Sodium in PDB 5ewm: Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101
Protein crystallography data
The structure of Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101, PDB code: 5ewm
was solved by
J.Pandit,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.41 /
2.76
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
268.400,
60.610,
144.500,
90.00,
116.27,
90.00
|
R / Rfree (%)
|
17.1 /
21.1
|
Other elements in 5ewm:
The structure of Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101 also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101
(pdb code 5ewm). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the
Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101, PDB code: 5ewm:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 5ewm
Go back to
Sodium Binding Sites List in 5ewm
Sodium binding site 1 out
of 5 in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na501
b:67.9
occ:1.00
|
O
|
A:ASP364
|
2.5
|
54.3
|
1.0
|
O
|
A:PHE137
|
2.5
|
43.1
|
1.0
|
O
|
A:HOH635
|
2.9
|
44.6
|
1.0
|
O
|
A:HOH671
|
3.0
|
42.1
|
1.0
|
O
|
A:HOH613
|
3.1
|
42.5
|
1.0
|
C
|
A:ASP364
|
3.5
|
52.7
|
1.0
|
C
|
A:PHE137
|
3.6
|
41.4
|
1.0
|
N
|
A:PHE137
|
4.1
|
37.3
|
1.0
|
CA
|
A:PHE137
|
4.1
|
35.6
|
1.0
|
O
|
A:TYR128
|
4.2
|
45.3
|
1.0
|
CB
|
A:PHE137
|
4.2
|
36.1
|
1.0
|
O
|
A:HIS134
|
4.2
|
44.0
|
1.0
|
N
|
A:GLY365
|
4.4
|
46.4
|
1.0
|
CA
|
A:ASP364
|
4.4
|
47.1
|
1.0
|
CA
|
A:GLY365
|
4.5
|
43.7
|
1.0
|
O
|
A:SER129
|
4.6
|
51.7
|
1.0
|
N
|
A:LEU138
|
4.7
|
38.4
|
1.0
|
CD1
|
A:PHE137
|
4.8
|
38.2
|
1.0
|
CB
|
A:ASP364
|
4.9
|
48.6
|
1.0
|
C
|
A:SER129
|
4.9
|
47.5
|
1.0
|
CA
|
A:SER129
|
4.9
|
38.2
|
1.0
|
C
|
A:GLY365
|
5.0
|
45.4
|
1.0
|
CA
|
A:LEU138
|
5.0
|
39.8
|
1.0
|
|
Sodium binding site 2 out
of 5 in 5ewm
Go back to
Sodium Binding Sites List in 5ewm
Sodium binding site 2 out
of 5 in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na508
b:45.8
occ:1.00
|
O
|
A:ARG398
|
2.3
|
57.5
|
1.0
|
O
|
A:VAL385
|
2.4
|
51.2
|
1.0
|
O
|
A:ASN396
|
2.6
|
58.8
|
1.0
|
OD1
|
A:ASN396
|
2.8
|
54.5
|
1.0
|
C
|
A:VAL385
|
3.4
|
50.1
|
1.0
|
N
|
A:ASN396
|
3.4
|
52.9
|
1.0
|
C
|
A:ARG398
|
3.4
|
55.5
|
1.0
|
C
|
A:ASN396
|
3.4
|
57.5
|
1.0
|
CA
|
A:VAL385
|
3.7
|
45.5
|
1.0
|
OE1
|
A:GLN395
|
3.8
|
57.0
|
1.0
|
CG
|
A:ASN396
|
3.8
|
60.5
|
1.0
|
CB
|
A:VAL385
|
3.8
|
48.7
|
1.0
|
CA
|
A:ASN396
|
3.9
|
52.2
|
1.0
|
N
|
A:ARG398
|
3.9
|
55.1
|
1.0
|
C
|
A:GLN395
|
4.1
|
57.2
|
1.0
|
CB
|
A:GLN395
|
4.1
|
49.6
|
1.0
|
CA
|
A:ARG398
|
4.2
|
54.2
|
1.0
|
CA
|
A:GLN395
|
4.3
|
48.0
|
1.0
|
N
|
A:LYS399
|
4.4
|
50.3
|
1.0
|
CB
|
A:ASN396
|
4.4
|
47.7
|
1.0
|
N
|
A:ASP397
|
4.5
|
54.0
|
1.0
|
N
|
A:GLY386
|
4.6
|
45.6
|
1.0
|
C
|
A:ASP397
|
4.6
|
59.3
|
1.0
|
CG1
|
A:VAL385
|
4.7
|
49.0
|
1.0
|
CD
|
A:GLN395
|
4.7
|
51.5
|
1.0
|
CB
|
A:ARG398
|
4.7
|
54.5
|
1.0
|
O
|
A:HOH625
|
4.7
|
47.8
|
1.0
|
CA
|
A:LYS399
|
4.7
|
50.3
|
1.0
|
ND2
|
A:ASN396
|
4.7
|
46.9
|
1.0
|
CG
|
A:GLN395
|
4.8
|
37.5
|
1.0
|
CA
|
A:ASP397
|
4.9
|
55.2
|
1.0
|
CG2
|
A:VAL385
|
4.9
|
46.9
|
1.0
|
|
Sodium binding site 3 out
of 5 in 5ewm
Go back to
Sodium Binding Sites List in 5ewm
Sodium binding site 3 out
of 5 in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na509
b:62.4
occ:1.00
|
O
|
A:ASN50
|
2.3
|
52.4
|
1.0
|
O
|
A:HIS53
|
2.7
|
56.9
|
1.0
|
O
|
A:LYS51
|
3.3
|
51.2
|
1.0
|
OG1
|
A:THR55
|
3.4
|
61.3
|
1.0
|
C
|
A:ASN50
|
3.5
|
50.4
|
1.0
|
C
|
A:LYS51
|
3.8
|
49.7
|
1.0
|
CA
|
A:LYS51
|
3.8
|
46.0
|
1.0
|
C
|
A:HIS53
|
4.0
|
56.2
|
1.0
|
N
|
A:LYS51
|
4.1
|
46.9
|
1.0
|
N
|
A:THR55
|
4.3
|
55.6
|
1.0
|
CB
|
A:THR55
|
4.3
|
61.5
|
1.0
|
CG2
|
A:THR55
|
4.4
|
54.0
|
1.0
|
CA
|
A:ASN50
|
4.7
|
43.6
|
1.0
|
N
|
A:HIS53
|
4.7
|
50.4
|
1.0
|
N
|
A:ARG52
|
4.9
|
45.7
|
1.0
|
CA
|
A:PHE54
|
4.9
|
51.4
|
1.0
|
N
|
A:PHE54
|
4.9
|
52.1
|
1.0
|
CA
|
A:THR55
|
4.9
|
55.9
|
1.0
|
CA
|
A:HIS53
|
4.9
|
50.2
|
1.0
|
|
Sodium binding site 4 out
of 5 in 5ewm
Go back to
Sodium Binding Sites List in 5ewm
Sodium binding site 4 out
of 5 in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na504
b:57.9
occ:1.00
|
O
|
D:SER312
|
2.2
|
80.2
|
1.0
|
O
|
B:ARG328
|
2.3
|
75.8
|
1.0
|
O
|
B:GLN331
|
2.5
|
65.6
|
1.0
|
O
|
B:HOH668
|
3.3
|
67.8
|
1.0
|
C
|
B:ARG328
|
3.3
|
77.0
|
1.0
|
C
|
D:SER312
|
3.4
|
79.0
|
1.0
|
C
|
B:GLN331
|
3.6
|
65.2
|
1.0
|
CA
|
B:ILE329
|
3.8
|
74.8
|
1.0
|
N
|
B:ILE329
|
4.0
|
74.1
|
1.0
|
C
|
B:ILE329
|
4.1
|
73.7
|
1.0
|
CG
|
B:ARG328
|
4.2
|
94.4
|
1.0
|
N
|
B:GLN331
|
4.2
|
62.8
|
1.0
|
N
|
D:PHE313
|
4.2
|
72.2
|
1.0
|
CA
|
D:PHE313
|
4.3
|
70.4
|
1.0
|
CB
|
D:PHE313
|
4.4
|
71.4
|
1.0
|
CA
|
B:GLN331
|
4.4
|
61.1
|
1.0
|
CA
|
B:ARG328
|
4.5
|
74.0
|
1.0
|
CA
|
D:SER312
|
4.5
|
77.0
|
1.0
|
O
|
B:ILE329
|
4.5
|
74.7
|
1.0
|
CB
|
D:SER312
|
4.6
|
81.5
|
1.0
|
N
|
B:TYR330
|
4.6
|
65.8
|
1.0
|
CB
|
B:ARG328
|
4.6
|
76.2
|
1.0
|
N
|
B:SER332
|
4.7
|
60.3
|
1.0
|
CA
|
B:SER332
|
4.9
|
60.3
|
1.0
|
CB
|
B:GLN331
|
4.9
|
60.4
|
1.0
|
|
Sodium binding site 5 out
of 5 in 5ewm
Go back to
Sodium Binding Sites List in 5ewm
Sodium binding site 5 out
of 5 in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na501
b:80.4
occ:1.00
|
O
|
C:ASP364
|
2.6
|
77.9
|
1.0
|
O
|
C:TYR128
|
2.9
|
70.0
|
1.0
|
O
|
C:PHE137
|
2.9
|
73.3
|
1.0
|
O
|
C:HOH601
|
3.5
|
69.6
|
1.0
|
OD1
|
C:ASP366
|
3.5
|
77.7
|
1.0
|
C
|
C:ASP364
|
3.7
|
78.8
|
1.0
|
CD1
|
C:PHE137
|
3.7
|
72.9
|
1.0
|
CA
|
C:SER129
|
3.7
|
63.8
|
1.0
|
C
|
C:PHE137
|
3.8
|
72.1
|
1.0
|
C
|
C:TYR128
|
3.8
|
68.0
|
1.0
|
C
|
C:GLY365
|
4.1
|
74.9
|
1.0
|
CA
|
C:GLY365
|
4.2
|
73.0
|
1.0
|
N
|
C:SER129
|
4.2
|
63.3
|
1.0
|
O
|
C:GLY365
|
4.2
|
73.1
|
1.0
|
CB
|
C:PHE137
|
4.3
|
68.8
|
1.0
|
CG
|
C:ASP366
|
4.3
|
79.6
|
1.0
|
N
|
C:GLY365
|
4.3
|
74.3
|
1.0
|
N
|
C:LEU138
|
4.4
|
68.4
|
1.0
|
CA
|
C:LEU138
|
4.4
|
67.9
|
1.0
|
N
|
C:ASP366
|
4.4
|
70.5
|
1.0
|
CG
|
C:PHE137
|
4.5
|
69.6
|
1.0
|
CB
|
C:SER129
|
4.6
|
66.0
|
1.0
|
C
|
C:SER129
|
4.6
|
68.3
|
1.0
|
CE1
|
C:PHE137
|
4.6
|
73.4
|
1.0
|
CA
|
C:PHE137
|
4.7
|
68.0
|
1.0
|
NE
|
C:ARG139
|
4.7
|
55.1
|
1.0
|
OD2
|
C:ASP366
|
4.8
|
87.2
|
1.0
|
O
|
C:SER129
|
4.8
|
69.4
|
1.0
|
CA
|
C:ASP364
|
4.8
|
76.5
|
1.0
|
OG
|
C:SER129
|
4.8
|
70.0
|
1.0
|
CB
|
C:ASP364
|
4.9
|
77.8
|
1.0
|
CG
|
C:ARG139
|
4.9
|
58.7
|
1.0
|
C
|
C:LEU138
|
5.0
|
70.2
|
1.0
|
|
Reference:
D.Stroebel,
D.L.Buhl,
J.D.Knafels,
P.K.Chanda,
M.Green,
S.Sciabola,
L.Mony,
P.Paoletti,
J.Pandit.
A Novel Binding Mode Reveals Two Distinct Classes of Nmda Receptor GLUN2B-Selective Antagonists. Mol.Pharmacol. V. 89 541 2016.
ISSN: ESSN 1521-0111
PubMed: 26912815
DOI: 10.1124/MOL.115.103036
Page generated: Mon Oct 7 20:53:37 2024
|