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Zinc in PDB 6lb2: Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Mono-Acyl Glycerol

Protein crystallography data

The structure of Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Mono-Acyl Glycerol, PDB code: 6lb2 was solved by Y.Shima, D.Morita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.15 / 1.69
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 252.541, 46.895, 85.091, 90.00, 90.76, 90.00
R / Rfree (%) 19.5 / 22.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Mono-Acyl Glycerol (pdb code 6lb2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Mono-Acyl Glycerol, PDB code: 6lb2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6lb2

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Zinc binding site 1 out of 8 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Mono-Acyl Glycerol


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 Mono-Acyl Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:19.4
occ:1.00
N A:ALA0 1.9 24.5 1.0
NE2 A:HIS3 2.0 15.3 1.0
O A:ALA0 2.1 25.2 1.0
OE1 A:GLN180 2.1 19.0 1.0
C A:ALA0 2.8 23.3 1.0
CA A:ALA0 2.8 23.3 1.0
CE1 A:HIS3 3.0 17.9 1.0
CD2 A:HIS3 3.1 19.9 1.0
CD A:GLN180 3.1 19.7 1.0
NE2 A:GLN180 3.3 17.6 1.0
CB A:ALA0 3.6 26.0 1.0
N A:GLY1 4.1 28.6 1.0
ND1 A:HIS3 4.1 12.9 1.0
O A:HOH600 4.2 26.2 1.0
CG A:HIS3 4.2 14.5 1.0
CG A:GLN180 4.5 19.9 1.0
O A:HOH522 4.5 31.2 1.0
O A:HOH564 4.8 32.0 1.0
CA A:GLY1 4.9 24.0 1.0
CB A:GLN180 4.9 15.4 1.0

Zinc binding site 2 out of 8 in 6lb2

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Zinc binding site 2 out of 8 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Mono-Acyl Glycerol


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 Mono-Acyl Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:23.6
occ:1.00
OE1 A:GLU138 2.0 31.8 1.0
O A:HOH549 2.1 25.9 1.0
OE2 A:GLU138 2.4 34.8 1.0
CD A:GLU138 2.5 35.3 1.0
CG A:GLU138 4.0 34.4 1.0
O A:HOH404 4.1 33.4 1.0
CB A:GLU138 4.8 33.1 1.0

Zinc binding site 3 out of 8 in 6lb2

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Zinc binding site 3 out of 8 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Mono-Acyl Glycerol


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 Mono-Acyl Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:30.7
occ:1.00
O A:HOH417 1.8 28.1 1.0
NE2 A:HIS197 2.1 26.7 1.0
O A:HOH576 2.2 34.8 1.0
CD2 A:HIS197 3.0 35.1 1.0
CE1 A:HIS197 3.1 28.7 1.0
OD2 A:ASP196 4.1 37.0 1.0
ND1 A:HIS197 4.2 33.8 1.0
CG A:HIS197 4.2 23.0 1.0
CB A:ASP196 4.4 20.3 1.0
CG A:ASP196 4.8 33.7 1.0

Zinc binding site 4 out of 8 in 6lb2

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Zinc binding site 4 out of 8 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Mono-Acyl Glycerol


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 Mono-Acyl Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:99.9
occ:1.00
ND1 A:HIS192 2.4 43.4 1.0
OG1 A:THR190 3.2 26.4 1.0
CG A:HIS192 3.2 51.0 1.0
O A:THR200 3.2 20.0 1.0
N A:HIS192 3.3 22.4 1.0
CB A:HIS192 3.3 33.0 1.0
CE1 A:HIS192 3.5 48.4 1.0
C A:HIS191 3.5 26.2 1.0
N A:HIS191 3.5 19.3 1.0
C A:THR190 3.6 25.8 1.0
CA A:HIS191 3.7 28.4 1.0
NH1 A:ARG202 3.7 26.2 1.0
O A:THR190 3.7 22.0 1.0
CA A:HIS192 3.9 21.6 1.0
CB A:THR190 3.9 26.6 1.0
O A:HOH469 3.9 30.3 1.0
C A:THR200 4.1 15.0 1.0
CB A:ARG202 4.1 15.9 1.0
O A:HOH567 4.1 30.9 1.0
CB A:THR200 4.2 21.0 1.0
O A:HIS191 4.2 29.2 1.0
CG2 A:THR200 4.3 23.4 1.0
N A:ARG202 4.3 18.0 1.0
CD2 A:HIS192 4.4 53.0 1.0
CA A:THR190 4.4 21.4 1.0
NE2 A:HIS192 4.5 64.6 1.0
CZ A:ARG202 4.7 24.7 1.0
CA A:THR200 4.8 19.6 1.0
CA A:ARG202 4.9 17.9 1.0
N A:LEU201 4.9 16.2 1.0
C A:LEU201 4.9 19.1 1.0
C A:HIS192 5.0 24.3 1.0
CA A:LEU201 5.0 19.9 1.0
O A:HIS192 5.0 26.1 1.0

Zinc binding site 5 out of 8 in 6lb2

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Zinc binding site 5 out of 8 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Mono-Acyl Glycerol


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 Mono-Acyl Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:15.8
occ:1.00
OE2 C:GLU254 2.0 17.0 1.0
NE2 C:HIS191 2.0 13.8 1.0
CD C:GLU254 2.8 13.9 1.0
OE1 C:GLU254 3.0 17.3 1.0
CE1 C:HIS191 3.0 15.7 1.0
CD2 C:HIS191 3.0 15.7 1.0
CB C:ALA199 3.7 16.2 1.0
ND1 C:HIS191 4.1 17.5 1.0
CG C:HIS191 4.2 17.0 1.0
OG C:SER251 4.2 20.1 1.0
CG C:GLU254 4.2 20.9 1.0
CB C:SER251 4.2 17.4 1.0
CA C:SER251 4.5 18.2 1.0
O C:HOH495 4.8 41.9 1.0
O C:SER251 4.9 21.3 1.0

Zinc binding site 6 out of 8 in 6lb2

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Zinc binding site 6 out of 8 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Mono-Acyl Glycerol


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 Mono-Acyl Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:21.9
occ:1.00
OE2 C:GLU58 2.0 17.9 1.0
OE1 C:GLU61 2.1 17.0 1.0
CD C:GLU58 2.8 19.8 1.0
OE1 C:GLU58 3.0 23.5 1.0
CD C:GLU61 3.0 33.9 1.0
OE2 C:GLU61 3.2 31.0 1.0
O C:HOH417 3.4 34.9 1.0
CG C:GLU58 4.3 16.4 1.0
CG C:GLU61 4.4 26.2 1.0
O C:HOH432 4.6 27.7 1.0
CB C:GLU61 4.7 22.2 1.0

Zinc binding site 7 out of 8 in 6lb2

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Zinc binding site 7 out of 8 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Mono-Acyl Glycerol


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 Mono-Acyl Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn303

b:58.0
occ:0.46
ND1 C:HIS197 1.9 31.0 0.6
CE1 C:HIS197 2.2 27.7 0.6
CB C:ASP196 2.7 24.1 1.0
CG C:HIS197 3.2 34.0 0.6
CA C:ASP196 3.3 19.2 1.0
C C:ASP196 3.3 17.6 1.0
NE2 C:HIS197 3.4 27.8 0.6
ND1 C:HIS197 3.5 31.9 0.4
N C:ASP196 3.5 21.2 1.0
N C:HIS197 3.6 18.7 0.6
N C:HIS197 3.6 18.9 0.4
O C:ASP196 3.8 17.8 1.0
CD2 C:HIS197 3.8 29.7 0.6
CG C:ASP196 4.0 47.0 1.0
CB C:HIS197 4.0 23.4 0.6
CB C:HIS197 4.1 26.0 0.4
CG C:HIS197 4.3 22.7 0.4
OD2 C:ASP196 4.3 47.1 1.0
CA C:HIS197 4.3 21.6 0.6
CA C:HIS197 4.4 21.1 0.4
CE1 C:HIS197 4.6 27.4 0.4
O C:HOH411 4.7 28.1 1.0
C C:SER195 4.8 18.0 1.0
OG C:SER195 5.0 20.6 1.0

Zinc binding site 8 out of 8 in 6lb2

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Zinc binding site 8 out of 8 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Mono-Acyl Glycerol


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 Mono-Acyl Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn303

b:60.2
occ:0.54
NE2 C:HIS197 2.1 28.1 0.4
CD2 C:HIS197 3.0 26.8 0.4
CE1 C:HIS197 3.1 27.4 0.4
OE1 C:GLU198 4.0 32.6 1.0
CD C:GLU198 4.1 33.2 1.0
CG C:HIS197 4.2 22.7 0.4
ND1 C:HIS197 4.2 31.9 0.4
CG C:GLU198 4.4 28.4 1.0
OE2 C:GLU198 4.5 35.2 1.0

Reference:

Y.Shima, D.Morita, T.Mizutani, N.Mori, B.Mikami, M.Sugita. Crystal Structures of Lysophospholipid-Bound Mhc Class I Molecules. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32269076
DOI: 10.1074/JBC.RA119.011932
Page generated: Wed Dec 16 12:14:12 2020

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