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Iodine in PDB 6y54: Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab

Protein crystallography data

The structure of Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab, PDB code: 6y54 was solved by L.Dello Iacono, P.Henriques, R.Adamo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.74 / 2.67
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.609, 153.205, 101.051, 90.00, 91.53, 90.00
R / Rfree (%) 21 / 26.7

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab (pdb code 6y54). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab, PDB code: 6y54:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 6y54

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Iodine binding site 1 out of 9 in the Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
H:I301

b:46.8
occ:0.88
 N H:TRP155 3.7 13.7 1.0
CA H:GLY158 3.9 56.4 1.0
CA H:THR154 4.2 41.3 1.0
CG2 H:VAL164 4.2 14.4 1.0
CA H:SER161 4.2 65.8 1.0
CB H:TRP155 4.3 16.9 1.0
CG1 H:VAL164 4.3 18.9 1.0
C H:THR154 4.4 44.5 1.0
CB H:VAL164 4.5 22.5 1.0
N H:SER161 4.5 69.2 1.0
O H:TRP155 4.5 28.6 1.0
C H:GLY158 4.5 62.8 1.0
CB H:THR154 4.5 46.2 1.0
CA H:TRP155 4.5 17.1 1.0
CD1 H:TRP155 4.6 16.2 1.0
N H:GLY158 4.7 59.2 1.0
O H:GLY158 4.7 68.5 1.0
C H:LEU160 4.7 45.7 1.0
O H:LEU160 4.7 42.9 1.0
OG H:SER161 4.8 51.3 1.0
O H:LEU153 4.8 46.1 1.0
CG H:TRP155 4.9 17.1 1.0
CB H:SER161 4.9 51.9 1.0
C H:TRP155 5.0 31.1 1.0

Iodine binding site 2 out of 9 in 6y54

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Iodine binding site 2 out of 9 in the Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
H:I302

b:61.7
occ:0.84
 OH H:TYR103 3.4 54.1 1.0
CA M:PRO201 3.8 55.2 1.0
O M:THR205 3.9 35.8 1.0
CG M:LYS206 4.0 39.2 1.0
N M:THR205 4.1 41.5 1.0
CA M:SER204 4.2 42.2 1.0
N M:PRO201 4.3 48.7 1.0
C M:THR205 4.3 36.7 1.0
C M:SER204 4.3 40.8 1.0
CZ H:TYR103 4.3 49.8 1.0
CE1 H:TYR103 4.3 46.5 1.0
CB M:PRO201 4.4 52.0 1.0
O M:HIS200 4.4 37.7 1.0
C M:HIS200 4.5 36.7 1.0
CB M:LYS206 4.5 41.8 1.0
CG M:PRO201 4.6 30.0 1.0
CD M:LYS206 4.7 39.8 1.0
CE M:LYS206 4.8 36.5 1.0
N M:LYS206 4.8 49.5 1.0
C M:PRO201 4.8 46.0 1.0
SD H:MET101 4.8 60.5 1.0
N M:HIS200 4.8 28.4 1.0
O M:PRO201 4.8 53.9 1.0
CB M:ALA199 4.8 29.8 1.0
CA M:THR205 4.9 40.6 1.0
CD M:PRO201 4.9 36.3 1.0

Iodine binding site 3 out of 9 in 6y54

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Iodine binding site 3 out of 9 in the Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
L:I301

b:41.8
occ:0.95
 CD L:ARG193 4.0 32.9 1.0
CA L:GLU190 4.0 35.1 1.0
CB L:GLU190 4.0 24.6 1.0
NE L:ARG193 4.1 41.2 1.0
N L:GLU190 4.1 39.1 1.0
NH1 L:ARG193 4.1 37.5 1.0
CZ L:ARG193 4.2 45.0 1.0
CG L:GLU190 4.3 30.1 1.0
C L:ASP189 4.4 54.2 1.0
O L:ASP189 4.4 53.3 1.0
CB L:ASP189 4.7 47.7 1.0
NH2 L:ARG193 4.9 47.2 1.0

Iodine binding site 4 out of 9 in 6y54

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Iodine binding site 4 out of 9 in the Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
L:I302

b:0.4
occ:1.00
 OD2 L:ASP170 4.0 70.4 1.0
CB L:PRO45 4.1 91.5 1.0
NZ L:LYS108 4.1 38.1 1.0
CG L:ASP170 4.2 56.0 1.0
CA L:GLY89 4.3 48.5 1.0
CD1 L:LEU88 4.3 48.5 1.0
CD L:PRO45 4.4 93.5 1.0
OD1 L:ASP170 4.5 63.0 1.0
CG L:PRO45 4.5 0.1 1.0
CA L:PRO45 4.5 84.2 1.0
CG2 L:VAL90 4.6 35.8 1.0
CB L:ASP170 4.6 40.8 1.0
C L:GLY89 4.7 47.1 1.0
CG L:LYS108 4.7 37.4 1.0
N L:PRO45 4.7 86.5 1.0
N L:GLY89 4.7 48.9 1.0
CD L:LYS108 4.8 37.3 1.0
N L:VAL90 4.9 41.3 1.0

Iodine binding site 5 out of 9 in 6y54

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Iodine binding site 5 out of 9 in the Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
M:I301

b:37.1
occ:0.68
 N M:TRP155 3.5 48.2 1.0
CA M:THR154 3.8 30.9 1.0
C M:THR154 4.2 41.1 1.0
CB M:THR154 4.2 42.5 1.0
CA M:SER161 4.2 52.0 1.0
CG1 M:VAL164 4.3 35.6 1.0
CG2 M:THR154 4.3 29.5 1.0
CA M:GLY158 4.3 52.6 1.0
CG2 M:VAL164 4.3 36.9 1.0
CB M:TRP155 4.4 31.5 1.0
O M:TRP155 4.4 52.6 1.0
CB M:SER161 4.4 52.5 1.0
CD1 M:TRP155 4.5 23.9 1.0
CA M:TRP155 4.5 37.1 1.0
N M:SER161 4.5 51.3 1.0
CB M:VAL164 4.6 40.9 1.0
O M:LEU153 4.7 53.7 1.0
C M:GLY158 4.7 61.1 1.0
O M:GLY158 4.8 68.0 1.0
N M:GLY158 4.8 58.3 1.0
CG M:TRP155 4.9 28.4 1.0
C M:LEU160 5.0 52.0 1.0
C M:TRP155 5.0 47.9 1.0
N M:THR154 5.0 28.1 1.0

Iodine binding site 6 out of 9 in 6y54

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Iodine binding site 6 out of 9 in the Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
M:I302

b:38.0
occ:0.47
 CB H:LYS23 4.1 38.0 1.0
CD H:LYS23 4.1 44.0 1.0
CB M:LYS23 4.2 29.0 1.0
CG2 H:THR78 4.2 33.5 1.0
CD M:LYS23 4.3 47.4 1.0
OG M:SER21 4.3 35.9 1.0
CB H:SER21 4.4 46.5 1.0
CB M:SER21 4.4 27.4 1.0
CG H:LYS23 4.5 46.5 1.0
OG H:SER21 4.6 38.0 1.0
OG1 M:THR78 4.7 42.1 1.0
CG2 M:THR78 4.7 47.7 1.0
CG M:LYS23 4.8 31.8 1.0

Iodine binding site 7 out of 9 in 6y54

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Iodine binding site 7 out of 9 in the Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
M:I303

b:59.4
occ:0.88
 OH M:TYR103 3.4 45.5 1.0
CA H:PRO201 3.8 43.8 1.0
O H:THR205 3.8 28.0 1.0
CE M:MET101 3.9 45.5 1.0
CB H:LYS206 4.0 33.2 1.0
CG H:LYS206 4.1 43.3 1.0
CA H:SER204 4.1 48.2 0.6
CA H:SER204 4.2 48.3 0.4
N H:PRO201 4.2 42.8 1.0
C H:SER204 4.2 44.1 1.0
N H:THR205 4.2 35.0 1.0
C H:THR205 4.2 24.5 1.0
CZ M:TYR103 4.3 42.9 1.0
CE1 M:TYR103 4.3 44.0 1.0
CB H:PRO201 4.4 41.1 1.0
CG H:PRO201 4.4 37.0 1.0
C H:HIS200 4.5 36.7 1.0
CD H:LYS206 4.5 35.5 1.0
O H:HIS200 4.6 37.1 1.0
CB H:ALA199 4.6 34.0 1.0
N H:HIS200 4.6 21.9 1.0
N H:LYS206 4.7 34.0 1.0
CD H:PRO201 4.7 40.2 1.0
O H:SER204 4.7 45.8 1.0
CA H:LYS206 4.8 36.5 1.0
CA H:THR205 4.9 22.5 1.0
C H:PRO201 5.0 43.4 1.0
N H:SER204 5.0 51.4 1.0

Iodine binding site 8 out of 9 in 6y54

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Iodine binding site 8 out of 9 in the Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
M:I304

b:58.6
occ:0.52
 C M:GLY26 4.0 44.0 1.0
CB H:ALA202 4.1 35.2 1.0
N M:TYR27 4.2 51.2 1.0
O M:GLY26 4.2 49.5 1.0
CA M:GLY26 4.3 40.8 1.0
CA H:ALA202 4.4 33.8 1.0
CA M:TYR27 4.4 41.5 1.0
C M:TYR27 4.7 56.1 1.0
O M:TYR27 4.8 62.0 1.0
O H:ALA202 4.8 43.8 1.0
CD2 H:LEU11 4.9 38.4 1.0
N M:GLY26 4.9 42.7 1.0
CB H:LEU11 4.9 25.7 1.0
CG2 H:THR117 4.9 34.0 1.0

Iodine binding site 9 out of 9 in 6y54

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Iodine binding site 9 out of 9 in the Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of A Neisseria Meningitidis Serogroup A Capsular Oligosaccharide Bound to A Functional Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
N:I301

b:43.9
occ:0.93
 CB N:GLU190 3.9 25.3 1.0
CA N:GLU190 4.1 38.7 1.0
CD N:ARG193 4.1 37.8 1.0
NH1 N:ARG193 4.1 25.3 1.0
O N:ASP189 4.1 57.7 1.0
N N:GLU190 4.3 36.1 1.0
C N:ASP189 4.3 46.0 1.0
NE N:ARG193 4.4 37.0 1.0
CZ N:ARG193 4.4 35.3 1.0
CG N:GLU190 4.5 40.8 1.0
CB N:ASP189 4.8 37.8 1.0

Reference:

P.Henriques, L.Dello Iacono, A.Gimeno, A.Biolchi, M.R.Romano, A.Arda, G.J.L.Bernardes, J.Jimenez-Barbero, F.Berti, R.Rappuoli, R.Adamo. Structure of A Protective Epitope Reveals the Importance of Acetylation of Neisseria Meningitidis Serogroup A Capsular Polysaccharide. Proc.Natl.Acad.Sci.Usa V. 117 29795 2020.
ISSN: ESSN 1091-6490
PubMed: 33158970
DOI: 10.1073/PNAS.2011385117
Page generated: Mon Aug 12 00:37:04 2024

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