N A:TYR93 4.6 24.7 1.0
HD1 A:TYR93 4.6 21.3 1.0
HA A:TYR93 4.7 29.0 1.0
CA A:CYS100 4.7 23.8 1.0
HA A:CYS90 4.7 21.9 1.0
H A:LYS92 4.8 26.2 1.0
HA A:CYS100 4.8 28.6 1.0
HA A:CYS106 4.8 19.0 1.0
CA A:TYR93 4.9 24.2 1.0
HH22 A:ARG72 4.9 22.5 1.0
HD1 A:HIS110 4.9 16.6 1.0
HD2 A:PRO101 5.0 22.8 1.0
HB3 A:TYR93 5.0 23.6 1.0

Zinc binding site 3 out of 6 in 5elh

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Zinc binding site 3 out of 6 in the Crystal Structure of Mouse Unkempt Zinc Fingers 1-3 (ZNF1-3), Bound to Rna


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 Mouse Unkempt Zinc Fingers 1-3 (ZNF1-3), Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:39.7
occ:1.00
NE2 A:HIS151 2.1 28.4 1.0
SG A:CYS130 2.3 34.9 1.0
SG A:CYS147 2.4 26.3 1.0
SG A:CYS140 2.4 35.9 1.0
HE1 A:HIS151 2.5 37.8 1.0
HB2 A:CYS140 2.6 42.9 1.0
CE1 A:HIS151 2.6 31.5 1.0
CB A:CYS140 3.0 35.7 1.0
HB2 A:CYS130 3.1 33.0 1.0
CB A:CYS130 3.2 27.5 1.0
HB2 A:CYS147 3.3 35.7 1.0
CB A:CYS147 3.3 29.7 1.0
CD2 A:HIS151 3.3 32.2 1.0
HB3 A:CYS130 3.3 33.0 1.0
HD22 A:ASN143 3.5 62.5 1.0
HB2 A:HIS132 3.5 52.9 1.0
HB3 A:CYS147 3.5 35.7 1.0
HB3 A:CYS140 3.6 42.9 1.0
HD2 A:HIS132 3.6 61.7 1.0
HD2 A:HIS151 3.8 38.7 1.0
HB2 A:PHE149 3.8 27.3 1.0
ND1 A:HIS151 3.8 35.2 1.0
HB2 A:ASN143 4.0 60.0 1.0
HA A:CYS140 4.1 50.6 1.0
CA A:CYS140 4.2 42.2 1.0
CG A:HIS151 4.2 33.5 1.0
ND2 A:ASN143 4.3 52.1 1.0
CD2 A:HIS132 4.4 51.4 1.0
H A:PHE149 4.5 26.7 1.0
CB A:HIS132 4.5 44.1 1.0
HD1 A:HIS151 4.5 42.2 1.0
H A:ASN143 4.6 56.7 1.0
CA A:CYS130 4.6 29.5 1.0
H A:HIS132 4.6 50.1 1.0
HD21 A:ASN143 4.7 62.5 1.0
CA A:CYS147 4.7 26.5 1.0
CB A:PHE149 4.8 22.8 1.0
HA A:CYS130 4.8 35.4 1.0
O A:PHE149 4.8 23.3 1.0
CG A:HIS132 4.8 49.2 1.0
CB A:ASN143 4.9 50.0 1.0
HA A:CYS147 4.9 31.8 1.0
H A:CYS140 4.9 54.2 1.0
H A:LYS142 5.0 52.8 1.0
HB3 A:HIS132 5.0 52.9 1.0

Zinc binding site 4 out of 6 in 5elh

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Zinc binding site 4 out of 6 in the Crystal Structure of Mouse Unkempt Zinc Fingers 1-3 (ZNF1-3), Bound to Rna


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 Mouse Unkempt Zinc Fingers 1-3 (ZNF1-3), Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:27.8
occ:1.00
NE2 B:HIS65 2.0 19.4 1.0
SG B:CYS45 2.3 19.1 1.0
SG B:CYS53 2.3 18.2 1.0
SG B:CYS61 2.3 17.7 1.0
HB2 B:CYS45 2.8 23.1 1.0
CE1 B:HIS65 2.8 19.7 1.0
HE1 B:HIS65 3.0 23.7 1.0
HB2 B:CYS61 3.0 16.4 1.0
CB B:CYS45 3.0 19.3 1.0
CD2 B:HIS65 3.1 16.7 1.0
HB2 B:CYS53 3.1 28.0 1.0
CB B:CYS61 3.2 13.7 1.0
HB3 B:CYS45 3.3 23.1 1.0
CB B:CYS53 3.3 23.4 1.0
HD2 B:HIS65 3.4 20.0 1.0
HB2 B:PHE48 3.5 24.9 1.0
HB3 B:CYS61 3.5 16.4 1.0
HB3 B:CYS53 3.6 28.0 1.0
O B:HOH344 4.0 23.8 1.0
HB2 B:GLN55 4.0 28.6 1.0
ND1 B:HIS65 4.0 17.8 1.0
H B:PHE48 4.1 22.9 1.0
HB2 B:HIS63 4.1 19.1 1.0
HB2 B:LEU47 4.2 34.1 1.0
CG B:HIS65 4.2 20.4 1.0
O B:HOH443 4.4 37.3 1.0
CB B:PHE48 4.4 20.8 1.0
CA B:CYS45 4.5 23.8 1.0
HB3 B:PHE48 4.5 24.9 1.0
H B:HIS63 4.6 16.9 1.0
CA B:CYS61 4.6 17.2 1.0
HD2 B:HIS63 4.6 32.8 1.0
HA B:CYS61 4.6 20.6 1.0
CA B:CYS53 4.6 24.1 1.0
H B:GLN55 4.6 24.7 1.0
HA B:CYS45 4.6 28.6 1.0
HA B:CYS53 4.7 28.9 1.0
N B:PHE48 4.7 19.1 1.0
HD1 B:HIS65 4.8 21.4 1.0
HE1 B:TYR59 4.8 23.6 1.0
O B:HIS63 4.9 14.3 1.0
CB B:GLN55 5.0 23.9 1.0
HD12 B:LEU47 5.0 43.6 1.0

Zinc binding site 5 out of 6 in 5elh

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Zinc binding site 5 out of 6 in the Crystal Structure of Mouse Unkempt Zinc Fingers 1-3 (ZNF1-3), Bound to Rna


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 Mouse Unkempt Zinc Fingers 1-3 (ZNF1-3), Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:29.0
occ:1.00
NE2 B:HIS110 2.1 14.5 1.0
SG B:CYS106 2.3 20.8 1.0
SG B:CYS100 2.3 17.9 1.0
SG B:CYS90 2.4 21.4 1.0
HB2 B:CYS106 3.0 19.9 1.0
CD2 B:HIS110 3.0 21.4 1.0
HB2 B:CYS90 3.0 23.7 1.0
CB B:CYS106 3.1 16.6 1.0
HB2 B:CYS100 3.1 25.9 1.0
CE1 B:HIS110 3.1 20.1 1.0
HD2 B:HIS110 3.1 25.6 1.0
HB3 B:CYS106 3.2 19.9 1.0
CB B:CYS90 3.2 19.8 1.0
CB B:CYS100 3.3 21.6 1.0
HE1 B:HIS110 3.3 24.2 1.0
HB3 B:CYS90 3.5 23.7 1.0
HB2 B:TYR93 3.6 26.8 1.0
HB3 B:CYS100 3.6 25.9 1.0
HB2 B:PHE108 4.1 27.8 1.0
O B:HOH430 4.2 33.7 1.0
CG B:HIS110 4.2 15.5 1.0
ND1 B:HIS110 4.2 16.6 1.0
HB2 B:GLU102 4.3 48.9 1.0
O B:HOH355 4.3 49.0 1.0
HB2 B:LYS92 4.4 26.5 1.0
H B:TYR93 4.4 27.7 1.0
HG2 B:GLU102 4.5 62.6 1.0
CB B:TYR93 4.5 22.3 1.0
CA B:CYS106 4.5 20.0 1.0
H B:PHE108 4.6 24.3 1.0
HD2 B:PHE108 4.6 36.3 1.0
H B:GLU102 4.6 30.9 1.0
HD1 B:TYR93 4.6 18.5 1.0
CA B:CYS90 4.7 19.2 1.0
HA B:TYR93 4.7 25.4 1.0
CA B:CYS100 4.7 22.0 1.0
N B:TYR93 4.7 23.1 1.0
O B:PHE108 4.7 16.6 1.0
HA B:CYS100 4.7 26.4 1.0
H B:LYS92 4.8 29.7 1.0
HA B:CYS106 4.8 24.1 1.0
HA B:CYS90 4.8 23.0 1.0
HD2 B:PRO101 4.8 32.1 1.0
O B:GLY103 4.8 25.2 1.0
CA B:TYR93 4.9 21.1 1.0
HB3 B:TYR93 5.0 26.8 1.0
HD1 B:HIS110 5.0 19.9 1.0

Zinc binding site 6 out of 6 in 5elh

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Zinc binding site 6 out of 6 in the Crystal Structure of Mouse Unkempt Zinc Fingers 1-3 (ZNF1-3), Bound to Rna


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 Mouse Unkempt Zinc Fingers 1-3 (ZNF1-3), Bound to Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn203

b:25.5
occ:1.00
NE2 B:HIS151 2.1 19.9 1.0
SG B:CYS140 2.3 15.5 1.0
SG B:CYS147 2.3 14.0 1.0
SG B:CYS130 2.4 17.4 1.0
HB2 B:CYS140 2.5 16.1 1.0
CE1 B:HIS151 2.9 20.5 1.0
CB B:CYS140 3.0 13.4 1.0
HE1 B:HIS151 3.0 24.6 1.0
HB2 B:CYS130 3.0 27.6 1.0
CB B:CYS130 3.1 23.0 1.0
CD2 B:HIS151 3.2 18.7 1.0
HB3 B:CYS130 3.3 27.6 1.0
HB2 B:CYS147 3.3 22.0 1.0
CB B:CYS147 3.3 18.3 1.0
HB3 B:CYS147 3.5 22.0 1.0
HD2 B:HIS151 3.5 22.4 1.0
HB2 B:ASN143 3.6 17.5 1.0
HB2 B:HIS132 3.6 25.9 1.0
HB3 B:CYS140 3.6 16.1 1.0
HD22 B:ASN143 3.7 23.1 1.0
HD2 B:HIS132 3.7 32.3 1.0
HB2 B:PHE149 3.8 16.4 1.0
HA B:CYS140 3.9 24.8 1.0
CA B:CYS140 4.1 20.6 1.0
ND1 B:HIS151 4.1 19.6 1.0
ND2 B:ASN143 4.2 19.2 1.0
CG B:HIS151 4.3 19.1 1.0
H B:ASN143 4.3 26.5 1.0
H B:PHE149 4.4 15.2 1.0
CB B:ASN143 4.5 14.6 1.0
H B:HIS132 4.5 19.0 1.0
CD2 B:HIS132 4.5 26.9 1.0
CB B:HIS132 4.5 21.6 1.0
CA B:CYS130 4.6 20.9 1.0
O R:HOH110 4.7 17.2 1.0
HD21 B:ASN143 4.7 23.1 1.0
CB B:PHE149 4.7 13.6 1.0
O B:PHE149 4.7 14.9 1.0
CG B:ASN143 4.7 20.8 1.0
CA B:CYS147 4.7 14.6 1.0
HA B:CYS130 4.8 25.0 1.0
HD1 B:HIS151 4.8 23.5 1.0
H B:CYS140 4.9 17.5 1.0
HA B:CYS147 4.9 17.5 1.0
HB3 B:PHE149 4.9 16.4 1.0
N B:CYS140 4.9 14.6 1.0
CG B:HIS132 4.9 25.5 1.0
H B:LYS142 4.9 29.6 1.0
HB3 B:ASN143 5.0 17.5 1.0

Reference:

J.Murn, M.Teplova, K.Zarnack, Y.Shi, D.J.Patel. Recognition of Distinct Rna Motifs By the Clustered Ccch Zinc Fingers of Neuronal Protein Unkempt. Nat.Struct.Mol.Biol. V. 23 16 2016.
ISSN: ESSN 1545-9985
PubMed: 26641712
DOI: 10.1038/NSMB.3140
Page generated: Wed Dec 16 06:10:07 2020

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