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Zinc in PDB 4oxc: Crystal Structure of Xiap BIR1 Domain

Protein crystallography data

The structure of Crystal Structure of Xiap BIR1 Domain, PDB code: 4oxc was solved by M.Milani, F.Cossu, E.Mastrangelo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.19 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 36.630, 72.390, 69.870, 90.00, 95.69, 90.00
R / Rfree (%) 17.6 / 25.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Xiap BIR1 Domain (pdb code 4oxc). 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 Xiap BIR1 Domain, PDB code: 4oxc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4oxc

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Zinc binding site 1 out of 4 in the Crystal Structure of Xiap BIR1 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 Xiap BIR1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:43.0
occ:1.00
SG A:CYS63 2.1 43.7 1.0
NE2 A:HIS83 2.1 37.7 1.0
SG A:CYS90 2.3 53.8 1.0
SG A:CYS66 2.3 44.6 1.0
CE1 A:HIS83 3.0 38.0 1.0
CB A:CYS63 3.0 48.2 1.0
CB A:CYS90 3.1 51.5 1.0
CD2 A:HIS83 3.2 43.5 1.0
CB A:CYS66 3.4 56.2 1.0
N A:CYS66 3.9 50.2 1.0
ND1 A:HIS83 4.1 41.5 1.0
CA A:CYS66 4.2 47.2 1.0
CG A:HIS83 4.3 39.3 1.0
CA A:CYS90 4.5 50.9 1.0
CA A:CYS63 4.5 42.5 1.0
OG A:SER87 4.5 71.7 1.0
C A:CYS63 4.9 36.9 1.0
CB A:SER65 4.9 41.9 1.0
CB A:SER87 4.9 46.5 1.0
C A:CYS66 4.9 47.7 1.0

Zinc binding site 2 out of 4 in 4oxc

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Zinc binding site 2 out of 4 in the Crystal Structure of Xiap BIR1 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 Xiap BIR1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:59.3
occ:1.00
SG B:CYS66 2.2 71.1 1.0
NE2 B:HIS83 2.2 42.5 1.0
SG B:CYS90 2.2 71.3 1.0
SG B:CYS63 2.3 62.5 1.0
CE1 B:HIS83 3.0 47.7 1.0
CB B:CYS63 3.2 62.9 1.0
CB B:CYS66 3.2 63.7 1.0
CD2 B:HIS83 3.3 55.3 1.0
CB B:CYS90 3.4 82.7 1.0
N B:CYS66 3.6 65.3 1.0
CA B:CYS66 4.0 60.0 1.0
ND1 B:HIS83 4.2 45.1 1.0
OG B:SER87 4.2 59.6 1.0
CG B:HIS83 4.4 46.1 1.0
CB B:SER65 4.4 77.3 1.0
CA B:CYS90 4.5 77.2 1.0
CA B:CYS63 4.7 56.9 1.0
CG1 B:ILE93 4.7 90.4 1.0
C B:SER65 4.7 64.7 1.0
OG B:SER65 4.8 87.8 1.0
C B:CYS66 4.8 53.1 1.0
N B:SER65 4.9 82.3 1.0
CA B:SER65 4.9 72.5 1.0
N B:HIS67 5.0 58.3 1.0

Zinc binding site 3 out of 4 in 4oxc

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Zinc binding site 3 out of 4 in the Crystal Structure of Xiap BIR1 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 Xiap BIR1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn500

b:39.5
occ:1.00
NE2 C:HIS83 2.1 44.0 1.0
SG C:CYS66 2.1 46.4 1.0
SG C:CYS63 2.2 46.2 1.0
SG C:CYS90 2.3 45.5 1.0
CE1 C:HIS83 2.8 43.5 1.0
CB C:CYS63 3.2 44.6 1.0
CD2 C:HIS83 3.3 46.1 1.0
CB C:CYS66 3.3 51.1 1.0
CB C:CYS90 3.3 56.2 1.0
N C:CYS66 3.8 52.3 1.0
ND1 C:HIS83 4.0 44.6 1.0
CA C:CYS66 4.1 45.8 1.0
CG C:HIS83 4.3 39.6 1.0
OG C:SER87 4.3 42.2 1.0
CB C:SER65 4.5 52.1 1.0
CG1 C:ILE93 4.6 56.3 1.0
CA C:CYS90 4.6 50.6 1.0
CA C:CYS63 4.6 43.8 1.0
CB C:PHE92 4.8 46.2 1.0
C C:SER65 4.8 42.4 1.0
C C:CYS66 4.9 41.3 1.0

Zinc binding site 4 out of 4 in 4oxc

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Zinc binding site 4 out of 4 in the Crystal Structure of Xiap BIR1 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 Xiap BIR1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn500

b:56.2
occ:1.00
SG D:CYS90 2.1 71.4 1.0
SG D:CYS63 2.1 50.7 1.0
SG D:CYS66 2.2 57.1 1.0
NE2 D:HIS83 2.3 45.2 1.0
CE1 D:HIS83 2.9 47.6 1.0
CB D:CYS66 3.1 58.2 1.0
CB D:CYS63 3.2 56.1 1.0
CB D:CYS90 3.2 70.7 1.0
CD2 D:HIS83 3.4 52.0 1.0
N D:CYS66 3.6 64.8 1.0
CA D:CYS66 3.9 55.3 1.0
ND1 D:HIS83 4.1 51.0 1.0
OG D:SER87 4.3 51.5 1.0
CG D:HIS83 4.4 48.4 1.0
CA D:CYS90 4.5 68.0 1.0
CB D:SER65 4.6 54.1 1.0
CA D:CYS63 4.6 57.5 1.0
CG1 D:ILE93 4.7 64.4 1.0
C D:CYS66 4.7 47.5 1.0
C D:SER65 4.7 60.5 1.0
CB D:PHE92 4.9 72.4 1.0
N D:HIS67 5.0 50.3 1.0

Reference:

F.Cossu, M.Milani, S.Grassi, F.Malvezzi, A.Corti, M.Bolognesi, E.Mastrangelo. NF023 Binding to Xiap-BIR1: Searching Drugs For Regulation of the Nf-Kappa B Pathway. Proteins 2015.
ISSN: ESSN 1097-0134
PubMed: 25619915
DOI: 10.1002/PROT.24766
Page generated: Wed Dec 16 05:39:47 2020

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