Atomistry » Calcium » PDB 4zmq-5a3y » 4zrw
Atomistry »
  Calcium »
    PDB 4zmq-5a3y »
      4zrw »

Calcium in PDB 4zrw: Structure of Cow Mincle Complexed with Trehalose

Protein crystallography data

The structure of Structure of Cow Mincle Complexed with Trehalose, PDB code: 4zrw was solved by H.Feinberg, N.D.S.Rambaruth, M.E.Taylor, K.Drickamer, W.I.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.35 / 2.60
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 97.800, 97.800, 45.200, 90.00, 90.00, 120.00
R / Rfree (%) 15.2 / 20.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Cow Mincle Complexed with Trehalose (pdb code 4zrw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of Cow Mincle Complexed with Trehalose, PDB code: 4zrw:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4zrw

Go back to Calcium Binding Sites List in 4zrw
Calcium binding site 1 out of 3 in the Structure of Cow Mincle Complexed with Trehalose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Cow Mincle Complexed with Trehalose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:38.0
occ:1.00
OD1 A:ASP193 2.2 34.9 1.0
O4P A:TRE301 2.4 34.1 1.0
OD1 A:ASN192 2.4 34.0 1.0
OD1 A:ASN170 2.4 37.3 1.0
OE1 A:GLU176 2.5 36.1 1.0
OE1 A:GLU168 2.5 40.6 1.0
O3P A:TRE301 2.5 38.9 1.0
O A:ASP193 2.6 33.9 1.0
C3P A:TRE301 3.2 35.6 1.0
C4P A:TRE301 3.3 38.1 1.0
CG A:ASP193 3.3 37.0 1.0
CD A:GLU168 3.4 38.4 1.0
CG A:ASN170 3.4 36.0 1.0
CD A:GLU176 3.4 34.0 1.0
CG A:ASN192 3.4 36.0 1.0
C A:ASP193 3.6 31.5 1.0
OE2 A:GLU168 3.7 38.9 1.0
N A:ASP193 3.7 35.3 1.0
OE2 A:GLU176 3.8 34.2 1.0
ND2 A:ASN170 3.8 35.0 1.0
ND2 A:ASN192 3.9 34.2 1.0
OD2 A:ASP193 4.0 37.3 1.0
CA A:ASP193 4.0 30.3 1.0
N A:ASN170 4.2 35.7 1.0
CB A:ASP193 4.3 34.4 1.0
C5P A:TRE301 4.6 39.5 1.0
CG A:GLU168 4.6 35.2 1.0
CG A:GLU176 4.7 31.6 1.0
C2P A:TRE301 4.7 32.5 1.0
CB A:ASN170 4.7 37.1 1.0
CG A:LEU172 4.7 33.4 1.0
C A:ASN192 4.7 35.6 1.0
CB A:ASN192 4.7 33.4 1.0
CB A:GLU176 4.8 32.8 1.0
CD1 A:LEU172 4.8 30.4 1.0
N A:VAL194 4.8 32.7 1.0
N A:ASN171 4.8 36.6 1.0
CA A:ASN170 4.9 38.0 1.0
CA A:ASN192 4.9 32.1 1.0

Calcium binding site 2 out of 3 in 4zrw

Go back to Calcium Binding Sites List in 4zrw
Calcium binding site 2 out of 3 in the Structure of Cow Mincle Complexed with Trehalose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Cow Mincle Complexed with Trehalose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:33.1
occ:1.00
O A:HOH432 2.3 33.2 1.0
O A:HOH434 2.4 33.0 1.0
OD1 A:ASN118 2.4 36.0 1.0
O A:VAL116 2.4 36.3 1.0
OE2 A:GLU122 2.4 32.5 1.0
OE2 A:GLU205 2.4 41.0 1.0
OE1 A:GLU205 2.6 35.0 1.0
CD A:GLU205 2.8 37.3 1.0
OE1 A:GLU122 2.9 43.4 1.0
CD A:GLU122 3.0 39.0 1.0
C A:VAL116 3.6 34.5 1.0
CG A:ASN118 3.6 33.5 1.0
OH A:TYR91 4.1 36.8 1.0
O A:HOH404 4.2 41.5 1.0
O A:HOH426 4.3 33.0 1.0
N A:ASN118 4.3 35.6 1.0
N A:VAL116 4.3 33.6 1.0
CA A:VAL116 4.3 30.9 1.0
CG A:GLU205 4.4 35.8 1.0
CB A:ASN118 4.4 36.6 1.0
CB A:VAL116 4.4 33.8 1.0
CG A:GLU122 4.5 35.7 1.0
N A:ILE117 4.6 31.0 1.0
ND2 A:ASN118 4.6 30.2 1.0
CA A:ILE117 4.7 31.8 1.0
O A:HOH428 4.7 40.8 1.0
CG2 A:VAL115 4.7 26.2 1.0
CG1 A:VAL116 4.9 29.5 1.0
CE2 A:TYR91 5.0 32.2 1.0
C A:ILE117 5.0 38.0 1.0

Calcium binding site 3 out of 3 in 4zrw

Go back to Calcium Binding Sites List in 4zrw
Calcium binding site 3 out of 3 in the Structure of Cow Mincle Complexed with Trehalose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Cow Mincle Complexed with Trehalose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:35.1
occ:1.00
OD1 A:ASP177 2.4 38.6 1.0
O A:HOH419 2.4 34.9 1.0
O A:GLU176 2.4 34.1 1.0
OD1 A:ASN171 2.5 35.2 1.0
OE1 A:GLU146 2.6 37.3 1.0
OD1 A:ASP142 2.6 38.6 1.0
OE2 A:GLU146 2.6 32.1 1.0
OD2 A:ASP142 2.6 36.6 1.0
CD A:GLU146 2.9 37.3 1.0
CG A:ASP142 2.9 36.0 1.0
CG A:ASP177 3.4 41.5 1.0
C A:GLU176 3.4 37.6 1.0
CG A:ASN171 3.4 35.3 1.0
CA A:ASP177 3.7 35.6 1.0
N A:ASP177 4.0 35.5 1.0
CB A:ASP177 4.1 38.5 1.0
CB A:ASN171 4.2 27.7 1.0
ND2 A:ASN171 4.2 37.0 1.0
CZ2 A:TRP149 4.3 36.2 1.0
OD2 A:ASP177 4.3 42.6 1.0
CG A:GLU146 4.4 32.6 1.0
CB A:ASP142 4.5 36.1 1.0
N A:GLU176 4.5 31.6 1.0
CA A:GLU176 4.5 33.2 1.0
CA A:ASN171 4.7 32.9 1.0
CH2 A:TRP149 4.7 34.5 1.0
OD2 A:ASP193 4.7 37.3 1.0
O A:ASP142 4.7 41.5 1.0
O A:HOH402 4.8 44.0 1.0
C A:ASP177 4.9 36.0 1.0

Reference:

H.Feinberg, N.D.Rambaruth, S.A.Jegouzo, K.M.Jacobsen, R.Djurhuus, T.B.Poulsen, W.I.Weis, M.E.Taylor, K.Drickamer. Binding Sites For Acylated Trehalose Analogs of Glycolipid Ligands on An Extended Carbohydrate Recognition Domain of the Macrophage Receptor Mincle. J.Biol.Chem. V. 291 21222 2016.
ISSN: ESSN 1083-351X
PubMed: 27542410
DOI: 10.1074/JBC.M116.749515
Page generated: Sun Jul 14 16:06:29 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy