Fluorine in PDB 6lly: Cryoem Structure of SERCA2B Wt in E2-BEF3- State

Enzymatic activity of Cryoem Structure of SERCA2B Wt in E2-BEF3- State

All present enzymatic activity of Cryoem Structure of SERCA2B Wt in E2-BEF3- State:
7.2.2.10;

Other elements in 6lly:

The structure of Cryoem Structure of SERCA2B Wt in E2-BEF3- State also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Cryoem Structure of SERCA2B Wt in E2-BEF3- State (pdb code 6lly). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Cryoem Structure of SERCA2B Wt in E2-BEF3- State, PDB code: 6lly:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6lly

Go back to Fluorine Binding Sites List in 6lly
Fluorine binding site 1 out of 3 in the Cryoem Structure of SERCA2B Wt in E2-BEF3- State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryoem Structure of SERCA2B Wt in E2-BEF3- State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:19.8
occ:0.00
 F1 A:BEF2001 0.0 19.8 0.0
BE A:BEF2001 1.5 19.8 0.0
OD2 A:ASP351 2.1 23.2 1.0
MG A:MG2002 2.3 9.7 1.0
OD1 A:ASP351 2.4 23.2 1.0
F3 A:BEF2001 2.5 19.8 0.0
F2 A:BEF2001 2.6 19.8 0.0
CG A:ASP351 2.6 23.2 1.0
O A:THR353 3.1 20.2 1.0
CA A:GLY182 3.5 10.9 1.0
ND2 A:ASN705 3.6 13.9 1.0
CB A:THR353 3.7 20.2 1.0
N A:THR353 3.8 20.2 1.0
C A:THR353 4.0 20.2 1.0
CA A:THR353 4.0 20.2 1.0
CB A:ASP351 4.1 23.2 1.0
OD1 A:ASN705 4.2 13.9 1.0
OD1 A:ASP702 4.3 18.5 1.0
O A:SER178 4.3 9.4 1.0
CG A:ASN705 4.3 13.9 1.0
NZ A:LYS683 4.4 13.3 1.0
O A:GLY182 4.4 10.9 1.0
OG1 A:THR353 4.4 20.2 1.0
N A:GLY182 4.4 10.9 1.0
C A:GLY182 4.5 10.9 1.0
OD2 A:ASP706 4.5 15.0 1.0
N A:LYS352 4.6 20.2 1.0
CG2 A:THR353 4.7 20.2 1.0
OG1 A:THR624 4.7 12.3 1.0
OD1 A:ASP706 4.8 15.0 1.0
C A:LYS352 4.8 20.2 1.0

Fluorine binding site 2 out of 3 in 6lly

Go back to Fluorine Binding Sites List in 6lly
Fluorine binding site 2 out of 3 in the Cryoem Structure of SERCA2B Wt in E2-BEF3- State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryoem Structure of SERCA2B Wt in E2-BEF3- State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:19.8
occ:0.00
 F2 A:BEF2001 0.0 19.8 0.0
BE A:BEF2001 1.6 19.8 0.0
OG1 A:THR624 2.3 12.3 1.0
OD1 A:ASP351 2.4 23.2 1.0
F3 A:BEF2001 2.5 19.8 0.0
F1 A:BEF2001 2.6 19.8 0.0
N A:THR353 2.9 20.2 1.0
CB A:THR624 3.3 12.3 1.0
CG A:ASP351 3.4 23.2 1.0
N A:LYS352 3.4 20.2 1.0
OG1 A:THR353 3.4 20.2 1.0
CB A:THR353 3.4 20.2 1.0
O A:GLY182 3.6 10.9 1.0
CA A:THR624 3.7 12.3 1.0
CB A:LYS352 3.7 20.2 1.0
OD2 A:ASP351 3.7 23.2 1.0
CA A:THR353 3.7 20.2 1.0
C A:LYS352 3.8 20.2 1.0
CA A:LYS352 3.8 20.2 1.0
N A:GLY625 3.8 10.5 1.0
CA A:GLY182 4.0 10.9 1.0
C A:GLY182 4.3 10.9 1.0
C A:THR624 4.3 12.3 1.0
O A:THR353 4.3 20.2 1.0
C A:ASP351 4.4 23.2 1.0
CE A:LYS352 4.5 20.2 1.0
C A:THR353 4.5 20.2 1.0
MG A:MG2002 4.5 9.7 1.0
CG2 A:THR624 4.6 12.3 1.0
CB A:ASP351 4.6 23.2 1.0
N A:ASP626 4.6 13.8 1.0
NZ A:LYS683 4.7 13.3 1.0
CA A:ASP351 4.7 23.2 1.0
CG A:LYS352 4.8 20.2 1.0
NZ A:LYS352 4.8 20.2 1.0
CA A:GLY625 4.9 10.5 1.0
CG2 A:THR353 4.9 20.2 1.0
ND2 A:ASN705 4.9 13.9 1.0
O A:LYS352 4.9 20.2 1.0
N A:THR624 5.0 12.3 1.0

Fluorine binding site 3 out of 3 in 6lly

Go back to Fluorine Binding Sites List in 6lly
Fluorine binding site 3 out of 3 in the Cryoem Structure of SERCA2B Wt in E2-BEF3- State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryoem Structure of SERCA2B Wt in E2-BEF3- State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:19.8
occ:0.00
 F3 A:BEF2001 0.0 19.8 0.0
BE A:BEF2001 1.5 19.8 0.0
OD1 A:ASP351 2.4 23.2 1.0
F2 A:BEF2001 2.5 19.8 0.0
F1 A:BEF2001 2.5 19.8 0.0
ND2 A:ASN705 2.6 13.9 1.0
NZ A:LYS683 2.7 13.3 1.0
N A:GLY625 2.9 10.5 1.0
CG A:ASP351 3.4 23.2 1.0
OG1 A:THR624 3.5 12.3 1.0
CA A:THR624 3.6 12.3 1.0
CA A:GLY182 3.6 10.9 1.0
C A:THR624 3.6 12.3 1.0
CE A:LYS683 3.6 13.3 1.0
CA A:GLY625 3.7 10.5 1.0
OD2 A:ASP351 3.8 23.2 1.0
CG A:ASN705 3.9 13.9 1.0
CB A:THR624 4.1 12.3 1.0
O A:THR181 4.2 11.7 1.0
OD1 A:ASP706 4.3 15.0 1.0
N A:GLY182 4.4 10.9 1.0
O A:ILE623 4.4 12.2 1.0
OD1 A:ASN705 4.5 13.9 1.0
C A:GLY182 4.6 10.9 1.0
O A:GLY182 4.6 10.9 1.0
C A:THR181 4.6 11.7 1.0
CB A:ASP351 4.7 23.2 1.0
C A:GLY625 4.7 10.5 1.0
MG A:MG2002 4.7 9.7 1.0
N A:THR624 4.8 12.3 1.0
O A:THR624 4.8 12.3 1.0
N A:ASP626 4.8 13.8 1.0
N A:LYS352 4.9 20.2 1.0
CB A:ASN705 5.0 13.9 1.0

Reference:

Y.Zhang, M.Inoue, A.Tsutsumi, S.Watanabe, T.Nishizawa, K.Nagata, M.Kikkawa, K.Inaba. Cryo-Em Structures of SERCA2B Reveal the Mechanism of Regulation By the Luminal Extension Tail. Sci Adv V. 6 B0147 2020.
ISSN: ESSN 2375-2548
PubMed: 32851169
DOI: 10.1126/SCIADV.ABB0147
Page generated: Sun Dec 13 12:56:35 2020

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