Chlorine in PDB 6ldy: Structure Antibody D6 in Complex with Methylated Peptide

Protein crystallography data

The structure of Structure Antibody D6 in Complex with Methylated Peptide, PDB code: 6ldy 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) 40.18 / 1.77
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 41.520, 76.210, 79.210, 85.58, 84.20, 76.03
R / Rfree (%) 18.5 / 21.8

Other elements in 6ldy:

The structure of Structure Antibody D6 in Complex with Methylated Peptide also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure Antibody D6 in Complex with Methylated Peptide (pdb code 6ldy). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure Antibody D6 in Complex with Methylated Peptide, PDB code: 6ldy:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6ldy

Go back to Chlorine Binding Sites List in 6ldy
Chlorine binding site 1 out of 4 in the Structure Antibody D6 in Complex with Methylated Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure Antibody D6 in Complex with Methylated Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:23.0
occ:1.00
 O A:HOH430 2.8 40.7 1.0
O A:HOH425 3.1 25.2 1.0
N A:TYR46 3.3 19.8 1.0
N B:PHE103 3.4 24.2 1.0
CA B:GLY102 3.8 26.9 1.0
CB A:TYR46 3.8 20.8 1.0
CA A:GLU45 3.9 20.6 1.0
CD2 B:PHE103 4.0 21.6 1.0
C A:GLU45 4.1 20.2 1.0
C B:GLY102 4.1 25.2 1.0
CB B:PHE103 4.1 21.7 1.0
CA A:TYR46 4.2 19.8 1.0
O A:HOH569 4.2 41.2 1.0
O A:LEU44 4.2 20.8 1.0
O B:PHE103 4.2 22.4 1.0
CA B:PHE103 4.3 22.4 1.0
CG A:GLU45 4.3 22.3 1.0
O B:HOH568 4.5 35.8 1.0
CG B:PHE103 4.6 21.4 1.0
O A:TYR46 4.6 21.2 1.0
CB A:GLU45 4.6 21.4 1.0
C B:PHE103 4.8 22.4 1.0
CA A:CA301 4.8 45.8 1.0
N A:GLU45 4.8 20.2 1.0
O B:HOH496 4.9 31.0 1.0
C A:LEU44 4.9 20.3 1.0
C A:TYR46 4.9 19.9 1.0
O B:HOH440 4.9 35.1 1.0

Chlorine binding site 2 out of 4 in 6ldy

Go back to Chlorine Binding Sites List in 6ldy
Chlorine binding site 2 out of 4 in the Structure Antibody D6 in Complex with Methylated Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure Antibody D6 in Complex with Methylated Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl302

b:29.9
occ:1.00
 O H:HOH448 3.1 26.3 1.0
O H:HOH523 3.1 40.1 1.0
N H:TYR46 3.3 25.4 1.0
N L:PHE103 3.4 29.2 1.0
CA L:GLY102 3.7 32.9 1.0
CA H:GLU45 3.8 25.8 1.0
CB H:TYR46 3.8 26.0 1.0
C H:GLU45 4.0 25.0 1.0
C L:GLY102 4.0 31.1 1.0
CD2 L:PHE103 4.1 26.8 1.0
CG H:GLU45 4.1 26.8 1.0
CA H:TYR46 4.2 24.6 1.0
CB L:PHE103 4.3 26.9 1.0
O L:PHE103 4.3 28.8 1.0
O H:LEU44 4.3 27.3 1.0
O L:HOH472 4.4 51.1 1.0
CA L:PHE103 4.4 28.2 1.0
CB H:GLU45 4.5 26.1 1.0
O H:TYR46 4.6 23.2 1.0
O L:SER101 4.6 35.8 1.0
CG L:PHE103 4.7 26.5 1.0
N H:GLU45 4.8 25.3 1.0
C L:PHE103 4.9 28.3 1.0
N L:GLY102 4.9 34.2 1.0
C H:TYR46 4.9 23.5 1.0
O L:HOH398 4.9 36.6 1.0
C H:LEU44 5.0 26.4 1.0

Chlorine binding site 3 out of 4 in 6ldy

Go back to Chlorine Binding Sites List in 6ldy
Chlorine binding site 3 out of 4 in the Structure Antibody D6 in Complex with Methylated Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure Antibody D6 in Complex with Methylated Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl303

b:31.3
occ:1.00
 N H:GLY145 3.1 16.4 1.0
NE2 H:GLN172 3.2 41.7 1.0
O H:HOH544 3.2 35.8 1.0
O H:HOH413 3.4 31.6 1.0
CA H:GLY145 3.6 16.8 1.0
O H:TYR177 3.8 15.7 1.0
CB H:LYS144 3.9 20.4 1.0
CD H:GLN172 4.0 41.9 1.0
C H:LYS144 4.1 16.5 1.0
CB H:SER178 4.2 19.5 1.0
CA H:LYS144 4.3 17.5 1.0
CB H:LEU176 4.3 18.8 1.0
CG H:GLN172 4.3 38.3 1.0
C H:TYR177 4.3 16.5 1.0
CE H:LYS144 4.4 30.7 1.0
CG H:LYS144 4.6 23.7 1.0
C H:LEU176 4.7 18.3 1.0
CB H:GLN172 4.7 33.9 1.0
OG H:SER178 4.7 21.8 1.0
N H:TYR177 4.8 17.8 1.0
N H:SER178 4.8 17.0 1.0
C H:GLY145 4.9 16.5 1.0
O H:HOH479 4.9 23.0 0.5
OE1 H:GLN172 4.9 44.4 1.0
O H:LEU176 4.9 19.1 1.0
CA H:SER178 4.9 17.4 1.0
CD H:LYS144 5.0 26.9 1.0
CD1 H:LEU176 5.0 20.1 1.0

Chlorine binding site 4 out of 4 in 6ldy

Go back to Chlorine Binding Sites List in 6ldy
Chlorine binding site 4 out of 4 in the Structure Antibody D6 in Complex with Methylated Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure Antibody D6 in Complex with Methylated Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl304

b:31.8
occ:1.00
 O H:HOH547 2.9 28.3 1.0
O H:HOH438 3.0 21.7 0.6
N H:LEU10 3.2 20.9 1.0
CB H:LEU10 3.4 24.8 1.0
O H:HOH447 3.4 35.7 1.0
CB H:ARG9 3.7 20.8 1.0
CD H:PRO148 3.7 17.0 1.0
CG H:PRO148 3.8 17.1 1.0
CA H:ARG9 3.9 19.4 1.0
CG H:PRO117 3.9 20.4 1.0
CB H:ALA200 3.9 16.0 1.0
CA H:LEU10 4.0 22.4 1.0
C H:ARG9 4.0 20.4 1.0
CD2 H:LEU10 4.3 26.2 1.0
CG H:LEU10 4.5 26.0 1.0
CB H:PRO117 4.5 19.7 1.0
O H:LEU10 4.5 22.4 1.0
CA H:ALA200 4.8 16.4 1.0
C H:LEU10 4.8 22.9 1.0
CG H:ARG9 4.8 22.1 1.0
O H:ALA200 4.9 17.6 1.0
CD H:PRO117 5.0 21.1 1.0
CB H:PRO148 5.0 16.5 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: Sat Dec 12 13:16:54 2020

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