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
Go back to
Zinc Binding Sites List in 6lb2
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
Go back to
Zinc Binding Sites List in 6lb2
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
Go back to
Zinc Binding Sites List in 6lb2
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
Go back to
Zinc Binding Sites List in 6lb2
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
Go back to
Zinc Binding Sites List in 6lb2
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
Go back to
Zinc Binding Sites List in 6lb2
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
Go back to
Zinc Binding Sites List in 6lb2
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
Go back to
Zinc Binding Sites List in 6lb2
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: Tue Oct 29 02:28:40 2024
|