Atomistry » Zinc » PDB 2ivh-2jaz » 2iyk
Atomistry »
  Zinc »
    PDB 2ivh-2jaz »
      2iyk »

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

Go back to Zinc Binding Sites List in 2iyk
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

Go back to Zinc Binding Sites List in 2iyk
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

Go back to Zinc Binding Sites List in 2iyk
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

Go back to Zinc Binding Sites List in 2iyk
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

Go back to Zinc Binding Sites List in 2iyk
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

Go back to Zinc Binding Sites List in 2iyk
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

Last articles

Mg in 3CMR
Mg in 3CMQ
Mg in 3CLY
Mg in 3CK5
Mg in 3CLC
Mg in 3CKG
Mg in 3CKE
Mg in 3CK4
Mg in 3CJO
Mg in 3CJ8
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy