Calcium 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:

Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure Antibody D6 in Complex with Methylated Peptide, PDB code: 6ldy:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6ldy

Go back to Calcium Binding Sites List in 6ldy
Calcium binding site 1 out of 2 in the Structure Antibody D6 in Complex with Methylated Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca301

b:45.8
occ:1.00
O A:HOH569 2.3 41.2 1.0
O A:HOH566 2.3 48.7 1.0
O A:HOH552 2.3 34.2 1.0
O A:HOH430 2.4 40.7 1.0
O B:HOH440 2.5 35.1 1.0
O B:HOH589 2.8 56.8 1.0
O A:HOH442 4.3 21.5 1.0
O A:LEU44 4.6 20.8 1.0
O A:HOH496 4.6 28.7 0.6
O B:HOH438 4.7 26.6 0.6
O B:PHE103 4.7 22.4 1.0
CL A:CL302 4.8 23.0 1.0

Calcium binding site 2 out of 2 in 6ldy

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca301

b:50.0
occ:1.00
O L:HOH472 2.1 51.1 1.0
O H:HOH567 2.3 25.7 0.6
O H:HOH523 2.3 40.1 1.0
O L:HOH346 4.4 28.8 1.0
O L:PHE103 4.9 28.8 1.0
O H:LEU44 4.9 27.3 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 06:21:16 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy