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

Protein crystallography data

The structure of Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Lysophosphatidylethanolamine, PDB code: 6lam 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) 40.09 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 251.879, 46.729, 84.983, 90.00, 90.80, 90.00
R / Rfree (%) 19.1 / 22.9

Other elements in 6lam:

The structure of Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Lysophosphatidylethanolamine also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

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

Zinc binding site 1 out of 7 in 6lam

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Zinc binding site 1 out of 7 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Lysophosphatidylethanolamine


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

b:17.2
occ:0.49
ZN A:ZN301 0.0 17.2 0.5
ZN A:ZN301 1.2 16.1 0.5
OE2 A:GLU61 2.1 19.2 1.0
OE1 A:GLU58 2.3 23.5 1.0
CD A:GLU61 2.8 36.9 1.0
OE1 A:GLU61 2.8 33.2 1.0
CD A:GLU58 3.1 21.0 1.0
OE2 A:GLU58 3.3 24.4 1.0
CG A:GLU61 4.2 31.8 1.0
CG A:GLU58 4.6 20.2 1.0
CB A:GLU61 4.7 22.9 1.0

Zinc binding site 2 out of 7 in 6lam

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Zinc binding site 2 out of 7 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Lysophosphatidylethanolamine


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

b:16.1
occ:0.51
ZN A:ZN301 0.0 16.1 0.5
ZN A:ZN301 1.2 17.2 0.5
OE1 A:GLU58 2.0 23.5 1.0
OE2 A:GLU61 2.2 19.2 1.0
OE2 A:GLU58 2.3 24.4 1.0
CD A:GLU58 2.5 21.0 1.0
CD A:GLU61 3.2 36.9 1.0
OE1 A:GLU61 3.6 33.2 1.0
CG A:GLU58 4.0 20.2 1.0
O A:HOH440 4.3 28.4 1.0
CG A:GLU61 4.5 31.8 1.0
CB A:GLU61 4.6 22.9 1.0
CB A:GLU58 4.9 21.4 1.0

Zinc binding site 3 out of 7 in 6lam

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Zinc binding site 3 out of 7 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Lysophosphatidylethanolamine


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 Lysophosphatidylethanolamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:19.5
occ:1.00
OE1 A:GLU254 2.0 18.8 1.0
NE2 A:HIS191 2.1 17.0 1.0
CD A:GLU254 2.8 16.0 1.0
OE2 A:GLU254 2.9 19.9 1.0
CE1 A:HIS191 3.0 20.8 1.0
CD2 A:HIS191 3.0 19.0 1.0
CB A:ALA199 3.7 16.7 1.0
ND1 A:HIS191 4.1 18.6 1.0
CG A:HIS191 4.2 21.9 1.0
OG A:SER251 4.2 20.9 1.0
CG A:GLU254 4.2 21.3 1.0
CB A:SER251 4.3 18.7 1.0
CA A:SER251 4.5 19.7 1.0
O A:SER251 4.9 22.5 1.0

Zinc binding site 4 out of 7 in 6lam

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Zinc binding site 4 out of 7 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Lysophosphatidylethanolamine


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

b:20.4
occ:1.00
N C:ALA0 2.0 26.3 1.0
NE2 C:HIS3 2.1 17.5 1.0
OE1 C:GLN180 2.1 20.1 1.0
O C:ALA0 2.1 22.3 1.0
C C:ALA0 2.8 23.3 1.0
CA C:ALA0 2.9 22.5 1.0
CE1 C:HIS3 3.0 19.4 1.0
CD C:GLN180 3.1 20.7 1.0
CD2 C:HIS3 3.1 19.9 1.0
NE2 C:GLN180 3.3 17.1 1.0
CB C:ALA0 3.6 23.2 1.0
ND1 C:HIS3 4.1 13.3 1.0
N C:GLY1 4.2 27.9 1.0
O C:HOH564 4.2 25.7 1.0
CG C:HIS3 4.2 15.0 1.0
O C:HOH453 4.5 36.6 1.0
CG C:GLN180 4.5 18.9 1.0
O C:HOH444 4.7 29.5 1.0
O2 C:EDO307 4.7 26.6 1.0
CA C:GLY1 4.9 24.8 1.0
CB C:GLN180 4.9 16.6 1.0

Zinc binding site 5 out of 7 in 6lam

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Zinc binding site 5 out of 7 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Lysophosphatidylethanolamine


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

b:32.3
occ:1.00
NE2 C:HIS197 2.1 27.4 1.0
O1 C:EDO310 2.3 31.1 1.0
O2 C:EDO310 2.3 28.8 1.0
C1 C:EDO310 2.9 38.0 1.0
C2 C:EDO310 3.0 44.4 1.0
CD2 C:HIS197 3.1 29.4 1.0
CE1 C:HIS197 3.2 26.3 1.0
OD2 C:ASP196 4.0 36.5 1.0
CG C:HIS197 4.2 25.9 1.0
ND1 C:HIS197 4.3 32.1 1.0
CB C:ASP196 4.3 21.2 1.0
O C:HOH531 4.6 26.9 1.0
CG C:ASP196 4.6 31.9 1.0

Zinc binding site 6 out of 7 in 6lam

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Zinc binding site 6 out of 7 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*098 Complexed with Lysophosphatidylethanolamine


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

b:25.8
occ:1.00
OE2 C:GLU138 2.0 31.1 1.0
O C:HOH523 2.2 26.6 1.0
OE1 C:GLU138 2.4 33.3 1.0
CD C:GLU138 2.5 23.1 1.0
CG C:GLU138 4.0 32.3 1.0
O C:HOH407 4.1 31.9 1.0
CB C:GLU138 4.8 28.3 1.0

Zinc binding site 7 out of 7 in 6lam

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


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

b:86.7
occ:1.00
ND1 C:HIS192 2.1 52.8 1.0
CG C:HIS192 2.9 41.0 1.0
CE1 C:HIS192 3.0 41.4 1.0
CB C:HIS192 3.2 33.1 1.0
OD2 D:ASP98 3.3 82.0 1.0
CG D:ASP98 3.7 72.7 1.0
O D:ASP98 3.8 58.6 1.0
CD2 C:HIS192 4.0 40.5 1.0
NE2 C:HIS192 4.0 45.9 1.0
OD1 D:ASP98 4.1 66.4 1.0
CA C:HIS192 4.1 27.7 1.0
CB D:ASP98 4.4 61.0 1.0
C D:ASP98 4.7 50.8 1.0
O C:HIS191 4.8 26.5 1.0
O C:HOH532 4.9 31.9 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 12:14:09 2020

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