Sodium in PDB 6q4r: High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor
Protein crystallography data
The structure of High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor, PDB code: 6q4r
was solved by
P.Giastas,
M.Neu,
P.Rowland,
E.Stratikos,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
91.45 /
1.60
|
Space group
|
P 2 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.683,
116.669,
147.267,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18 /
21.3
|
Other elements in 6q4r:
The structure of High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor
(pdb code 6q4r). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the
High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor, PDB code: 6q4r:
Jump to Sodium binding site number:
1;
2;
3;
Sodium binding site 1 out
of 3 in 6q4r
Go back to
Sodium Binding Sites List in 6q4r
Sodium binding site 1 out
of 3 in the High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1044
b:35.0
occ:1.00
|
H30
|
A:HJ51009
|
2.7
|
24.2
|
1.0
|
OG
|
A:SER870
|
3.0
|
19.3
|
1.0
|
O
|
A:HOH1489
|
3.0
|
28.8
|
0.7
|
NE2
|
A:GLN315
|
3.2
|
19.1
|
1.0
|
N
|
A:SER870
|
3.2
|
17.3
|
1.0
|
OG
|
A:SER868
|
3.5
|
18.9
|
0.1
|
N
|
A:SER869
|
3.5
|
17.4
|
1.0
|
H7
|
A:HJ51009
|
3.6
|
33.6
|
1.0
|
C30
|
A:HJ51009
|
3.6
|
20.2
|
1.0
|
CG
|
A:GLN315
|
3.7
|
17.4
|
1.0
|
CB
|
A:SER870
|
3.8
|
18.4
|
1.0
|
CB
|
A:SER869
|
3.8
|
23.5
|
1.0
|
H6
|
A:HJ51009
|
3.8
|
33.2
|
1.0
|
H29
|
A:HJ51009
|
3.8
|
25.7
|
1.0
|
CB
|
A:SER868
|
3.9
|
17.0
|
0.1
|
CD
|
A:GLN315
|
3.9
|
20.9
|
1.0
|
CB
|
A:SER868
|
3.9
|
16.4
|
0.9
|
CA
|
A:SER869
|
4.0
|
19.3
|
1.0
|
C
|
A:SER869
|
4.0
|
18.6
|
1.0
|
CA
|
A:SER870
|
4.0
|
13.3
|
1.0
|
C7
|
A:HJ51009
|
4.1
|
28.0
|
1.0
|
C29
|
A:HJ51009
|
4.2
|
21.4
|
1.0
|
C6
|
A:HJ51009
|
4.2
|
27.7
|
1.0
|
C
|
A:SER868
|
4.3
|
17.3
|
1.0
|
O
|
A:HOH1523
|
4.3
|
26.6
|
0.8
|
CA
|
A:SER868
|
4.5
|
15.4
|
0.9
|
CA
|
A:SER868
|
4.5
|
16.7
|
0.1
|
OG
|
A:SER868
|
4.5
|
15.8
|
0.9
|
OG
|
A:SER869
|
4.6
|
26.3
|
1.0
|
O
|
A:HOH1493
|
4.7
|
26.1
|
0.9
|
C31
|
A:HJ51009
|
4.7
|
21.3
|
1.0
|
H31
|
A:HJ51009
|
4.8
|
25.6
|
1.0
|
O
|
A:GLN315
|
4.9
|
17.1
|
1.0
|
CB
|
A:GLN315
|
4.9
|
12.2
|
1.0
|
O
|
A:HOH1274
|
4.9
|
25.5
|
1.0
|
|
Sodium binding site 2 out
of 3 in 6q4r
Go back to
Sodium Binding Sites List in 6q4r
Sodium binding site 2 out
of 3 in the High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1045
b:35.0
occ:1.00
|
O
|
A:HOH1401
|
2.9
|
16.5
|
1.0
|
OG
|
A:SER316
|
2.9
|
13.7
|
0.6
|
N
|
A:SER316
|
3.0
|
12.8
|
1.0
|
H5
|
A:HJ51009
|
3.2
|
29.4
|
1.0
|
CE2
|
A:PHE314
|
3.4
|
17.7
|
1.0
|
N
|
A:GLN315
|
3.4
|
13.9
|
1.0
|
H6
|
A:HJ51009
|
3.5
|
33.2
|
1.0
|
CB
|
A:GLN315
|
3.5
|
12.2
|
1.0
|
CB
|
A:SER316
|
3.6
|
15.7
|
0.6
|
CD2
|
A:PHE314
|
3.7
|
14.6
|
1.0
|
CZ
|
A:PHE314
|
3.7
|
15.0
|
1.0
|
CB
|
A:SER316
|
3.7
|
15.9
|
0.4
|
CG
|
A:GLN181
|
3.7
|
18.7
|
1.0
|
CA
|
A:GLN315
|
3.8
|
16.1
|
1.0
|
CD
|
A:GLN181
|
3.8
|
19.1
|
1.0
|
C
|
A:GLN315
|
3.8
|
18.9
|
1.0
|
OE1
|
A:GLN181
|
3.8
|
16.8
|
1.0
|
CA
|
A:SER316
|
3.9
|
14.6
|
0.6
|
CA
|
A:SER316
|
3.9
|
14.7
|
0.4
|
C5
|
A:HJ51009
|
4.0
|
24.5
|
1.0
|
C6
|
A:HJ51009
|
4.1
|
27.7
|
1.0
|
CE1
|
A:PHE314
|
4.2
|
16.9
|
1.0
|
CG
|
A:PHE314
|
4.2
|
14.1
|
1.0
|
O
|
A:HOH1663
|
4.5
|
51.0
|
1.0
|
CD1
|
A:PHE314
|
4.5
|
14.1
|
1.0
|
NE2
|
A:GLN181
|
4.5
|
19.0
|
1.0
|
C
|
A:PHE314
|
4.5
|
13.0
|
1.0
|
CB
|
A:GLN181
|
4.5
|
16.9
|
1.0
|
O
|
A:PHE159
|
4.6
|
15.9
|
1.0
|
C
|
A:SER316
|
4.6
|
15.4
|
1.0
|
CG
|
A:GLN315
|
4.6
|
17.4
|
1.0
|
O
|
A:SER316
|
4.7
|
15.7
|
1.0
|
CA
|
A:PHE314
|
5.0
|
13.8
|
1.0
|
|
Sodium binding site 3 out
of 3 in 6q4r
Go back to
Sodium Binding Sites List in 6q4r
Sodium binding site 3 out
of 3 in the High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1046
b:35.0
occ:1.00
|
O
|
A:HOH1853
|
2.7
|
27.1
|
1.0
|
OE2
|
A:GLU431
|
2.8
|
22.3
|
1.0
|
O
|
A:HOH1600
|
2.9
|
21.6
|
1.0
|
N
|
A:CYS907
|
3.1
|
17.0
|
1.0
|
SG
|
A:CYS907
|
3.4
|
19.4
|
1.0
|
CB
|
A:CYS907
|
3.5
|
20.1
|
1.0
|
CD
|
A:GLU431
|
3.6
|
21.9
|
1.0
|
N
|
A:ARG906
|
3.6
|
16.2
|
1.0
|
CG
|
A:GLU431
|
3.6
|
15.9
|
1.0
|
CD2
|
A:LEU905
|
3.9
|
21.5
|
1.0
|
CA
|
A:CYS907
|
3.9
|
16.6
|
1.0
|
CB
|
A:LEU905
|
4.1
|
16.4
|
1.0
|
C
|
A:ARG906
|
4.1
|
18.1
|
1.0
|
CA
|
A:ARG906
|
4.1
|
17.4
|
1.0
|
C
|
A:LEU905
|
4.2
|
16.3
|
1.0
|
CB
|
A:ARG906
|
4.3
|
17.7
|
1.0
|
O
|
A:HOH1641
|
4.3
|
31.4
|
1.0
|
CA
|
A:GLY867
|
4.3
|
15.2
|
1.0
|
CB
|
A:ALA872
|
4.4
|
15.5
|
1.0
|
CA
|
A:LEU905
|
4.4
|
19.5
|
1.0
|
O
|
A:HOH1400
|
4.4
|
30.3
|
1.0
|
CG
|
A:LEU905
|
4.5
|
20.2
|
1.0
|
O
|
A:GLY867
|
4.6
|
20.8
|
1.0
|
OE1
|
A:GLU431
|
4.7
|
23.0
|
1.0
|
CB
|
A:GLU431
|
4.7
|
15.7
|
1.0
|
C
|
A:GLY867
|
4.7
|
17.0
|
1.0
|
O
|
A:HOH1406
|
4.8
|
17.2
|
0.8
|
CA
|
A:ALA872
|
4.9
|
15.5
|
1.0
|
N
|
A:GLY867
|
4.9
|
17.6
|
1.0
|
|
Reference:
P.Giastas,
M.Neu,
P.Rowland,
E.Stratikos.
High-Resolution Crystal Structure of Endoplasmic Reticulum Aminopeptidase 1 with Bound Phosphinic Transition-State Analogue Inhibitor. Acs Med.Chem.Lett. V. 10 708 2019.
ISSN: ISSN 1948-5875
PubMed: 31097987
DOI: 10.1021/ACSMEDCHEMLETT.9B00002
Page generated: Tue Oct 8 12:47:59 2024
|