Zinc in PDB 4zfz: Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein

Protein crystallography data

The structure of Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein, PDB code: 4zfz was solved by D.Morita, M.Sugita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.18 / 1.76
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.402, 85.179, 127.990, 89.20, 79.57, 90.02
R / Rfree (%) 19.5 / 22.8

Other elements in 4zfz:

The structure of Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein (pdb code 4zfz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein, PDB code: 4zfz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 in 4zfz

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Zinc binding site 1 out of 18 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein


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 Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:26.8
occ:1.00
 OE1 A:GLU254 1.6 17.5 1.0
NE2 A:HIS191 2.0 28.5 1.0
CD A:GLU254 2.6 38.1 1.0
CD2 A:HIS191 2.9 27.5 1.0
OE2 A:GLU254 3.0 28.5 1.0
CE1 A:HIS191 3.1 32.0 1.0
CB A:ALA199 3.6 26.1 1.0
CG A:GLU254 4.0 28.0 1.0
CG A:HIS191 4.1 31.8 1.0
ND1 A:HIS191 4.2 28.0 1.0
OG A:SER251 4.3 28.7 1.0
CB A:SER251 4.5 31.7 1.0
CA A:SER251 4.6 32.7 1.0
NE1 A:TRP274 4.7 30.5 1.0
O A:HOH414 4.9 37.3 1.0

Zinc binding site 2 out of 18 in 4zfz

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Zinc binding site 2 out of 18 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein


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 Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:24.4
occ:1.00
 OE1 A:GLU58 1.9 20.5 1.0
OE1 A:GLU61 2.0 22.2 1.0
CD A:GLU58 2.8 24.1 1.0
CD A:GLU61 2.8 25.7 1.0
OE2 A:GLU58 2.9 20.5 1.0
OE2 A:GLU61 3.1 22.6 1.0
CG A:GLU58 4.2 20.7 1.0
CG A:GLU61 4.3 20.9 1.0
CB A:GLU61 4.7 23.4 1.0
O A:HOH433 4.9 25.0 1.0

Zinc binding site 3 out of 18 in 4zfz

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Zinc binding site 3 out of 18 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein


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 Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:69.6
occ:1.00
 ND1 A:HIS192 2.3 55.9 1.0
OD2 B:ASP98 2.4 77.2 1.0
CG A:HIS192 3.0 49.4 1.0
O B:HOH253 3.0 59.6 1.0
CE1 A:HIS192 3.2 50.5 1.0
O A:HOH534 3.2 56.6 1.0
CG B:ASP98 3.3 63.7 1.0
CB A:HIS192 3.3 38.1 1.0
O B:HOH201 3.6 40.3 1.0
OD1 B:ASP98 3.8 59.7 1.0
O B:ASP98 4.0 58.4 1.0
CD2 A:HIS192 4.0 45.7 1.0
NE2 A:HIS192 4.1 49.2 1.0
CA A:HIS192 4.2 31.1 1.0
CB B:ASP98 4.3 57.9 1.0
O B:HOH213 4.6 46.8 1.0
O A:HIS191 4.7 34.2 1.0
C B:ASP98 4.8 51.5 1.0
O A:HOH496 4.9 41.8 1.0

Zinc binding site 4 out of 18 in 4zfz

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Zinc binding site 4 out of 18 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein


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 Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:23.9
occ:1.00
 N A:ALA0 2.0 26.1 1.0
NE2 A:HIS3 2.1 23.1 1.0
O A:ALA0 2.1 22.9 1.0
OE1 A:GLN180 2.1 21.3 1.0
C A:ALA0 2.8 26.3 1.0
CA A:ALA0 2.8 25.9 1.0
CD2 A:HIS3 3.0 24.9 1.0
CE1 A:HIS3 3.0 23.8 1.0
CD A:GLN180 3.1 22.4 1.0
NE2 A:GLN180 3.4 20.9 1.0
CB A:ALA0 3.6 24.0 1.0
N A:GLY1 4.1 29.2 1.0
ND1 A:HIS3 4.2 17.0 1.0
CG A:HIS3 4.2 17.4 1.0
CG A:GLN180 4.5 25.6 1.0
O A:HOH481 4.5 41.0 1.0
O1 A:EDO305 4.6 26.2 1.0
O A:HOH409 4.7 36.3 1.0
CA A:GLY1 4.8 28.9 1.0
CB A:GLN180 4.9 25.5 1.0

Zinc binding site 5 out of 18 in 4zfz

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Zinc binding site 5 out of 18 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein


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 Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:75.3
occ:1.00
 NE2 B:HIS51 2.2 40.5 1.0
O2 B:EDO109 2.4 64.1 1.0
O B:HOH257 2.9 67.6 1.0
CD2 B:HIS51 3.1 38.7 1.0
O1 B:EDO109 3.2 60.8 1.0
CE1 B:HIS51 3.3 41.0 1.0
C2 B:EDO109 3.5 61.6 1.0
C1 B:EDO109 3.5 55.5 1.0
O B:HOH252 4.1 54.6 1.0
CG B:HIS51 4.3 32.0 1.0
O B:HOH247 4.3 34.0 1.0
O B:HOH234 4.3 40.9 1.0
ND1 B:HIS51 4.3 30.4 1.0

Zinc binding site 6 out of 18 in 4zfz

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Zinc binding site 6 out of 18 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein


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 Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn102

b:37.9
occ:1.00
 O1 B:EDO108 1.7 27.6 1.0
O B:HOH211 1.9 38.4 1.0
OE2 B:GLU36 2.2 45.4 1.0
NE2 D:HIS197 2.2 32.4 1.0
OE1 B:GLU36 2.4 38.2 1.0
O2 B:EDO108 2.4 49.4 1.0
C1 B:EDO108 2.5 40.0 1.0
CD B:GLU36 2.6 35.8 1.0
C2 B:EDO108 2.8 42.7 1.0
CD2 D:HIS197 3.1 36.5 1.0
CE1 D:HIS197 3.3 32.5 1.0
OD2 D:ASP196 4.1 42.2 1.0
CG B:GLU36 4.1 31.6 1.0
CG D:HIS197 4.3 30.5 1.0
CB D:ASP196 4.4 29.3 1.0
ND1 D:HIS197 4.4 33.7 1.0
OD1 B:ASN83 4.5 44.6 1.0
O D:HOH513 4.7 37.7 1.0
CG D:ASP196 4.7 38.1 1.0
CB B:GLU36 4.9 30.3 1.0

Zinc binding site 7 out of 18 in 4zfz

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Zinc binding site 7 out of 18 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein


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 Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:26.4
occ:1.00
 OE2 D:GLU254 1.6 18.6 1.0
NE2 D:HIS191 2.1 28.6 1.0
CD D:GLU254 2.6 37.4 1.0
CD2 D:HIS191 2.9 29.3 1.0
OE1 D:GLU254 3.0 26.4 1.0
CE1 D:HIS191 3.1 31.6 1.0
CB D:ALA199 3.6 26.6 1.0
CG D:GLU254 4.0 27.6 1.0
CG D:HIS191 4.1 31.3 1.0
ND1 D:HIS191 4.2 29.0 1.0
OG D:SER251 4.4 30.1 1.0
CB D:SER251 4.5 29.2 1.0
CA D:SER251 4.6 33.4 1.0
NE1 D:TRP274 4.8 33.2 1.0

Zinc binding site 8 out of 18 in 4zfz

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Zinc binding site 8 out of 18 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein


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 Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:76.1
occ:1.00
 ND1 D:HIS192 2.3 56.5 1.0
OD2 E:ASP98 2.5 74.7 1.0
O E:HOH255 2.6 60.3 1.0
CG D:HIS192 3.1 49.0 1.0
CE1 D:HIS192 3.3 49.1 1.0
CG E:ASP98 3.3 62.0 1.0
O E:HOH201 3.3 40.5 1.0
O D:HOH532 3.4 60.5 1.0
CB D:HIS192 3.4 35.7 1.0
O D:HOH559 3.6 50.0 1.0
OD1 E:ASP98 3.8 61.5 1.0
O E:ASP98 3.9 56.5 1.0
CA D:HIS192 4.2 31.3 1.0
CD2 D:HIS192 4.3 45.8 1.0
NE2 D:HIS192 4.3 47.0 1.0
CB E:ASP98 4.4 56.3 1.0
O D:HIS191 4.6 32.2 1.0
C E:ASP98 4.7 53.1 1.0

Zinc binding site 9 out of 18 in 4zfz

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Zinc binding site 9 out of 18 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein


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 Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn303

b:24.8
occ:1.00
 OE1 D:GLN180 2.0 22.9 1.0
O D:ALA0 2.1 23.8 1.0
N D:ALA0 2.1 25.2 1.0
NE2 D:HIS3 2.1 21.7 1.0
C D:ALA0 2.8 24.3 1.0
CA D:ALA0 2.9 28.3 1.0
CD D:GLN180 3.0 22.9 1.0
CE1 D:HIS3 3.1 22.1 1.0
CD2 D:HIS3 3.1 23.3 1.0
NE2 D:GLN180 3.4 19.6 1.0
CB D:ALA0 3.6 26.7 1.0
N D:GLY1 4.1 28.4 1.0
ND1 D:HIS3 4.2 18.2 1.0
CG D:HIS3 4.2 20.5 1.0
CG D:GLN180 4.4 25.6 1.0
O1 D:EDO304 4.7 27.3 1.0
O D:HOH413 4.7 35.8 1.0
CB D:GLN180 4.8 23.4 1.0
CA D:GLY1 4.8 29.5 1.0

Zinc binding site 10 out of 18 in 4zfz

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Zinc binding site 10 out of 18 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein


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 Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Myristoylated 5-Mer Lipopeptide Derived From Siv Nef Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn101

b:75.1
occ:1.00
 NE2 E:HIS51 2.2 42.5 1.0
O E:HOH256 2.7 72.1 1.0
C1 E:EDO108 2.7 53.9 1.0
CD2 E:HIS51 3.1 39.2 1.0
CE1 E:HIS51 3.2 39.4 1.0
C2 E:EDO108 3.4 51.2 1.0
O2 E:EDO108 3.5 57.9 1.0
O1 E:EDO108 3.5 55.7 1.0
O E:HOH254 3.9 50.1 1.0
O E:HOH241 4.2 36.5 1.0
CG E:HIS51 4.3 33.8 1.0
ND1 E:HIS51 4.3 33.1 1.0
O E:HOH246 4.4 34.6 1.0

Reference:

D.Morita, Y.Yamamoto, T.Mizutani, T.Ishikawa, J.Suzuki, T.Igarashi, N.Mori, T.Shiina, H.Inoko, H.Fujita, K.Iwai, Y.Tanaka, B.Mikami, M.Sugita. Crystal Structure of the N-Myristoylated Lipopeptide-Bound Mhc Class I Complex Nat Commun V. 7 10356 2016.
ISSN: ESSN 2041-1723
PubMed: 26758274
DOI: 10.1038/NCOMMS10356
Page generated: Wed Dec 16 05:59:09 2020

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