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Sodium in PDB 6vfr: Crystal Structure of Human Protocadherin 18 EC1-EC4

Protein crystallography data

The structure of Crystal Structure of Human Protocadherin 18 EC1-EC4, PDB code: 6vfr was solved by O.J.Harrison, J.Brasch, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.90 / 2.79
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 126.959, 176.942, 71.872, 90.00, 101.42, 90.00
R / Rfree (%) 23.6 / 27.2

Other elements in 6vfr:

The structure of Crystal Structure of Human Protocadherin 18 EC1-EC4 also contains other interesting chemical elements:

Calcium (Ca) 18 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Protocadherin 18 EC1-EC4 (pdb code 6vfr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Protocadherin 18 EC1-EC4, PDB code: 6vfr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6vfr

Go back to Sodium Binding Sites List in 6vfr
Sodium binding site 1 out of 2 in the Crystal Structure of Human Protocadherin 18 EC1-EC4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Protocadherin 18 EC1-EC4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na524

b:77.6
occ:1.00
O A:ARG276 2.2 84.5 1.0
O A:HOH613 2.2 0.9 1.0
O A:LEU241 2.2 82.5 1.0
OD1 A:ASN242 2.4 96.1 1.0
OD1 A:ASP240 2.4 0.8 1.0
O A:HOH621 2.5 87.1 1.0
C A:LEU241 3.2 98.8 1.0
C A:ARG276 3.4 0.2 1.0
CG A:ASP240 3.5 0.7 1.0
CG A:ASN242 3.6 0.6 1.0
HA3 A:GLY277 3.7 0.3 1.0
OD2 A:ASP240 3.9 0.3 1.0
CA A:ASN242 3.9 96.7 1.0
N A:ASN242 3.9 95.8 1.0
HA A:ARG276 4.0 0.7 1.0
N A:LEU241 4.1 97.1 1.0
HD2 A:HIS278 4.1 0.6 1.0
HB3 A:ARG276 4.1 0.4 1.0
H A:LEU241 4.2 0.5 1.0
CA A:ARG276 4.2 0.5 1.0
CA A:LEU241 4.3 0.3 1.0
CB A:ASN242 4.3 97.1 1.0
N A:GLY277 4.3 0.8 1.0
C A:ASP240 4.3 0.2 1.0
CA A:GLY277 4.3 0.3 1.0
HH A:TYR256 4.4 0.1 1.0
O A:GLY277 4.5 85.6 1.0
HE2 A:TYR256 4.6 0.8 1.0
C A:GLY277 4.6 0.9 1.0
HE2 A:HIS278 4.6 0.9 1.0
ND2 A:ASN242 4.6 0.5 1.0
O A:ASP240 4.6 90.8 1.0
HA A:ASP240 4.6 0.0 1.0
OH A:TYR256 4.6 0.9 1.0
CD2 A:HIS278 4.7 0.5 1.0
CB A:ARG276 4.7 0.5 1.0
CB A:ASP240 4.7 0.6 1.0
C1 A:NAG501 4.8 0.4 1.0
CE2 A:TYR256 4.8 95.7 1.0
CA A:ASP240 4.8 0.8 1.0
HB2 A:LEU241 4.8 0.5 1.0
CZ A:TYR256 4.9 96.2 1.0
HA A:LEU241 4.9 0.2 1.0
NE2 A:HIS278 4.9 0.2 1.0

Sodium binding site 2 out of 2 in 6vfr

Go back to Sodium Binding Sites List in 6vfr
Sodium binding site 2 out of 2 in the Crystal Structure of Human Protocadherin 18 EC1-EC4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Protocadherin 18 EC1-EC4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na521

b:76.7
occ:1.00
O B:LEU241 2.2 78.9 1.0
O B:HOH606 2.2 0.5 1.0
O B:HOH605 2.2 88.3 1.0
O B:ARG276 2.3 81.2 1.0
OD1 B:ASN242 2.5 0.4 1.0
OD1 B:ASP240 2.5 0.8 1.0
C B:LEU241 3.2 84.6 1.0
CG B:ASP240 3.3 0.3 1.0
C B:ARG276 3.5 95.8 1.0
OD2 B:ASP240 3.6 0.3 1.0
CG B:ASN242 3.7 0.2 1.0
HA3 B:GLY277 3.9 0.1 1.0
N B:ASN242 3.9 94.8 1.0
HD2 B:HIS278 4.0 0.8 1.0
CA B:ASN242 4.0 97.6 1.0
HB2 B:ARG276 4.0 0.5 1.0
N B:LEU241 4.0 0.9 1.0
H B:LEU241 4.2 0.3 1.0
C B:ASP240 4.2 0.0 1.0
CA B:LEU241 4.2 97.5 1.0
HA B:ARG276 4.3 0.7 1.0
CB B:ASN242 4.3 0.3 1.0
CA B:ARG276 4.4 0.3 1.0
O B:ASP240 4.5 85.8 1.0
N B:GLY277 4.5 99.4 1.0
CA B:GLY277 4.5 96.7 1.0
O B:GLY277 4.5 97.3 1.0
HA B:ASP240 4.6 0.6 1.0
C B:GLY277 4.6 0.1 1.0
CB B:ASP240 4.6 0.9 1.0
HH B:TYR256 4.6 0.1 1.0
CD2 B:HIS278 4.6 0.8 1.0
CB B:ARG276 4.7 0.8 1.0
ND2 B:ASN242 4.7 0.5 1.0
CA B:ASP240 4.7 98.8 1.0
OH B:TYR256 4.8 0.0 1.0
HA B:LEU241 4.9 1.0 1.0
HB2 B:LEU241 4.9 0.5 1.0
O B:HOH614 4.9 98.0 1.0
NE2 B:HIS278 4.9 0.3 1.0
C1 B:NAG502 5.0 0.4 1.0

Reference:

O.J.Harrison, J.Brasch, P.S.Katsamba, G.Ahlsen, A.J.Noble, H.Dan, R.V.Sampogna, C.S.Potter, B.Carragher, B.Honig, L.Shapiro. Family-Wide Structural and Biophysical Analysis of Binding Interactions Among Non-Clustered Delta-Protocadherins. Cell Rep V. 30 2655 2020.
ISSN: ESSN 2211-1247
PubMed: 32101743
DOI: 10.1016/J.CELREP.2020.02.003
Page generated: Tue Oct 8 14:22:54 2024

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