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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:

Fluorine (F) 6 atoms

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

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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

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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

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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

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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

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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

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