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Calcium 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:

Zinc (Zn) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex, PDB code: 3zni:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3zni

Go back to Calcium Binding Sites List in 3zni
Calcium binding site 1 out of 4 in the Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca1430

b:51.5
occ:1.00
 OD1 A:ASP221 2.3 35.1 1.0
OD1 A:ASN225 2.4 37.4 1.0
O A:TYR227 2.4 29.0 1.0
OE2 A:GLU232 2.5 35.4 1.0
OG1 A:THR223 2.7 31.1 1.0
OE1 A:GLU232 2.8 32.8 1.0
CD A:GLU232 3.0 34.5 1.0
O A:HOH2047 3.1 29.2 1.0
CG A:ASN225 3.3 35.2 1.0
CG A:ASP221 3.4 36.0 1.0
C A:TYR227 3.5 30.1 1.0
ND2 A:ASN225 3.8 33.6 1.0
N A:ASN225 4.0 40.5 1.0
CB A:THR223 4.0 29.4 1.0
N A:THR223 4.0 31.5 1.0
N A:TYR227 4.1 30.0 1.0
N A:CYS224 4.1 40.0 1.0
CA A:ASP221 4.1 34.0 1.0
OD2 A:ASP221 4.2 39.2 1.0
CB A:ASP221 4.3 36.9 1.0
CA A:THR223 4.3 34.1 1.0
CA A:TYR227 4.3 30.9 1.0
C A:ASP221 4.4 32.9 1.0
C A:THR223 4.4 37.6 1.0
CB A:ASN225 4.5 33.3 1.0
N A:ILE228 4.5 29.7 1.0
CG A:GLU232 4.5 31.1 1.0
N A:LEU222 4.6 30.8 1.0
CA A:ASN225 4.6 38.1 1.0
CA A:ILE228 4.6 27.0 1.0
N A:ASP226 4.7 36.1 1.0
CG2 A:THR223 4.7 25.8 1.0
CB A:TYR227 4.7 30.6 1.0
C A:ASN225 4.8 38.0 1.0
CD1 A:ILE228 4.9 27.2 1.0
O A:ASP221 4.9 34.8 1.0
CA A:CYS224 4.9 42.0 1.0
C A:CYS224 4.9 41.0 1.0
N A:SER229 4.9 24.0 1.0

Calcium binding site 2 out of 4 in 3zni

Go back to Calcium Binding Sites List in 3zni
Calcium binding site 2 out of 4 in the Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
E:Ca1430

b:52.6
occ:1.00
 O E:TYR227 2.3 38.4 1.0
OD1 E:ASP221 2.3 34.4 1.0
OD1 E:ASN225 2.4 31.8 1.0
OE2 E:GLU232 2.4 36.4 1.0
OG1 E:THR223 2.8 30.9 1.0
OE1 E:GLU232 2.8 34.9 1.0
CD E:GLU232 3.0 35.0 1.0
O E:HOH2075 3.1 37.1 1.0
C E:TYR227 3.4 37.6 1.0
CG E:ASN225 3.4 34.9 1.0
CG E:ASP221 3.4 33.1 1.0
N E:TYR227 3.9 34.1 1.0
ND2 E:ASN225 4.0 35.8 1.0
N E:ASN225 4.0 35.1 1.0
CB E:THR223 4.1 30.9 1.0
N E:THR223 4.1 28.2 1.0
CA E:ASP221 4.1 32.8 1.0
CA E:TYR227 4.1 36.7 1.0
OD2 E:ASP221 4.2 34.1 1.0
N E:CYS224 4.2 31.5 1.0
CB E:ASP221 4.3 32.1 1.0
N E:ILE228 4.4 35.7 1.0
C E:ASP221 4.4 28.9 1.0
CA E:THR223 4.4 30.2 1.0
CB E:TYR227 4.5 37.9 1.0
C E:THR223 4.5 30.6 1.0
CG E:GLU232 4.5 29.3 1.0
CA E:ILE228 4.5 31.7 1.0
CB E:ASN225 4.6 36.0 1.0
N E:LEU222 4.6 27.2 1.0
N E:ASP226 4.6 35.9 1.0
CA E:ASN225 4.6 37.8 1.0
C E:ASN225 4.8 37.0 1.0
CG2 E:THR223 4.8 23.3 1.0
N E:SER229 4.9 27.4 1.0
CD1 E:ILE228 4.9 30.3 1.0
O E:ASP221 4.9 29.6 1.0
C E:CYS224 5.0 34.7 1.0
CA E:CYS224 5.0 32.9 1.0

Calcium binding site 3 out of 4 in 3zni

Go back to Calcium Binding Sites List in 3zni
Calcium binding site 3 out of 4 in the Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
I:Ca1429

b:61.5
occ:1.00
 OD1 I:ASP221 2.4 41.6 1.0
O I:TYR227 2.4 46.3 1.0
OE2 I:GLU232 2.4 46.1 1.0
OD1 I:ASN225 2.4 44.5 1.0
OG1 I:THR223 2.6 32.4 1.0
OE1 I:GLU232 2.8 47.6 1.0
CD I:GLU232 2.9 45.0 1.0
O I:HOH2041 3.2 41.4 1.0
CG I:ASP221 3.3 43.7 1.0
CG I:ASN225 3.3 45.6 1.0
C I:TYR227 3.5 44.4 1.0
ND2 I:ASN225 3.8 45.5 1.0
CB I:THR223 3.8 32.3 1.0
N I:THR223 3.9 37.3 1.0
OD2 I:ASP221 4.0 48.7 1.0
CA I:ASP221 4.0 35.6 1.0
N I:ASN225 4.1 45.6 1.0
N I:TYR227 4.1 44.8 1.0
N I:CYS224 4.1 39.6 1.0
CA I:THR223 4.2 37.3 1.0
CB I:ASP221 4.2 38.0 1.0
C I:ASP221 4.3 35.4 1.0
CA I:TYR227 4.3 46.4 1.0
C I:THR223 4.3 39.8 1.0
CG I:GLU232 4.4 41.0 1.0
CG2 I:THR223 4.5 30.1 1.0
N I:LEU222 4.5 32.4 1.0
N I:ILE228 4.5 41.5 1.0
CB I:ASN225 4.5 45.9 1.0
CA I:ILE228 4.6 39.7 1.0
CB I:TYR227 4.7 47.6 1.0
CA I:ASN225 4.7 46.1 1.0
N I:ASP226 4.8 46.9 1.0
O I:ASP221 4.8 39.2 1.0
CD1 I:ILE228 4.9 39.3 1.0
N I:SER229 4.9 37.0 1.0
C I:ASN225 4.9 46.2 1.0
CA I:CYS224 5.0 41.4 1.0

Calcium binding site 4 out of 4 in 3zni

Go back to Calcium Binding Sites List in 3zni
Calcium binding site 4 out of 4 in the Structure of PHOSPHOTYR363-Cbl-B - UBCH5B-Ub - Zap-70 Peptide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
M:Ca1430

b:55.9
occ:1.00
 O M:TYR227 2.3 35.3 1.0
OD1 M:ASP221 2.4 42.1 1.0
OD1 M:ASN225 2.4 38.6 1.0
OE2 M:GLU232 2.5 35.9 1.0
OE1 M:GLU232 2.7 38.5 1.0
OG1 M:THR223 2.7 31.5 1.0
CD M:GLU232 2.9 38.2 1.0
O M:HOH2041 3.1 36.8 1.0
CG M:ASP221 3.3 43.1 1.0
CG M:ASN225 3.4 38.9 1.0
C M:TYR227 3.5 36.7 1.0
OD2 M:ASP221 3.9 45.7 1.0
CB M:THR223 4.0 35.0 1.0
N M:THR223 4.0 35.0 1.0
ND2 M:ASN225 4.0 39.2 1.0
N M:ASN225 4.0 41.2 1.0
N M:TYR227 4.1 36.2 1.0
CA M:ASP221 4.1 41.1 1.0
N M:CYS224 4.2 31.7 1.0
CB M:ASP221 4.2 43.2 1.0
CA M:TYR227 4.3 37.2 1.0
CA M:THR223 4.3 33.9 1.0
C M:ASP221 4.3 41.1 1.0
C M:THR223 4.4 34.4 1.0
N M:ILE228 4.4 35.7 1.0
CG M:GLU232 4.5 37.2 1.0
CA M:ILE228 4.5 34.8 1.0
N M:LEU222 4.5 40.0 1.0
CB M:ASN225 4.6 38.3 1.0
CG2 M:THR223 4.6 31.0 1.0
CB M:TYR227 4.6 40.2 1.0
CD1 M:ILE228 4.7 31.7 1.0
CA M:ASN225 4.7 41.6 1.0
N M:ASP226 4.8 37.5 1.0
C M:ASN225 4.9 38.9 1.0
O M:ASP221 4.9 43.0 1.0
N M:SER229 4.9 36.7 1.0
CA M:CYS224 5.0 36.9 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 Jul 13 21:41:21 2024

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