Calcium in PDB 6rym: Structure of Carbohydrate Recognition Domain with Glcnac Bound

Protein crystallography data

The structure of Structure of Carbohydrate Recognition Domain with Glcnac Bound, PDB code: 6rym 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) 25.11 / 1.46
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 50.225, 50.225, 51.925, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 18.4

Calcium Binding Sites:

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

Calcium binding site 1 out of 2 in 6rym

Go back to Calcium Binding Sites List in 6rym
Calcium binding site 1 out of 2 in the Structure of Carbohydrate Recognition Domain with Glcnac 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 Carbohydrate Recognition Domain with Glcnac Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:12.0
occ:1.00
OD1 A:ASP338 2.3 13.8 1.0
O4 A:NAG404 2.4 13.3 0.5
OE1 A:GLU325 2.4 13.6 1.0
O3 A:NAG404 2.4 13.7 0.5
OD1 A:ASN337 2.4 12.2 1.0
OD1 A:ASN317 2.4 17.6 1.0
O A:ASP338 2.5 10.7 1.0
O4 A:NDG403 2.5 13.2 0.5
OE1 A:GLU315 2.6 13.3 1.0
O3 A:NDG403 2.8 14.0 0.5
C4 A:NAG404 3.2 15.2 0.5
C3 A:NAG404 3.3 14.8 0.5
CD A:GLU325 3.4 13.0 1.0
CG A:ASP338 3.4 13.0 1.0
C4 A:NDG403 3.4 15.1 0.5
CD A:GLU315 3.4 12.9 1.0
CG A:ASN337 3.4 10.1 1.0
CG A:ASN317 3.4 20.6 1.0
C A:ASP338 3.5 9.2 1.0
C3 A:NDG403 3.5 14.7 0.5
N A:ASP338 3.7 10.0 1.0
OE2 A:GLU315 3.7 13.4 1.0
OE2 A:GLU325 3.7 14.4 1.0
ND2 A:ASN337 3.9 11.1 1.0
ND2 A:ASN317 3.9 21.1 1.0
CA A:ASP338 4.0 10.4 1.0
OD2 A:ASP338 4.2 13.1 1.0
CB A:ASP338 4.2 11.3 1.0
N A:ASN317 4.3 20.0 1.0
O A:SER319 4.5 28.5 1.0
C A:ASN337 4.5 10.5 1.0
CG A:GLU325 4.6 12.8 1.0
CB A:ASN317 4.7 20.6 1.0
C2 A:NAG404 4.7 15.5 0.5
C5 A:NAG404 4.7 16.4 0.5
CG A:GLU315 4.7 13.6 1.0
N A:VAL339 4.7 9.8 1.0
CB A:ASN337 4.7 9.6 1.0
N A:ASN318 4.8 22.1 1.0
N A:SER319 4.8 25.6 1.0
CB A:GLU325 4.8 12.2 1.0
C5 A:NDG403 4.8 15.7 0.5
CA A:ASN337 4.8 9.3 1.0
C2 A:NDG403 4.9 15.2 0.5
CA A:ASN317 4.9 22.3 1.0
C A:SER319 5.0 27.6 1.0

Calcium binding site 2 out of 2 in 6rym

Go back to Calcium Binding Sites List in 6rym
Calcium binding site 2 out of 2 in the Structure of Carbohydrate Recognition Domain with Glcnac 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 Carbohydrate Recognition Domain with Glcnac Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:22.8
occ:1.00
OD2 A:ASP291 2.3 19.3 1.0
O A:HOH528 2.3 21.1 1.0
OE2 A:GLU295 2.6 32.7 1.0
OE1 A:GLU295 2.6 30.0 1.0
O A:GLU325 2.6 15.6 1.0
OD1 A:ASN318 2.7 24.4 1.0
OD1 A:ASP291 2.7 17.1 1.0
OD1 A:ASN326 2.8 18.8 1.0
CG A:ASP291 2.8 17.0 1.0
CD A:GLU295 2.9 31.8 1.0
CG A:ASN318 3.4 24.3 1.0
C A:GLU325 3.5 13.2 1.0
CA A:ASN326 3.8 12.2 1.0
CG A:ASN326 3.9 15.5 1.0
CB A:ASN318 4.0 23.8 1.0
N A:ASN326 4.1 12.2 1.0
ND2 A:ASN318 4.2 25.2 1.0
CB A:ASN326 4.3 12.9 1.0
CB A:ASP291 4.3 15.3 1.0
CG A:GLU295 4.4 30.2 1.0
N A:GLU325 4.4 14.1 1.0
O A:HOH541 4.4 26.4 1.0
CZ A:PHE298 4.5 13.2 1.0
CA A:ASN318 4.6 24.2 1.0
CA A:GLU325 4.6 13.6 1.0
N A:GLY296 4.6 25.8 1.0
OD2 A:ASP338 4.6 13.1 1.0
O A:HOH629 4.7 27.5 1.0
O A:ASP291 4.8 16.7 1.0
CA A:GLU295 4.9 28.8 1.0
C A:ASN326 5.0 10.5 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: Sat Dec 12 07:31:41 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