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Zinc in PDB 3r8b: Crystal Structure of Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8

Protein crystallography data

The structure of Crystal Structure of Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8, PDB code: 3r8b was solved by D.A.Bonsor, E.J.Sundberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.57 / 2.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 109.954, 160.370, 186.265, 90.00, 90.00, 90.00
R / Rfree (%) 24.6 / 26.5

Other elements in 3r8b:

The structure of Crystal Structure of Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8 also contains other interesting chemical elements:

Chlorine (Cl) 14 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8 (pdb code 3r8b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Crystal Structure of Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8, PDB code: 3r8b:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in 3r8b

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Zinc binding site 1 out of 24 in the Crystal Structure of Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8


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 Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn121

b:60.4
occ:1.00
OD1 D:ASP59 2.0 42.6 1.0
OD2 D:ASP59 2.2 40.8 1.0
CG D:ASP59 2.4 40.4 1.0
OE1 B:GLU42 2.4 49.7 1.0
OE2 B:GLU42 2.5 47.6 1.0
CD B:GLU42 2.7 47.1 1.0
CL D:CL123 2.9 24.4 1.0
CL D:CL124 3.1 33.0 1.0
NH2 B:ARG44 3.1 53.7 1.0
ZN P:ZN121 3.3 63.6 1.0
OD1 F:ASP59 3.6 42.6 1.0
NH1 B:ARG44 3.7 54.7 1.0
CZ B:ARG44 3.7 52.4 1.0
CB D:ASP59 3.9 39.4 1.0
CG F:ASP59 4.2 40.5 1.0
CG B:GLU42 4.2 43.9 1.0
OD2 F:ASP59 4.4 41.1 1.0
NH2 P:ARG44 4.7 53.7 1.0
CA D:ASP59 4.7 39.2 1.0
NE B:ARG44 4.8 49.2 1.0

Zinc binding site 2 out of 24 in 3r8b

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Zinc binding site 2 out of 24 in the Crystal Structure of Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8


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 Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn121

b:63.6
occ:1.00
OD1 F:ASP59 2.3 42.6 1.0
OD2 F:ASP59 2.4 41.1 1.0
OE1 P:GLU42 2.6 49.5 1.0
OE2 P:GLU42 2.6 47.6 1.0
CG F:ASP59 2.6 40.5 1.0
CL D:CL123 2.7 24.4 1.0
NH2 P:ARG44 2.9 53.7 1.0
CD P:GLU42 2.9 47.0 1.0
ZN B:ZN121 3.3 60.4 1.0
CL D:CL124 3.4 33.0 1.0
NH1 P:ARG44 3.4 54.7 1.0
CZ P:ARG44 3.5 52.5 1.0
OD1 D:ASP59 3.5 42.6 1.0
CB F:ASP59 4.2 39.5 1.0
CG D:ASP59 4.2 40.4 1.0
CG P:GLU42 4.3 43.8 1.0
OD2 D:ASP59 4.6 40.8 1.0
NE P:ARG44 4.6 49.0 1.0
NH2 B:ARG44 4.7 53.7 1.0
CA F:ASP59 5.0 39.1 1.0

Zinc binding site 3 out of 24 in 3r8b

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Zinc binding site 3 out of 24 in the Crystal Structure of Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8


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 Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn121

b:60.1
occ:1.00
OD1 P:ASP59 2.1 42.6 1.0
OD2 P:ASP59 2.4 41.2 1.0
OE1 F:GLU42 2.5 49.6 1.0
CG P:ASP59 2.6 40.7 1.0
OE2 F:GLU42 2.7 47.6 1.0
CL B:CL123 2.7 21.7 1.0
CD F:GLU42 2.9 46.9 1.0
NH2 F:ARG44 2.9 53.7 1.0
ZN D:ZN121 3.0 57.0 1.0
CL B:CL124 3.1 37.8 1.0
OD1 B:ASP59 3.5 42.7 1.0
NH1 F:ARG44 3.6 54.7 1.0
CZ F:ARG44 3.6 52.5 1.0
CG B:ASP59 4.1 40.3 1.0
CB P:ASP59 4.1 39.5 1.0
CG F:GLU42 4.3 43.8 1.0
OD2 B:ASP59 4.4 40.8 1.0
NH2 D:ARG44 4.4 53.7 1.0
NE F:ARG44 4.7 49.1 1.0
CA P:ASP59 4.9 39.2 1.0

Zinc binding site 4 out of 24 in 3r8b

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Zinc binding site 4 out of 24 in the Crystal Structure of Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8


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 Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn121

b:57.0
occ:1.00
OD1 B:ASP59 2.1 42.7 1.0
OE1 D:GLU42 2.4 49.7 1.0
OD2 B:ASP59 2.4 40.8 1.0
CG B:ASP59 2.6 40.3 1.0
OE2 D:GLU42 2.6 47.7 1.0
CL B:CL123 2.7 21.7 1.0
CD D:GLU42 2.8 47.1 1.0
NH2 D:ARG44 2.9 53.7 1.0
ZN F:ZN121 3.0 60.1 1.0
CL B:CL124 3.5 37.8 1.0
OD1 P:ASP59 3.6 42.6 1.0
CZ D:ARG44 3.6 52.5 1.0
NH1 D:ARG44 3.7 54.7 1.0
CB B:ASP59 4.1 39.5 1.0
CG P:ASP59 4.3 40.7 1.0
CG D:GLU42 4.3 43.8 1.0
NH2 F:ARG44 4.4 53.7 1.0
OD2 P:ASP59 4.6 41.2 1.0
NE D:ARG44 4.8 49.0 1.0
CA B:ASP59 4.8 39.1 1.0

Zinc binding site 5 out of 24 in 3r8b

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Zinc binding site 5 out of 24 in the Crystal Structure of Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8


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 Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn122

b:36.6
occ:1.00
OD2 O:ASP206 1.9 32.8 1.0
NE2 B:HIS50 2.0 32.9 1.0
NE2 D:HIS41 2.0 44.2 1.0
OE1 B:GLU56 2.1 30.3 1.0
OE2 B:GLU56 2.2 30.4 1.0
CD B:GLU56 2.4 32.2 1.0
CG O:ASP206 2.6 35.9 1.0
OD1 O:ASP206 2.6 35.2 1.0
CE1 D:HIS41 2.8 45.4 1.0
CE1 B:HIS50 2.9 34.3 1.0
CD2 B:HIS50 3.1 32.4 1.0
CD2 D:HIS41 3.2 44.2 1.0
CE B:MET48 3.2 39.6 1.0
CG B:GLU56 4.0 33.0 1.0
CB O:ASP206 4.0 36.4 1.0
ND1 D:HIS41 4.0 45.4 1.0
ND1 B:HIS50 4.0 34.0 1.0
CG B:HIS50 4.1 33.2 1.0
CG D:HIS41 4.2 44.1 1.0
SD B:MET48 4.5 40.5 1.0
CB B:GLU56 4.8 34.0 1.0
OH A:TYR91 4.8 41.5 1.0

Zinc binding site 6 out of 24 in 3r8b

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Zinc binding site 6 out of 24 in the Crystal Structure of Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8


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 Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn122

b:33.2
occ:1.00
NE2 D:HIS50 2.0 33.1 1.0
OE1 D:GLU56 2.0 29.9 1.0
OD2 E:ASP206 2.0 33.0 1.0
NE2 B:HIS41 2.1 44.2 1.0
OE2 D:GLU56 2.2 30.6 1.0
CD D:GLU56 2.4 32.1 1.0
CG E:ASP206 2.7 35.8 1.0
OD1 E:ASP206 2.7 34.8 1.0
CE1 D:HIS50 2.9 34.3 1.0
CE1 B:HIS41 3.0 45.6 1.0
CD2 D:HIS50 3.0 32.5 1.0
CE D:MET48 3.2 39.5 1.0
CD2 B:HIS41 3.2 44.1 1.0
CG D:GLU56 3.9 33.1 1.0
ND1 D:HIS50 4.0 33.9 1.0
CB E:ASP206 4.1 36.4 1.0
CG D:HIS50 4.1 33.3 1.0
ND1 B:HIS41 4.2 45.7 1.0
CG B:HIS41 4.3 44.2 1.0
SD D:MET48 4.3 40.4 1.0
CB D:GLU56 4.7 34.0 1.0

Zinc binding site 7 out of 24 in 3r8b

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Zinc binding site 7 out of 24 in the Crystal Structure of Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn121

b:29.7
occ:1.00
NE2 J:HIS50 2.0 32.8 1.0
OE1 J:GLU56 2.1 29.9 1.0
OE2 J:GLU56 2.2 30.5 1.0
CD J:GLU56 2.5 32.1 1.0
CE1 J:HIS50 2.9 34.0 1.0
CD2 J:HIS50 3.1 32.5 1.0
CE J:MET48 3.2 39.6 1.0
CG J:GLU56 4.0 32.9 1.0
ND1 J:HIS50 4.1 33.8 1.0
CG J:HIS50 4.2 33.2 1.0
SD J:MET48 4.4 40.7 1.0
OH I:TYR91 4.8 41.5 1.0
CB J:GLU56 4.8 34.0 1.0

Zinc binding site 8 out of 24 in 3r8b

Go back to Zinc Binding Sites List in 3r8b
Zinc binding site 8 out of 24 in the Crystal Structure of Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn122

b:36.3
occ:1.00
OD2 C:ASP206 1.9 33.0 1.0
NE2 P:HIS41 2.0 44.0 1.0
OE1 F:GLU56 2.1 30.1 1.0
NE2 F:HIS50 2.1 33.0 1.0
OE2 F:GLU56 2.2 30.3 1.0
CD F:GLU56 2.5 32.1 1.0
CG C:ASP206 2.6 35.9 1.0
OD1 C:ASP206 2.6 35.3 1.0
CE1 P:HIS41 2.9 45.5 1.0
CE1 F:HIS50 3.0 34.1 1.0
CD2 P:HIS41 3.1 44.0 1.0
CD2 F:HIS50 3.2 32.6 1.0
CE F:MET48 3.4 39.5 1.0
CB C:ASP206 4.0 36.4 1.0
ND1 P:HIS41 4.0 45.6 1.0
CG F:GLU56 4.0 33.0 1.0
ND1 F:HIS50 4.1 33.8 1.0
CG P:HIS41 4.2 44.1 1.0
CG F:HIS50 4.2 33.1 1.0
SD F:MET48 4.6 40.0 1.0
OH E:TYR91 4.8 41.5 1.0
CB F:GLU56 4.8 34.0 1.0

Zinc binding site 9 out of 24 in 3r8b

Go back to Zinc Binding Sites List in 3r8b
Zinc binding site 9 out of 24 in the Crystal Structure of Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn121

b:35.4
occ:1.00
OE1 L:GLU56 2.0 30.4 1.0
NE2 L:HIS50 2.1 33.2 1.0
OE2 L:GLU56 2.3 30.4 1.0
CD L:GLU56 2.5 32.2 1.0
CE1 L:HIS50 2.9 34.3 1.0
CD2 L:HIS50 3.1 32.8 1.0
CE L:MET48 3.2 39.8 1.0
CG L:GLU56 4.0 33.0 1.0
ND1 L:HIS50 4.1 34.1 1.0
CG L:HIS50 4.2 33.4 1.0
SD L:MET48 4.4 40.6 1.0
CB L:GLU56 4.8 34.1 1.0
OH K:TYR91 4.8 41.6 1.0

Zinc binding site 10 out of 24 in 3r8b

Go back to Zinc Binding Sites List in 3r8b
Zinc binding site 10 out of 24 in the Crystal Structure of Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Staphylococcal Enterotoxin B in Complex with An Affinity Matured Mouse Tcr VBETA8.2 Protein, G5-8 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn121

b:34.5
occ:1.00
NE2 H:HIS50 2.0 33.0 1.0
OE1 H:GLU56 2.1 30.0 1.0
OE2 H:GLU56 2.1 30.5 1.0
CD H:GLU56 2.4 32.2 1.0
CE1 H:HIS50 2.8 34.3 1.0
CD2 H:HIS50 3.0 32.6 1.0
CE H:MET48 3.3 39.8 1.0
CG H:GLU56 4.0 33.0 1.0
ND1 H:HIS50 4.0 34.0 1.0
CG H:HIS50 4.1 33.3 1.0
SD H:MET48 4.5 40.6 1.0
CB H:GLU56 4.7 34.1 1.0
OH G:TYR91 4.9 41.5 1.0

Reference:

D.A.Bonsor, S.Postel, B.G.Pierce, N.Wang, P.Zhu, R.A.Buonpane, Z.Weng, D.M.Kranz, E.J.Sundberg. Molecular Basis of A Million-Fold Affinity Maturation Process in A Protein-Protein Interaction. J.Mol.Biol. V. 411 321 2011.
ISSN: ISSN 0022-2836
PubMed: 21689661
DOI: 10.1016/J.JMB.2011.06.009
Page generated: Wed Dec 16 04:46:56 2020

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