Atomistry » Zinc » PDB 4i9i-4ii1 » 4ic3
Atomistry »
  Zinc »
    PDB 4i9i-4ii1 »
      4ic3 »

Zinc in PDB 4ic3: Crystal Structure of the F495L Mutant Xiap Ring Domain

Protein crystallography data

The structure of Crystal Structure of the F495L Mutant Xiap Ring Domain, PDB code: 4ic3 was solved by Y.Nakatani, C.L.Day, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.34 / 1.78
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.735, 48.471, 39.967, 90.00, 97.47, 90.00
R / Rfree (%) 17.6 / 22.2

Other elements in 4ic3:

The structure of Crystal Structure of the F495L Mutant Xiap Ring Domain also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the F495L Mutant Xiap Ring Domain (pdb code 4ic3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the F495L Mutant Xiap Ring Domain, PDB code: 4ic3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4ic3

Go back to Zinc Binding Sites List in 4ic3
Zinc binding site 1 out of 4 in the Crystal Structure of the F495L Mutant Xiap Ring Domain


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 F495L Mutant Xiap Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:20.0
occ:1.00
SG A:CYS453 2.3 23.3 1.0
SG A:CYS474 2.3 21.1 1.0
SG A:CYS450 2.3 19.2 1.0
SG A:CYS471 2.4 21.5 1.0
CB A:CYS450 3.1 19.8 1.0
CB A:CYS474 3.1 20.4 1.0
CB A:CYS453 3.2 24.5 1.0
CB A:CYS471 3.6 20.5 1.0
N A:CYS453 3.7 20.5 1.0
NH2 A:ARG456 3.9 32.6 1.0
N A:CYS471 4.0 17.2 1.0
CA A:CYS453 4.0 22.6 1.0
NE A:ARG456 4.1 32.4 1.0
N A:CYS474 4.2 19.5 1.0
CA A:CYS474 4.3 21.7 1.0
CA A:CYS471 4.4 17.9 1.0
CZ A:ARG456 4.5 35.1 1.0
CB A:ILE452 4.6 18.3 1.0
CA A:CYS450 4.6 20.0 1.0
C A:ILE452 4.8 22.0 1.0
N A:MET454 4.8 24.7 1.0
C A:CYS453 4.8 27.2 1.0
C A:CYS471 4.9 18.8 1.0

Zinc binding site 2 out of 4 in 4ic3

Go back to Zinc Binding Sites List in 4ic3
Zinc binding site 2 out of 4 in the Crystal Structure of the F495L Mutant Xiap Ring Domain


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 F495L Mutant Xiap Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:20.1
occ:1.00
ND1 A:HIS467 2.0 24.5 1.0
SG A:CYS481 2.3 20.2 1.0
SG A:CYS484 2.3 23.0 1.0
SG A:CYS465 2.4 20.3 1.0
CE1 A:HIS467 3.0 27.4 1.0
CB A:CYS481 3.0 21.8 1.0
CG A:HIS467 3.0 23.1 1.0
CB A:CYS465 3.2 21.6 1.0
CB A:HIS467 3.4 21.1 1.0
CB A:CYS484 3.5 25.3 1.0
N A:CYS484 3.9 23.4 1.0
NE2 A:HIS467 4.1 28.7 1.0
CD2 A:HIS467 4.1 26.7 1.0
CA A:CYS484 4.2 26.3 1.0
N A:HIS467 4.4 16.5 1.0
CB A:MET483 4.5 27.8 1.0
CA A:CYS481 4.5 22.6 1.0
CA A:HIS467 4.5 17.2 1.0
CA A:CYS465 4.5 20.1 1.0
C A:CYS465 4.7 19.1 1.0
C A:MET483 4.8 25.8 1.0
C A:CYS484 4.9 27.1 1.0
CB A:THR486 4.9 23.4 1.0
O A:CYS465 4.9 20.5 1.0
C A:CYS481 4.9 23.1 1.0
N A:MET483 5.0 24.3 1.0
CA A:MET483 5.0 25.6 1.0
OG1 A:THR486 5.0 24.8 1.0

Zinc binding site 3 out of 4 in 4ic3

Go back to Zinc Binding Sites List in 4ic3
Zinc binding site 3 out of 4 in the Crystal Structure of the F495L Mutant Xiap Ring Domain


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 F495L Mutant Xiap Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:16.8
occ:1.00
SG B:CYS450 2.3 14.1 1.0
SG B:CYS453 2.4 17.9 1.0
SG B:CYS471 2.4 15.2 1.0
SG B:CYS474 2.4 18.1 1.0
CB B:CYS450 3.1 14.0 1.0
CB B:CYS474 3.2 18.1 1.0
CB B:CYS453 3.3 21.1 1.0
CB B:CYS471 3.6 14.9 1.0
N B:CYS453 3.7 19.2 1.0
N B:CYS471 3.9 11.3 1.0
CA B:CYS453 4.1 20.6 1.0
NH2 B:ARG456 4.1 25.6 1.0
N B:CYS474 4.2 16.2 1.0
CA B:CYS474 4.3 18.8 1.0
CA B:CYS471 4.3 14.8 1.0
CA B:CYS450 4.6 14.0 1.0
NE B:ARG456 4.6 23.5 1.0
O B:HOH1138 4.6 31.3 1.0
CB B:ILE452 4.7 18.8 1.0
CZ B:ARG456 4.8 23.0 1.0
C B:ILE452 4.9 22.4 1.0
C B:CYS453 4.9 19.2 1.0
N B:MET454 4.9 18.5 1.0
CG2 B:ILE452 5.0 22.3 1.0
C B:THR470 5.0 12.6 1.0

Zinc binding site 4 out of 4 in 4ic3

Go back to Zinc Binding Sites List in 4ic3
Zinc binding site 4 out of 4 in the Crystal Structure of the F495L Mutant Xiap Ring Domain


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 F495L Mutant Xiap Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:11.3
occ:1.00
ND1 B:HIS467 2.0 16.2 1.0
SG B:CYS484 2.3 11.0 1.0
SG B:CYS465 2.3 11.9 1.0
SG B:CYS481 2.4 12.5 1.0
CE1 B:HIS467 2.9 16.4 1.0
CB B:CYS481 3.0 11.5 1.0
CG B:HIS467 3.0 16.3 1.0
CB B:CYS465 3.2 12.3 1.0
CB B:CYS484 3.4 13.2 1.0
CB B:HIS467 3.4 13.9 1.0
N B:CYS484 3.9 13.6 1.0
NE2 B:HIS467 4.1 19.2 1.0
CD2 B:HIS467 4.1 19.7 1.0
CA B:CYS484 4.2 13.0 1.0
N B:HIS467 4.4 12.5 1.0
CA B:CYS481 4.5 11.6 1.0
CB B:MET483 4.5 16.2 1.0
CA B:HIS467 4.5 14.3 1.0
CA B:CYS465 4.6 13.5 1.0
C B:CYS465 4.8 13.2 1.0
C B:MET483 4.8 16.3 1.0
OG1 B:THR486 4.9 11.6 1.0
C B:CYS484 4.9 13.8 1.0
O B:HOH1104 5.0 14.6 1.0
CB B:THR486 5.0 13.4 1.0
N B:TYR485 5.0 13.7 1.0
N B:MET483 5.0 13.9 1.0

Reference:

Y.Nakatani, T.Kleffmann, K.Linke, S.M.Condon, M.G.Hinds, C.L.Day. Regulation of Ubiquitin Transfer By Xiap, A Dimeric Ring E3 Ligase Biochem.J. V. 450 629 2013.
ISSN: ISSN 0264-6021
PubMed: 23259674
DOI: 10.1042/BJ20121702
Page generated: Sun Oct 27 00:39:10 2024

Last articles

Na in 1NJI
Na in 1N8R
Na in 1M90
Na in 1NJ9
Na in 1NHX
Na in 1ND4
Na in 1NHJ
Na in 1NAI
Na in 1NAH
Na in 1N82
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy