Atomistry » Calcium » PDB 5fk0-5g38 » 5fma
Atomistry »
  Calcium »
    PDB 5fk0-5g38 »
      5fma »

Calcium in PDB 5fma: Human Notch 1, Egf 4-7

Protein crystallography data

The structure of Human Notch 1, Egf 4-7, PDB code: 5fma was solved by P.C.Weisshuhn, D.Sheppard, P.Taylor, P.Whiteman, S.M.Lea, P.A.Handford, C.Redfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.42 / 2.46
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.940, 86.830, 53.450, 90.00, 107.58, 90.00
R / Rfree (%) 25.9 / 26.3

Other elements in 5fma:

The structure of Human Notch 1, Egf 4-7 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Notch 1, Egf 4-7 (pdb code 5fma). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Human Notch 1, Egf 4-7, PDB code: 5fma:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5fma

Go back to Calcium Binding Sites List in 5fma
Calcium binding site 1 out of 5 in the Human Notch 1, Egf 4-7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Notch 1, Egf 4-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1295

b:49.1
occ:1.00
OD1 A:ASN197 2.3 38.1 1.0
OE1 A:GLU181 2.4 53.6 1.0
OD2 A:ASP178 2.5 52.2 1.0
O A:SER201 2.6 47.0 1.0
O A:GLU198 2.6 53.5 1.0
O A:VAL179 2.6 49.6 1.0
OD1 A:ASP178 2.7 57.3 1.0
CG A:ASP178 3.0 52.0 1.0
CD A:GLU181 3.4 67.2 1.0
CG A:ASN197 3.4 46.5 1.0
C A:SER201 3.5 47.4 1.0
OE2 A:GLU181 3.7 56.3 1.0
N A:SER201 3.7 46.1 1.0
C A:GLU198 3.8 54.4 1.0
C A:VAL179 3.8 50.0 1.0
ND2 A:ASN197 3.9 37.4 1.0
N A:GLU198 3.9 50.6 1.0
CA A:SER201 4.0 45.4 1.0
N A:GLY200 4.2 48.4 1.0
N A:GLU181 4.4 49.1 1.0
C A:GLY200 4.4 50.2 1.0
CB A:ASP178 4.5 44.9 1.0
CA A:ASN180 4.5 47.0 1.0
CA A:GLU198 4.5 50.7 1.0
N A:VAL179 4.5 44.9 1.0
N A:TYR202 4.6 43.4 1.0
N A:ASN180 4.6 47.5 1.0
CB A:ASN197 4.7 45.0 1.0
CG A:GLU181 4.7 56.2 1.0
O A:SER169 4.7 43.0 1.0
CA A:GLY200 4.8 47.6 1.0
CA A:VAL179 4.8 45.1 1.0
N A:VAL199 4.8 51.3 1.0
C A:ASN197 4.9 53.5 1.0
CA A:ASN197 4.9 49.2 1.0
CG2 A:VAL179 4.9 49.1 1.0
C A:VAL199 5.0 53.4 1.0

Calcium binding site 2 out of 5 in 5fma

Go back to Calcium Binding Sites List in 5fma
Calcium binding site 2 out of 5 in the Human Notch 1, Egf 4-7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Notch 1, Egf 4-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1296

b:72.2
occ:1.00
OD1 A:ASN257 2.2 85.6 1.0
OD2 A:ASP274 2.2 71.3 1.0
O A:ILE258 2.2 70.1 1.0
O A:GLY275 2.3 59.1 1.0
OD1 A:ASP274 2.6 76.2 1.0
CG A:ASP274 2.7 70.1 1.0
OD2 A:ASP260 2.7 73.6 1.0
CG A:ASN257 3.3 89.2 1.0
C A:ILE258 3.4 70.5 1.0
C A:GLY275 3.6 60.1 1.0
CG A:ASP260 3.7 71.3 1.0
ND2 A:ASN257 3.9 79.5 1.0
N A:GLY275 4.0 56.4 1.0
N A:ASP260 4.1 64.4 1.0
N A:ILE258 4.1 67.9 1.0
CB A:ASP274 4.2 58.5 1.0
N A:ASP259 4.3 66.2 1.0
CA A:ASP259 4.3 65.3 1.0
CA A:ILE258 4.3 68.0 1.0
C A:ASN257 4.4 71.0 1.0
CA A:GLY275 4.4 56.2 1.0
CB A:ASN257 4.4 67.2 1.0
OD1 A:ASP260 4.5 72.2 1.0
CB A:ASP260 4.5 66.1 1.0
N A:VAL276 4.5 57.7 1.0
C A:ASP259 4.6 68.9 1.0
O A:THR278 4.6 56.3 1.0
CA A:VAL276 4.7 58.3 1.0
C A:ASP274 4.7 59.9 1.0
N A:ASN277 4.7 58.5 1.0
O A:ASN257 4.7 70.0 1.0
CA A:ASP274 4.8 56.8 1.0
CA A:ASN257 4.9 67.7 1.0
O A:GLY248 4.9 70.8 1.0
CA A:ASP260 5.0 64.4 1.0

Calcium binding site 3 out of 5 in 5fma

Go back to Calcium Binding Sites List in 5fma
Calcium binding site 3 out of 5 in the Human Notch 1, Egf 4-7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Notch 1, Egf 4-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1297

b:74.1
occ:1.00
NE2 A:GLN177 3.6 86.7 1.0
CE1 A:HIS171 3.9 50.2 1.0
O A:ASP178 3.9 47.4 1.0
CB A:GLN177 4.2 46.6 1.0
CD A:GLN177 4.5 90.2 1.0
NE2 A:HIS171 4.5 50.7 1.0
CG A:GLN177 4.6 65.3 1.0
ND1 A:HIS171 5.0 50.8 1.0

Calcium binding site 4 out of 5 in 5fma

Go back to Calcium Binding Sites List in 5fma
Calcium binding site 4 out of 5 in the Human Notch 1, Egf 4-7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Notch 1, Egf 4-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1295

b:46.9
occ:1.00
OD1 B:ASN197 2.3 43.6 1.0
OD2 B:ASP178 2.4 58.6 1.0
O B:VAL179 2.5 43.2 1.0
OE1 B:GLU181 2.5 40.8 1.0
OD1 B:ASP178 2.6 54.9 1.0
O B:GLU198 2.6 48.8 1.0
O B:SER201 2.8 47.5 1.0
CG B:ASP178 2.8 54.7 1.0
CG B:ASN197 3.3 51.7 1.0
CD B:GLU181 3.5 56.4 1.0
C B:VAL179 3.6 44.2 1.0
ND2 B:ASN197 3.7 45.4 1.0
C B:SER201 3.8 49.0 1.0
C B:GLU198 3.8 49.4 1.0
OE2 B:GLU181 3.9 52.0 1.0
N B:SER201 3.9 46.0 1.0
N B:GLU198 4.0 45.6 1.0
N B:VAL179 4.3 42.0 1.0
CA B:SER201 4.3 45.6 1.0
N B:GLY200 4.3 47.2 1.0
CB B:ASP178 4.3 45.5 1.0
CA B:ASN180 4.3 40.1 1.0
N B:ASN180 4.4 40.9 1.0
N B:GLU181 4.4 42.0 1.0
CA B:GLU198 4.5 45.5 1.0
CA B:VAL179 4.6 41.3 1.0
CB B:ASN197 4.6 43.1 1.0
C B:GLY200 4.6 50.1 1.0
O B:SER169 4.6 45.1 1.0
N B:TYR202 4.8 47.2 1.0
C B:ASP178 4.8 46.1 1.0
C B:ASN197 4.8 48.8 1.0
CA B:ASN197 4.8 44.9 1.0
N B:VAL199 4.8 46.4 1.0
CA B:GLY200 4.9 47.2 1.0
CG B:GLU181 4.9 50.0 1.0
C B:ASN180 4.9 44.9 1.0

Calcium binding site 5 out of 5 in 5fma

Go back to Calcium Binding Sites List in 5fma
Calcium binding site 5 out of 5 in the Human Notch 1, Egf 4-7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human Notch 1, Egf 4-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1296

b:72.0
occ:1.00
O B:ILE258 2.3 85.0 1.0
O B:GLY275 2.3 77.5 1.0
OD1 B:ASN257 2.3 83.2 1.0
OD2 B:ASP260 2.4 99.9 1.0
OD2 B:ASP274 2.7 82.0 1.0
OD1 B:ASP274 2.9 88.4 1.0
CG B:ASP274 3.1 81.9 1.0
CG B:ASP260 3.4 93.6 1.0
CG B:ASN257 3.5 92.1 1.0
C B:ILE258 3.5 84.6 1.0
C B:GLY275 3.5 78.3 1.0
ND2 B:ASN257 4.1 82.8 1.0
OD1 B:ASP260 4.1 94.1 1.0
N B:ILE258 4.1 80.3 1.0
N B:GLY275 4.2 73.5 1.0
N B:ASN277 4.2 76.3 1.0
N B:ASP260 4.2 80.4 1.0
CB B:ASP260 4.3 83.6 1.0
CA B:ILE258 4.3 80.4 1.0
N B:VAL276 4.4 75.8 1.0
CA B:VAL276 4.4 75.9 1.0
N B:ASP259 4.5 80.6 1.0
CA B:GLY275 4.5 74.2 1.0
O B:THR278 4.5 76.4 1.0
C B:ASN257 4.5 82.4 1.0
CB B:ASP274 4.6 72.5 1.0
CA B:ASP259 4.6 80.1 1.0
CB B:ASN257 4.6 77.0 1.0
O B:GLY248 4.6 82.8 1.0
C B:ASP259 4.7 84.2 1.0
C B:VAL276 4.8 80.3 1.0
CB B:ILE258 4.8 84.8 1.0
C B:ASP274 4.9 75.9 1.0
CA B:ASP260 4.9 80.6 1.0
O B:ASN257 5.0 81.0 1.0

Reference:

P.C.Weisshuhn, D.Sheppard, P.Taylor, P.Whiteman, S.M.Lea, P.A.Handford, C.Redfield. Non-Linear and Flexible Regions of the Human NOTCH1 Extracellular Domain Revealed By High-Resolution Structural Studies. Structure V. 24 555 2016.
ISSN: ISSN 0969-2126
PubMed: 26996961
DOI: 10.1016/J.STR.2016.02.010
Page generated: Sat Dec 12 05:25:15 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