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Sodium in PDB 6mjj: Crystal Structure of the MCD1D/Xxm (JJ290) /Inktcr Ternary Complex

Protein crystallography data

The structure of Crystal Structure of the MCD1D/Xxm (JJ290) /Inktcr Ternary Complex, PDB code: 6mjj was solved by D.M.Zajonc, A.Bitra, J.Janssens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.87 / 1.93
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 78.999, 191.279, 151.264, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 21.6

Other elements in 6mjj:

The structure of Crystal Structure of the MCD1D/Xxm (JJ290) /Inktcr Ternary Complex also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the MCD1D/Xxm (JJ290) /Inktcr Ternary Complex (pdb code 6mjj). 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 MCD1D/Xxm (JJ290) /Inktcr Ternary Complex, PDB code: 6mjj:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 6mjj

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Sodium binding site 1 out of 9 in the Crystal Structure of the MCD1D/Xxm (JJ290) /Inktcr Ternary Complex


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 MCD1D/Xxm (JJ290) /Inktcr Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na605

b:40.8
occ:1.00
 O C:LEU99 2.7 18.7 1.0
O D:HOH474 2.7 30.7 1.0
NE C:ARG101 3.1 24.0 1.0
C C:LEU99 3.4 18.8 1.0
CG A:GLU83 3.5 19.6 1.0
CD C:ARG101 3.6 22.9 1.0
CD A:GLU83 3.6 19.9 1.0
O C:GLY100 3.7 20.2 1.0
OE2 A:GLU83 3.7 21.0 1.0
O C:HOH829 3.8 21.5 1.0
CG C:ARG101 3.9 22.1 1.0
OH D:TYR50 3.9 21.8 1.0
O A:HOH441 4.0 22.9 1.0
C C:GLY100 4.0 19.9 1.0
CA C:LEU99 4.1 19.6 1.0
CZ C:ARG101 4.1 24.3 1.0
OE1 A:GLU83 4.1 20.6 1.0
N C:GLY100 4.2 19.0 1.0
NH2 A:ARG79 4.3 19.1 1.0
NH2 C:ARG101 4.3 24.4 1.0
NE A:ARG79 4.4 19.6 1.0
N C:ARG101 4.4 19.3 1.0
O C:ALA98 4.5 21.1 1.0
CB A:GLU83 4.5 19.3 1.0
CA C:GLY100 4.5 19.6 1.0
CZ A:ARG79 4.5 20.0 1.0
O C:HOH797 4.8 20.6 1.0
OH D:TYR48 4.9 18.7 1.0
CA C:ARG101 4.9 19.6 1.0
CB C:ARG101 5.0 20.5 1.0
CB C:LEU99 5.0 20.4 1.0

Sodium binding site 2 out of 9 in 6mjj

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Sodium binding site 2 out of 9 in the Crystal Structure of the MCD1D/Xxm (JJ290) /Inktcr Ternary Complex


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 MCD1D/Xxm (JJ290) /Inktcr Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na606

b:47.3
occ:1.00
 O C:PHE104 2.8 17.7 1.0
O C:HOH728 2.8 30.5 1.0
O2 C:GOL609 2.8 63.8 1.0
OG1 C:THR2 2.9 44.8 1.0
O C:VAL4 3.4 21.1 1.0
O1 C:GOL609 3.5 66.8 1.0
CG2 C:THR2 3.7 44.0 1.0
CB C:THR2 3.7 43.6 1.0
N C:ALA106 3.7 18.9 1.0
CA C:GLY105 3.8 19.2 1.0
C1 C:GOL609 3.8 65.0 1.0
C C:PHE104 3.8 18.3 1.0
C C:GLY105 3.9 19.1 1.0
C2 C:GOL609 3.9 65.9 1.0
O C:HOH838 3.9 52.1 1.0
N D:GLY42 4.0 23.4 1.0
O D:HOH472 4.2 45.3 1.0
N C:GLY105 4.3 18.6 1.0
CA D:GLY42 4.4 23.0 1.0
CB C:ALA106 4.4 20.9 1.0
CA C:ALA106 4.5 20.3 1.0
C C:VAL4 4.6 21.6 1.0
O C:GLY105 4.6 18.7 1.0
C3 C:GOL609 4.7 66.6 1.0
CB C:VAL4 4.9 21.0 1.0
N C:VAL4 5.0 22.2 1.0
C D:HIS41 5.0 25.1 1.0

Sodium binding site 3 out of 9 in 6mjj

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Sodium binding site 3 out of 9 in the Crystal Structure of the MCD1D/Xxm (JJ290) /Inktcr Ternary Complex


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 MCD1D/Xxm (JJ290) /Inktcr Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na607

b:47.5
occ:1.00
 N C:VAL20 3.5 23.6 1.0
O C:VAL20 3.5 23.0 1.0
O C:HOH716 3.6 24.3 1.0
CB C:CYS19 3.8 26.2 1.0
CD1 C:LEU11 3.9 20.3 1.0
CA C:CYS19 4.0 25.0 1.0
C C:CYS19 4.2 24.0 1.0
C C:VAL20 4.3 23.6 1.0
CA C:VAL20 4.3 24.2 1.0
CB C:VAL20 4.7 25.3 1.0
O C:HOH739 4.7 41.5 1.0

Sodium binding site 4 out of 9 in 6mjj

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Sodium binding site 4 out of 9 in the Crystal Structure of the MCD1D/Xxm (JJ290) /Inktcr Ternary Complex


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 MCD1D/Xxm (JJ290) /Inktcr Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na608

b:41.2
occ:1.00
 OG C:SER46 2.9 21.2 1.0
CB C:SER46 3.7 21.1 1.0
N C:THR48 3.7 21.3 1.0
O C:HOH826 3.7 54.0 1.0
C C:LEU47 3.8 21.0 1.0
O C:SER46 3.8 20.4 1.0
C C:SER46 3.9 20.9 1.0
CA C:THR48 3.9 21.8 1.0
O C:LEU47 3.9 21.2 1.0
O C:HOH764 4.2 57.4 1.0
NH1 C:ARG34 4.2 22.1 1.0
N C:LEU47 4.2 20.2 1.0
C C:THR48 4.2 21.1 1.0
O C:HOH814 4.3 40.5 1.0
CA C:SER46 4.4 20.4 1.0
CA C:LEU47 4.5 20.3 1.0
N C:VAL49 4.5 20.8 0.5
N C:VAL49 4.6 20.7 0.5
CG2 C:VAL49 4.6 21.7 0.5
O C:HOH742 4.7 41.9 1.0
O C:THR48 4.8 20.3 1.0

Sodium binding site 5 out of 9 in 6mjj

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Sodium binding site 5 out of 9 in the Crystal Structure of the MCD1D/Xxm (JJ290) /Inktcr Ternary Complex


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 MCD1D/Xxm (JJ290) /Inktcr Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na610

b:27.8
occ:1.00
 O A:HOH406 2.5 34.3 1.0
NA A:NA309 2.8 28.4 1.0
O C:GLY96 2.9 20.4 1.0
O A:ALA152 3.0 18.8 1.0
N A:GLN154 3.3 21.1 1.0
CA C:GLY96 3.7 19.1 1.0
C C:GLY96 3.7 19.1 1.0
CB A:GLN154 3.9 25.6 1.0
CE2 D:TYR98 3.9 23.3 1.0
CG A:GLN154 3.9 28.8 1.0
CD2 D:TYR98 3.9 22.1 1.0
CA A:ASP153 3.9 19.1 1.0
O A:HOH423 4.0 31.8 1.0
O A:HOH607 4.0 34.5 1.0
O2 D:GOL301 4.1 45.7 1.0
C A:ALA152 4.1 18.9 1.0
C A:ASP153 4.1 19.9 1.0
CA A:GLN154 4.2 22.5 1.0
OE1 A:GLN154 4.3 34.9 1.0
O D:HOH577 4.3 34.5 1.0
N A:ASP153 4.5 18.3 1.0
OD1 A:ASP153 4.5 17.9 1.0
CD A:GLN154 4.6 32.0 1.0
C1 D:GOL301 4.6 47.5 1.0
N A:GLY155 4.6 19.9 1.0
C2 D:GOL301 4.9 44.8 1.0
ND2 C:ASN31 4.9 18.5 1.0
C A:GLN154 5.0 21.1 1.0
OD1 C:ASN31 5.0 19.2 1.0

Sodium binding site 6 out of 9 in 6mjj

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Sodium binding site 6 out of 9 in the Crystal Structure of the MCD1D/Xxm (JJ290) /Inktcr Ternary Complex


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 MCD1D/Xxm (JJ290) /Inktcr Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na302

b:32.6
occ:1.00
 O D:HOH565 2.4 36.0 1.0
OH D:TYR33 2.8 20.1 1.0
O D:ASP95 2.9 19.8 1.0
C D:GLY94 3.4 18.7 1.0
CA D:GLY94 3.5 18.8 1.0
CB C:ALA98 3.6 19.3 1.0
ND2 D:ASN31 3.6 18.9 1.0
O D:GLY94 3.7 18.6 1.0
CZ D:TYR33 3.7 19.7 1.0
O D:GLY97 3.7 18.9 1.0
CE1 D:TYR33 3.7 19.4 1.0
CB D:ASN31 3.8 19.2 1.0
N D:ASP95 3.9 18.9 1.0
O D:HOH440 4.0 20.9 1.0
N D:GLY94 4.0 18.7 1.0
C D:ASP95 4.0 19.9 1.0
CA C:ALA98 4.1 19.3 1.0
O D:HOH572 4.1 31.1 1.0
CG D:ASN31 4.2 19.6 1.0
O D:THR99 4.2 20.6 1.0
CA D:ASP95 4.5 20.1 1.0
CG D:GLN100 4.6 18.5 1.0
C D:SER93 4.9 18.7 1.0
C D:GLY97 4.9 19.8 1.0
O C:ALA98 5.0 21.1 1.0
CE2 D:TYR33 5.0 19.1 1.0
O D:ASN31 5.0 18.7 1.0

Sodium binding site 7 out of 9 in 6mjj

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Sodium binding site 7 out of 9 in the Crystal Structure of the MCD1D/Xxm (JJ290) /Inktcr Ternary Complex


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 MCD1D/Xxm (JJ290) /Inktcr Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na303

b:62.3
occ:1.00
 O D:HOH560 2.6 48.6 1.0
NZ D:LYS65 3.7 39.8 1.0
OE1 D:GLU79 3.7 47.8 1.0
NZ D:LYS18 3.8 40.8 1.0
OE2 D:GLU79 3.8 48.8 1.0
CE D:LYS18 4.2 39.2 1.0
CD D:GLU79 4.2 44.8 1.0
CD1 D:ILE77 4.2 32.5 1.0
CG2 D:ILE77 4.4 30.0 1.0
CD D:LYS65 4.6 36.0 1.0
CE D:LYS65 4.7 38.0 1.0

Sodium binding site 8 out of 9 in 6mjj

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Sodium binding site 8 out of 9 in the Crystal Structure of the MCD1D/Xxm (JJ290) /Inktcr Ternary Complex


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 MCD1D/Xxm (JJ290) /Inktcr Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na304

b:63.3
occ:1.00
 OG D:SER128 3.2 37.0 1.0
N C:GLN125 3.6 33.1 1.0
O C:GLN125 3.8 32.8 1.0
CB D:ALA130 3.9 32.4 1.0
CG C:PRO203 4.0 56.4 1.0
CB D:SER128 4.1 34.1 1.0
CB C:GLN125 4.1 36.5 1.0
CA C:GLN125 4.3 34.7 1.0
C C:GLN125 4.5 33.7 1.0
CA C:TYR124 4.5 32.5 1.0
C C:TYR124 4.5 32.5 1.0
O C:HOH719 4.6 41.5 1.0
O D:HOH587 4.6 43.7 1.0
CB C:TYR124 4.8 32.1 1.0
CB C:PRO203 4.8 56.8 1.0
N D:ALA130 4.9 31.0 1.0
CD1 C:TYR124 4.9 31.7 1.0

Sodium binding site 9 out of 9 in 6mjj

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Sodium binding site 9 out of 9 in the Crystal Structure of the MCD1D/Xxm (JJ290) /Inktcr Ternary Complex


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 MCD1D/Xxm (JJ290) /Inktcr Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na309

b:28.4
occ:1.00
 O A:HOH607 2.6 34.5 1.0
NA C:NA610 2.8 27.8 1.0
ND2 C:ASN31 2.9 18.5 1.0
N A:GLY155 3.1 19.9 1.0
O C:HOH800 3.5 50.1 1.0
O3 A:JU4308 3.7 20.1 1.0
CA A:GLY155 3.7 19.7 1.0
OD1 A:ASP153 3.8 17.9 1.0
N A:GLN154 3.8 21.1 1.0
CG C:ASN31 3.8 18.9 1.0
CA C:GLY96 3.9 19.1 1.0
OD1 C:ASN31 3.9 19.2 1.0
CAY A:JU4308 4.0 35.9 1.0
C A:GLN154 4.0 21.1 1.0
CB A:GLN154 4.1 25.6 1.0
CA A:GLN154 4.2 22.5 1.0
CAZ A:JU4308 4.3 33.3 1.0
O A:HOH406 4.4 34.3 1.0
O D:HOH577 4.5 34.5 1.0
C A:ASP153 4.5 19.9 1.0
O C:GLY96 4.7 20.4 1.0
N C:GLY96 4.8 18.7 1.0
C C:GLY96 4.8 19.1 1.0
CA A:ASP153 4.8 19.1 1.0
CAX A:JU4308 4.8 38.7 1.0
CG A:ASP153 4.9 18.4 1.0
CG A:GLN154 5.0 28.8 1.0
O C:HOH850 5.0 43.0 1.0
CE2 D:TYR98 5.0 23.3 1.0

Reference:

J.Janssens, A.Bitra, J.Wang, T.Decruy, K.Venken, J.Van Der Eycken, D.Elewaut, D.M.Zajonc, S.Van Calenbergh. 4"-O-Alkylated Alpha-Galactosylceramide Analogues As Inkt-Cell Antigens: Synthetic, Biological, and Structural Studies. Chemmedchem V. 14 147 2019.
ISSN: ESSN 1860-7187
PubMed: 30556652
DOI: 10.1002/CMDC.201800649
Page generated: Tue Oct 8 11:56:44 2024

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