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Zinc in PDB 3zni: Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex

Enzymatic activity of Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex

All present enzymatic activity of Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex:
2.7.10.2; 6.3.2.19;

Protein crystallography data

The structure of Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex, PDB code: 3zni was solved by H.Dou, L.Buetow, G.J.Sibbet, K.Cameron, D.T.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.54 / 2.21
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.970, 131.800, 122.000, 90.00, 91.92, 90.00
R / Rfree (%) 17.5 / 21.1

Other elements in 3zni:

The structure of Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex (pdb code 3zni). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex, PDB code: 3zni:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3zni

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Zinc binding site 1 out of 8 in the Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1428

b:40.3
occ:1.00
 SG A:CYS396 2.3 42.2 1.0
SG A:CYS376 2.4 38.6 1.0
SG A:CYS373 2.4 36.9 1.0
SG A:CYS393 2.4 39.5 1.0
CB A:CYS376 3.2 37.5 1.0
CB A:CYS396 3.2 31.6 1.0
CB A:CYS373 3.3 40.1 1.0
CB A:CYS393 3.6 38.6 1.0
N A:CYS376 3.6 35.2 1.0
CA A:CYS376 4.0 40.6 1.0
N A:CYS393 4.2 38.1 1.0
N A:CYS396 4.2 35.4 1.0
CA A:CYS396 4.3 34.7 1.0
CA A:CYS393 4.4 39.9 1.0
CB A:ILE375 4.4 30.3 1.0
ND2 A:ASN379 4.6 50.1 1.0
C A:ILE375 4.7 36.5 1.0
O A:CYS393 4.7 40.5 1.0
CA A:CYS373 4.7 41.4 1.0
CB A:ASN379 4.8 48.9 1.0
C A:CYS393 4.9 42.5 1.0
CA A:ILE375 4.9 33.0 1.0
N A:ILE375 4.9 37.1 1.0
C A:CYS373 5.0 43.3 1.0

Zinc binding site 2 out of 8 in 3zni

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Zinc binding site 2 out of 8 in the Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1429

b:28.8
occ:1.00
 ND1 A:HIS390 2.0 32.4 1.0
SG A:CYS408 2.2 26.1 1.0
SG A:CYS411 2.4 27.6 1.0
SG A:CYS388 2.4 28.1 1.0
CE1 A:HIS390 2.9 32.5 1.0
CB A:CYS408 3.0 29.2 1.0
CG A:HIS390 3.0 32.0 1.0
CB A:CYS388 3.2 28.3 1.0
CB A:HIS390 3.4 29.9 1.0
CB A:CYS411 3.5 21.1 1.0
N A:CYS411 3.9 24.1 1.0
NE2 A:HIS390 4.1 33.7 1.0
CD2 A:HIS390 4.1 29.6 1.0
CA A:CYS411 4.3 24.3 1.0
N A:HIS390 4.4 33.6 1.0
CA A:CYS408 4.5 28.7 1.0
CA A:CYS388 4.5 31.0 1.0
CA A:HIS390 4.5 34.5 1.0
CB A:PHE410 4.6 29.3 1.0
C A:PHE410 4.7 29.6 1.0
C A:CYS388 4.7 35.7 1.0
N A:PHE410 4.8 25.7 1.0
CA A:PHE410 4.9 28.4 1.0
O A:HOH2111 5.0 30.4 1.0
C A:CYS408 5.0 29.4 1.0
O A:CYS388 5.0 34.0 1.0
CB A:CYS413 5.0 28.2 0.5
C A:CYS411 5.0 27.6 1.0

Zinc binding site 3 out of 8 in 3zni

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Zinc binding site 3 out of 8 in the Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1428

b:38.1
occ:1.00
 SG E:CYS373 2.3 33.7 1.0
SG E:CYS396 2.3 40.9 1.0
SG E:CYS393 2.5 36.9 1.0
SG E:CYS376 2.5 37.1 1.0
CB E:CYS373 3.2 34.4 1.0
CB E:CYS396 3.3 37.1 1.0
CB E:CYS376 3.3 39.9 1.0
CB E:CYS393 3.4 42.2 1.0
N E:CYS376 3.6 40.8 1.0
N E:CYS393 4.0 38.6 1.0
CA E:CYS376 4.1 39.3 1.0
CA E:CYS393 4.2 43.2 1.0
N E:CYS396 4.3 34.3 1.0
CB E:ILE375 4.3 29.6 1.0
CA E:CYS396 4.4 37.0 1.0
O E:HOH2160 4.6 49.9 1.0
ND2 E:ASN379 4.6 57.5 1.0
CA E:CYS373 4.6 34.3 1.0
O E:CYS393 4.6 41.1 1.0
C E:ILE375 4.7 39.3 1.0
C E:CYS393 4.7 44.1 1.0
CB E:ASN379 4.8 52.9 1.0
O E:CYS373 4.8 37.8 1.0
C E:CYS373 4.9 38.3 1.0
CA E:ILE375 4.9 33.1 1.0
N E:ILE375 4.9 34.1 1.0
CG2 E:ILE375 4.9 30.0 1.0

Zinc binding site 4 out of 8 in 3zni

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Zinc binding site 4 out of 8 in the Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1429

b:31.4
occ:1.00
 ND1 E:HIS390 2.0 34.3 1.0
SG E:CYS408 2.3 28.1 1.0
SG E:CYS411 2.3 31.0 1.0
SG E:CYS388 2.4 30.1 1.0
CE1 E:HIS390 2.9 38.2 1.0
CB E:CYS408 3.0 31.1 1.0
CG E:HIS390 3.0 33.6 1.0
CB E:CYS388 3.1 28.1 1.0
CB E:HIS390 3.4 30.7 1.0
CB E:CYS411 3.5 27.4 1.0
N E:CYS411 3.8 31.2 1.0
NE2 E:HIS390 4.1 40.4 1.0
CD2 E:HIS390 4.1 36.3 1.0
CA E:CYS411 4.2 35.9 1.0
N E:HIS390 4.4 32.8 1.0
CA E:CYS408 4.5 30.3 1.0
CA E:CYS388 4.5 32.1 1.0
CA E:HIS390 4.6 34.2 1.0
CB E:PHE410 4.6 28.2 1.0
C E:PHE410 4.6 32.2 1.0
C E:CYS388 4.7 34.2 1.0
O E:HOH2080 4.8 40.1 1.0
C E:CYS411 4.8 32.9 1.0
N E:PHE410 4.9 28.2 1.0
CA E:PHE410 4.9 29.1 1.0
O E:CYS388 4.9 36.9 1.0
C E:CYS408 5.0 33.1 1.0
O E:HOH2156 5.0 41.7 1.0
N E:ARG412 5.0 32.7 1.0

Zinc binding site 5 out of 8 in 3zni

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Zinc binding site 5 out of 8 in the Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1427

b:51.7
occ:1.00
 SG I:CYS376 2.3 47.5 1.0
SG I:CYS396 2.3 45.4 1.0
SG I:CYS373 2.3 56.5 1.0
SG I:CYS393 2.4 56.8 1.0
CB I:CYS373 3.2 50.1 1.0
CB I:CYS396 3.3 45.7 1.0
CB I:CYS376 3.4 50.8 1.0
CB I:CYS393 3.4 52.4 1.0
N I:CYS376 3.6 44.2 1.0
N I:CYS393 4.0 45.5 1.0
CA I:CYS376 4.1 44.4 1.0
CA I:CYS393 4.2 50.3 1.0
N I:CYS396 4.3 47.5 1.0
CB I:ILE375 4.3 41.0 1.0
CA I:CYS396 4.4 46.4 1.0
CA I:CYS373 4.6 50.8 1.0
O I:CYS393 4.6 47.2 1.0
ND2 I:ASN379 4.7 77.8 1.0
C I:ILE375 4.7 42.7 1.0
CB I:ASN379 4.7 72.8 1.0
C I:CYS393 4.8 49.0 1.0
N I:ILE375 4.9 40.3 1.0
CA I:ILE375 4.9 39.5 1.0
C I:CYS373 4.9 49.3 1.0
O I:CYS373 4.9 50.2 1.0

Zinc binding site 6 out of 8 in 3zni

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Zinc binding site 6 out of 8 in the Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1428

b:37.1
occ:1.00
 ND1 I:HIS390 2.0 41.8 1.0
SG I:CYS408 2.2 32.6 1.0
SG I:CYS411 2.2 38.5 1.0
SG I:CYS388 2.3 38.4 1.0
CE1 I:HIS390 2.8 43.5 1.0
CB I:CYS408 2.9 31.9 1.0
CG I:HIS390 3.1 41.7 1.0
CB I:CYS388 3.1 35.1 1.0
CB I:CYS411 3.5 32.0 1.0
CB I:HIS390 3.6 42.0 1.0
N I:CYS411 3.8 32.4 1.0
NE2 I:HIS390 4.0 44.8 1.0
CD2 I:HIS390 4.1 43.8 1.0
CA I:CYS411 4.2 33.3 1.0
CA I:CYS408 4.4 31.5 1.0
CA I:CYS388 4.5 41.1 1.0
N I:HIS390 4.5 47.0 1.0
CB I:PHE410 4.5 35.2 1.0
C I:PHE410 4.6 34.7 1.0
CA I:HIS390 4.7 45.1 1.0
C I:CYS388 4.7 44.1 1.0
N I:PHE410 4.9 29.6 1.0
CB I:CYS413 4.9 34.8 0.5
CA I:PHE410 4.9 32.8 1.0
C I:CYS411 4.9 37.8 1.0
O I:CYS388 5.0 42.4 1.0
C I:CYS408 5.0 34.8 1.0

Zinc binding site 7 out of 8 in 3zni

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Zinc binding site 7 out of 8 in the Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn1428

b:42.8
occ:1.00
 SG M:CYS396 2.3 43.8 1.0
SG M:CYS373 2.3 42.5 1.0
SG M:CYS376 2.4 43.3 1.0
SG M:CYS393 2.5 43.6 1.0
CB M:CYS373 3.2 42.5 1.0
CB M:CYS376 3.3 41.6 1.0
CB M:CYS396 3.3 42.2 1.0
CB M:CYS393 3.4 48.3 1.0
N M:CYS376 3.6 39.5 1.0
N M:CYS393 4.0 44.2 1.0
CA M:CYS376 4.1 44.0 1.0
CA M:CYS393 4.2 45.8 1.0
N M:CYS396 4.3 44.8 1.0
CB M:ILE375 4.4 37.1 1.0
CA M:CYS396 4.4 42.2 1.0
O M:CYS393 4.6 46.4 1.0
CA M:CYS373 4.6 44.9 1.0
C M:ILE375 4.7 40.5 1.0
C M:CYS393 4.7 46.9 1.0
CB M:ASN379 4.8 58.9 1.0
C M:CYS373 4.8 45.4 1.0
O M:CYS373 4.8 44.2 1.0
N M:ILE375 4.9 39.8 1.0
ND2 M:ASN379 4.9 60.0 1.0
CA M:ILE375 4.9 37.6 1.0
O M:ASN379 4.9 59.3 1.0

Zinc binding site 8 out of 8 in 3zni

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Zinc binding site 8 out of 8 in the Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn1429

b:37.6
occ:1.00
 ND1 M:HIS390 2.0 35.7 1.0
SG M:CYS408 2.2 35.0 1.0
SG M:CYS411 2.3 33.1 1.0
SG M:CYS388 2.4 35.4 1.0
CE1 M:HIS390 2.8 38.7 1.0
CB M:CYS408 2.9 33.0 1.0
CG M:HIS390 3.1 38.0 1.0
CB M:CYS388 3.1 33.3 1.0
CB M:CYS411 3.5 36.5 1.0
CB M:HIS390 3.5 34.6 1.0
N M:CYS411 3.8 32.5 1.0
NE2 M:HIS390 4.0 41.0 1.0
CD2 M:HIS390 4.1 41.4 1.0
CA M:CYS411 4.2 35.7 1.0
CA M:CYS408 4.4 31.8 1.0
N M:HIS390 4.5 40.6 1.0
CA M:CYS388 4.5 37.1 1.0
CB M:PHE410 4.5 32.6 1.0
C M:PHE410 4.6 32.5 1.0
CA M:HIS390 4.6 38.4 1.0
C M:CYS388 4.7 37.6 1.0
N M:PHE410 4.8 30.4 1.0
CA M:PHE410 4.9 30.2 1.0
C M:CYS411 4.9 37.1 1.0
O M:CYS388 4.9 38.7 1.0
O M:HOH2049 4.9 32.9 1.0
CB M:CYS413 4.9 37.0 0.5
C M:CYS408 5.0 33.0 1.0

Reference:

H.Dou, L.Buetow, G.J.Sibbet, K.Cameron, D.T.Huang. Essentiality of A Non-Ring Element in Priming Donor Ubiquitin For Catalysis By A Monomeric E3. Nat.Struct.Mol.Biol. V. 20 982 2013.
ISSN: ISSN 1545-9993
PubMed: 23851457
DOI: 10.1038/NSMB.2621
Page generated: Sat Oct 26 18:30:42 2024

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