Atomistry » Calcium » PDB 6q77-6qpc » 6qpc
Atomistry »
  Calcium »
    PDB 6q77-6qpc »
      6qpc »

Calcium in PDB 6qpc: Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc (pdb code 6qpc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc, PDB code: 6qpc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6qpc

Go back to Calcium Binding Sites List in 6qpc
Calcium binding site 1 out of 4 in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:65.0
occ:1.00
OE2 A:GLU699 2.5 67.6 1.0
OE1 A:GLU670 2.5 68.7 1.0
OE1 A:GLU699 2.5 67.6 1.0
CD A:GLU699 2.8 67.6 1.0
OD1 A:ASN621 3.0 73.7 1.0
OE2 A:GLU670 3.0 68.7 1.0
CD A:GLU670 3.1 68.7 1.0
OE1 A:GLU624 3.7 73.4 1.0
CB A:ASN620 3.7 70.3 1.0
CG A:ASN621 3.8 73.7 1.0
O A:ALA617 3.9 70.6 1.0
N A:ASN621 4.2 73.7 1.0
ND2 A:ASN621 4.2 73.7 1.0
CG A:ASN620 4.3 70.3 1.0
CG A:GLU699 4.3 67.6 1.0
CA A:ALA617 4.3 70.6 1.0
C A:ASN620 4.4 70.3 1.0
CE A:MET671 4.4 61.4 1.0
CG A:GLU670 4.4 68.7 1.0
CA A:CA1002 4.5 73.7 1.0
O A:LYS616 4.5 71.4 1.0
ND2 A:ASN695 4.5 67.6 1.0
OD1 A:ASN695 4.5 67.6 1.0
CD A:GLU624 4.6 73.4 1.0
C A:ALA617 4.6 70.6 1.0
ND2 A:ASN620 4.6 70.3 1.0
NZ A:LYS616 4.6 71.4 1.0
CA A:ASN620 4.6 70.3 1.0
CA A:ASN621 4.7 73.7 1.0
CB A:ASN621 4.8 73.7 1.0
OE2 A:GLU624 4.9 73.4 1.0
O A:ASN620 4.9 70.3 1.0
OD1 A:ASN620 4.9 70.3 1.0
CG A:ASN695 5.0 67.6 1.0

Calcium binding site 2 out of 4 in 6qpc

Go back to Calcium Binding Sites List in 6qpc
Calcium binding site 2 out of 4 in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:73.7
occ:1.00
OE2 A:GLU670 2.5 68.7 1.0
OD1 A:ASP703 2.5 71.8 1.0
OD2 A:ASP703 2.5 71.8 1.0
OE2 A:GLU624 2.5 73.4 1.0
OE2 A:GLU699 2.6 67.6 1.0
CG A:ASP703 2.8 71.8 1.0
OE1 A:GLU667 2.9 71.3 1.0
CD A:GLU624 3.4 73.4 1.0
OE1 A:GLU624 3.5 73.4 1.0
CD A:GLU699 3.5 67.6 1.0
OH A:TYR299 3.6 64.3 1.0
CD A:GLU670 3.6 68.7 1.0
CG A:GLU699 3.8 67.6 1.0
CD A:GLU667 4.0 71.3 1.0
CG A:GLU670 4.2 68.7 1.0
CB A:ASP703 4.3 71.8 1.0
CA A:CA1001 4.5 65.0 1.0
CB A:GLU667 4.5 71.3 1.0
OE1 A:GLU670 4.6 68.7 1.0
CA A:GLU667 4.6 71.3 1.0
OE1 A:GLU699 4.7 67.6 1.0
O A:GLU667 4.8 71.3 1.0
OE2 A:GLU667 4.8 71.3 1.0
CG A:GLU624 4.8 73.4 1.0
O A:GLU699 4.8 67.6 1.0
CZ A:TYR299 4.8 64.3 1.0
CG A:GLU667 4.9 71.3 1.0

Calcium binding site 3 out of 4 in 6qpc

Go back to Calcium Binding Sites List in 6qpc
Calcium binding site 3 out of 4 in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1001

b:65.0
occ:1.00
OE2 B:GLU699 2.5 67.6 1.0
OE1 B:GLU670 2.5 68.7 1.0
OE1 B:GLU699 2.5 67.6 1.0
CD B:GLU699 2.8 67.6 1.0
OD1 B:ASN621 3.0 73.7 1.0
OE2 B:GLU670 3.0 68.7 1.0
CD B:GLU670 3.1 68.7 1.0
OE1 B:GLU624 3.7 73.4 1.0
CB B:ASN620 3.7 70.3 1.0
CG B:ASN621 3.8 73.7 1.0
O B:ALA617 3.9 70.6 1.0
N B:ASN621 4.2 73.7 1.0
ND2 B:ASN621 4.2 73.7 1.0
CG B:ASN620 4.3 70.3 1.0
CG B:GLU699 4.3 67.6 1.0
CA B:ALA617 4.3 70.6 1.0
C B:ASN620 4.4 70.3 1.0
CE B:MET671 4.4 61.4 1.0
CG B:GLU670 4.4 68.7 1.0
CA B:CA1002 4.5 73.7 1.0
O B:LYS616 4.5 71.4 1.0
ND2 B:ASN695 4.5 67.6 1.0
OD1 B:ASN695 4.5 67.6 1.0
CD B:GLU624 4.6 73.4 1.0
C B:ALA617 4.6 70.6 1.0
ND2 B:ASN620 4.6 70.3 1.0
NZ B:LYS616 4.6 71.4 1.0
CA B:ASN620 4.6 70.3 1.0
CA B:ASN621 4.7 73.7 1.0
CB B:ASN621 4.8 73.7 1.0
OE2 B:GLU624 4.9 73.4 1.0
O B:ASN620 4.9 70.3 1.0
OD1 B:ASN620 4.9 70.3 1.0
CG B:ASN695 5.0 67.6 1.0

Calcium binding site 4 out of 4 in 6qpc

Go back to Calcium Binding Sites List in 6qpc
Calcium binding site 4 out of 4 in the Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of Calcium-Bound MTMEM16F Lipid Scramblase in Nanodisc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1002

b:73.7
occ:1.00
OE2 B:GLU670 2.5 68.7 1.0
OD1 B:ASP703 2.5 71.8 1.0
OD2 B:ASP703 2.5 71.8 1.0
OE2 B:GLU624 2.5 73.4 1.0
OE2 B:GLU699 2.6 67.6 1.0
CG B:ASP703 2.8 71.8 1.0
OE1 B:GLU667 2.9 71.3 1.0
CD B:GLU624 3.4 73.4 1.0
OE1 B:GLU624 3.5 73.4 1.0
CD B:GLU699 3.5 67.6 1.0
OH B:TYR299 3.6 64.3 1.0
CD B:GLU670 3.6 68.7 1.0
CG B:GLU699 3.8 67.6 1.0
CD B:GLU667 4.0 71.3 1.0
CG B:GLU670 4.2 68.7 1.0
CB B:ASP703 4.3 71.8 1.0
CA B:CA1001 4.5 65.0 1.0
CB B:GLU667 4.5 71.3 1.0
OE1 B:GLU670 4.6 68.7 1.0
CA B:GLU667 4.6 71.3 1.0
OE1 B:GLU699 4.7 67.6 1.0
O B:GLU667 4.8 71.3 1.0
OE2 B:GLU667 4.8 71.3 1.0
CG B:GLU624 4.8 73.4 1.0
O B:GLU699 4.8 67.6 1.0
CZ B:TYR299 4.8 64.3 1.0
CG B:GLU667 4.9 71.3 1.0

Reference:

C.Alvadia, N.K.Lim, V.Clerico Mosina, G.T.Oostergetel, R.Dutzler, C.Paulino. Cryo-Em Structures and Functional Characterization of the Murine Lipid Scramblase TMEM16F. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 30785399
DOI: 10.7554/ELIFE.44365
Page generated: Tue Jul 16 13:56:49 2024

Last articles

W in 8QLN
W in 8RJA
V in 8WTN
Te in 8QLN
Re in 9GHX
Rb in 8Z5C
Ni in 9C0T
Ni in 9C0S
Ni in 9GP1
Ni in 9FYO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy