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Iodine in PDB 6ldv: Structure Antibody F9 in Complex with Methylated Peptide

Protein crystallography data

The structure of Structure Antibody F9 in Complex with Methylated Peptide, PDB code: 6ldv was solved by J.M.M.Caaveiro, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.32 / 1.90
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.764, 63.526, 125.856, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 22.9

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Iodine atom in the Structure Antibody F9 in Complex with Methylated Peptide (pdb code 6ldv). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 11 binding sites of Iodine where determined in the Structure Antibody F9 in Complex with Methylated Peptide, PDB code: 6ldv:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in 6ldv

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Iodine binding site 1 out of 11 in the Structure Antibody F9 in Complex with Methylated Peptide


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure Antibody F9 in Complex with Methylated Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:I301

b:23.1
occ:0.80
 N H:LEU10 3.6 16.2 1.0
CB H:ARG9 3.7 22.1 1.0
CB H:LEU10 4.1 17.5 1.0
CA H:ARG9 4.1 18.2 1.0
CG H:PRO117 4.2 16.7 1.0
CB H:ALA200 4.2 17.9 1.0
CD H:PRO148 4.2 14.7 1.0
O H:ALA200 4.3 15.9 1.0
CG H:PRO148 4.4 15.3 1.0
C H:ARG9 4.4 18.7 1.0
CA H:LEU10 4.5 17.1 1.0
O H:HOH469 4.6 15.8 1.0
O H:LEU10 4.6 16.5 1.0
CA H:ALA200 4.7 17.4 1.0
CB H:PRO117 4.8 16.2 1.0
C H:ALA200 4.8 16.8 1.0
CG H:ARG9 4.8 24.2 1.0

Iodine binding site 2 out of 11 in 6ldv

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Iodine binding site 2 out of 11 in the Structure Antibody F9 in Complex with Methylated Peptide


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure Antibody F9 in Complex with Methylated Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:I302

b:26.3
occ:0.60
 OG H:SER30 3.3 25.3 1.0
CB H:SER27 4.2 18.9 1.0
CB H:SER30 4.2 21.8 1.0
CG2 P:THR12 4.7 27.4 1.0

Iodine binding site 3 out of 11 in 6ldv

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Iodine binding site 3 out of 11 in the Structure Antibody F9 in Complex with Methylated Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure Antibody F9 in Complex with Methylated Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:I303

b:25.4
occ:0.60
 I H:IOD303 0.0 25.4 0.6
I H:IOD303 1.9 38.3 0.2
OE1 H:GLN172 3.1 57.2 1.0
O H:HOH527 3.4 16.2 0.6
N H:GLY145 3.6 19.3 1.0
CD H:GLN172 3.7 57.5 1.0
CG H:GLN172 3.9 50.8 1.0
CA H:GLY145 4.0 19.3 1.0
CB H:GLN172 4.0 48.4 1.0
CB H:LYS144 4.1 23.1 1.0
O H:TYR177 4.1 16.6 1.0
CE H:LYS144 4.2 28.9 1.0
CB H:LEU176 4.2 21.2 1.0
CB H:SER178 4.3 18.9 1.0
O H:LEU176 4.4 25.2 1.0
C H:TYR177 4.5 18.1 1.0
C H:LEU176 4.5 23.3 1.0
C H:LYS144 4.6 18.8 1.0
CA H:LYS144 4.6 19.6 1.0
OG H:SER174 4.7 46.3 1.0
NE2 H:GLN172 4.7 58.4 1.0
CG H:LYS144 4.8 24.6 1.0
N H:TYR177 4.8 22.1 1.0
O H:HOH560 4.9 20.1 0.6
OG H:SER178 4.9 24.6 1.0
N H:SER178 5.0 17.4 1.0

Iodine binding site 4 out of 11 in 6ldv

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Iodine binding site 4 out of 11 in the Structure Antibody F9 in Complex with Methylated Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure Antibody F9 in Complex with Methylated Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:I303

b:38.3
occ:0.25
 I H:IOD303 0.0 38.3 0.2
I H:IOD303 1.9 25.4 0.6
O H:HOH527 3.2 16.2 0.6
CE H:LYS144 3.7 28.9 1.0
CA H:GLY145 3.7 19.3 1.0
I H:IOD305 3.7 46.4 0.2
N H:GLY145 3.9 19.3 1.0
CD1 H:LEU176 4.2 20.4 1.0
CB H:LEU176 4.5 21.2 1.0
OG H:SER174 4.5 46.3 1.0
CB H:LYS144 4.5 23.1 1.0
O H:HOH560 4.6 20.1 0.6
NZ H:LYS144 4.6 28.4 1.0
CG H:LYS144 4.6 24.6 1.0
C H:LYS144 4.7 18.8 1.0
CD H:LYS144 4.8 27.0 1.0
OE1 H:GLN172 4.9 57.2 1.0
CG H:LEU176 5.0 20.0 1.0

Iodine binding site 5 out of 11 in 6ldv

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Iodine binding site 5 out of 11 in the Structure Antibody F9 in Complex with Methylated Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure Antibody F9 in Complex with Methylated Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:I304

b:41.8
occ:0.70
 CD H:LYS204 3.8 34.4 1.0
CA H:ASN202 3.8 20.1 1.0
CA H:PRO199 3.9 17.7 1.0
C H:ASN202 3.9 18.3 1.0
O H:THR203 4.1 15.5 1.0
CB H:ALA197 4.2 16.1 1.0
N H:THR203 4.2 16.6 1.0
N H:PRO199 4.2 17.5 1.0
CG H:LYS204 4.2 29.4 1.0
O H:ASN202 4.4 17.7 1.0
C H:HIS198 4.4 16.3 1.0
O H:HIS198 4.4 16.5 1.0
N H:HIS198 4.6 15.1 1.0
C H:THR203 4.6 16.6 1.0
CB H:PRO199 4.6 18.9 1.0
CB H:ASN202 4.7 24.0 1.0
CE H:LYS204 4.8 40.1 1.0
N H:ASN202 4.8 17.8 1.0
CA H:ALA197 4.8 15.8 1.0
CG H:PRO199 4.9 19.6 1.0
O H:HOH407 4.9 35.2 1.0
O H:HOH525 4.9 25.9 0.6
CD H:PRO199 4.9 17.9 1.0
C H:PRO199 5.0 17.2 1.0
O H:PRO199 5.0 16.2 1.0

Iodine binding site 6 out of 11 in 6ldv

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Iodine binding site 6 out of 11 in the Structure Antibody F9 in Complex with Methylated Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure Antibody F9 in Complex with Methylated Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:I305

b:38.7
occ:0.50
 I H:IOD305 0.0 38.7 0.5
I H:IOD305 2.7 46.4 0.2
O L:HOH555 2.9 22.4 1.0
OG H:SER121 3.7 17.9 1.0
CB H:SER121 3.8 17.4 1.0
CZ H:PHE123 4.0 14.7 1.0
CE2 H:PHE123 4.1 15.3 1.0
CG2 L:THR131 4.2 17.7 1.0
CG H:LYS144 4.5 24.6 1.0
CB L:THR131 4.6 17.9 1.0
O H:HOH406 4.7 22.6 1.0
CE H:LYS144 4.7 28.9 1.0
CD H:LYS144 4.7 27.0 1.0
OG1 L:THR131 4.9 17.2 1.0

Iodine binding site 7 out of 11 in 6ldv

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Iodine binding site 7 out of 11 in the Structure Antibody F9 in Complex with Methylated Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure Antibody F9 in Complex with Methylated Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:I305

b:46.4
occ:0.20
 I H:IOD305 0.0 46.4 0.2
I H:IOD305 2.7 38.7 0.5
NZ H:LYS118 3.2 29.4 1.0
CA H:GLY145 3.6 19.3 1.0
I H:IOD303 3.7 38.3 0.2
O H:HOH406 4.0 22.6 1.0
O L:HOH555 4.1 22.4 1.0
CE H:LYS118 4.2 28.0 1.0
N H:GLY145 4.3 19.3 1.0
O H:LYS144 4.5 17.9 1.0
C H:LYS144 4.6 18.8 1.0
O H:GLY145 4.6 18.8 1.0
CG H:LYS144 4.7 24.6 1.0
OG H:SER121 4.7 17.9 1.0
C H:GLY145 4.7 18.0 1.0
CD1 H:LEU176 4.7 20.4 1.0
CE H:LYS144 4.7 28.9 1.0
CB H:SER121 4.9 17.4 1.0

Iodine binding site 8 out of 11 in 6ldv

Go back to Iodine Binding Sites List in 6ldv
Iodine binding site 8 out of 11 in the Structure Antibody F9 in Complex with Methylated Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure Antibody F9 in Complex with Methylated Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
L:I301

b:41.6
occ:0.50
 I L:IOD301 0.0 41.6 0.5
I L:IOD301 2.8 50.8 0.3
N L:ALA14 3.4 21.2 1.0
O L:HOH487 3.5 27.2 1.0
CB L:ALA14 3.8 22.8 1.0
CA L:ALA13 4.1 22.8 1.0
CA L:ALA14 4.2 22.0 1.0
C L:ALA13 4.3 22.1 1.0
CB L:ALA13 4.3 23.0 1.0
I L:IOD303 4.4 50.0 0.5
CA L:GLY17 4.8 19.8 1.0
O L:ALA14 4.8 19.8 1.0

Iodine binding site 9 out of 11 in 6ldv

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Iodine binding site 9 out of 11 in the Structure Antibody F9 in Complex with Methylated Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure Antibody F9 in Complex with Methylated Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
L:I301

b:50.8
occ:0.30
 I L:IOD301 0.0 50.8 0.3
I L:IOD301 2.8 41.6 0.5
O L:HOH487 3.6 27.2 1.0
O L:HOH497 4.1 30.1 1.0
I L:IOD303 4.3 50.0 0.5
O L:SER12 4.5 24.4 1.0
CB L:ALA13 4.6 23.0 1.0
CA L:ALA13 4.6 22.8 1.0
O L:THR18 4.9 19.0 1.0

Iodine binding site 10 out of 11 in 6ldv

Go back to Iodine Binding Sites List in 6ldv
Iodine binding site 10 out of 11 in the Structure Antibody F9 in Complex with Methylated Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure Antibody F9 in Complex with Methylated Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
L:I302

b:48.0
occ:0.50
 NH2 H:ARG165 3.7 32.7 0.5
O H:HOH419 3.8 21.6 0.5
NH1 H:ARG165 4.0 31.9 0.5
CB L:ASN141 4.0 27.9 1.0
CZ H:ARG165 4.1 31.1 0.5
OG1 L:THR118 4.2 28.2 1.0
CD L:LYS142 4.3 29.3 1.0
CB L:LYS142 4.3 24.7 1.0
NH2 H:ARG165 4.5 26.2 0.5
CG L:ASN141 4.8 33.2 1.0
CG L:LYS142 4.9 27.6 1.0

Reference:

M.Ishii, M.Nakakido, J.M.M.Caaveiro, D.Kuroda, C.Okumura, T.Maruyama, K.Entzminger, K.Tsumoto. Structural Basis For Antigen Recognition By Methylated Lysine Specific Antibodies To Be Published.
Page generated: Sun Dec 13 19:46:13 2020

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