Iodine in PDB 6b8o: Wt Ig-Like V Domain with Phosphatidylserine

Protein crystallography data

The structure of Wt Ig-Like V Domain with Phosphatidylserine, PDB code: 6b8o was solved by A.Sudom, Z.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.36 / 2.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 160.331, 160.331, 86.205, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 26.1

Iodine Binding Sites:

The binding sites of Iodine atom in the Wt Ig-Like V Domain with Phosphatidylserine (pdb code 6b8o). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Wt Ig-Like V Domain with Phosphatidylserine, PDB code: 6b8o:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 6b8o

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Iodine binding site 1 out of 7 in the Wt Ig-Like V Domain with Phosphatidylserine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Wt Ig-Like V Domain with Phosphatidylserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I202

b:36.3
occ:1.00
 N A:LEU71 3.6 37.2 1.0
N A:TRP70 3.7 34.9 1.0
CB A:LEU69 3.9 38.2 1.0
CA A:LEU69 4.0 39.6 1.0
CB A:LEU71 4.0 37.3 1.0
CG A:LEU71 4.0 36.8 1.0
C A:LEU69 4.0 37.1 1.0
CD2 A:LEU69 4.2 38.5 1.0
CD1 A:LEU71 4.3 35.6 1.0
CA A:LEU71 4.4 38.5 1.0
CA A:TRP70 4.5 36.1 1.0
C A:TRP70 4.6 40.6 1.0
CG A:LEU69 4.6 37.9 1.0
CB A:TRP70 4.7 36.9 1.0
O A:LEU69 4.9 40.3 1.0

Iodine binding site 2 out of 7 in 6b8o

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Iodine binding site 2 out of 7 in the Wt Ig-Like V Domain with Phosphatidylserine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Wt Ig-Like V Domain with Phosphatidylserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I203

b:52.8
occ:1.00
 OG A:SER35 3.3 46.0 1.0
N C:ASN99 3.5 43.7 1.0
CD A:PRO37 3.6 43.7 1.0
N C:SER31 3.7 39.4 1.0
CB A:PRO37 3.8 39.3 1.0
CB C:SER31 3.8 39.8 1.0
CG A:PRO37 3.9 43.5 1.0
N A:PRO37 3.9 42.6 1.0
CA C:ASN99 4.0 44.1 1.0
CB A:SER35 4.0 39.9 1.0
CG C:ARG98 4.0 42.0 1.0
C C:GLN30 4.1 42.4 1.0
CA C:SER31 4.2 45.3 1.0
O A:SER35 4.2 38.7 1.0
C A:SER35 4.3 42.4 1.0
O C:GLY29 4.3 42.9 1.0
CA C:GLN30 4.3 46.1 1.0
CA A:PRO37 4.3 41.4 1.0
CG2 A:THR92 4.4 42.4 1.0
C A:CYS36 4.4 46.6 1.0
CB C:ASN99 4.5 42.7 1.0
C C:ARG98 4.5 44.3 1.0
N A:CYS36 4.5 42.4 1.0
CA C:ARG98 4.7 38.5 1.0
O C:GLN30 4.7 41.7 1.0
OG C:SER31 4.7 56.8 1.0
NH1 A:ARG122 4.7 48.7 1.0
CA A:CYS36 4.8 46.1 1.0
CA A:SER35 4.8 40.7 1.0
OG1 A:THR92 4.8 45.1 1.0
C C:GLY29 5.0 51.7 1.0
CB C:ARG98 5.0 38.0 1.0

Iodine binding site 3 out of 7 in 6b8o

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Iodine binding site 3 out of 7 in the Wt Ig-Like V Domain with Phosphatidylserine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Wt Ig-Like V Domain with Phosphatidylserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I204

b:58.1
occ:1.00
 OG A:SER31 2.9 64.8 1.0
N A:ASN99 3.4 34.4 1.0
CB B:SER35 3.6 53.6 1.0
CG B:PRO37 3.7 49.2 1.0
OG B:SER35 3.8 57.4 1.0
N B:PRO37 3.8 44.9 1.0
CB B:PRO37 3.8 48.1 1.0
CG A:ARG98 3.9 43.9 1.0
N A:SER31 3.9 42.8 1.0
CD B:PRO37 3.9 47.1 1.0
CG2 B:THR92 4.1 42.4 1.0
CA A:ASN99 4.1 39.3 1.0
CB A:SER31 4.1 45.8 1.0
C A:GLN30 4.2 48.0 1.0
CA B:PRO37 4.2 45.0 1.0
CA A:SER31 4.3 41.2 1.0
C B:SER35 4.3 47.6 1.0
C B:CYS36 4.3 53.6 1.0
N B:CYS36 4.4 48.4 1.0
C A:ARG98 4.4 45.9 1.0
CA A:ARG98 4.5 42.2 1.0
CA A:GLN30 4.5 42.8 1.0
O A:GLY29 4.6 45.7 1.0
CB A:ASN99 4.6 38.6 1.0
O B:SER35 4.6 55.8 1.0
CA B:SER35 4.6 52.0 1.0
OG1 B:THR92 4.6 46.3 1.0
CA B:CYS36 4.8 52.0 1.0
CB A:ARG98 4.8 41.9 1.0
O A:GLN30 4.9 52.4 1.0
CD A:ARG98 4.9 44.6 1.0

Iodine binding site 4 out of 7 in 6b8o

Go back to Iodine Binding Sites List in 6b8o
Iodine binding site 4 out of 7 in the Wt Ig-Like V Domain with Phosphatidylserine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Wt Ig-Like V Domain with Phosphatidylserine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I202

b:40.3
occ:1.00
 N B:LEU71 3.7 37.1 1.0
N B:TRP70 3.7 34.0 1.0
CB B:LEU69 3.9 42.5 1.0
CG B:LEU71 3.9 38.8 1.0
CA B:LEU69 4.0 40.9 1.0
CB B:LEU71 4.0 37.5 1.0
C B:LEU69 4.1 38.5 1.0
CD1 B:LEU71 4.1 40.3 1.0
CD2 B:LEU69 4.4 45.3 1.0
CA B:LEU71 4.5 36.4 1.0
CA B:TRP70 4.6 35.5 1.0
C B:TRP70 4.6 35.4 1.0
CG B:LEU69 4.7 41.7 1.0
O B:LEU69 4.8 41.1 1.0
CB B:TRP70 4.8 37.1 1.0

Iodine binding site 5 out of 7 in 6b8o

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Iodine binding site 5 out of 7 in the Wt Ig-Like V Domain with Phosphatidylserine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Wt Ig-Like V Domain with Phosphatidylserine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I203

b:57.5
occ:1.00
 N B:ASN99 3.5 45.4 1.0
OG C:SER35 3.7 50.1 1.0
N B:SER31 3.7 52.7 1.0
CB C:PRO37 3.8 45.7 1.0
CB C:SER35 3.8 48.3 1.0
CB B:SER31 3.8 46.9 1.0
CD C:PRO37 3.8 44.0 1.0
N C:PRO37 3.9 40.6 1.0
CG C:PRO37 4.0 47.3 1.0
CG2 C:THR92 4.1 46.3 1.0
CA B:ASN99 4.1 51.4 1.0
CG B:ARG98 4.1 37.3 1.0
C B:GLN30 4.1 48.5 1.0
CA B:SER31 4.1 47.7 1.0
CA C:PRO37 4.2 43.8 1.0
CA B:GLN30 4.4 46.9 1.0
C C:SER35 4.4 44.5 1.0
C B:ARG98 4.5 42.2 1.0
CB B:ASN99 4.5 55.6 1.0
C C:CYS36 4.5 39.7 1.0
OG1 C:THR92 4.5 49.4 1.0
CA B:ARG98 4.5 41.1 1.0
N C:CYS36 4.6 44.0 1.0
O C:SER35 4.6 45.3 1.0
O B:GLY29 4.7 50.7 1.0
O B:GLN30 4.7 40.4 1.0
CA C:SER35 4.7 46.6 1.0
CB B:ARG98 4.8 39.8 1.0
CB C:THR92 5.0 45.0 1.0
CA C:CYS36 5.0 41.7 1.0

Iodine binding site 6 out of 7 in 6b8o

Go back to Iodine Binding Sites List in 6b8o
Iodine binding site 6 out of 7 in the Wt Ig-Like V Domain with Phosphatidylserine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Wt Ig-Like V Domain with Phosphatidylserine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I202

b:35.1
occ:1.00
 N C:LEU71 3.6 36.6 1.0
N C:TRP70 3.7 34.7 1.0
CB C:LEU69 4.0 36.9 1.0
CB C:LEU71 4.0 34.5 1.0
CA C:LEU69 4.0 36.8 1.0
C C:LEU69 4.0 33.8 1.0
CG C:LEU71 4.0 36.8 1.0
CD1 C:LEU71 4.3 37.0 1.0
CA C:LEU71 4.4 37.0 1.0
CA C:TRP70 4.5 37.6 1.0
CD2 C:LEU69 4.5 41.6 1.0
C C:TRP70 4.5 39.6 1.0
CG C:LEU69 4.7 36.2 1.0
CB C:TRP70 4.8 37.1 1.0
O C:LEU69 4.8 38.6 1.0

Iodine binding site 7 out of 7 in 6b8o

Go back to Iodine Binding Sites List in 6b8o
Iodine binding site 7 out of 7 in the Wt Ig-Like V Domain with Phosphatidylserine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Wt Ig-Like V Domain with Phosphatidylserine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I202

b:74.8
occ:1.00
 NH2 E:ARG76 3.4 59.2 1.0
OG E:SER31 3.6 54.5 1.0
NH2 E:ARG98 3.9 97.2 1.0
CA C:LYS42 4.0 46.3 1.0
NE2 E:GLN33 4.0 56.6 1.0
CG2 E:THR96 4.1 52.4 1.0
NE E:ARG98 4.1 86.3 1.0
N C:LYS42 4.1 47.2 1.0
CB E:SER31 4.3 57.4 1.0
O C:MET41 4.3 48.6 1.0
C C:MET41 4.3 43.9 1.0
CZ E:ARG76 4.4 63.3 1.0
CZ E:ARG98 4.5 96.8 1.0
CB C:LYS42 4.6 58.0 1.0
NH1 E:ARG76 4.6 55.8 1.0
CB C:MET41 4.6 50.6 1.0

Reference:

A.Sudom, S.Talreja, J.Danao, E.Bragg, R.Kegel, X.Min, J.Richardson, Z.Zhang, N.Sharkov, E.Marcora, S.Thibault, J.Bradley, S.Wood, A.C.Lim, H.Chen, S.Wang, I.N.Foltz, S.Sambashivan, Z.Wang. Molecular Basis For the Loss-of-Function Effects of the Alzheimer'S Disease-Associated R47H Variant of the Immune Receptor TREM2. J. Biol. Chem. V. 293 12634 2018.
ISSN: ESSN 1083-351X
PubMed: 29794134
DOI: 10.1074/JBC.RA118.002352
Page generated: Sun Dec 13 19:42:50 2020

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