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Sodium in PDB 7lu6: Crystal Structure of the Mouse KIRREL3 D1 Homodimer

Protein crystallography data

The structure of Crystal Structure of the Mouse KIRREL3 D1 Homodimer, PDB code: 7lu6 was solved by C.A.Roman, J.S.Pak, J.Wang, E.Ozkan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.52 / 1.95
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 63.241, 63.241, 347.809, 90, 90, 120
R / Rfree (%) 16 / 19.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Mouse KIRREL3 D1 Homodimer (pdb code 7lu6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of the Mouse KIRREL3 D1 Homodimer, PDB code: 7lu6:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 7lu6

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Sodium binding site 1 out of 8 in the Crystal Structure of the Mouse KIRREL3 D1 Homodimer


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 the Mouse KIRREL3 D1 Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1001

b:17.1
occ:1.00
 O A:TYR96 2.2 12.9 1.0
O A:TYR99 2.3 14.0 1.0
O A:LEU93 2.3 14.3 1.0
C A:LEU93 3.2 13.0 1.0
C A:TYR96 3.3 14.8 1.0
C A:TYR99 3.5 14.0 1.0
CB A:LEU93 3.6 14.5 1.0
CA A:LEU93 4.0 16.0 1.0
N A:SER94 4.1 14.5 1.0
N A:PRO97 4.1 19.2 1.0
CA A:PRO97 4.1 14.8 1.0
N A:TYR99 4.2 14.7 1.0
CA A:SER94 4.2 15.4 1.0
CA A:TYR96 4.2 14.2 1.0
N A:TYR96 4.3 15.2 1.0
C A:PRO97 4.3 15.1 1.0
CA A:TYR99 4.3 12.1 1.0
O A:PRO97 4.5 18.8 1.0
CB A:TYR96 4.5 13.3 1.0
N A:LEU100 4.5 16.6 1.0
CD1 A:LEU100 4.6 13.4 1.0
CA A:LEU100 4.6 15.2 1.0
N A:LEU93 4.7 13.3 1.0
CB A:TYR99 4.7 12.1 1.0
C A:SER94 4.8 18.6 1.0
N A:GLN98 4.9 14.2 1.0

Sodium binding site 2 out of 8 in 7lu6

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Sodium binding site 2 out of 8 in the Crystal Structure of the Mouse KIRREL3 D1 Homodimer


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 the Mouse KIRREL3 D1 Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1001

b:22.0
occ:1.00
 O B:TYR99 2.3 16.0 1.0
O B:TYR96 2.4 18.2 1.0
O B:LEU93 2.4 14.9 1.0
C B:LEU93 3.2 14.0 1.0
C B:TYR96 3.4 16.6 1.0
C B:TYR99 3.6 15.1 1.0
CB B:LEU93 3.6 14.6 1.0
CA B:LEU93 3.9 13.9 1.0
N B:SER94 4.0 16.4 1.0
CA B:PRO97 4.1 20.2 1.0
CA B:SER94 4.2 15.4 1.0
N B:PRO97 4.2 18.9 1.0
N B:TYR99 4.2 16.3 1.0
C B:PRO97 4.3 18.2 1.0
CA B:TYR96 4.4 16.3 1.0
CA B:TYR99 4.4 15.5 1.0
N B:TYR96 4.5 20.3 1.0
O B:PRO97 4.5 18.5 1.0
N B:LEU100 4.5 15.4 1.0
N B:LEU93 4.6 15.9 1.0
O B:HOH1108 4.6 14.1 1.0
CA B:LEU100 4.6 17.7 1.0
CD2 B:LEU100 4.7 18.4 1.0
CB B:TYR96 4.7 15.7 1.0
C B:SER94 4.7 15.9 1.0
CB B:TYR99 4.8 15.0 1.0
N B:GLN98 4.9 18.5 1.0
CG B:LEU93 5.0 12.6 1.0

Sodium binding site 3 out of 8 in 7lu6

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Sodium binding site 3 out of 8 in the Crystal Structure of the Mouse KIRREL3 D1 Homodimer


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 Mouse KIRREL3 D1 Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1001

b:31.4
occ:1.00
 O C:HOH1152 2.1 24.0 1.0
O C:TYR99 2.3 25.0 1.0
O C:TYR96 2.3 24.5 1.0
O C:HOH1151 2.5 18.7 1.0
O C:LEU93 2.6 21.8 1.0
C C:TYR96 3.3 22.6 1.0
C C:LEU93 3.3 21.8 1.0
C C:TYR99 3.5 27.7 1.0
CB C:LEU93 3.7 20.9 1.0
O C:HOH1163 3.9 26.6 1.0
CD2 C:LEU100 4.0 31.5 1.0
CA C:PRO97 4.1 24.6 1.0
N C:PRO97 4.1 25.0 1.0
CA C:LEU93 4.1 19.8 1.0
N C:SER94 4.1 20.0 1.0
CA C:SER94 4.2 23.4 1.0
N C:TYR99 4.2 25.6 1.0
CA C:TYR96 4.3 21.0 1.0
CA C:TYR99 4.3 20.0 1.0
N C:TYR96 4.3 22.7 1.0
C C:PRO97 4.3 26.1 1.0
O C:PRO97 4.4 25.7 1.0
N C:LEU100 4.4 25.6 1.0
CB C:TYR99 4.6 21.1 1.0
CB C:TYR96 4.6 22.0 1.0
C C:SER94 4.6 25.0 1.0
CA C:LEU100 4.6 23.2 1.0
N C:LEU93 4.7 20.9 1.0
CG C:LEU100 4.9 28.9 1.0
N C:GLN98 4.9 25.9 1.0
O C:HOH1116 4.9 21.1 1.0
O C:SER94 4.9 23.5 1.0

Sodium binding site 4 out of 8 in 7lu6

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Sodium binding site 4 out of 8 in the Crystal Structure of the Mouse KIRREL3 D1 Homodimer


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 Mouse KIRREL3 D1 Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1001

b:21.9
occ:1.00
 O D:HOH1165 2.1 24.8 1.0
O D:TYR96 2.3 17.7 1.0
O D:LEU93 2.4 17.8 1.0
O D:TYR99 2.4 18.6 1.0
O D:HOH1162 2.5 14.4 1.0
C D:LEU93 3.2 17.2 1.0
C D:TYR96 3.3 17.1 1.0
C D:TYR99 3.6 18.8 1.0
CB D:LEU93 3.7 13.2 1.0
CA D:LEU93 4.0 19.4 1.0
N D:SER94 4.0 17.1 1.0
N D:PRO97 4.0 15.2 1.0
CA D:PRO97 4.1 15.3 1.0
CA D:SER94 4.1 17.1 1.0
O D:HOH1106 4.1 28.6 1.0
CD2 D:LEU100 4.2 21.9 1.0
CA D:TYR96 4.2 15.9 1.0
O D:HOH1167 4.2 31.7 1.0
N D:TYR96 4.2 15.4 1.0
N D:TYR99 4.3 14.3 1.0
C D:PRO97 4.4 15.3 1.0
CB D:TYR96 4.4 16.5 1.0
CA D:TYR99 4.4 15.3 1.0
C D:SER94 4.6 17.0 1.0
N D:LEU100 4.6 16.8 1.0
N D:LEU93 4.6 23.3 1.0
O D:PRO97 4.7 20.4 1.0
O D:HOH1108 4.7 20.4 1.0
CA D:LEU100 4.7 16.9 1.0
CB D:TYR99 4.7 12.1 1.0
O D:SER94 4.9 16.7 1.0
N D:GLN98 4.9 17.9 1.0
CG D:LEU100 5.0 22.1 1.0

Sodium binding site 5 out of 8 in 7lu6

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Sodium binding site 5 out of 8 in the Crystal Structure of the Mouse KIRREL3 D1 Homodimer


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 Mouse KIRREL3 D1 Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1001

b:53.6
occ:1.00
 O E:HOH1119 2.1 43.2 1.0
O E:ASP92 2.2 44.2 1.0
O E:TYR96 2.2 46.6 1.0
O E:LEU93 2.3 44.8 1.0
O E:TYR99 2.4 41.0 1.0
C E:LEU93 3.0 44.0 1.0
C E:TYR96 3.3 50.7 1.0
C E:ASP92 3.3 50.7 1.0
CB E:LEU93 3.5 47.1 1.0
C E:TYR99 3.6 39.4 1.0
CA E:LEU93 3.6 47.6 1.0
N E:LEU93 3.9 50.9 1.0
N E:SER94 3.9 43.6 1.0
CD2 E:LEU100 4.0 48.4 1.0
CA E:PRO97 4.0 42.2 1.0
N E:PRO97 4.1 47.9 1.0
N E:TYR99 4.1 35.1 1.0
C E:PRO97 4.2 43.7 1.0
CA E:SER94 4.2 43.4 1.0
CA E:TYR96 4.3 43.6 1.0
CA E:TYR99 4.3 34.0 1.0
O E:HOH1112 4.3 49.6 1.0
O E:PRO97 4.4 37.5 1.0
N E:TYR96 4.4 51.5 1.0
CA E:ASP92 4.6 49.4 1.0
N E:LEU100 4.6 34.7 1.0
CB E:TYR96 4.6 40.3 1.0
CB E:TYR99 4.7 38.7 1.0
C E:SER94 4.7 45.6 1.0
N E:GLN98 4.7 43.6 1.0
CG E:LEU93 4.8 39.7 1.0
CG E:LEU100 4.8 42.3 1.0
CA E:LEU100 4.8 33.4 1.0
O E:SER94 5.0 48.6 1.0

Sodium binding site 6 out of 8 in 7lu6

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Sodium binding site 6 out of 8 in the Crystal Structure of the Mouse KIRREL3 D1 Homodimer


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 Mouse KIRREL3 D1 Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na1001

b:72.6
occ:1.00
 O F:TYR96 2.1 54.4 1.0
O F:LEU93 2.2 64.5 1.0
O F:ASP92 2.4 56.7 1.0
O F:TYR99 2.5 58.1 1.0
C F:LEU93 3.0 60.4 1.0
C F:TYR96 3.1 55.5 1.0
C F:ASP92 3.6 64.0 1.0
C F:TYR99 3.6 58.4 1.0
CB F:LEU93 3.6 59.1 1.0
CA F:LEU93 3.7 60.5 1.0
N F:SER94 3.8 58.2 1.0
N F:PRO97 3.9 57.7 1.0
CA F:PRO97 3.9 60.3 1.0
CA F:SER94 4.0 59.2 1.0
CA F:TYR96 4.0 54.6 1.0
N F:TYR96 4.1 55.5 1.0
N F:LEU93 4.1 66.1 1.0
N F:TYR99 4.1 60.1 1.0
C F:PRO97 4.2 60.5 1.0
CA F:TYR99 4.3 55.6 1.0
C F:SER94 4.4 59.2 1.0
CB F:TYR96 4.4 53.5 1.0
O F:PRO97 4.4 57.8 1.0
O F:SER94 4.6 61.1 1.0
N F:LEU100 4.6 58.0 1.0
CB F:TYR99 4.6 51.0 1.0
N F:GLN98 4.7 55.4 1.0
CA F:ASP92 4.8 67.0 1.0
CA F:LEU100 4.9 55.6 1.0
CG F:LEU93 4.9 57.8 1.0
N F:SER95 5.0 57.6 1.0

Sodium binding site 7 out of 8 in 7lu6

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Sodium binding site 7 out of 8 in the Crystal Structure of the Mouse KIRREL3 D1 Homodimer


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 Mouse KIRREL3 D1 Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na1001

b:79.5
occ:1.00
 O G:TYR96 2.1 60.5 1.0
O G:LEU93 2.3 70.4 1.0
O G:TYR99 2.3 58.8 1.0
O G:HOH1108 2.3 58.3 1.0
O G:ASP92 2.4 69.6 1.0
C G:LEU93 3.0 69.3 1.0
C G:TYR96 3.2 62.4 1.0
C G:TYR99 3.4 61.3 1.0
CB G:LEU93 3.4 65.3 1.0
C G:ASP92 3.5 62.2 1.0
CA G:LEU93 3.6 65.5 1.0
N G:LEU93 4.0 63.7 1.0
N G:SER94 4.0 66.0 1.0
CD2 G:LEU100 4.0 66.0 1.0
CA G:PRO97 4.1 66.5 1.0
N G:TYR99 4.1 62.4 1.0
N G:PRO97 4.1 65.4 1.0
CA G:TYR99 4.2 59.1 1.0
CA G:TYR96 4.2 62.3 1.0
N G:TYR96 4.2 64.3 1.0
C G:PRO97 4.3 64.4 1.0
CA G:SER94 4.3 65.8 1.0
N G:LEU100 4.3 60.0 1.0
O G:PRO97 4.4 64.3 1.0
CB G:TYR99 4.4 54.2 1.0
CB G:TYR96 4.5 60.9 1.0
CA G:LEU100 4.6 62.6 1.0
CG G:LEU93 4.7 63.1 1.0
CG G:LEU100 4.7 64.5 1.0
CA G:ASP92 4.7 65.6 1.0
C G:SER94 4.7 66.6 1.0
N G:GLN98 4.9 63.1 1.0

Sodium binding site 8 out of 8 in 7lu6

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Sodium binding site 8 out of 8 in the Crystal Structure of the Mouse KIRREL3 D1 Homodimer


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 Mouse KIRREL3 D1 Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1001

b:60.9
occ:1.00
 O H:ASP92 2.1 50.4 1.0
O H:TYR96 2.3 47.0 1.0
O H:TYR99 2.3 44.5 1.0
O H:HOH1110 2.4 44.8 1.0
O H:LEU93 2.4 47.9 1.0
C H:LEU93 3.1 51.7 1.0
C H:ASP92 3.3 51.3 1.0
C H:TYR96 3.4 45.9 1.0
C H:TYR99 3.6 43.5 1.0
CB H:LEU93 3.6 49.0 1.0
CA H:LEU93 3.7 47.3 1.0
CD2 H:LEU100 3.7 53.2 1.0
OD1 H:ASP92 3.8 68.1 1.0
N H:LEU93 3.9 53.0 1.0
N H:SER94 4.0 53.6 1.0
CA H:PRO97 4.2 47.6 1.0
N H:PRO97 4.2 48.3 1.0
CA H:SER94 4.2 51.7 1.0
N H:TYR99 4.3 41.8 1.0
C H:PRO97 4.3 51.5 1.0
CA H:TYR96 4.4 45.9 1.0
CG H:ASP92 4.4 64.1 1.0
N H:TYR96 4.4 52.1 1.0
O H:PRO97 4.4 48.1 1.0
CA H:TYR99 4.4 40.6 1.0
CA H:ASP92 4.5 57.0 1.0
N H:LEU100 4.5 44.1 1.0
O H:HOH1104 4.5 50.2 1.0
C H:SER94 4.6 49.8 1.0
CA H:LEU100 4.6 42.9 1.0
CB H:TYR96 4.7 44.1 1.0
CG H:LEU100 4.7 53.4 1.0
CB H:TYR99 4.7 40.4 1.0
CG H:LEU93 4.8 43.3 1.0
O H:SER94 4.9 55.1 1.0
OD2 H:ASP92 4.9 66.1 1.0
N H:GLN98 5.0 49.9 1.0

Reference:

J.Wang, N.Vaddadi, J.S.Pak, Y.Park, S.Quilez, C.A.Roman, E.Dumontier, J.W.Thornton, J.F.Cloutier, E.Ozkan. Molecular and Structural Basis of Olfactory Sensory Neuron Axon Coalescence By Kirrel Receptors. Cell Rep V. 37 09940 2021.
ISSN: ESSN 2211-1247
PubMed: 34731636
DOI: 10.1016/J.CELREP.2021.109940
Page generated: Tue Oct 8 17:46:07 2024

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