Zinc in PDB 7apz: Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding

Protein crystallography data

The structure of Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding, PDB code: 7apz was solved by S.Halabi, J.Kaufman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.28 / 1.97
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 82.803, 82.803, 263.071, 90, 90, 120
R / Rfree (%) 21 / 25.5

Other elements in 7apz:

The structure of Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding (pdb code 7apz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding, PDB code: 7apz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 7apz

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Zinc binding site 1 out of 10 in the Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:30.2
occ:1.00
 O A:HOH351 1.9 36.9 1.0
NE2 A:HIS37 2.1 26.0 1.0
O A:HOH355 2.1 30.6 1.0
O A:HOH359 2.2 40.0 1.0
O A:HOH358 2.7 37.6 1.0
CD2 A:HIS37 3.0 22.9 1.0
CE1 A:HIS37 3.1 24.4 1.0
CG A:HIS37 4.2 21.6 1.0
ND1 A:HIS37 4.2 22.9 1.0
CG1 A:VAL140 4.5 24.8 1.0
CG2 A:VAL46 4.9 24.5 1.0
CB A:VAL46 5.0 22.6 1.0
CG1 A:VAL46 5.0 23.9 1.0

Zinc binding site 2 out of 10 in 7apz

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Zinc binding site 2 out of 10 in the Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:48.4
occ:1.00
 O A:HOH353 2.2 27.3 1.0
ND1 A:HIS171 2.4 24.9 1.0
O A:HOH363 2.4 37.1 1.0
CG A:HIS171 3.3 28.7 1.0
CE1 A:HIS171 3.3 28.5 1.0
CB A:HIS171 3.5 28.1 1.0
OG1 A:THR90 4.1 27.7 1.0
CB A:ALA174 4.1 50.5 1.0
CA A:THR90 4.2 26.7 1.0
CB A:PHE88 4.3 29.0 1.0
O A:TRP172 4.3 34.5 1.0
CD A:PRO91 4.4 29.4 1.0
CD2 A:HIS171 4.4 29.8 1.0
NE2 A:HIS171 4.5 27.4 1.0
O A:VAL89 4.5 23.9 1.0
N A:THR90 4.6 27.9 1.0
CB A:THR90 4.6 27.5 1.0
C A:VAL89 4.7 28.0 1.0
CA A:HIS171 4.7 29.5 1.0
CD2 A:PHE88 4.7 31.1 1.0
C A:HIS171 4.8 29.5 1.0
CA A:ALA174 4.9 53.4 1.0
CG2 A:THR90 4.9 28.9 1.0
O A:HIS171 4.9 32.0 1.0

Zinc binding site 3 out of 10 in 7apz

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Zinc binding site 3 out of 10 in the Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn206

b:87.4
occ:1.00
 OE1 A:GLU39 2.4 59.5 1.0
O A:HOH343 2.4 49.6 1.0
OD2 A:ASP41 3.1 69.1 1.0
CD A:GLU39 3.2 59.3 1.0
CG A:GLU39 3.3 48.1 1.0
CB A:ASP41 3.4 52.4 1.0
CG A:ASP41 3.7 63.6 1.0
O A:HOH315 3.9 54.8 1.0
OE2 A:GLU39 4.4 63.5 1.0
CB A:ALA42 4.5 38.0 1.0
N A:ALA42 4.7 41.3 1.0
CA A:ASP41 4.7 45.8 1.0
CB A:GLU39 4.8 37.5 1.0
OD1 A:ASP41 4.9 68.0 1.0
C A:ASP41 5.0 46.4 1.0

Zinc binding site 4 out of 10 in 7apz

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Zinc binding site 4 out of 10 in the Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn210

b:68.7
occ:0.50
 N B:MET-25 4.0 44.3 1.0
OG A:SER57 4.1 28.9 1.0
C A:ALA56 4.2 23.3 1.0
N A:SER57 4.3 22.4 1.0
CA A:ALA56 4.4 23.8 1.0
CB A:SER57 4.4 24.9 1.0
O B:MET-25 4.4 31.4 1.0
CA B:MET-25 4.5 37.5 1.0
O A:ALA56 4.5 24.6 1.0
N A:ALA56 4.5 25.5 1.0
C B:MET-25 4.6 35.2 1.0
O A:PHE55 4.6 25.0 1.0
C A:PHE55 4.6 25.7 1.0
CA A:SER57 5.0 23.4 1.0

Zinc binding site 5 out of 10 in 7apz

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Zinc binding site 5 out of 10 in the Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn212

b:98.1
occ:1.00
 O A:HOH354 2.2 57.2 1.0
O A:HOH308 2.3 57.9 1.0
OD2 A:ASP20 2.4 53.4 1.0
OD1 A:ASP20 2.7 48.9 1.0
CG A:ASP20 2.9 47.7 1.0
CB A:ASP20 4.4 44.5 1.0
N A:GLY18 4.7 37.8 1.0
CB A:GLU17 4.8 34.9 1.0
CA A:GLU17 5.0 34.6 1.0

Zinc binding site 6 out of 10 in 7apz

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Zinc binding site 6 out of 10 in the Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn207

b:44.8
occ:1.00
 NE2 B:HIS39 2.2 29.3 1.0
O B:HOH301 2.3 40.4 1.0
O B:HOH353 2.3 24.0 1.0
CD2 B:HIS39 3.0 27.9 1.0
CE1 B:HIS39 3.3 28.8 1.0
O B:HOH325 3.9 35.5 1.0
CG B:HIS39 4.2 27.6 1.0
CB B:ASP41 4.2 33.0 1.0
OD2 B:ASP41 4.3 31.4 1.0
ND1 B:HIS39 4.3 27.9 1.0
CG B:ASP41 4.8 33.7 1.0
CB B:VAL48 4.9 28.5 1.0
CG2 B:VAL48 4.9 30.8 1.0
CG1 B:VAL48 5.0 27.8 1.0

Zinc binding site 7 out of 10 in 7apz

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Zinc binding site 7 out of 10 in the Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn209

b:29.2
occ:1.00
 ND1 B:HIS16 2.1 23.5 1.0
CG B:HIS16 3.1 23.5 1.0
O B:HOH342 3.1 34.8 1.0
CE1 B:HIS16 3.1 27.6 1.0
CB B:HIS16 3.3 21.8 1.0
CD2 B:LEU18 4.1 37.4 1.0
CD2 B:HIS16 4.2 25.9 1.0
NE2 B:HIS16 4.2 27.0 1.0
CG2 A:VAL6 4.2 25.9 1.0
NH1 B:ARG25 4.5 42.3 1.0
CA B:HIS16 4.5 22.7 1.0
NH2 A:ARG4 4.6 31.6 1.0

Zinc binding site 8 out of 10 in 7apz

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Zinc binding site 8 out of 10 in the Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn210

b:91.0
occ:1.00
 OE2 B:GLU22 2.4 60.1 1.0
OE1 B:GLU22 3.0 64.3 1.0
CD B:GLU22 3.0 57.5 1.0
O7 B:NAG208 4.3 58.1 1.0
CB B:ARG23 4.4 34.3 1.0
CG B:GLU22 4.5 52.3 1.0
CG B:ARG23 4.9 34.2 1.0
O B:GLU22 5.0 35.7 1.0

Zinc binding site 9 out of 10 in 7apz

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Zinc binding site 9 out of 10 in the Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn213

b:121.3
occ:1.00
 OE2 B:GLU96 2.6 63.5 1.0
CD B:GLU96 3.4 51.5 1.0
N B:ARG181 3.7 54.2 1.0
CA B:LEU180 3.8 42.8 1.0
O B:SER179 3.9 36.6 1.0
CD2 B:LEU180 4.0 35.3 1.0
OE1 B:GLU96 4.1 55.4 1.0
C B:LEU180 4.3 45.0 1.0
CG B:GLU96 4.3 47.0 1.0
CB B:LEU180 4.5 43.7 1.0
CB B:ARG181 4.6 70.3 1.0
C B:SER179 4.7 37.0 1.0
N B:LEU180 4.8 40.1 1.0
CA B:ARG181 4.8 62.6 1.0
CG B:LEU180 4.9 40.0 1.0

Zinc binding site 10 out of 10 in 7apz

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Zinc binding site 10 out of 10 in the Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn214

b:79.2
occ:1.00
 O B:HOH314 2.0 52.4 1.0
OD1 B:ASP146 2.3 54.1 1.0
CG B:ASP146 3.0 44.5 1.0
OD2 B:ASP146 3.2 56.5 1.0
N B:VAL147 4.3 29.2 1.0
O B:VAL147 4.3 34.6 1.0
CB B:ASP146 4.4 40.7 1.0
CB B:VAL147 4.7 29.2 1.0
CA B:ASP146 4.9 34.0 1.0
CA B:VAL147 5.0 27.1 1.0
CG2 B:VAL147 5.0 32.0 1.0

Reference:

S.Halabi, J.Kaufman. Clip Peptide Bound to Chicken Mhc Class II Molecule (Bl-2) From B2 Haplotype with A Decamer Mode of Binding To Be Published.
Page generated: Fri Nov 5 16:47:58 2021

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