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Sodium in PDB 5ewl: Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Mk-22

Protein crystallography data

The structure of Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Mk-22, PDB code: 5ewl was solved by J.Pandit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.04 / 2.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 268.880, 59.940, 144.450, 90.00, 116.51, 90.00
R / Rfree (%) 16.2 / 21.7

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 Mk-22 (pdb code 5ewl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 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 Mk-22, PDB code: 5ewl:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5ewl

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Sodium binding site 1 out of 6 in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Mk-22


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 Mk-22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:66.3
occ:1.00
 O A:ASP364 2.5 52.2 1.0
O A:PHE137 2.6 44.0 1.0
O A:HOH638 2.7 32.4 1.0
C A:ASP364 3.2 51.2 1.0
C A:PHE137 3.8 42.0 1.0
N A:GLY365 3.8 46.0 1.0
CA A:GLY365 4.0 43.2 1.0
NZ A:LYS343 4.1 51.2 1.0
CA A:ASP364 4.1 47.1 1.0
N A:PHE137 4.3 38.1 1.0
O A:HIS134 4.4 45.0 1.0
CA A:PHE137 4.5 34.7 1.0
CB A:PHE137 4.7 34.8 1.0
CG A:LYS131 4.7 67.6 1.0
C A:GLY365 4.8 42.3 1.0
CB A:ASP364 4.8 48.9 1.0
CE A:LYS343 4.8 42.4 1.0
N A:LEU138 4.8 39.0 1.0
O A:TYR128 5.0 46.7 1.0

Sodium binding site 2 out of 6 in 5ewl

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Sodium binding site 2 out of 6 in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Mk-22


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 Mk-22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na509

b:49.5
occ:1.00
 O A:ASN50 2.4 44.8 1.0
O A:HIS53 2.8 53.3 1.0
O A:LYS51 3.2 46.9 1.0
OG1 A:THR55 3.2 62.7 1.0
C A:ASN50 3.6 44.3 1.0
C A:LYS51 3.7 46.8 1.0
CA A:LYS51 3.9 43.4 1.0
C A:HIS53 4.0 52.6 1.0
N A:LYS51 4.2 42.5 1.0
CB A:THR55 4.4 59.7 1.0
N A:THR55 4.4 56.3 1.0
CG2 A:THR55 4.5 50.2 1.0
N A:HIS53 4.6 48.6 1.0
N A:ARG52 4.7 42.3 1.0
CA A:ASN50 4.7 39.6 1.0
CA A:HIS53 4.9 48.9 1.0
N A:PHE54 5.0 48.9 1.0
CA A:PHE54 5.0 50.3 1.0

Sodium binding site 3 out of 6 in 5ewl

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Sodium binding site 3 out of 6 in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Mk-22


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 Mk-22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na510

b:43.7
occ:1.00
 O A:ASN396 2.3 53.6 1.0
O A:ARG398 2.5 57.3 1.0
O A:VAL385 2.5 53.8 1.0
OD1 A:ASN396 2.9 46.8 1.0
N A:ASN396 3.2 49.8 1.0
C A:ASN396 3.3 54.6 1.0
C A:VAL385 3.4 51.8 1.0
C A:ARG398 3.6 56.1 1.0
CA A:ASN396 3.7 49.6 1.0
CA A:VAL385 3.8 44.8 1.0
CG A:ASN396 3.8 57.9 1.0
N A:ARG398 3.8 52.9 1.0
CB A:VAL385 3.8 45.8 1.0
OE1 A:GLN395 4.0 65.6 1.0
C A:GLN395 4.0 53.5 1.0
CB A:GLN395 4.1 46.1 1.0
CA A:ARG398 4.2 52.7 1.0
CA A:GLN395 4.3 45.5 1.0
CB A:ASN396 4.3 45.7 1.0
N A:ASP397 4.4 52.7 1.0
C A:ASP397 4.6 55.7 1.0
N A:LYS399 4.6 52.2 1.0
N A:GLY386 4.6 48.0 1.0
CB A:ARG398 4.7 51.9 1.0
O A:HOH663 4.7 39.5 1.0
ND2 A:ASN396 4.8 46.7 1.0
CG1 A:VAL385 4.8 44.0 1.0
CG2 A:VAL385 4.8 44.2 1.0
CD A:GLN395 4.8 62.6 1.0
CA A:ASP397 4.8 53.8 1.0
CG A:GLN395 4.8 45.4 1.0
CA A:LYS399 4.8 51.8 1.0

Sodium binding site 4 out of 6 in 5ewl

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Sodium binding site 4 out of 6 in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Mk-22


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 Mk-22 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:67.6
occ:1.00
 O B:SER312 2.2 75.5 1.0
O D:GLN331 2.5 71.4 1.0
O D:ARG328 2.6 79.1 1.0
O B:HOH658 2.9 53.9 1.0
C B:SER312 3.5 76.0 1.0
C D:ARG328 3.7 80.9 1.0
C D:GLN331 3.7 72.7 1.0
CA D:ILE329 4.2 74.7 1.0
CB B:PHE313 4.3 68.2 1.0
N D:ILE329 4.3 75.2 1.0
N B:PHE313 4.3 69.8 1.0
CB B:SER312 4.4 82.5 1.0
C D:ILE329 4.4 75.8 1.0
CA B:PHE313 4.4 67.5 1.0
CA B:SER312 4.5 75.8 1.0
N D:GLN331 4.5 71.8 1.0
N D:SER332 4.6 69.0 1.0
O D:ILE329 4.6 75.3 1.0
O D:HOH627 4.7 56.8 1.0
CA D:SER332 4.7 68.1 1.0
CA D:GLN331 4.7 70.3 1.0
CA D:ARG328 4.7 83.2 1.0
CB D:SER332 4.8 70.3 1.0
CB D:ARG328 4.8 83.3 1.0
N D:TYR330 4.9 70.8 1.0

Sodium binding site 5 out of 6 in 5ewl

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Sodium binding site 5 out of 6 in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Mk-22


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 Mk-22 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na504

b:60.9
occ:1.00
 O D:SER312 2.2 79.0 1.0
O B:ARG328 2.4 71.8 1.0
O B:GLN331 2.5 65.3 1.0
C D:SER312 3.4 78.5 1.0
C B:ARG328 3.5 73.0 1.0
C B:GLN331 3.7 63.6 1.0
CA B:ILE329 4.0 67.8 1.0
N B:ILE329 4.2 68.0 1.0
CB D:PHE313 4.2 70.7 1.0
CA D:PHE313 4.2 70.0 1.0
N D:PHE313 4.2 71.8 1.0
C B:ILE329 4.2 70.6 1.0
CG B:ARG328 4.3 96.2 1.0
N B:GLN331 4.4 60.9 1.0
O B:ILE329 4.5 72.2 1.0
CA D:SER312 4.5 77.1 1.0
CB D:SER312 4.6 81.7 1.0
CA B:ARG328 4.6 71.0 1.0
N B:SER332 4.6 57.6 1.0
CA B:GLN331 4.6 59.7 1.0
CA B:SER332 4.7 57.0 1.0
CB B:ARG328 4.7 72.8 1.0
N B:TYR330 4.8 64.3 1.0
CB B:SER332 4.9 62.7 1.0

Sodium binding site 6 out of 6 in 5ewl

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Sodium binding site 6 out of 6 in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Mk-22


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Mk-22 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:70.6
occ:1.00
 O C:PHE137 2.6 64.5 1.0
O C:HOH603 2.6 55.1 1.0
O C:ASP364 3.0 60.5 1.0
O C:TYR128 3.3 64.5 1.0
O C:HIS134 3.5 60.6 1.0
C C:PHE137 3.6 64.8 1.0
O C:HOH618 3.8 57.1 1.0
CB C:PHE137 3.9 64.1 1.0
CA C:PHE137 4.1 63.5 1.0
C C:ASP364 4.1 64.4 1.0
N C:PHE137 4.2 65.5 1.0
CA C:SER129 4.2 56.5 1.0
C C:SER129 4.3 59.7 1.0
O C:SER129 4.3 59.4 1.0
C C:TYR128 4.4 63.0 1.0
CD1 C:PHE137 4.5 67.5 1.0
C C:HIS134 4.7 61.1 1.0
CG C:PHE137 4.7 64.8 1.0
N C:SER129 4.8 57.8 1.0
N C:LEU138 4.8 60.3 1.0
CA C:LYS131 4.8 56.3 1.0
CB C:HIS134 4.9 55.4 1.0
N C:LYS131 4.9 56.9 1.0
CA C:ASP364 4.9 63.0 1.0
N C:ASP130 5.0 55.8 1.0
CB C:ASP364 5.0 63.9 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 20:53:31 2024

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