Atomistry » Calcium » PDB 6ry5-6sau » 6ryj
Atomistry »
  Calcium »
    PDB 6ry5-6sau »
      6ryj »

Calcium in PDB 6ryj: Structure of Conglutinin Carbohydrate Recognition Domain with Ethylene Glycol Bound

Protein crystallography data

The structure of Structure of Conglutinin Carbohydrate Recognition Domain with Ethylene Glycol Bound, PDB code: 6ryj was solved by A.K.Shrive, T.J.Greenhough, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.64 / 1.25
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 50.822, 50.822, 52.837, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 20.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Conglutinin Carbohydrate Recognition Domain with Ethylene Glycol Bound (pdb code 6ryj). 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 of Conglutinin Carbohydrate Recognition Domain with Ethylene Glycol Bound, PDB code: 6ryj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6ryj

Go back to Calcium Binding Sites List in 6ryj
Calcium binding site 1 out of 2 in the Structure of Conglutinin Carbohydrate Recognition Domain with Ethylene Glycol Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Conglutinin Carbohydrate Recognition Domain with Ethylene Glycol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca400

b:15.9
occ:1.00
OD1 A:ASP338 2.3 15.0 1.0
OD1 A:ASN317 2.5 24.1 1.0
OD1 A:ASN337 2.5 13.4 1.0
O2 A:EDO402 2.5 18.7 1.0
OE1 A:GLU325 2.5 16.8 1.0
O1 A:EDO402 2.6 17.4 1.0
O A:ASP338 2.6 13.1 1.0
OE1 A:GLU315 2.6 18.5 1.0
C2 A:EDO402 3.4 19.5 1.0
CG A:ASP338 3.4 14.9 1.0
C1 A:EDO402 3.4 18.9 1.0
CD A:GLU315 3.5 18.8 1.0
CG A:ASN317 3.5 26.8 1.0
CD A:GLU325 3.5 15.4 1.0
CG A:ASN337 3.5 12.7 1.0
C A:ASP338 3.6 11.5 1.0
N A:ASP338 3.8 11.9 1.0
OE2 A:GLU315 3.8 18.6 1.0
OE2 A:GLU325 3.8 18.5 1.0
ND2 A:ASN337 3.9 12.7 1.0
ND2 A:ASN317 4.0 27.2 1.0
CA A:ASP338 4.0 12.4 1.0
OD2 A:ASP338 4.2 16.8 1.0
CB A:ASP338 4.3 13.3 1.0
N A:ASN317 4.3 26.6 1.0
C A:ASN337 4.6 11.1 1.0
O A:SER319 4.7 38.7 1.0
CB A:ASN317 4.7 26.6 1.0
CG A:GLU315 4.7 18.1 1.0
CG A:GLU325 4.8 16.2 1.0
N A:ASN318 4.8 30.1 1.0
CB A:ASN337 4.8 11.6 1.0
N A:VAL339 4.8 11.6 1.0
CA A:ASN317 4.9 28.1 1.0
CB A:GLU325 4.9 16.2 1.0
N A:SER319 4.9 35.7 1.0
CA A:ASN337 5.0 10.9 1.0

Calcium binding site 2 out of 2 in 6ryj

Go back to Calcium Binding Sites List in 6ryj
Calcium binding site 2 out of 2 in the Structure of Conglutinin Carbohydrate Recognition Domain with Ethylene Glycol Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Conglutinin Carbohydrate Recognition Domain with Ethylene Glycol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:39.6
occ:1.00
O A:HOH512 2.3 29.2 1.0
OD2 A:ASP291 2.3 24.9 1.0
OE2 A:GLU295 2.7 47.3 1.0
O A:GLU325 2.8 18.0 1.0
OD1 A:ASP291 2.9 22.9 1.0
CG A:ASP291 2.9 21.8 1.0
OD1 A:ASN326 3.0 20.6 1.0
OE1 A:GLU295 3.1 48.1 1.0
OD1 A:ASN318 3.1 36.9 1.0
CD A:GLU295 3.2 46.4 1.0
CG A:ASN318 3.6 35.6 1.0
C A:GLU325 3.6 15.5 1.0
CA A:ASN326 3.9 14.0 1.0
CG A:ASN326 4.1 18.4 1.0
CB A:ASN318 4.1 33.0 1.0
N A:ASN326 4.2 14.2 1.0
ND2 A:ASN318 4.3 37.0 1.0
CB A:ASP291 4.4 18.3 1.0
N A:GLU325 4.5 19.8 1.0
CB A:ASN326 4.5 15.0 1.0
CG A:GLU295 4.6 43.6 1.0
CZ A:PHE298 4.6 16.7 1.0
CA A:GLU325 4.7 16.5 1.0
CA A:ASN318 4.8 32.9 1.0
OD2 A:ASP338 4.8 16.8 1.0
N A:GLY296 4.9 36.5 1.0

Reference:

J.M.Paterson, A.J.Shaw, I.Burns, A.W.Dodds, A.Prasad, K.B.Reid, T.J.Greenhough, A.K.Shrive. Atomic-Resolution Crystal Structures of the Immune Protein Conglutinin From Cow Reveal Specific Interactions of Its Binding Site Withn-Acetylglucosamine. J.Biol.Chem. V. 294 17155 2019.
ISSN: ESSN 1083-351X
PubMed: 31562242
DOI: 10.1074/JBC.RA119.010271
Page generated: Tue Jul 16 14:28:47 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy