Magnesium in PDB 8fc9: Cryo-Em Structure of the Human TRPV4 - Rhoa, Apo Condition
Enzymatic activity of Cryo-Em Structure of the Human TRPV4 - Rhoa, Apo Condition
All present enzymatic activity of Cryo-Em Structure of the Human TRPV4 - Rhoa, Apo Condition:
3.6.5.2;
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Cryo-Em Structure of the Human TRPV4 - Rhoa, Apo Condition
(pdb code 8fc9). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Cryo-Em Structure of the Human TRPV4 - Rhoa, Apo Condition, PDB code: 8fc9:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8fc9
Go back to
Magnesium Binding Sites List in 8fc9
Magnesium binding site 1 out
of 4 in the Cryo-Em Structure of the Human TRPV4 - Rhoa, Apo Condition
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Cryo-Em Structure of the Human TRPV4 - Rhoa, Apo Condition within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg301
b:130.8
occ:1.00
|
O
|
E:THR37
|
2.1
|
153.4
|
1.0
|
|
OG1
|
E:THR19
|
2.3
|
153.1
|
1.0
|
|
HG1
|
E:THR19
|
2.4
|
153.1
|
1.0
|
|
O1B
|
E:GDP302
|
2.5
|
162.5
|
1.0
|
|
HA
|
E:THR37
|
2.8
|
153.4
|
1.0
|
|
C
|
E:THR37
|
2.9
|
153.4
|
1.0
|
|
HB
|
E:THR19
|
3.3
|
153.1
|
1.0
|
|
CB
|
E:THR19
|
3.3
|
153.1
|
1.0
|
|
CA
|
E:THR37
|
3.4
|
153.4
|
1.0
|
|
HG21
|
E:THR19
|
3.4
|
153.1
|
1.0
|
|
O
|
E:PRO36
|
3.6
|
154.8
|
1.0
|
|
O3B
|
E:GDP302
|
3.7
|
162.5
|
1.0
|
|
PB
|
E:GDP302
|
3.7
|
162.5
|
1.0
|
|
O2A
|
E:GDP302
|
3.8
|
162.5
|
1.0
|
|
HA
|
E:VAL38
|
3.9
|
146.3
|
1.0
|
|
CG2
|
E:THR19
|
3.9
|
153.1
|
1.0
|
|
N
|
E:VAL38
|
3.9
|
146.3
|
1.0
|
|
HB2
|
E:ALA61
|
4.0
|
158.0
|
1.0
|
|
H
|
E:THR19
|
4.1
|
153.1
|
1.0
|
|
OG1
|
E:THR37
|
4.1
|
153.4
|
1.0
|
|
N
|
E:THR37
|
4.4
|
153.4
|
1.0
|
|
C
|
E:PRO36
|
4.4
|
154.8
|
1.0
|
|
HG12
|
E:VAL38
|
4.4
|
146.3
|
1.0
|
|
CB
|
E:THR37
|
4.4
|
153.4
|
1.0
|
|
HG23
|
E:THR19
|
4.4
|
153.1
|
1.0
|
|
CA
|
E:VAL38
|
4.4
|
146.3
|
1.0
|
|
HZ3
|
E:LYS18
|
4.5
|
156.0
|
1.0
|
|
OD2
|
E:ASP59
|
4.5
|
143.7
|
1.0
|
|
HG12
|
E:VAL35
|
4.6
|
156.5
|
1.0
|
|
CA
|
E:THR19
|
4.6
|
153.1
|
1.0
|
|
HG1
|
E:THR37
|
4.6
|
153.4
|
1.0
|
|
H
|
E:VAL38
|
4.6
|
146.3
|
1.0
|
|
PA
|
E:GDP302
|
4.6
|
162.5
|
1.0
|
|
HG22
|
E:THR19
|
4.6
|
153.1
|
1.0
|
|
O3A
|
E:GDP302
|
4.7
|
162.5
|
1.0
|
|
N
|
E:THR19
|
4.7
|
153.1
|
1.0
|
|
HB1
|
E:ALA61
|
4.7
|
158.0
|
1.0
|
|
O2B
|
E:GDP302
|
4.7
|
162.5
|
1.0
|
|
O1A
|
E:GDP302
|
4.8
|
162.5
|
1.0
|
|
CB
|
E:ALA61
|
4.8
|
158.0
|
1.0
|
|
HG13
|
E:VAL38
|
4.8
|
146.3
|
1.0
|
|
HB
|
E:THR37
|
4.9
|
153.4
|
1.0
|
|
HA
|
E:THR19
|
4.9
|
153.1
|
1.0
|
|
CG1
|
E:VAL38
|
5.0
|
146.3
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8fc9
Go back to
Magnesium Binding Sites List in 8fc9
Magnesium binding site 2 out
of 4 in the Cryo-Em Structure of the Human TRPV4 - Rhoa, Apo Condition
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Cryo-Em Structure of the Human TRPV4 - Rhoa, Apo Condition within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg301
b:130.8
occ:1.00
|
O
|
F:THR37
|
2.1
|
153.4
|
1.0
|
|
OG1
|
F:THR19
|
2.3
|
153.1
|
1.0
|
|
HG1
|
F:THR19
|
2.4
|
153.1
|
1.0
|
|
O1B
|
F:GDP302
|
2.5
|
162.5
|
1.0
|
|
HA
|
F:THR37
|
2.8
|
153.4
|
1.0
|
|
C
|
F:THR37
|
2.9
|
153.4
|
1.0
|
|
HB
|
F:THR19
|
3.3
|
153.1
|
1.0
|
|
CB
|
F:THR19
|
3.3
|
153.1
|
1.0
|
|
CA
|
F:THR37
|
3.4
|
153.4
|
1.0
|
|
HG21
|
F:THR19
|
3.4
|
153.1
|
1.0
|
|
O
|
F:PRO36
|
3.6
|
154.8
|
1.0
|
|
O3B
|
F:GDP302
|
3.7
|
162.5
|
1.0
|
|
PB
|
F:GDP302
|
3.7
|
162.5
|
1.0
|
|
O2A
|
F:GDP302
|
3.8
|
162.5
|
1.0
|
|
HA
|
F:VAL38
|
3.9
|
146.3
|
1.0
|
|
CG2
|
F:THR19
|
3.9
|
153.1
|
1.0
|
|
N
|
F:VAL38
|
3.9
|
146.3
|
1.0
|
|
HB2
|
F:ALA61
|
4.0
|
158.0
|
1.0
|
|
H
|
F:THR19
|
4.1
|
153.1
|
1.0
|
|
OG1
|
F:THR37
|
4.1
|
153.4
|
1.0
|
|
N
|
F:THR37
|
4.4
|
153.4
|
1.0
|
|
C
|
F:PRO36
|
4.4
|
154.8
|
1.0
|
|
HG12
|
F:VAL38
|
4.4
|
146.3
|
1.0
|
|
CB
|
F:THR37
|
4.4
|
153.4
|
1.0
|
|
HG23
|
F:THR19
|
4.4
|
153.1
|
1.0
|
|
CA
|
F:VAL38
|
4.4
|
146.3
|
1.0
|
|
HZ3
|
F:LYS18
|
4.5
|
156.0
|
1.0
|
|
OD2
|
F:ASP59
|
4.5
|
143.7
|
1.0
|
|
HG12
|
F:VAL35
|
4.6
|
156.5
|
1.0
|
|
CA
|
F:THR19
|
4.6
|
153.1
|
1.0
|
|
HG1
|
F:THR37
|
4.6
|
153.4
|
1.0
|
|
H
|
F:VAL38
|
4.6
|
146.3
|
1.0
|
|
PA
|
F:GDP302
|
4.6
|
162.5
|
1.0
|
|
HG22
|
F:THR19
|
4.6
|
153.1
|
1.0
|
|
O3A
|
F:GDP302
|
4.7
|
162.5
|
1.0
|
|
N
|
F:THR19
|
4.7
|
153.1
|
1.0
|
|
HB1
|
F:ALA61
|
4.7
|
158.0
|
1.0
|
|
O2B
|
F:GDP302
|
4.7
|
162.5
|
1.0
|
|
O1A
|
F:GDP302
|
4.8
|
162.5
|
1.0
|
|
CB
|
F:ALA61
|
4.8
|
158.0
|
1.0
|
|
HG13
|
F:VAL38
|
4.8
|
146.3
|
1.0
|
|
HB
|
F:THR37
|
4.9
|
153.4
|
1.0
|
|
HA
|
F:THR19
|
4.9
|
153.1
|
1.0
|
|
CG1
|
F:VAL38
|
5.0
|
146.3
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8fc9
Go back to
Magnesium Binding Sites List in 8fc9
Magnesium binding site 3 out
of 4 in the Cryo-Em Structure of the Human TRPV4 - Rhoa, Apo Condition
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Cryo-Em Structure of the Human TRPV4 - Rhoa, Apo Condition within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg301
b:130.8
occ:1.00
|
O
|
G:THR37
|
2.1
|
153.4
|
1.0
|
|
OG1
|
G:THR19
|
2.3
|
153.1
|
1.0
|
|
HG1
|
G:THR19
|
2.4
|
153.1
|
1.0
|
|
O1B
|
G:GDP302
|
2.5
|
162.5
|
1.0
|
|
HA
|
G:THR37
|
2.8
|
153.4
|
1.0
|
|
C
|
G:THR37
|
2.9
|
153.4
|
1.0
|
|
HB
|
G:THR19
|
3.3
|
153.1
|
1.0
|
|
CB
|
G:THR19
|
3.3
|
153.1
|
1.0
|
|
CA
|
G:THR37
|
3.4
|
153.4
|
1.0
|
|
HG21
|
G:THR19
|
3.4
|
153.1
|
1.0
|
|
O
|
G:PRO36
|
3.6
|
154.8
|
1.0
|
|
O3B
|
G:GDP302
|
3.7
|
162.5
|
1.0
|
|
PB
|
G:GDP302
|
3.7
|
162.5
|
1.0
|
|
O2A
|
G:GDP302
|
3.8
|
162.5
|
1.0
|
|
HA
|
G:VAL38
|
3.9
|
146.3
|
1.0
|
|
CG2
|
G:THR19
|
3.9
|
153.1
|
1.0
|
|
N
|
G:VAL38
|
3.9
|
146.3
|
1.0
|
|
HB2
|
G:ALA61
|
4.0
|
158.0
|
1.0
|
|
H
|
G:THR19
|
4.1
|
153.1
|
1.0
|
|
OG1
|
G:THR37
|
4.1
|
153.4
|
1.0
|
|
N
|
G:THR37
|
4.4
|
153.4
|
1.0
|
|
C
|
G:PRO36
|
4.4
|
154.8
|
1.0
|
|
HG12
|
G:VAL38
|
4.4
|
146.3
|
1.0
|
|
CB
|
G:THR37
|
4.4
|
153.4
|
1.0
|
|
HG23
|
G:THR19
|
4.4
|
153.1
|
1.0
|
|
CA
|
G:VAL38
|
4.4
|
146.3
|
1.0
|
|
HZ3
|
G:LYS18
|
4.5
|
156.0
|
1.0
|
|
OD2
|
G:ASP59
|
4.5
|
143.7
|
1.0
|
|
HG12
|
G:VAL35
|
4.6
|
156.5
|
1.0
|
|
CA
|
G:THR19
|
4.6
|
153.1
|
1.0
|
|
HG1
|
G:THR37
|
4.6
|
153.4
|
1.0
|
|
H
|
G:VAL38
|
4.6
|
146.3
|
1.0
|
|
PA
|
G:GDP302
|
4.6
|
162.5
|
1.0
|
|
HG22
|
G:THR19
|
4.6
|
153.1
|
1.0
|
|
O3A
|
G:GDP302
|
4.7
|
162.5
|
1.0
|
|
N
|
G:THR19
|
4.7
|
153.1
|
1.0
|
|
HB1
|
G:ALA61
|
4.7
|
158.0
|
1.0
|
|
O2B
|
G:GDP302
|
4.7
|
162.5
|
1.0
|
|
O1A
|
G:GDP302
|
4.8
|
162.5
|
1.0
|
|
CB
|
G:ALA61
|
4.8
|
158.0
|
1.0
|
|
HG13
|
G:VAL38
|
4.8
|
146.3
|
1.0
|
|
HB
|
G:THR37
|
4.9
|
153.4
|
1.0
|
|
HA
|
G:THR19
|
4.9
|
153.1
|
1.0
|
|
CG1
|
G:VAL38
|
5.0
|
146.3
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8fc9
Go back to
Magnesium Binding Sites List in 8fc9
Magnesium binding site 4 out
of 4 in the Cryo-Em Structure of the Human TRPV4 - Rhoa, Apo Condition
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Cryo-Em Structure of the Human TRPV4 - Rhoa, Apo Condition within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg301
b:130.8
occ:1.00
|
O
|
H:THR37
|
2.1
|
153.4
|
1.0
|
|
OG1
|
H:THR19
|
2.3
|
153.1
|
1.0
|
|
HG1
|
H:THR19
|
2.4
|
153.1
|
1.0
|
|
O1B
|
H:GDP302
|
2.5
|
162.5
|
1.0
|
|
HA
|
H:THR37
|
2.8
|
153.4
|
1.0
|
|
C
|
H:THR37
|
2.9
|
153.4
|
1.0
|
|
HB
|
H:THR19
|
3.3
|
153.1
|
1.0
|
|
CB
|
H:THR19
|
3.3
|
153.1
|
1.0
|
|
CA
|
H:THR37
|
3.4
|
153.4
|
1.0
|
|
HG21
|
H:THR19
|
3.4
|
153.1
|
1.0
|
|
O
|
H:PRO36
|
3.6
|
154.8
|
1.0
|
|
O3B
|
H:GDP302
|
3.7
|
162.5
|
1.0
|
|
PB
|
H:GDP302
|
3.7
|
162.5
|
1.0
|
|
O2A
|
H:GDP302
|
3.8
|
162.5
|
1.0
|
|
HA
|
H:VAL38
|
3.9
|
146.3
|
1.0
|
|
CG2
|
H:THR19
|
3.9
|
153.1
|
1.0
|
|
N
|
H:VAL38
|
3.9
|
146.3
|
1.0
|
|
HB2
|
H:ALA61
|
4.0
|
158.0
|
1.0
|
|
H
|
H:THR19
|
4.1
|
153.1
|
1.0
|
|
OG1
|
H:THR37
|
4.1
|
153.4
|
1.0
|
|
N
|
H:THR37
|
4.4
|
153.4
|
1.0
|
|
C
|
H:PRO36
|
4.4
|
154.8
|
1.0
|
|
HG12
|
H:VAL38
|
4.4
|
146.3
|
1.0
|
|
CB
|
H:THR37
|
4.4
|
153.4
|
1.0
|
|
HG23
|
H:THR19
|
4.4
|
153.1
|
1.0
|
|
CA
|
H:VAL38
|
4.4
|
146.3
|
1.0
|
|
HZ3
|
H:LYS18
|
4.5
|
156.0
|
1.0
|
|
OD2
|
H:ASP59
|
4.5
|
143.7
|
1.0
|
|
HG12
|
H:VAL35
|
4.6
|
156.5
|
1.0
|
|
CA
|
H:THR19
|
4.6
|
153.1
|
1.0
|
|
HG1
|
H:THR37
|
4.6
|
153.4
|
1.0
|
|
H
|
H:VAL38
|
4.6
|
146.3
|
1.0
|
|
PA
|
H:GDP302
|
4.6
|
162.5
|
1.0
|
|
HG22
|
H:THR19
|
4.6
|
153.1
|
1.0
|
|
O3A
|
H:GDP302
|
4.7
|
162.5
|
1.0
|
|
N
|
H:THR19
|
4.7
|
153.1
|
1.0
|
|
HB1
|
H:ALA61
|
4.7
|
158.0
|
1.0
|
|
O2B
|
H:GDP302
|
4.7
|
162.5
|
1.0
|
|
O1A
|
H:GDP302
|
4.8
|
162.5
|
1.0
|
|
CB
|
H:ALA61
|
4.8
|
158.0
|
1.0
|
|
HG13
|
H:VAL38
|
4.8
|
146.3
|
1.0
|
|
HB
|
H:THR37
|
4.9
|
153.4
|
1.0
|
|
HA
|
H:THR19
|
4.9
|
153.1
|
1.0
|
|
Reference:
D.H.Kwon,
F.Zhang,
B.A.Mccray,
S.Feng,
M.Kumar,
J.M.Sullivan,
W.Im,
C.J.Sumner,
S.Y.Lee.
TRPV4-Rho Gtpase Complex Structures Reveal Mechanisms of Gating and Disease. Nat Commun V. 14 3732 2023.
ISSN: ESSN 2041-1723
PubMed: 37353484
DOI: 10.1038/S41467-023-39345-0
Page generated: Fri Oct 4 02:26:57 2024
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