Atomistry » Calcium » PDB 8clg-8db9 » 8d1f
Atomistry »
  Calcium »
    PDB 8clg-8db9 »
      8d1f »

Calcium in PDB 8d1f: HBEST2 5MM CA2+ (CA2+-Bound) Closed State

Other elements in 8d1f:

The structure of HBEST2 5MM CA2+ (CA2+-Bound) Closed State also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the HBEST2 5MM CA2+ (CA2+-Bound) Closed State (pdb code 8d1f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the HBEST2 5MM CA2+ (CA2+-Bound) Closed State, PDB code: 8d1f:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 8d1f

Go back to Calcium Binding Sites List in 8d1f
Calcium binding site 1 out of 5 in the HBEST2 5MM CA2+ (CA2+-Bound) Closed State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of HBEST2 5MM CA2+ (CA2+-Bound) Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:1.6
occ:1.00
O C:ASN296 2.3 1.1 1.0
O C:GLN293 2.5 1.9 1.0
O D:ALA10 2.5 1.7 1.0
OD1 C:ASP304 2.5 1.2 1.0
O C:HOH603 2.6 1.3 1.0
OD2 C:ASP301 2.6 2.1 1.0
OD2 C:ASP304 2.6 1.2 1.0
CG C:ASP304 2.9 1.2 1.0
HB2 C:ASP301 3.3 2.1 1.0
C C:ASN296 3.5 1.1 1.0
CG C:ASP301 3.5 2.1 1.0
HA D:ASN11 3.5 3.2 1.0
C C:GLN293 3.6 1.9 1.0
H C:GLY299 3.6 2.9 1.0
HA C:PRO297 3.6 1.4 1.0
HA C:GLN293 3.6 1.9 1.0
C D:ALA10 3.7 1.7 1.0
H C:ASN296 3.8 1.1 1.0
HA3 C:GLY299 3.8 2.9 1.0
H C:ASP301 3.9 2.1 1.0
CB C:ASP301 3.9 2.1 1.0
HB3 C:ASN296 3.9 1.1 1.0
HG3 C:GLN293 4.0 1.9 1.0
CA C:GLN293 4.2 1.9 1.0
HG2 C:GLN293 4.2 1.9 1.0
CA C:PRO297 4.2 1.4 1.0
CA D:ASN11 4.3 3.2 1.0
N C:PRO297 4.3 1.4 1.0
N C:GLY299 4.3 2.9 1.0
H D:ALA12 4.4 4.5 1.0
CB C:ASP304 4.4 1.2 1.0
CA C:ASN296 4.4 1.1 1.0
N D:ASN11 4.4 3.2 1.0
HA D:ALA10 4.4 1.7 1.0
O D:VAL9 4.4 2.1 1.0
N C:ASN296 4.5 1.1 1.0
O C:HOH677 4.5 1.6 1.0
CA C:GLY299 4.5 2.9 1.0
OD1 C:ASP301 4.5 2.1 1.0
HA C:LEU294 4.5 1.6 1.0
HB3 C:ASP301 4.5 2.1 1.0
CG C:GLN293 4.5 1.9 1.0
O C:GLU292 4.6 2.8 1.0
C C:PRO297 4.6 1.4 1.0
CB C:ASN296 4.6 1.1 1.0
N C:LEU294 4.7 1.6 1.0
CA D:ALA10 4.7 1.7 1.0
N C:ASP301 4.7 2.1 1.0
HA C:ASP304 4.7 1.2 1.0
HB3 C:ASP304 4.8 1.2 1.0
N D:ALA12 4.8 4.5 1.0
HB2 C:ASP304 4.8 1.2 1.0
C D:ASN11 4.9 3.2 1.0
CA C:ASP301 4.9 2.1 1.0
CA C:LEU294 4.9 1.6 1.0
H C:PHE298 5.0 1.7 1.0
N C:PHE298 5.0 1.7 1.0
C C:GLY299 5.0 2.9 1.0

Calcium binding site 2 out of 5 in 8d1f

Go back to Calcium Binding Sites List in 8d1f
Calcium binding site 2 out of 5 in the HBEST2 5MM CA2+ (CA2+-Bound) Closed State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of HBEST2 5MM CA2+ (CA2+-Bound) Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca501

b:1.6
occ:1.00
O E:ASN296 2.3 1.1 1.0
O E:GLN293 2.5 1.9 1.0
OD1 E:ASP304 2.5 1.2 1.0
O A:ALA10 2.5 1.7 1.0
O E:HOH603 2.6 1.3 1.0
OD2 E:ASP301 2.6 2.1 1.0
OD2 E:ASP304 2.6 1.2 1.0
CG E:ASP304 2.9 1.2 1.0
HB2 E:ASP301 3.3 2.1 1.0
C E:ASN296 3.5 1.1 1.0
CG E:ASP301 3.5 2.1 1.0
HA A:ASN11 3.5 3.2 1.0
C E:GLN293 3.6 1.9 1.0
H E:GLY299 3.6 2.9 1.0
HA E:PRO297 3.6 1.4 1.0
HA E:GLN293 3.6 1.9 1.0
C A:ALA10 3.7 1.7 1.0
H E:ASN296 3.8 1.1 1.0
HA3 E:GLY299 3.8 2.9 1.0
H E:ASP301 3.9 2.1 1.0
CB E:ASP301 3.9 2.1 1.0
HB3 E:ASN296 3.9 1.1 1.0
HG3 E:GLN293 4.0 1.9 1.0
CA E:GLN293 4.2 1.9 1.0
HG2 E:GLN293 4.2 1.9 1.0
CA E:PRO297 4.2 1.4 1.0
CA A:ASN11 4.3 3.2 1.0
N E:PRO297 4.3 1.4 1.0
N E:GLY299 4.3 2.9 1.0
H A:ALA12 4.4 4.5 1.0
CB E:ASP304 4.4 1.2 1.0
CA E:ASN296 4.4 1.1 1.0
N A:ASN11 4.4 3.2 1.0
HA A:ALA10 4.4 1.7 1.0
O A:VAL9 4.4 2.1 1.0
N E:ASN296 4.5 1.1 1.0
O E:HOH677 4.5 1.6 1.0
CA E:GLY299 4.5 2.9 1.0
OD1 E:ASP301 4.5 2.1 1.0
HA E:LEU294 4.5 1.6 1.0
HB3 E:ASP301 4.5 2.1 1.0
CG E:GLN293 4.5 1.9 1.0
O E:GLU292 4.6 2.8 1.0
C E:PRO297 4.6 1.4 1.0
CB E:ASN296 4.6 1.1 1.0
N E:LEU294 4.7 1.6 1.0
CA A:ALA10 4.7 1.7 1.0
N E:ASP301 4.7 2.1 1.0
HA E:ASP304 4.7 1.2 1.0
HB3 E:ASP304 4.8 1.2 1.0
N A:ALA12 4.8 4.5 1.0
HB2 E:ASP304 4.8 1.2 1.0
C A:ASN11 4.9 3.2 1.0
CA E:ASP301 4.9 2.1 1.0
CA E:LEU294 4.9 1.6 1.0
H E:PHE298 5.0 1.7 1.0
N E:PHE298 5.0 1.7 1.0
C E:GLY299 5.0 2.9 1.0

Calcium binding site 3 out of 5 in 8d1f

Go back to Calcium Binding Sites List in 8d1f
Calcium binding site 3 out of 5 in the HBEST2 5MM CA2+ (CA2+-Bound) Closed State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of HBEST2 5MM CA2+ (CA2+-Bound) Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:1.6
occ:1.00
O A:ASN296 2.3 1.1 1.0
O A:GLN293 2.5 1.9 1.0
O B:ALA10 2.5 1.7 1.0
OD1 A:ASP304 2.5 1.2 1.0
O A:HOH603 2.6 1.3 1.0
OD2 A:ASP301 2.6 2.1 1.0
OD2 A:ASP304 2.6 1.2 1.0
CG A:ASP304 2.9 1.2 1.0
HB2 A:ASP301 3.3 2.1 1.0
C A:ASN296 3.5 1.1 1.0
CG A:ASP301 3.5 2.1 1.0
HA B:ASN11 3.5 3.2 1.0
C A:GLN293 3.6 1.9 1.0
H A:GLY299 3.6 2.9 1.0
HA A:PRO297 3.6 1.4 1.0
HA A:GLN293 3.6 1.9 1.0
C B:ALA10 3.7 1.7 1.0
H A:ASN296 3.8 1.1 1.0
HA3 A:GLY299 3.8 2.9 1.0
H A:ASP301 3.9 2.1 1.0
CB A:ASP301 3.9 2.1 1.0
HB3 A:ASN296 4.0 1.1 1.0
HG3 A:GLN293 4.0 1.9 1.0
CA A:GLN293 4.2 1.9 1.0
HG2 A:GLN293 4.2 1.9 1.0
CA A:PRO297 4.2 1.4 1.0
CA B:ASN11 4.3 3.2 1.0
N A:PRO297 4.3 1.4 1.0
N A:GLY299 4.3 2.9 1.0
H B:ALA12 4.4 4.5 1.0
CB A:ASP304 4.4 1.2 1.0
N B:ASN11 4.4 3.2 1.0
CA A:ASN296 4.4 1.1 1.0
HA B:ALA10 4.4 1.7 1.0
O B:VAL9 4.4 2.1 1.0
N A:ASN296 4.5 1.1 1.0
O A:HOH677 4.5 1.6 1.0
CA A:GLY299 4.5 2.9 1.0
OD1 A:ASP301 4.5 2.1 1.0
HA A:LEU294 4.5 1.6 1.0
HB3 A:ASP301 4.5 2.1 1.0
CG A:GLN293 4.5 1.9 1.0
O A:GLU292 4.6 2.8 1.0
C A:PRO297 4.6 1.4 1.0
CB A:ASN296 4.6 1.1 1.0
N A:LEU294 4.7 1.6 1.0
CA B:ALA10 4.7 1.7 1.0
N A:ASP301 4.7 2.1 1.0
HA A:ASP304 4.7 1.2 1.0
HB3 A:ASP304 4.8 1.2 1.0
N B:ALA12 4.8 4.5 1.0
HB2 A:ASP304 4.8 1.2 1.0
C B:ASN11 4.9 3.2 1.0
CA A:ASP301 4.9 2.1 1.0
CA A:LEU294 4.9 1.6 1.0
H A:PHE298 5.0 1.7 1.0
N A:PHE298 5.0 1.7 1.0
C A:GLY299 5.0 2.9 1.0

Calcium binding site 4 out of 5 in 8d1f

Go back to Calcium Binding Sites List in 8d1f
Calcium binding site 4 out of 5 in the HBEST2 5MM CA2+ (CA2+-Bound) Closed State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of HBEST2 5MM CA2+ (CA2+-Bound) Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:1.6
occ:1.00
O D:ASN296 2.3 1.1 1.0
O D:GLN293 2.5 1.9 1.0
O E:ALA10 2.5 1.7 1.0
OD1 D:ASP304 2.5 1.2 1.0
O D:HOH603 2.6 1.3 1.0
OD2 D:ASP301 2.6 2.1 1.0
OD2 D:ASP304 2.6 1.2 1.0
CG D:ASP304 2.9 1.2 1.0
HB2 D:ASP301 3.3 2.1 1.0
C D:ASN296 3.5 1.1 1.0
CG D:ASP301 3.5 2.1 1.0
HA E:ASN11 3.5 3.2 1.0
C D:GLN293 3.6 1.9 1.0
H D:GLY299 3.6 2.9 1.0
HA D:PRO297 3.6 1.4 1.0
HA D:GLN293 3.6 1.9 1.0
C E:ALA10 3.7 1.7 1.0
H D:ASN296 3.8 1.1 1.0
HA3 D:GLY299 3.8 2.9 1.0
H D:ASP301 3.9 2.1 1.0
CB D:ASP301 3.9 2.1 1.0
HB3 D:ASN296 3.9 1.1 1.0
HG3 D:GLN293 4.0 1.9 1.0
CA D:GLN293 4.2 1.9 1.0
HG2 D:GLN293 4.2 1.9 1.0
CA D:PRO297 4.2 1.4 1.0
CA E:ASN11 4.3 3.2 1.0
N D:PRO297 4.3 1.4 1.0
N D:GLY299 4.3 2.9 1.0
H E:ALA12 4.4 4.5 1.0
CB D:ASP304 4.4 1.2 1.0
N E:ASN11 4.4 3.2 1.0
CA D:ASN296 4.4 1.1 1.0
HA E:ALA10 4.4 1.7 1.0
O E:VAL9 4.4 2.1 1.0
N D:ASN296 4.5 1.1 1.0
O D:HOH677 4.5 1.6 1.0
CA D:GLY299 4.5 2.9 1.0
OD1 D:ASP301 4.5 2.1 1.0
HA D:LEU294 4.5 1.6 1.0
HB3 D:ASP301 4.5 2.1 1.0
CG D:GLN293 4.5 1.9 1.0
O D:GLU292 4.6 2.8 1.0
C D:PRO297 4.6 1.4 1.0
CB D:ASN296 4.6 1.1 1.0
N D:LEU294 4.7 1.6 1.0
CA E:ALA10 4.7 1.7 1.0
N D:ASP301 4.7 2.1 1.0
HA D:ASP304 4.7 1.2 1.0
HB3 D:ASP304 4.8 1.2 1.0
N E:ALA12 4.8 4.5 1.0
HB2 D:ASP304 4.8 1.2 1.0
C E:ASN11 4.9 3.2 1.0
CA D:ASP301 4.9 2.1 1.0
CA D:LEU294 4.9 1.6 1.0
H D:PHE298 5.0 1.7 1.0
N D:PHE298 5.0 1.7 1.0
C D:GLY299 5.0 2.9 1.0

Calcium binding site 5 out of 5 in 8d1f

Go back to Calcium Binding Sites List in 8d1f
Calcium binding site 5 out of 5 in the HBEST2 5MM CA2+ (CA2+-Bound) Closed State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of HBEST2 5MM CA2+ (CA2+-Bound) Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:1.6
occ:1.00
O B:ASN296 2.3 1.1 1.0
O B:GLN293 2.5 1.9 1.0
OD1 B:ASP304 2.5 1.2 1.0
O C:ALA10 2.5 1.7 1.0
O B:HOH603 2.6 1.3 1.0
OD2 B:ASP301 2.6 2.1 1.0
OD2 B:ASP304 2.6 1.2 1.0
CG B:ASP304 2.9 1.2 1.0
HB2 B:ASP301 3.3 2.1 1.0
C B:ASN296 3.5 1.1 1.0
CG B:ASP301 3.5 2.1 1.0
HA C:ASN11 3.5 3.2 1.0
C B:GLN293 3.6 1.9 1.0
H B:GLY299 3.6 2.9 1.0
HA B:PRO297 3.6 1.4 1.0
HA B:GLN293 3.6 1.9 1.0
C C:ALA10 3.7 1.7 1.0
H B:ASN296 3.8 1.1 1.0
HA3 B:GLY299 3.8 2.9 1.0
H B:ASP301 3.9 2.1 1.0
CB B:ASP301 3.9 2.1 1.0
HB3 B:ASN296 3.9 1.1 1.0
HG3 B:GLN293 4.0 1.9 1.0
CA B:GLN293 4.2 1.9 1.0
HG2 B:GLN293 4.2 1.9 1.0
CA B:PRO297 4.2 1.4 1.0
CA C:ASN11 4.3 3.2 1.0
N B:PRO297 4.3 1.4 1.0
N B:GLY299 4.3 2.9 1.0
H C:ALA12 4.4 4.5 1.0
CB B:ASP304 4.4 1.2 1.0
CA B:ASN296 4.4 1.1 1.0
N C:ASN11 4.4 3.2 1.0
HA C:ALA10 4.4 1.7 1.0
O C:VAL9 4.4 2.1 1.0
N B:ASN296 4.5 1.1 1.0
O B:HOH677 4.5 1.6 1.0
CA B:GLY299 4.5 2.9 1.0
OD1 B:ASP301 4.5 2.1 1.0
HA B:LEU294 4.5 1.6 1.0
HB3 B:ASP301 4.5 2.1 1.0
CG B:GLN293 4.5 1.9 1.0
O B:GLU292 4.6 2.8 1.0
C B:PRO297 4.6 1.4 1.0
CB B:ASN296 4.6 1.1 1.0
N B:LEU294 4.7 1.6 1.0
CA C:ALA10 4.7 1.7 1.0
N B:ASP301 4.7 2.1 1.0
HA B:ASP304 4.7 1.2 1.0
HB3 B:ASP304 4.8 1.2 1.0
N C:ALA12 4.8 4.5 1.0
HB2 B:ASP304 4.8 1.2 1.0
C C:ASN11 4.9 3.2 1.0
CA B:ASP301 4.9 2.1 1.0
CA B:LEU294 4.9 1.6 1.0
H B:PHE298 5.0 1.7 1.0
N B:PHE298 5.0 1.7 1.0
C B:GLY299 5.0 2.9 1.0

Reference:

A.P.Owji, J.Wang, A.Kittredge, Z.Clark, Y.Zhang, W.A.Hendrickson, T.Yang. Structures and Gating Mechanisms of Human Bestrophin Anion Channels. Nat Commun V. 13 3836 2022.
ISSN: ESSN 2041-1723
PubMed: 35789156
DOI: 10.1038/S41467-022-31437-7
Page generated: Thu Jul 10 03:48:12 2025

Last articles

Mg in 6VZS
Mg in 6VZT
Mg in 6VZR
Mg in 6VZQ
Mg in 6VZ8
Mg in 6VZ9
Mg in 6VYD
Mg in 6VZ4
Mg in 6VWP
Mg in 6VWW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy