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Zinc in PDB 6lah: Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Lysophosphatidylcholine

Protein crystallography data

The structure of Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Lysophosphatidylcholine, PDB code: 6lah 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) 40.17 / 1.87
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 251.438, 46.443, 84.928, 90.00, 90.90, 90.00
R / Rfree (%) 19.4 / 23

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

Zinc binding site 1 out of 6 in 6lah

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Zinc binding site 1 out of 6 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Lysophosphatidylcholine


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 Lysophosphatidylcholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:28.4
occ:1.00
OE1 A:GLU61 2.1 18.4 0.5
OE2 A:GLU58 2.1 26.8 1.0
OE1 A:GLU61 2.3 21.2 0.5
OE1 A:GLU58 2.7 31.3 1.0
CD A:GLU58 2.7 30.3 1.0
CD A:GLU61 2.9 23.5 0.5
OE2 A:GLU61 3.2 24.3 0.5
CD A:GLU61 3.2 25.4 0.5
OE2 A:GLU61 3.5 22.4 0.5
CG A:GLU58 4.2 23.3 1.0
O A:HOH407 4.3 34.0 1.0
CG A:GLU61 4.3 18.1 0.5
CG A:GLU61 4.5 24.0 0.5
CB A:GLU61 4.6 22.3 0.5
CB A:GLU61 4.7 22.3 0.5

Zinc binding site 2 out of 6 in 6lah

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Zinc binding site 2 out of 6 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Lysophosphatidylcholine


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 Lysophosphatidylcholine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:22.9
occ:1.00
OE2 C:GLU58 2.0 20.2 1.0
OE2 C:GLU61 2.0 19.2 1.0
CD C:GLU58 2.7 23.8 1.0
CD C:GLU61 2.8 21.9 1.0
OE1 C:GLU58 2.9 20.4 1.0
OE1 C:GLU61 2.9 24.7 1.0
O C:HOH463 3.9 23.0 1.0
CG C:GLU61 4.2 20.0 1.0
CG C:GLU58 4.2 18.8 1.0
CB C:GLU61 4.6 19.0 1.0
O C:HOH420 4.8 22.7 1.0

Zinc binding site 3 out of 6 in 6lah

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Zinc binding site 3 out of 6 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Lysophosphatidylcholine


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 Lysophosphatidylcholine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:26.8
occ:1.00
N C:ALA0 2.0 34.8 1.0
O C:ALA0 2.1 27.3 1.0
OE1 C:GLN180 2.1 26.4 1.0
NE2 C:HIS3 2.1 22.6 1.0
C C:ALA0 2.8 28.8 1.0
CA C:ALA0 2.9 29.9 1.0
CD2 C:HIS3 3.1 24.8 1.0
CE1 C:HIS3 3.1 27.5 1.0
CD C:GLN180 3.1 27.2 1.0
NE2 C:GLN180 3.5 25.0 1.0
CB C:ALA0 3.6 29.1 1.0
N C:GLY1 4.1 28.1 1.0
ND1 C:HIS3 4.2 19.1 1.0
CG C:HIS3 4.2 23.3 1.0
CG C:GLN180 4.5 21.1 1.0
O C:HOH408 4.6 33.5 1.0
O2 C:EDO310 4.8 32.0 1.0
CA C:GLY1 4.8 25.3 1.0
CB C:GLN180 4.9 23.8 1.0

Zinc binding site 4 out of 6 in 6lah

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Zinc binding site 4 out of 6 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Lysophosphatidylcholine


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 Lysophosphatidylcholine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn303

b:41.0
occ:1.00
NE2 C:HIS197 2.1 36.9 1.0
O C:HOH437 2.2 30.8 1.0
CD2 C:HIS197 3.0 33.2 1.0
CE1 C:HIS197 3.1 31.1 1.0
OD2 C:ASP196 4.0 42.7 1.0
ND1 C:HIS197 4.2 34.7 1.0
CG C:HIS197 4.2 31.3 1.0
CB C:ASP196 4.4 30.4 1.0
CG C:ASP196 4.7 35.8 1.0
O C:HOH504 4.8 31.1 1.0

Zinc binding site 5 out of 6 in 6lah

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Zinc binding site 5 out of 6 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Lysophosphatidylcholine


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 Lysophosphatidylcholine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn304

b:32.1
occ:1.00
OE1 C:GLU138 2.1 31.1 1.0
OE2 C:GLU138 2.3 37.8 1.0
CD C:GLU138 2.5 34.7 1.0
CG C:GLU138 4.0 36.4 1.0
O C:HOH407 4.3 38.0 1.0
CB C:GLU138 4.8 36.5 1.0

Zinc binding site 6 out of 6 in 6lah

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


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 Lysophosphatidylcholine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn305

b:0.5
occ:1.00
ND1 C:HIS192 2.5 45.5 1.0
CE1 C:HIS192 3.4 42.8 1.0
OD2 D:ASP98 3.4 52.5 1.0
CG C:HIS192 3.5 44.6 1.0
CB C:HIS192 3.8 32.1 1.0
CG D:ASP98 3.8 53.9 1.0
OD1 D:ASP98 4.1 60.6 1.0
CA C:HIS192 4.4 30.8 1.0
NE2 C:HIS192 4.5 43.1 1.0
O C:HIS191 4.6 32.8 1.0
CD2 C:HIS192 4.6 36.8 1.0
CB D:ASP98 4.7 42.5 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 12:14:07 2020

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