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Sodium in PDB 3d5k: Crystal Structure of the Oprm Channel in A Non-Symmetrical Space Group

Protein crystallography data

The structure of Crystal Structure of the Oprm Channel in A Non-Symmetrical Space Group, PDB code: 3d5k was solved by G.Phan, I.Broutin, A.Ducruix, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.900, 70.200, 344.500, 90.00, 90.00, 90.00
R / Rfree (%) 23.6 / 29.3

Other elements in 3d5k:

The structure of Crystal Structure of the Oprm Channel in A Non-Symmetrical Space Group also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Oprm Channel in A Non-Symmetrical Space Group (pdb code 3d5k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Crystal Structure of the Oprm Channel in A Non-Symmetrical Space Group, PDB code: 3d5k:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 3d5k

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Sodium binding site 1 out of 9 in the Crystal Structure of the Oprm Channel in A Non-Symmetrical Space Group


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Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Oprm Channel in A Non-Symmetrical Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na475

b:30.8
occ:1.00
 OD2 A:ASP371 2.4 26.0 1.0
O C:GLN229 2.9 23.2 1.0
CG A:ASP371 3.4 24.8 1.0
NE2 A:GLN367 3.7 24.2 1.0
OD1 A:ASP371 3.7 25.4 1.0
CB C:ALA233 3.8 23.4 1.0
C C:GLN229 3.8 23.1 1.0
CB C:GLN229 4.1 22.6 1.0
N C:ALA233 4.2 23.5 1.0
CA C:GLN229 4.3 22.8 1.0
CA C:ALA233 4.4 23.5 1.0
CD A:GLN367 4.5 25.1 1.0
CG A:GLN367 4.7 23.4 1.0
CB A:ASP371 4.7 23.8 1.0
CB C:ASN232 4.9 23.9 1.0
CG C:GLN229 4.9 22.7 1.0
N C:ASP230 4.9 23.7 1.0

Sodium binding site 2 out of 9 in 3d5k

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Sodium binding site 2 out of 9 in the Crystal Structure of the Oprm Channel in A Non-Symmetrical Space Group


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Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Oprm Channel in A Non-Symmetrical Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na476

b:28.9
occ:1.00
 NE2 A:GLN154 3.0 21.4 1.0
O A:TRP450 3.1 39.1 1.0
NE1 A:TRP40 3.3 35.3 1.0
N A:GLN452 3.9 41.0 1.0
CD1 A:LEU57 3.9 25.0 1.0
CB A:GLN452 4.0 41.5 1.0
CD A:GLN154 4.0 22.4 1.0
C A:TRP450 4.1 39.3 1.0
CA A:GLN452 4.2 41.5 1.0
CE2 A:TRP40 4.2 35.7 1.0
OE1 A:GLN154 4.3 23.6 1.0
C A:ASN451 4.3 40.7 1.0
CD1 A:TRP40 4.3 36.0 1.0
CZ2 A:TRP40 4.4 36.0 1.0
CA A:ASN451 4.7 40.4 1.0
N A:ASN451 4.8 39.8 1.0
CG A:GLN452 4.8 41.8 1.0
O A:GLY449 4.9 37.5 1.0
O A:ASN451 4.9 40.7 1.0

Sodium binding site 3 out of 9 in 3d5k

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Sodium binding site 3 out of 9 in the Crystal Structure of the Oprm Channel in A Non-Symmetrical Space Group


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 the Oprm Channel in A Non-Symmetrical Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na476

b:26.6
occ:1.00
 OH C:TYR24 2.8 24.2 1.0
OD1 B:ASN232 3.1 22.1 1.0
O B:ALA228 3.2 22.5 1.0
CZ C:TYR24 3.7 23.7 1.0
CB B:GLN231 3.8 23.9 1.0
CE1 C:TYR24 3.8 24.1 1.0
CG B:ASN232 3.9 22.9 1.0
CB C:PRO19 3.9 24.8 1.0
C B:ALA228 4.0 22.6 1.0
CA B:ALA228 4.1 22.5 1.0
O B:HOH623 4.1 46.0 1.0
ND2 B:ASN232 4.2 23.2 1.0
CB B:ALA228 4.3 22.5 1.0
CG C:PRO19 4.3 24.6 1.0
N B:ASN232 4.3 23.1 1.0
OE1 B:GLN231 4.4 28.8 1.0
CD B:GLN231 4.4 28.3 1.0
CG B:GLN231 4.7 25.5 1.0
O B:HOH522 4.7 31.3 1.0
C B:GLN231 4.7 23.4 1.0
NE2 B:GLN231 4.8 29.1 1.0
CA B:GLN231 4.8 23.6 1.0
CE2 C:TYR24 4.9 24.1 1.0
CA B:ASN232 5.0 22.9 1.0

Sodium binding site 4 out of 9 in 3d5k

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Sodium binding site 4 out of 9 in the Crystal Structure of the Oprm Channel in A Non-Symmetrical Space Group


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 the Oprm Channel in A Non-Symmetrical Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na477

b:29.2
occ:1.00
 O B:LEU256 2.9 34.4 1.0
N B:ASP46 3.2 25.7 1.0
CB B:ASP46 3.4 25.5 1.0
N B:ARG45 3.4 26.1 1.0
C B:LEU256 3.8 34.7 1.0
CA B:PHE44 3.9 25.6 1.0
CB B:PHE44 3.9 25.4 1.0
CA B:ASP46 3.9 25.3 1.0
C B:PHE44 4.0 25.9 1.0
CD2 B:LEU49 4.0 22.2 1.0
CD2 B:LEU257 4.1 34.0 1.0
CB B:LEU256 4.2 34.8 1.0
CD2 B:PHE44 4.2 23.8 1.0
C B:ARG45 4.2 26.1 1.0
CA B:ARG45 4.3 26.3 1.0
CA B:LEU256 4.3 34.9 1.0
CG B:PHE44 4.6 24.2 1.0
O B:ASP46 4.7 24.9 1.0
CG B:ASP46 4.7 25.7 1.0
CD2 B:LEU256 4.8 34.3 1.0
CB B:ARG45 4.8 26.6 1.0
CB B:LEU49 4.8 23.3 1.0
C B:ASP46 4.9 25.0 1.0
N B:LEU257 4.9 34.6 1.0
CG B:LEU49 5.0 22.9 1.0

Sodium binding site 5 out of 9 in 3d5k

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Sodium binding site 5 out of 9 in the Crystal Structure of the Oprm Channel in A Non-Symmetrical Space Group


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 the Oprm Channel in A Non-Symmetrical Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na478

b:25.8
occ:1.00
 O B:HOH513 2.6 22.2 1.0
O B:THR146 2.8 22.5 1.0
O B:ALA66 3.0 21.9 1.0
CG2 B:THR146 3.5 22.5 1.0
N B:GLN150 3.5 20.8 1.0
C B:ALA66 3.8 22.0 1.0
CB B:ALA149 3.8 20.9 1.0
C B:THR146 3.8 22.6 1.0
C B:ALA149 3.9 21.0 1.0
CA B:GLN150 3.9 20.7 1.0
CA B:ALA66 3.9 22.0 1.0
CG2 B:VAL70 4.0 23.8 1.0
CB B:ASN69 4.0 23.4 1.0
CB B:GLN150 4.0 20.9 1.0
CB B:ALA66 4.1 22.1 1.0
CA B:THR146 4.3 22.6 1.0
CA B:ALA149 4.4 21.0 1.0
O B:ALA149 4.5 21.1 1.0
CB B:THR146 4.5 22.5 1.0
N B:VAL70 4.5 24.0 1.0
OD1 B:ASN69 4.6 24.4 1.0
CG B:ASN69 4.8 23.7 1.0
C B:ASN69 4.9 23.7 1.0
CA B:ASN69 4.9 23.4 1.0
N B:ALA149 5.0 21.2 1.0
CG B:GLN150 5.0 21.0 1.0

Sodium binding site 6 out of 9 in 3d5k

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Sodium binding site 6 out of 9 in the Crystal Structure of the Oprm Channel in A Non-Symmetrical Space Group


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 the Oprm Channel in A Non-Symmetrical Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na479

b:27.9
occ:1.00
 OE1 B:GLN154 3.1 21.0 1.0
O B:TRP450 3.3 29.1 1.0
NE1 B:TRP40 3.3 24.9 1.0
O B:HOH571 3.7 27.4 1.0
CD1 B:LEU57 3.7 21.2 1.0
N B:GLN452 3.9 30.8 1.0
O B:HOH625 3.9 42.4 1.0
CB B:GLN452 3.9 31.4 1.0
CE2 B:TRP40 4.2 24.8 1.0
CD B:GLN154 4.2 20.2 1.0
CA B:GLN452 4.2 31.5 1.0
CD1 B:TRP40 4.3 25.1 1.0
C B:TRP450 4.3 29.1 1.0
C B:ASN451 4.3 30.2 1.0
CZ2 B:TRP40 4.3 25.3 1.0
NE2 B:GLN154 4.6 20.0 1.0
OE1 B:GLN452 4.6 30.7 1.0
CA B:ASN451 4.7 29.9 1.0
CG B:GLN452 4.9 31.2 1.0
O B:ASN451 4.9 30.2 1.0
N B:ASN451 4.9 29.5 1.0

Sodium binding site 7 out of 9 in 3d5k

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Sodium binding site 7 out of 9 in the Crystal Structure of the Oprm Channel in A Non-Symmetrical Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the Oprm Channel in A Non-Symmetrical Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na480

b:28.1
occ:1.00
 O B:HOH544 3.0 20.9 1.0
O B:GLN418 3.0 26.6 1.0
OH B:TYR185 3.3 28.2 1.0
CE1 B:TYR185 3.7 28.0 1.0
C B:GLN418 3.9 26.6 1.0
CA B:GLN418 3.9 26.8 1.0
CZ B:TYR185 3.9 28.2 1.0
CD2 B:LEU421 4.0 23.6 1.0
CB B:LEU421 4.0 24.2 1.0
N B:PHE422 4.0 23.9 1.0
CG2 B:THR181 4.0 28.3 1.0
CB B:PHE422 4.1 23.9 1.0
CG B:LEU421 4.1 24.1 1.0
CB B:GLN418 4.3 26.9 1.0
CA B:PHE422 4.4 23.8 1.0
CG B:GLN418 4.6 26.7 1.0
C B:LEU421 4.7 24.1 1.0
CA B:LEU421 4.8 24.2 1.0
CD1 B:TYR185 4.9 28.3 1.0
OG1 B:THR181 4.9 28.9 1.0

Sodium binding site 8 out of 9 in 3d5k

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Sodium binding site 8 out of 9 in the Crystal Structure of the Oprm Channel in A Non-Symmetrical Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of the Oprm Channel in A Non-Symmetrical Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na475

b:29.8
occ:1.00
 O C:HOH478 2.5 24.2 1.0
O C:GLY263 2.6 30.6 1.0
N C:GLY29 3.5 35.9 1.0
C C:GLY263 3.8 30.8 1.0
CD1 C:TYR18 3.8 23.4 1.0
N C:THR28 3.8 34.7 1.0
CB C:ASN27 4.0 33.4 1.0
CA C:GLY29 4.0 36.5 1.0
OD1 C:ASN27 4.1 32.9 1.0
CG C:ASN27 4.1 33.1 1.0
CA C:ASN27 4.3 33.5 1.0
C C:ASN27 4.4 34.1 1.0
O C:GLY29 4.5 36.9 1.0
C C:THR28 4.5 35.6 1.0
CB C:ALA262 4.5 31.8 1.0
OG1 C:THR28 4.5 35.3 1.0
CA C:LEU264 4.6 30.5 1.0
N C:LEU264 4.6 30.6 1.0
CE1 C:TYR18 4.6 22.9 1.0
C C:GLY29 4.6 36.8 1.0
N C:GLY263 4.6 31.6 1.0
CB C:TYR18 4.7 24.6 1.0
CA C:THR28 4.7 35.2 1.0
CA C:GLY263 4.7 31.1 1.0
CG C:TYR18 4.7 23.9 1.0
CD2 C:LEU264 4.8 30.1 1.0
ND2 C:ASN27 4.9 30.9 1.0
N C:TYR18 5.0 25.2 1.0

Sodium binding site 9 out of 9 in 3d5k

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Sodium binding site 9 out of 9 in the Crystal Structure of the Oprm Channel in A Non-Symmetrical Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of the Oprm Channel in A Non-Symmetrical Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na476

b:30.3
occ:1.00
 O C:ALA361 2.8 21.0 1.0
OD1 C:ASP274 3.0 29.1 1.0
OD2 C:ASP274 3.2 28.9 1.0
CG C:ASP274 3.3 28.1 1.0
NH2 C:ARG272 3.4 29.2 1.0
NE C:ARG272 3.4 29.7 1.0
CZ C:ARG272 3.6 29.8 1.0
C C:ALA361 3.7 20.7 1.0
CA C:ALA361 3.8 20.8 1.0
N C:ALA365 4.1 20.4 1.0
CB C:ALA361 4.1 20.6 1.0
CB C:ALA365 4.1 20.2 1.0
CG1 C:ILE275 4.2 25.8 1.0
CB C:THR364 4.2 20.8 1.0
CD C:ARG272 4.4 29.8 1.0
CA C:ALA365 4.5 20.2 1.0
NH1 C:ARG272 4.5 29.7 1.0
O C:HOH613 4.5 30.9 1.0
CB C:ASP274 4.6 27.6 1.0
CG2 C:THR364 4.6 20.8 1.0
C C:THR364 4.8 20.5 1.0
N C:ILE275 4.8 26.5 1.0
C C:ASP274 4.8 27.0 1.0
N C:ILE362 4.9 20.5 1.0
CD1 C:ILE275 4.9 26.3 1.0

Reference:

G.Phan, H.Benabdelhak, M.B.Lascombe, P.Benas, S.Rety, M.Picard, A.Ducruix, C.Etchebest, I.Broutin. Structural and Dynamical Insights Into the Opening Mechanism of P. Aeruginosa Oprm Channel. Structure V. 18 507 2010.
ISSN: ISSN 0969-2126
PubMed: 20399187
DOI: 10.1016/J.STR.2010.01.018
Page generated: Mon Oct 7 08:09:56 2024

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