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Sodium in PDB 6mkb: Crystal Structure of Murine 4-1BB Ligand

Protein crystallography data

The structure of Crystal Structure of Murine 4-1BB Ligand, PDB code: 6mkb was solved by A.Bitra, D.M.Zajonc, T.Doukov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.14 / 2.50
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 77.362, 77.362, 118.236, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 24.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Murine 4-1BB Ligand (pdb code 6mkb). 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 Murine 4-1BB Ligand, PDB code: 6mkb:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6mkb

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Sodium binding site 1 out of 6 in the Crystal Structure of Murine 4-1BB Ligand


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 Murine 4-1BB Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:69.9
occ:1.00
 O A:LEU164 2.5 57.4 1.0
O A:LYS188 2.7 63.5 1.0
N A:VAL271 3.1 57.8 1.0
NE1 A:TRP166 3.1 51.9 1.0
CD1 A:TRP166 3.4 52.9 1.0
O A:VAL271 3.4 60.8 1.0
CG2 A:THR163 3.4 57.8 1.0
C A:LEU164 3.6 57.0 1.0
CB A:LYS188 3.6 67.7 1.0
CB A:SER270 3.8 62.8 1.0
C A:LYS188 3.8 66.7 1.0
CA A:SER270 3.8 57.5 1.0
C A:SER270 3.9 61.0 1.0
CA A:VAL271 3.9 56.0 1.0
N A:LEU164 3.9 54.0 1.0
C A:VAL271 4.1 60.4 1.0
CA A:LEU164 4.2 52.4 1.0
CB A:VAL271 4.3 57.2 1.0
CA A:LYS188 4.3 66.8 1.0
CE2 A:TRP166 4.4 51.5 1.0
C A:THR163 4.5 59.2 1.0
CB A:LEU164 4.5 50.6 1.0
N A:ASN165 4.7 51.8 1.0
CG A:TRP166 4.7 48.8 1.0
CB A:THR163 4.8 61.1 1.0
OG A:SER270 4.8 71.2 1.0
CG2 A:VAL271 4.8 57.0 1.0
CG A:LYS188 4.9 68.6 1.0
OH A:TYR183 4.9 65.6 1.0
CA A:THR163 4.9 56.9 1.0
CD A:LYS188 5.0 76.7 1.0

Sodium binding site 2 out of 6 in 6mkb

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Sodium binding site 2 out of 6 in the Crystal Structure of Murine 4-1BB Ligand


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 Murine 4-1BB Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:65.2
occ:1.00
 O A:ASN293 2.6 54.5 1.0
O A:LYS205 2.6 48.6 1.0
OG A:SER207 2.8 57.9 1.0
N A:SER290 3.1 51.3 1.0
O A:SER290 3.3 54.8 1.0
O A:HOH506 3.4 46.9 1.0
C A:LYS205 3.5 50.1 1.0
O A:GLU288 3.6 53.3 1.0
CB A:SER207 3.6 49.0 1.0
CA A:LEU289 3.7 51.2 1.0
C A:ASN293 3.8 54.9 1.0
N A:SER207 3.8 45.1 1.0
C A:LEU289 3.9 54.1 1.0
CB A:ASN293 4.1 47.7 1.0
CA A:SER290 4.1 52.4 1.0
CB A:LYS205 4.1 50.6 1.0
C A:SER290 4.1 56.4 1.0
OG A:SER290 4.1 61.9 1.0
CA A:SER207 4.3 45.4 1.0
C A:LEU206 4.3 49.4 1.0
N A:LEU206 4.3 46.4 1.0
C A:GLU288 4.4 56.2 1.0
CA A:LYS205 4.4 48.0 1.0
CA A:LEU206 4.5 46.6 1.0
N A:LEU289 4.5 53.6 1.0
CA A:ASN293 4.5 51.1 1.0
CD1 A:LEU252 4.6 62.0 1.0
CB A:LEU289 4.7 50.9 1.0
CB A:SER290 4.7 56.6 1.0
N A:THR294 4.8 52.0 1.0
CD2 A:LEU289 4.8 57.8 1.0
OG1 A:THR295 4.9 44.5 1.0
N A:ASN293 5.0 52.8 1.0

Sodium binding site 3 out of 6 in 6mkb

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Sodium binding site 3 out of 6 in the Crystal Structure of Murine 4-1BB Ligand


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 Murine 4-1BB Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na408

b:92.6
occ:1.00
 O B:ASN293 2.6 52.2 1.0
OG B:SER207 2.7 56.8 1.0
O B:LYS205 2.8 49.3 1.0
N B:SER290 3.1 48.9 1.0
O B:SER290 3.3 56.0 1.0
O B:HOH535 3.4 44.9 1.0
CB B:SER207 3.5 47.2 1.0
C B:LYS205 3.6 48.8 1.0
O B:GLU288 3.6 48.3 1.0
C B:ASN293 3.7 53.9 1.0
CB B:ASN293 3.7 53.9 1.0
N B:SER207 3.7 45.0 1.0
CA B:LEU289 3.8 46.3 1.0
C B:LEU289 3.9 52.6 1.0
OG B:SER290 4.0 58.5 1.0
CA B:SER290 4.0 50.4 1.0
C B:SER290 4.1 56.3 1.0
CB B:LYS205 4.1 48.5 1.0
CA B:SER207 4.2 45.8 1.0
CA B:ASN293 4.3 50.9 1.0
C B:LEU206 4.3 47.5 1.0
N B:LEU206 4.4 43.4 1.0
C B:GLU288 4.4 49.6 1.0
CA B:LYS205 4.5 47.2 1.0
CA B:LEU206 4.5 44.0 1.0
N B:LEU289 4.5 46.4 1.0
CD1 B:LEU252 4.6 51.6 1.0
CB B:SER290 4.6 54.1 1.0
CB B:LEU289 4.8 45.8 1.0
N B:THR294 4.8 50.7 1.0
N B:ASN293 4.9 52.3 1.0
CG B:ASN293 4.9 73.0 1.0
CD2 B:LEU289 4.9 48.4 1.0
ND2 B:ASN293 5.0 63.4 1.0
OG1 B:THR295 5.0 42.8 1.0

Sodium binding site 4 out of 6 in 6mkb

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Sodium binding site 4 out of 6 in the Crystal Structure of Murine 4-1BB Ligand


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 Murine 4-1BB Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na404

b:54.7
occ:1.00
 O C:ASN293 2.6 52.4 1.0
O C:LYS205 2.7 47.8 1.0
OG C:SER207 2.8 58.2 1.0
N C:SER290 3.1 48.0 1.0
NA C:NA405 3.3 57.3 1.0
O C:SER290 3.4 55.7 1.0
C C:LYS205 3.5 48.2 1.0
CB C:SER207 3.6 48.6 1.0
O C:GLU288 3.6 49.8 1.0
CA C:LEU289 3.7 45.5 1.0
N C:SER207 3.7 46.7 1.0
C C:ASN293 3.8 53.7 1.0
C C:LEU289 3.9 50.9 1.0
CB C:ASN293 4.0 52.4 1.0
CA C:SER290 4.1 48.8 1.0
CB C:LYS205 4.1 46.7 1.0
OG C:SER290 4.1 50.8 1.0
C C:SER290 4.1 55.8 1.0
CA C:SER207 4.3 47.1 1.0
C C:LEU206 4.3 50.5 1.0
N C:LEU206 4.3 46.0 1.0
CA C:LYS205 4.4 44.6 1.0
C C:GLU288 4.4 50.3 1.0
CA C:ASN293 4.4 50.4 1.0
CA C:LEU206 4.4 47.2 1.0
N C:LEU289 4.5 46.4 1.0
CD1 C:LEU252 4.5 53.1 1.0
CB C:SER290 4.7 50.0 1.0
CB C:LEU289 4.7 44.8 1.0
N C:THR294 4.8 50.7 1.0
CD2 C:LEU289 4.8 46.6 1.0
OG1 C:THR295 4.9 44.6 1.0
N C:ASN293 5.0 52.1 1.0

Sodium binding site 5 out of 6 in 6mkb

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Sodium binding site 5 out of 6 in the Crystal Structure of Murine 4-1BB Ligand


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 Murine 4-1BB Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na405

b:57.3
occ:1.00
 O C:HOH540 2.5 40.0 1.0
N C:THR295 2.9 48.0 1.0
O C:ASN293 3.1 52.4 1.0
OG1 C:THR295 3.2 44.6 1.0
NA C:NA404 3.3 54.7 1.0
N C:SER290 3.3 48.0 1.0
CA C:THR294 3.4 50.7 1.0
CB C:LEU289 3.4 44.8 1.0
C C:LEU289 3.5 50.9 1.0
CA C:LEU289 3.5 45.5 1.0
CB C:THR295 3.5 46.9 1.0
O C:SER290 3.6 55.7 1.0
C C:THR294 3.6 53.9 1.0
O C:LYS205 3.8 47.8 1.0
CA C:THR295 3.8 46.0 1.0
C C:ASN293 4.0 53.7 1.0
C C:SER290 4.0 55.8 1.0
CA C:SER290 4.1 48.8 1.0
N C:THR294 4.1 50.7 1.0
CG2 C:THR294 4.3 49.6 1.0
O C:LEU289 4.3 51.4 1.0
CG C:LEU289 4.4 48.4 1.0
CD2 C:LEU289 4.4 46.6 1.0
CB C:THR294 4.5 53.1 1.0
CB C:ALA153 4.8 46.2 1.0
CB C:LYS205 4.8 46.7 1.0
CD1 C:LEU289 4.8 48.8 1.0
O C:THR294 4.8 54.5 1.0
C C:LYS205 4.9 48.2 1.0
N C:LEU289 4.9 46.4 1.0
CG2 C:THR295 4.9 34.9 1.0
C C:THR295 4.9 49.0 1.0
O C:ALA153 5.0 53.2 1.0
O C:THR295 5.0 48.7 1.0
N C:TYR291 5.0 54.5 1.0

Sodium binding site 6 out of 6 in 6mkb

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Sodium binding site 6 out of 6 in the Crystal Structure of Murine 4-1BB Ligand


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 Murine 4-1BB Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:66.5
occ:1.00
 O D:LYS205 2.5 45.7 1.0
O D:ASN293 2.7 54.1 1.0
OG D:SER207 3.0 57.6 1.0
N D:SER290 3.0 50.4 1.0
O D:HOH507 3.3 42.6 1.0
O D:SER290 3.4 54.9 1.0
O D:GLU288 3.5 53.4 1.0
C D:LYS205 3.5 47.5 1.0
CA D:LEU289 3.5 50.5 1.0
C D:LEU289 3.7 54.6 1.0
CB D:SER207 3.8 49.2 1.0
N D:SER207 3.8 45.7 1.0
C D:ASN293 3.9 54.6 1.0
CA D:SER290 4.1 51.5 1.0
CB D:LYS205 4.1 47.8 1.0
C D:SER290 4.2 55.9 1.0
OG D:SER290 4.2 58.4 1.0
CB D:ASN293 4.2 48.4 1.0
C D:GLU288 4.3 55.0 1.0
C D:LEU206 4.3 49.9 1.0
N D:LEU289 4.3 52.7 1.0
N D:LEU206 4.3 44.6 1.0
CA D:SER207 4.4 46.1 1.0
CA D:LEU206 4.4 45.6 1.0
CA D:LYS205 4.4 45.5 1.0
CB D:LEU289 4.5 49.9 1.0
CA D:ASN293 4.6 51.1 1.0
CD2 D:LEU289 4.6 58.4 1.0
OG1 D:THR295 4.7 47.5 1.0
CB D:SER290 4.7 54.5 1.0
CD1 D:LEU252 4.8 64.4 1.0
N D:THR294 4.9 51.3 1.0
O D:LEU289 4.9 56.8 1.0

Reference:

A.Bitra, T.Doukov, G.Destito, M.Croft, D.M.Zajonc. Crystal Structure of the M4-1BB/4-1BBL Complex Reveals An Unusual Dimeric Ligand That Undergoes Structural Changes Upon 4-1BB Receptor Binding. J. Biol. Chem. V. 294 1831 2019.
ISSN: ESSN 1083-351X
PubMed: 30545939
DOI: 10.1074/JBC.RA118.006297
Page generated: Tue Oct 8 11:57:16 2024

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