Atomistry » Calcium » PDB 3b1u-3biw » 3b7y
Atomistry »
  Calcium »
    PDB 3b1u-3biw »
      3b7y »

Calcium in PDB 3b7y: Crystal Structure of the C2 Domain of the E3 Ubiquitin- Protein Ligase NEDD4

Protein crystallography data

The structure of Crystal Structure of the C2 Domain of the E3 Ubiquitin- Protein Ligase NEDD4, PDB code: 3b7y was solved by J.R.Walker, M.Ruzanov, C.Butler-Cole, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.23 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 38.778, 47.997, 50.786, 108.89, 111.11, 100.86
R / Rfree (%) 16.9 / 20.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the C2 Domain of the E3 Ubiquitin- Protein Ligase NEDD4 (pdb code 3b7y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the C2 Domain of the E3 Ubiquitin- Protein Ligase NEDD4, PDB code: 3b7y:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3b7y

Go back to Calcium Binding Sites List in 3b7y
Calcium binding site 1 out of 2 in the Crystal Structure of the C2 Domain of the E3 Ubiquitin- Protein Ligase NEDD4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the C2 Domain of the E3 Ubiquitin- Protein Ligase NEDD4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:87.0
occ:1.00
O A:ASN195 2.3 74.8 1.0
O A:THR198 2.3 79.6 1.0
OD1 A:ASP200 2.4 62.3 1.0
CG A:ASP200 3.4 61.1 1.0
C A:ASN195 3.4 76.2 1.0
C A:THR198 3.5 83.7 1.0
N A:ASP200 3.7 66.0 1.0
N A:ASN195 3.8 67.7 1.0
C A:ARG199 3.9 71.6 1.0
OD2 A:ASP200 3.9 60.9 1.0
CA A:ASN195 4.0 73.9 1.0
CB A:ASN195 4.2 76.0 1.0
CA A:ARG199 4.2 75.7 1.0
N A:ARG199 4.3 81.2 1.0
CA A:ASP200 4.3 63.2 1.0
N A:THR198 4.3 92.5 1.0
CB A:ASP200 4.4 58.2 1.0
O A:ARG199 4.5 71.5 1.0
N A:ARG196 4.5 88.9 1.0
CA A:THR198 4.6 90.5 1.0
C A:ARG196 4.8 95.4 1.0
O A:ARG196 4.9 97.2 1.0
CA A:ARG196 4.9 92.5 1.0
C A:GLU194 5.0 64.2 1.0

Calcium binding site 2 out of 2 in 3b7y

Go back to Calcium Binding Sites List in 3b7y
Calcium binding site 2 out of 2 in the Crystal Structure of the C2 Domain of the E3 Ubiquitin- Protein Ligase NEDD4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the C2 Domain of the E3 Ubiquitin- Protein Ligase NEDD4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:95.4
occ:1.00
O A:GLU194 2.4 65.0 1.0
OD2 A:ASP141 2.6 71.6 1.0
OD1 A:ASN195 2.8 75.4 1.0
OD1 A:ASP193 3.3 67.0 1.0
C A:GLU194 3.4 64.2 1.0
OD2 A:ASP193 3.6 66.0 1.0
CG A:ASP141 3.7 67.6 1.0
CG A:ASP193 3.7 65.1 1.0
CG A:ASN195 3.8 76.2 1.0
CA A:ASN195 3.9 73.9 1.0
N A:ASN195 4.0 67.7 1.0
CB A:ASP141 4.1 61.8 1.0
N A:ASP141 4.3 62.4 1.0
N A:GLU194 4.4 55.8 1.0
CB A:ASN195 4.4 76.0 1.0
CA A:GLU194 4.5 59.5 1.0
C A:ASP193 4.6 55.7 1.0
OD1 A:ASP141 4.7 65.7 1.0
CA A:ASP141 4.8 59.3 1.0
O A:ASP193 4.8 55.5 1.0
ND2 A:ASN195 4.8 74.8 1.0
CA A:SER140 4.9 71.6 1.0
N A:SER140 5.0 76.7 1.0
CB A:ASP193 5.0 56.3 1.0

Reference:

J.R.Walker, M.Ruzanov, C.Butler-Cole, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon. C2 Domain of the Human E3 Ubiquitin-Protein Ligase NEDD4. To Be Published.
Page generated: Sat Dec 12 04:05:42 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