Calcium in PDB 8ear: Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp
Other elements in 8ear:
The structure of Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp also contains other interesting chemical elements:
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
16;
Binding sites:
The binding sites of Calcium atom in the Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp
(pdb code 8ear). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the
Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp, PDB code: 8ear:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 16 in 8ear
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Calcium Binding Sites List in 8ear
Calcium binding site 1 out
of 16 in the Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp
![](/pictures/CA/pdb/ea/8ear-CA-sphere_01.jpg) Mono view
![](/pictures/CA/pdb/ea/8ear-CA-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2804
b:130.9
occ:1.00
|
OD1
|
A:ASN2583
|
2.8
|
38.6
|
0.5
|
CG
|
A:ASN2583
|
3.0
|
38.6
|
0.5
|
ND2
|
A:ASN2583
|
3.3
|
38.6
|
0.5
|
CE2
|
B:PHE2586
|
3.6
|
76.9
|
0.5
|
CB
|
A:ASN2583
|
3.7
|
38.6
|
0.5
|
CB
|
A:ASN2583
|
3.8
|
38.6
|
0.5
|
CZ
|
B:PHE2586
|
4.2
|
76.9
|
0.5
|
CD2
|
B:PHE2586
|
4.2
|
76.9
|
0.5
|
O
|
A:ILE2578
|
4.4
|
66.1
|
1.0
|
CA
|
A:ASN2583
|
4.4
|
38.6
|
0.5
|
CA
|
A:ASN2583
|
4.5
|
38.6
|
0.5
|
CD2
|
A:PHE2586
|
4.8
|
76.9
|
0.5
|
N
|
A:ASN2583
|
4.8
|
38.6
|
0.5
|
CE2
|
A:PHE2586
|
4.8
|
76.9
|
0.5
|
CG
|
A:ASN2583
|
4.9
|
38.6
|
0.5
|
N
|
A:ASN2583
|
4.9
|
38.6
|
0.5
|
|
Calcium binding site 2 out
of 16 in 8ear
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Calcium Binding Sites List in 8ear
Calcium binding site 2 out
of 16 in the Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp
![](/pictures/CA/pdb/ea/8ear-CA-sphere_02.jpg) Mono view
![](/pictures/CA/pdb/ea/8ear-CA-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2805
b:151.5
occ:1.00
|
OE1
|
A:GLU283
|
3.7
|
106.3
|
1.0
|
O
|
A:PHE53
|
3.9
|
107.4
|
1.0
|
CD
|
A:GLU283
|
4.1
|
106.3
|
1.0
|
OE2
|
A:GLU283
|
4.2
|
106.3
|
1.0
|
C
|
A:PHE53
|
4.3
|
107.4
|
1.0
|
CB
|
A:PHE53
|
4.4
|
107.4
|
1.0
|
CA
|
A:GLY237
|
4.5
|
88.4
|
1.0
|
CA
|
A:PHE53
|
4.7
|
107.4
|
1.0
|
N
|
A:PHE53
|
4.7
|
107.4
|
1.0
|
CG
|
A:GLU285
|
4.8
|
101.6
|
1.0
|
OE2
|
A:GLU285
|
4.9
|
101.6
|
1.0
|
N
|
A:ARG54
|
4.9
|
103.3
|
1.0
|
|
Calcium binding site 3 out
of 16 in 8ear
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Calcium Binding Sites List in 8ear
Calcium binding site 3 out
of 16 in the Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp
![](/pictures/CA/pdb/ea/8ear-CA-sphere_03.jpg) Mono view
![](/pictures/CA/pdb/ea/8ear-CA-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2806
b:110.4
occ:1.00
|
NE2
|
A:GLN2045
|
2.7
|
101.7
|
1.0
|
O
|
A:TYR2656
|
3.7
|
102.7
|
1.0
|
CD
|
A:GLN2045
|
3.7
|
101.7
|
1.0
|
CG
|
A:GLN2045
|
4.0
|
101.7
|
1.0
|
CG
|
A:GLU2042
|
4.2
|
96.0
|
1.0
|
NE2
|
A:HIS1980
|
4.3
|
104.8
|
1.0
|
OE2
|
A:GLU2042
|
4.4
|
96.0
|
1.0
|
CD
|
A:GLU2042
|
4.8
|
96.0
|
1.0
|
C
|
A:TYR2656
|
4.8
|
102.7
|
1.0
|
CE1
|
A:HIS1980
|
4.8
|
104.8
|
1.0
|
OE1
|
A:GLN2045
|
4.8
|
101.7
|
1.0
|
CB
|
A:GLN2045
|
4.9
|
101.7
|
1.0
|
|
Calcium binding site 4 out
of 16 in 8ear
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Calcium Binding Sites List in 8ear
Calcium binding site 4 out
of 16 in the Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp
![](/pictures/CA/pdb/ea/8ear-CA-sphere_04.jpg) Mono view
![](/pictures/CA/pdb/ea/8ear-CA-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2807
b:114.9
occ:1.00
|
OG
|
A:SER2545
|
3.4
|
76.0
|
1.0
|
ND1
|
A:HIS2541
|
3.4
|
68.0
|
1.0
|
OD1
|
D:ASP2551
|
3.5
|
89.5
|
1.0
|
NH2
|
A:ARG2544
|
3.7
|
77.1
|
1.0
|
CA
|
A:HIS2541
|
4.2
|
68.0
|
1.0
|
O
|
A:HIS2541
|
4.2
|
68.0
|
1.0
|
CB
|
A:HIS2541
|
4.3
|
68.0
|
1.0
|
CG
|
A:HIS2541
|
4.3
|
68.0
|
1.0
|
CE1
|
A:HIS2541
|
4.4
|
68.0
|
1.0
|
CG
|
D:ASP2551
|
4.5
|
89.5
|
1.0
|
CZ
|
A:ARG2544
|
4.5
|
77.1
|
1.0
|
CB
|
A:SER2545
|
4.7
|
76.0
|
1.0
|
C
|
A:HIS2541
|
4.7
|
68.0
|
1.0
|
OD2
|
D:ASP2551
|
4.8
|
89.5
|
1.0
|
N
|
A:SER2545
|
4.9
|
76.0
|
1.0
|
|
Calcium binding site 5 out
of 16 in 8ear
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Calcium Binding Sites List in 8ear
Calcium binding site 5 out
of 16 in the Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp
![](/pictures/CA/pdb/ea/8ear-CA-sphere_05.jpg) Mono view
![](/pictures/CA/pdb/ea/8ear-CA-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2805
b:133.3
occ:1.00
|
OD1
|
B:ASN2583
|
2.8
|
38.6
|
0.5
|
CG
|
B:ASN2583
|
3.0
|
38.6
|
0.5
|
ND2
|
B:ASN2583
|
3.3
|
38.6
|
0.5
|
CE2
|
C:PHE2586
|
3.6
|
76.9
|
0.5
|
CB
|
B:ASN2583
|
3.7
|
38.6
|
0.5
|
CB
|
B:ASN2583
|
3.8
|
38.6
|
0.5
|
CZ
|
C:PHE2586
|
4.2
|
76.9
|
0.5
|
CD2
|
C:PHE2586
|
4.2
|
76.9
|
0.5
|
O
|
B:ILE2578
|
4.3
|
66.1
|
1.0
|
CA
|
B:ASN2583
|
4.4
|
38.6
|
0.5
|
CA
|
B:ASN2583
|
4.4
|
38.6
|
0.5
|
CD2
|
B:PHE2586
|
4.8
|
76.9
|
0.5
|
N
|
B:ASN2583
|
4.8
|
38.6
|
0.5
|
CE2
|
B:PHE2586
|
4.8
|
76.9
|
0.5
|
CG
|
B:ASN2583
|
4.9
|
38.6
|
0.5
|
N
|
B:ASN2583
|
4.9
|
38.6
|
0.5
|
|
Calcium binding site 6 out
of 16 in 8ear
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Calcium Binding Sites List in 8ear
Calcium binding site 6 out
of 16 in the Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp
![](/pictures/CA/pdb/ea/8ear-CA-sphere_06.jpg) Mono view
![](/pictures/CA/pdb/ea/8ear-CA-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2806
b:150.6
occ:1.00
|
OE1
|
B:GLU283
|
3.7
|
106.3
|
1.0
|
O
|
B:PHE53
|
3.9
|
107.4
|
1.0
|
CD
|
B:GLU283
|
4.1
|
106.3
|
1.0
|
OE2
|
B:GLU283
|
4.2
|
106.3
|
1.0
|
C
|
B:PHE53
|
4.3
|
107.4
|
1.0
|
CB
|
B:PHE53
|
4.4
|
107.4
|
1.0
|
CA
|
B:GLY237
|
4.5
|
88.4
|
1.0
|
CA
|
B:PHE53
|
4.7
|
107.4
|
1.0
|
N
|
B:PHE53
|
4.7
|
107.4
|
1.0
|
CG
|
B:GLU285
|
4.8
|
101.6
|
1.0
|
OE2
|
B:GLU285
|
4.9
|
101.6
|
1.0
|
N
|
B:ARG54
|
4.9
|
103.3
|
1.0
|
|
Calcium binding site 7 out
of 16 in 8ear
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Calcium Binding Sites List in 8ear
Calcium binding site 7 out
of 16 in the Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp
![](/pictures/CA/pdb/ea/8ear-CA-sphere_07.jpg) Mono view
![](/pictures/CA/pdb/ea/8ear-CA-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2807
b:112.8
occ:1.00
|
NE2
|
B:GLN2045
|
2.7
|
101.7
|
1.0
|
O
|
B:TYR2656
|
3.7
|
102.7
|
1.0
|
CD
|
B:GLN2045
|
3.8
|
101.7
|
1.0
|
CG
|
B:GLN2045
|
4.0
|
101.7
|
1.0
|
CG
|
B:GLU2042
|
4.2
|
96.0
|
1.0
|
NE2
|
B:HIS1980
|
4.3
|
104.8
|
1.0
|
OE2
|
B:GLU2042
|
4.4
|
96.0
|
1.0
|
CD
|
B:GLU2042
|
4.8
|
96.0
|
1.0
|
C
|
B:TYR2656
|
4.8
|
102.7
|
1.0
|
CE1
|
B:HIS1980
|
4.8
|
104.8
|
1.0
|
OE1
|
B:GLN2045
|
4.8
|
101.7
|
1.0
|
CB
|
B:GLN2045
|
4.9
|
101.7
|
1.0
|
|
Calcium binding site 8 out
of 16 in 8ear
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Calcium Binding Sites List in 8ear
Calcium binding site 8 out
of 16 in the Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp
![](/pictures/CA/pdb/ea/8ear-CA-sphere_08.jpg) Mono view
![](/pictures/CA/pdb/ea/8ear-CA-sphere_08_stereo.jpg) Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2808
b:116.8
occ:1.00
|
OG
|
B:SER2545
|
3.4
|
76.0
|
1.0
|
ND1
|
B:HIS2541
|
3.4
|
68.0
|
1.0
|
OD1
|
A:ASP2551
|
3.5
|
89.5
|
1.0
|
NH2
|
B:ARG2544
|
3.7
|
77.1
|
1.0
|
CA
|
B:HIS2541
|
4.2
|
68.0
|
1.0
|
O
|
B:HIS2541
|
4.2
|
68.0
|
1.0
|
CB
|
B:HIS2541
|
4.3
|
68.0
|
1.0
|
CG
|
B:HIS2541
|
4.3
|
68.0
|
1.0
|
CE1
|
B:HIS2541
|
4.4
|
68.0
|
1.0
|
CG
|
A:ASP2551
|
4.5
|
89.5
|
1.0
|
CZ
|
B:ARG2544
|
4.5
|
77.1
|
1.0
|
C
|
B:HIS2541
|
4.7
|
68.0
|
1.0
|
CB
|
B:SER2545
|
4.7
|
76.0
|
1.0
|
OD2
|
A:ASP2551
|
4.8
|
89.5
|
1.0
|
N
|
B:SER2545
|
4.9
|
76.0
|
1.0
|
|
Calcium binding site 9 out
of 16 in 8ear
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Calcium Binding Sites List in 8ear
Calcium binding site 9 out
of 16 in the Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp
![](/pictures/CA/pdb/ea/8ear-CA-sphere_09.jpg) Mono view
![](/pictures/CA/pdb/ea/8ear-CA-sphere_09_stereo.jpg) Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2809
b:135.7
occ:1.00
|
OD1
|
C:ASN2583
|
2.8
|
38.6
|
0.5
|
CG
|
C:ASN2583
|
3.0
|
38.6
|
0.5
|
ND2
|
C:ASN2583
|
3.3
|
38.6
|
0.5
|
CE2
|
D:PHE2586
|
3.6
|
76.9
|
0.5
|
CB
|
C:ASN2583
|
3.7
|
38.6
|
0.5
|
CB
|
C:ASN2583
|
3.8
|
38.6
|
0.5
|
CZ
|
D:PHE2586
|
4.2
|
76.9
|
0.5
|
CD2
|
D:PHE2586
|
4.2
|
76.9
|
0.5
|
O
|
C:ILE2578
|
4.3
|
66.1
|
1.0
|
CA
|
C:ASN2583
|
4.4
|
38.6
|
0.5
|
CA
|
C:ASN2583
|
4.4
|
38.6
|
0.5
|
CD2
|
C:PHE2586
|
4.8
|
76.9
|
0.5
|
N
|
C:ASN2583
|
4.8
|
38.6
|
0.5
|
CE2
|
C:PHE2586
|
4.8
|
76.9
|
0.5
|
CG
|
C:ASN2583
|
4.8
|
38.6
|
0.5
|
N
|
C:ASN2583
|
4.9
|
38.6
|
0.5
|
|
Calcium binding site 10 out
of 16 in 8ear
Go back to
Calcium Binding Sites List in 8ear
Calcium binding site 10 out
of 16 in the Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp
![](/pictures/CA/pdb/ea/8ear-CA-sphere_10.jpg) Mono view
![](/pictures/CA/pdb/ea/8ear-CA-sphere_10_stereo.jpg) Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Structure of the Full-Length IP3R1 Channel Determined in the Presence of Calcium/IP3/Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2810
b:151.4
occ:1.00
|
OE1
|
C:GLU283
|
3.7
|
106.3
|
1.0
|
O
|
C:PHE53
|
3.9
|
107.4
|
1.0
|
CD
|
C:GLU283
|
4.1
|
106.3
|
1.0
|
OE2
|
C:GLU283
|
4.2
|
106.3
|
1.0
|
C
|
C:PHE53
|
4.3
|
107.4
|
1.0
|
CB
|
C:PHE53
|
4.4
|
107.4
|
1.0
|
CA
|
C:GLY237
|
4.5
|
88.4
|
1.0
|
CA
|
C:PHE53
|
4.7
|
107.4
|
1.0
|
N
|
C:PHE53
|
4.7
|
107.4
|
1.0
|
CG
|
C:GLU285
|
4.8
|
101.6
|
1.0
|
OE2
|
C:GLU285
|
4.9
|
101.6
|
1.0
|
N
|
C:ARG54
|
4.9
|
103.3
|
1.0
|
|
Reference:
G.Fan,
M.R.Baker,
L.E.Terry,
V.Arige,
M.Chen,
A.B.Seryshev,
M.L.Baker,
S.J.Ludtke,
D.I.Yule,
I.I.Serysheva.
Conformational Motions and Ligand-Binding Underlying Gating and Regulation in Ip 3 R Channel. Nat Commun V. 13 6942 2022.
ISSN: ESSN 2041-1723
PubMed: 36376291
DOI: 10.1038/S41467-022-34574-1
Page generated: Fri Jul 19 08:07:54 2024
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