Fluorine in PDB 7yam: Cryoem Structure of SPCA1A in E2P State

Enzymatic activity of Cryoem Structure of SPCA1A in E2P State

All present enzymatic activity of Cryoem Structure of SPCA1A in E2P State:
7.2.2.10;

Other elements in 7yam:

The structure of Cryoem Structure of SPCA1A in E2P 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 SPCA1A in E2P State (pdb code 7yam). 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 SPCA1A in E2P State, PDB code: 7yam:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7yam

Go back to Fluorine Binding Sites List in 7yam
Fluorine binding site 1 out of 3 in the Cryoem Structure of SPCA1A in E2P 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 SPCA1A in E2P State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:3.7
occ:1.00
 F1 A:BEF1001 0.0 3.7 1.0
BE A:BEF1001 1.5 3.7 1.0
MG A:MG1002 1.8 3.0 1.0
OD1 A:ASP350 2.3 2.5 1.0
OD2 A:ASP350 2.3 2.5 1.0
F3 A:BEF1001 2.5 3.7 1.0
F2 A:BEF1001 2.6 3.7 1.0
CG A:ASP350 2.6 2.5 1.0
O A:THR352 2.8 3.0 1.0
CB A:THR352 3.7 3.0 1.0
O A:SER186 3.7 10.1 1.0
C A:THR352 3.7 3.0 1.0
OD1 A:ASP644 3.9 4.4 1.0
CA A:GLY190 3.9 8.3 1.0
N A:THR352 4.0 3.0 1.0
CA A:THR352 4.0 3.0 1.0
CB A:ASP350 4.1 2.5 1.0
OD2 A:ASP648 4.2 4.6 1.0
ND2 A:ASN647 4.3 4.8 1.0
OD1 A:ASN647 4.4 4.8 1.0
CG2 A:THR352 4.5 3.0 1.0
N A:GLY190 4.6 8.3 1.0
OG1 A:THR352 4.6 3.0 1.0
OG1 A:THR570 4.8 2.9 1.0
CG A:ASN647 4.8 4.8 1.0
NZ A:LYS625 4.9 3.2 1.0
C A:SER186 4.9 10.1 1.0
C A:ASP350 4.9 2.5 1.0
N A:GLY353 5.0 2.9 1.0
CA A:ASP350 5.0 2.5 1.0
N A:LYS351 5.0 2.2 1.0
CG A:ASP644 5.0 4.4 1.0

Fluorine binding site 2 out of 3 in 7yam

Go back to Fluorine Binding Sites List in 7yam
Fluorine binding site 2 out of 3 in the Cryoem Structure of SPCA1A in E2P 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 SPCA1A in E2P State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:3.7
occ:1.00
 F2 A:BEF1001 0.0 3.7 1.0
BE A:BEF1001 1.6 3.7 1.0
OG1 A:THR570 2.2 2.9 1.0
OD1 A:ASP350 2.3 2.5 1.0
F3 A:BEF1001 2.5 3.7 1.0
F1 A:BEF1001 2.6 3.7 1.0
N A:THR352 2.9 3.0 1.0
CB A:THR352 3.2 3.0 1.0
OG1 A:THR352 3.3 3.0 1.0
CB A:THR570 3.4 2.9 1.0
CG A:ASP350 3.4 2.5 1.0
CA A:THR352 3.6 3.0 1.0
N A:LYS351 3.7 2.2 1.0
CA A:GLY190 3.7 8.3 1.0
O A:GLY190 3.9 8.3 1.0
OD2 A:ASP350 4.0 2.5 1.0
C A:LYS351 4.0 2.2 1.0
O A:THR352 4.0 3.0 1.0
CA A:THR570 4.0 2.9 1.0
MG A:MG1002 4.1 3.0 1.0
CA A:LYS351 4.2 2.2 1.0
N A:GLY571 4.2 3.6 1.0
CB A:LYS351 4.2 2.2 1.0
C A:THR352 4.3 3.0 1.0
C A:ASP350 4.3 2.5 1.0
C A:GLY190 4.3 8.3 1.0
CG2 A:THR570 4.6 2.9 1.0
CG2 A:THR352 4.6 3.0 1.0
CB A:ASP350 4.6 2.5 1.0
CA A:ASP350 4.6 2.5 1.0
C A:THR570 4.7 2.9 1.0
NZ A:LYS625 4.7 3.2 1.0
CE A:LYS351 4.9 2.2 1.0
N A:GLY190 4.9 8.3 1.0
O A:ILE569 4.9 2.2 1.0

Fluorine binding site 3 out of 3 in 7yam

Go back to Fluorine Binding Sites List in 7yam
Fluorine binding site 3 out of 3 in the Cryoem Structure of SPCA1A in E2P 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 SPCA1A in E2P State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:3.7
occ:1.00
 F3 A:BEF1001 0.0 3.7 1.0
BE A:BEF1001 1.5 3.7 1.0
OD1 A:ASP350 2.3 2.5 1.0
F2 A:BEF1001 2.5 3.7 1.0
F1 A:BEF1001 2.5 3.7 1.0
NZ A:LYS625 2.8 3.2 1.0
ND2 A:ASN647 2.9 4.8 1.0
CG A:ASP350 3.2 2.5 1.0
CG A:ASN647 3.7 4.8 1.0
OG1 A:THR570 3.7 2.9 1.0
OD2 A:ASP350 3.7 2.5 1.0
OD1 A:ASN647 3.8 4.8 1.0
CE A:LYS625 3.9 3.2 1.0
CA A:GLY190 3.9 8.3 1.0
N A:GLY571 3.9 3.6 1.0
MG A:MG1002 4.1 3.0 1.0
CA A:THR570 4.1 2.9 1.0
OD1 A:ASP648 4.2 4.6 1.0
OD2 A:ASP648 4.2 4.6 1.0
CB A:ASP350 4.3 2.5 1.0
CB A:THR570 4.4 2.9 1.0
N A:GLY190 4.4 8.3 1.0
C A:THR570 4.6 2.9 1.0
CG A:ASP648 4.6 4.6 1.0
O A:THR189 4.6 10.3 1.0
C A:THR189 4.7 10.3 1.0
O A:ILE569 4.7 2.2 1.0
CA A:ASP350 4.9 2.5 1.0
CA A:GLY571 4.9 3.6 1.0
CB A:ASN647 5.0 4.8 1.0

Reference:

Z.Chen, S.Watanabe, H.Hashida, M.Inoue, Y.Daigaku, M.Kikkawa, K.Inaba. Cryo-Em Structures of Human SPCA1A Reveal the Mechanism of Ca 2+ /Mn 2+ Transport Into the Golgi Apparatus. Sci Adv V. 9 D9742 2023.
ISSN: ESSN 2375-2548
PubMed: 36867705
DOI: 10.1126/SCIADV.ADD9742
Page generated: Fri Aug 2 15:43:01 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy