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Zinc in PDB 2iyk: Crystal Structure of the UPF2-Interacting Domain of Nonsense Mediated Mrna Decay Factor UPF1

Protein crystallography data

The structure of Crystal Structure of the UPF2-Interacting Domain of Nonsense Mediated Mrna Decay Factor UPF1, PDB code: 2iyk was solved by J.Kadlec, D.Guilligay, R.B.Ravelli, S.Cusack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.71 / 2.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.560, 72.980, 73.210, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 25.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the UPF2-Interacting Domain of Nonsense Mediated Mrna Decay Factor UPF1 (pdb code 2iyk). 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 the UPF2-Interacting Domain of Nonsense Mediated Mrna Decay Factor UPF1, PDB code: 2iyk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2iyk

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Zinc binding site 1 out of 6 in the Crystal Structure of the UPF2-Interacting Domain of Nonsense Mediated Mrna Decay Factor UPF1


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 the UPF2-Interacting Domain of Nonsense Mediated Mrna Decay Factor UPF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1163

b:51.4
occ:1.00
 SG A:CYS13 2.2 28.1 1.0
ND1 A:HIS45 2.2 26.6 1.0
SG A:CYS16 2.5 33.0 1.0
SG A:CYS35 2.5 24.9 1.0
CE1 A:HIS45 3.1 28.6 1.0
CB A:CYS13 3.2 28.1 1.0
CG A:HIS45 3.3 25.4 1.0
CB A:CYS35 3.5 23.9 1.0
CB A:CYS16 3.5 33.6 1.0
CB A:HIS45 3.7 23.4 1.0
N A:CYS16 3.9 32.4 1.0
N A:CYS35 4.0 22.0 1.0
CA A:CYS16 4.3 34.1 1.0
NE2 A:HIS45 4.3 28.8 1.0
CA A:CYS35 4.3 22.2 1.0
CB A:TYR15 4.3 29.8 1.0
CD2 A:HIS45 4.4 26.9 1.0
CD1 A:ILE18 4.6 30.9 1.0
CA A:CYS13 4.7 28.3 1.0
N A:GLY17 4.8 32.8 1.0
C A:TYR15 4.9 33.3 1.0
CB A:ILE18 4.9 29.6 1.0
C A:CYS35 4.9 21.6 1.0
O A:GLY37 4.9 25.6 1.0
O A:CYS35 4.9 21.1 1.0
CA A:TYR15 5.0 31.6 1.0
N A:TYR15 5.0 30.5 1.0
CG1 A:ILE18 5.0 30.9 1.0
C A:CYS16 5.0 34.6 1.0

Zinc binding site 2 out of 6 in 2iyk

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Zinc binding site 2 out of 6 in the Crystal Structure of the UPF2-Interacting Domain of Nonsense Mediated Mrna Decay Factor UPF1


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 the UPF2-Interacting Domain of Nonsense Mediated Mrna Decay Factor UPF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1164

b:48.0
occ:1.00
 NE2 A:HIS49 2.2 24.9 1.0
SG A:CYS27 2.4 23.3 1.0
SG A:CYS55 2.5 26.8 1.0
OG A:SER30 2.6 27.6 1.0
CD2 A:HIS49 3.1 22.7 1.0
CE1 A:HIS49 3.1 26.4 1.0
CB A:CYS55 3.3 23.7 1.0
CB A:SER30 3.3 30.3 1.0
CB A:CYS27 3.7 22.1 1.0
N A:SER30 3.8 29.5 1.0
CA A:SER30 4.2 31.2 1.0
CG A:HIS49 4.2 23.3 1.0
ND1 A:HIS49 4.2 26.0 1.0
CB A:ALA53 4.2 29.3 1.0
CB A:THR29 4.4 28.5 1.0
C A:THR29 4.7 31.0 1.0
CA A:CYS55 4.8 24.1 1.0
CA A:THR29 5.0 29.5 1.0
CA A:CYS27 5.0 22.1 1.0

Zinc binding site 3 out of 6 in 2iyk

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Zinc binding site 3 out of 6 in the Crystal Structure of the UPF2-Interacting Domain of Nonsense Mediated Mrna Decay Factor UPF1


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 the UPF2-Interacting Domain of Nonsense Mediated Mrna Decay Factor UPF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1165

b:38.5
occ:1.00
 SG A:CYS73 2.3 31.9 1.0
SG A:CYS103 2.3 21.9 1.0
SG A:CYS76 2.5 25.8 1.0
SG A:CYS99 2.5 23.1 1.0
CB A:CYS73 3.1 29.7 1.0
CB A:CYS99 3.3 21.2 1.0
CB A:CYS103 3.4 21.8 1.0
CB A:CYS76 3.5 25.5 1.0
N A:CYS76 3.8 25.9 1.0
N A:CYS99 3.9 21.1 1.0
CA A:CYS76 4.2 26.2 1.0
CA A:CYS99 4.2 21.1 1.0
CB A:ASN75 4.3 25.9 1.0
ND2 A:ASN75 4.3 26.0 1.0
CB A:CYS78 4.5 21.3 1.0
CA A:CYS73 4.6 30.1 1.0
C A:ASN75 4.7 27.0 1.0
C A:CYS76 4.8 25.9 1.0
CA A:CYS103 4.8 21.8 1.0
N A:GLY77 4.9 24.9 1.0
CG A:ASN75 4.9 26.6 1.0
CA A:ASN75 4.9 26.8 1.0
N A:CYS78 4.9 22.8 1.0
N A:ASN75 4.9 27.1 1.0
N A:CYS103 5.0 21.5 1.0

Zinc binding site 4 out of 6 in 2iyk

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Zinc binding site 4 out of 6 in the Crystal Structure of the UPF2-Interacting Domain of Nonsense Mediated Mrna Decay Factor UPF1


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 the UPF2-Interacting Domain of Nonsense Mediated Mrna Decay Factor UPF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1163

b:29.0
occ:1.00
 ND1 B:HIS45 2.2 20.0 1.0
SG B:CYS13 2.4 22.1 1.0
SG B:CYS35 2.5 19.4 1.0
SG B:CYS16 2.5 24.6 1.0
CE1 B:HIS45 3.1 20.8 1.0
CB B:CYS13 3.2 21.9 1.0
CG B:HIS45 3.2 19.3 1.0
CB B:CYS35 3.6 19.3 1.0
CB B:HIS45 3.6 18.3 1.0
CB B:CYS16 3.6 24.2 1.0
N B:CYS16 3.9 23.4 1.0
N B:CYS35 3.9 17.8 1.0
NE2 B:HIS45 4.3 21.1 1.0
CB B:TYR15 4.3 21.8 1.0
CA B:CYS35 4.3 18.4 1.0
CA B:CYS16 4.3 24.4 1.0
CD2 B:HIS45 4.3 20.2 1.0
CA B:CYS13 4.6 22.2 1.0
CD1 B:ILE18 4.8 23.8 1.0
C B:TYR15 4.8 23.6 1.0
O B:CYS35 4.8 17.8 1.0
C B:CYS35 4.9 18.2 1.0
N B:GLY17 4.9 24.3 1.0
CA B:TYR15 4.9 22.6 1.0
N B:TYR15 4.9 22.2 1.0
CB B:ILE18 5.0 23.4 1.0
O B:GLY37 5.0 20.3 1.0

Zinc binding site 5 out of 6 in 2iyk

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Zinc binding site 5 out of 6 in the Crystal Structure of the UPF2-Interacting Domain of Nonsense Mediated Mrna Decay Factor UPF1


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 the UPF2-Interacting Domain of Nonsense Mediated Mrna Decay Factor UPF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1164

b:45.6
occ:1.00
 SG B:CYS27 2.3 19.7 1.0
NE2 B:HIS49 2.3 20.8 1.0
SG B:CYS55 2.5 24.0 1.0
OG B:SER30 2.7 21.8 1.0
CD2 B:HIS49 3.2 19.2 1.0
CB B:CYS55 3.2 22.3 1.0
CE1 B:HIS49 3.3 21.2 1.0
CB B:SER30 3.4 23.8 1.0
CB B:CYS27 3.7 18.7 1.0
N B:SER30 3.8 23.7 1.0
CA B:SER30 4.2 24.5 1.0
CB B:ALA53 4.2 25.0 1.0
CG B:HIS49 4.3 19.3 1.0
ND1 B:HIS49 4.4 21.0 1.0
CB B:THR29 4.4 24.2 1.0
CA B:CYS55 4.7 23.5 1.0
C B:THR29 4.7 25.0 1.0
CA B:THR29 4.9 24.3 1.0

Zinc binding site 6 out of 6 in 2iyk

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Zinc binding site 6 out of 6 in the Crystal Structure of the UPF2-Interacting Domain of Nonsense Mediated Mrna Decay Factor UPF1


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 the UPF2-Interacting Domain of Nonsense Mediated Mrna Decay Factor UPF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1165

b:28.2
occ:1.00
 SG B:CYS103 2.3 22.0 1.0
SG B:CYS76 2.4 24.9 1.0
SG B:CYS73 2.5 21.3 1.0
SG B:CYS99 2.6 21.3 1.0
CB B:CYS73 3.2 20.8 1.0
CB B:CYS99 3.2 20.0 1.0
CB B:CYS103 3.4 21.1 1.0
CB B:CYS76 3.5 25.5 1.0
N B:CYS76 3.8 25.4 1.0
N B:CYS99 3.9 18.9 1.0
CA B:CYS76 4.2 26.0 1.0
CA B:CYS99 4.2 19.2 1.0
CB B:ASN75 4.3 25.4 1.0
ND2 B:ASN75 4.3 26.1 1.0
CB B:CYS78 4.5 20.1 1.0
CA B:CYS73 4.6 21.2 1.0
C B:ASN75 4.8 26.8 1.0
C B:CYS76 4.8 25.5 1.0
CA B:CYS103 4.8 21.8 1.0
CG B:ASN75 4.9 26.6 1.0
N B:CYS78 4.9 21.7 1.0
N B:GLY77 4.9 24.4 1.0
CA B:ASN75 4.9 26.3 1.0
N B:ASN75 5.0 26.1 1.0
N B:CYS103 5.0 21.7 1.0

Reference:

J.Kadlec, D.Guilligay, R.B.Ravelli, S.Cusack. Crystal Structure of the UPF2-Interacting Domain of Nonsense-Mediated Mrna Decay Factor UPF1. Rna V. 12 1817 2006.
ISSN: ISSN 1355-8382
PubMed: 16931876
DOI: 10.1261/RNA.177606
Page generated: Thu Oct 17 01:01:30 2024

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