Magnesium in PDB 5a3s: Crystal Structure of the (Sr) Calcium Atpase E2-Vanadate Complex Bound to Thapsigargin and Tnp-Atp
Enzymatic activity of Crystal Structure of the (Sr) Calcium Atpase E2-Vanadate Complex Bound to Thapsigargin and Tnp-Atp
All present enzymatic activity of Crystal Structure of the (Sr) Calcium Atpase E2-Vanadate Complex Bound to Thapsigargin and Tnp-Atp:
3.6.3.8;
Protein crystallography data
The structure of Crystal Structure of the (Sr) Calcium Atpase E2-Vanadate Complex Bound to Thapsigargin and Tnp-Atp, PDB code: 5a3s
was solved by
J.D.Clausen,
M.Bublitz,
B.Arnou,
C.Olesen,
J.P.Andersen,
J.V.Moller,
P.Nissen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
78.91 /
3.30
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
130.556,
93.778,
135.692,
90.00,
107.26,
90.00
|
R / Rfree (%)
|
21.1 /
24.5
|
Other elements in 5a3s:
The structure of Crystal Structure of the (Sr) Calcium Atpase E2-Vanadate Complex Bound to Thapsigargin and Tnp-Atp also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the (Sr) Calcium Atpase E2-Vanadate Complex Bound to Thapsigargin and Tnp-Atp
(pdb code 5a3s). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of the (Sr) Calcium Atpase E2-Vanadate Complex Bound to Thapsigargin and Tnp-Atp, PDB code: 5a3s:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5a3s
Go back to
Magnesium Binding Sites List in 5a3s
Magnesium binding site 1 out
of 4 in the Crystal Structure of the (Sr) Calcium Atpase E2-Vanadate Complex Bound to Thapsigargin and Tnp-Atp
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of the (Sr) Calcium Atpase E2-Vanadate Complex Bound to Thapsigargin and Tnp-Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1003
b:92.8
occ:1.00
|
O
|
A:HOH2001
|
1.9
|
0.6
|
1.0
|
OD2
|
A:ASP351
|
2.0
|
0.5
|
1.0
|
O
|
A:HOH2003
|
2.0
|
1.0
|
1.0
|
O
|
A:THR353
|
2.0
|
68.1
|
1.0
|
OD1
|
A:ASP703
|
2.1
|
83.7
|
1.0
|
O2
|
A:VN41001
|
2.1
|
1.0
|
1.0
|
CG
|
A:ASP351
|
3.1
|
92.3
|
1.0
|
CG
|
A:ASP703
|
3.2
|
84.1
|
1.0
|
C
|
A:THR353
|
3.3
|
65.3
|
1.0
|
V
|
A:VN41001
|
3.5
|
95.2
|
1.0
|
OD2
|
A:ASP703
|
3.6
|
1.0
|
1.0
|
OD1
|
A:ASP351
|
3.7
|
0.7
|
1.0
|
O
|
A:GLY182
|
3.9
|
64.0
|
1.0
|
OD2
|
A:ASP707
|
4.0
|
0.5
|
1.0
|
CA
|
A:THR353
|
4.2
|
57.7
|
1.0
|
N
|
A:GLY354
|
4.2
|
66.8
|
1.0
|
CB
|
A:ASP351
|
4.3
|
68.9
|
1.0
|
CB
|
A:THR353
|
4.3
|
65.4
|
1.0
|
CA
|
A:GLY354
|
4.3
|
66.7
|
1.0
|
N
|
A:GLY704
|
4.3
|
69.2
|
1.0
|
N
|
A:THR353
|
4.4
|
67.8
|
1.0
|
CB
|
A:ASP703
|
4.4
|
70.7
|
1.0
|
CG2
|
A:THR353
|
4.5
|
58.4
|
1.0
|
N
|
A:ASP703
|
4.5
|
62.4
|
1.0
|
O1
|
A:VN41001
|
4.5
|
1.0
|
1.0
|
O3
|
A:VN41001
|
4.5
|
85.6
|
1.0
|
OG1
|
A:THR355
|
4.6
|
71.2
|
1.0
|
N
|
A:THR355
|
4.7
|
53.2
|
1.0
|
C
|
A:ASP703
|
4.7
|
64.6
|
1.0
|
CA
|
A:GLY182
|
4.7
|
67.4
|
1.0
|
CA
|
A:ASP703
|
4.8
|
63.4
|
1.0
|
C
|
A:GLY354
|
4.8
|
62.4
|
1.0
|
CA
|
A:GLY704
|
4.8
|
89.4
|
1.0
|
C
|
A:GLY182
|
4.8
|
66.2
|
1.0
|
O
|
A:HOH2002
|
4.9
|
0.7
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5a3s
Go back to
Magnesium Binding Sites List in 5a3s
Magnesium binding site 2 out
of 4 in the Crystal Structure of the (Sr) Calcium Atpase E2-Vanadate Complex Bound to Thapsigargin and Tnp-Atp
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of the (Sr) Calcium Atpase E2-Vanadate Complex Bound to Thapsigargin and Tnp-Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1004
b:0.8
occ:1.00
|
OD1
|
A:ASN628
|
2.1
|
0.3
|
1.0
|
O
|
A:HOH2004
|
2.2
|
72.3
|
1.0
|
O2B
|
A:1281002
|
2.2
|
0.8
|
1.0
|
O3G
|
A:1281002
|
2.4
|
0.4
|
1.0
|
CG
|
A:ASN628
|
3.2
|
69.1
|
1.0
|
PB
|
A:1281002
|
3.4
|
0.1
|
1.0
|
PG
|
A:1281002
|
3.5
|
0.7
|
1.0
|
ND2
|
A:ASN628
|
3.7
|
59.5
|
1.0
|
O3B
|
A:1281002
|
3.7
|
0.7
|
1.0
|
N7
|
A:1281002
|
3.8
|
0.8
|
1.0
|
O3A
|
A:1281002
|
4.0
|
0.9
|
1.0
|
O1G
|
A:1281002
|
4.1
|
0.2
|
1.0
|
NH1
|
A:ARG560
|
4.2
|
0.4
|
1.0
|
C8
|
A:1281002
|
4.5
|
0.1
|
1.0
|
CB
|
A:ASN628
|
4.5
|
45.5
|
1.0
|
C5
|
A:1281002
|
4.6
|
0.2
|
1.0
|
N6
|
A:1281002
|
4.6
|
0.5
|
1.0
|
O1B
|
A:1281002
|
4.7
|
0.8
|
1.0
|
CZ
|
A:ARG560
|
4.8
|
0.3
|
1.0
|
O2G
|
A:1281002
|
4.8
|
0.1
|
1.0
|
C6
|
A:1281002
|
5.0
|
0.8
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5a3s
Go back to
Magnesium Binding Sites List in 5a3s
Magnesium binding site 3 out
of 4 in the Crystal Structure of the (Sr) Calcium Atpase E2-Vanadate Complex Bound to Thapsigargin and Tnp-Atp
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of the (Sr) Calcium Atpase E2-Vanadate Complex Bound to Thapsigargin and Tnp-Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1003
b:0.9
occ:1.00
|
O
|
B:HOH2001
|
2.0
|
91.9
|
1.0
|
OD2
|
B:ASP351
|
2.1
|
87.1
|
1.0
|
O
|
B:THR353
|
2.1
|
93.2
|
1.0
|
O
|
B:HOH2003
|
2.1
|
98.0
|
1.0
|
OD1
|
B:ASP703
|
2.1
|
98.3
|
1.0
|
O2
|
B:VN41001
|
2.2
|
0.0
|
1.0
|
CG
|
B:ASP703
|
3.0
|
92.1
|
1.0
|
OD2
|
B:ASP703
|
3.2
|
93.7
|
1.0
|
CG
|
B:ASP351
|
3.2
|
74.6
|
1.0
|
C
|
B:THR353
|
3.3
|
78.6
|
1.0
|
V
|
B:VN41001
|
3.6
|
88.6
|
1.0
|
OD2
|
B:ASP707
|
3.9
|
0.1
|
1.0
|
OD1
|
B:ASP351
|
3.9
|
65.9
|
1.0
|
O
|
B:GLY182
|
4.1
|
58.0
|
1.0
|
N
|
B:GLY354
|
4.2
|
78.3
|
1.0
|
CA
|
B:THR353
|
4.2
|
82.7
|
1.0
|
OG1
|
B:THR355
|
4.2
|
94.1
|
1.0
|
CB
|
B:ASP351
|
4.3
|
80.2
|
1.0
|
CA
|
B:GLY354
|
4.3
|
85.5
|
1.0
|
CB
|
B:THR353
|
4.3
|
81.3
|
1.0
|
CB
|
B:ASP703
|
4.4
|
89.3
|
1.0
|
N
|
B:GLY704
|
4.4
|
87.3
|
1.0
|
N
|
B:THR353
|
4.4
|
90.0
|
1.0
|
N
|
B:THR355
|
4.4
|
97.9
|
1.0
|
O3
|
B:VN41001
|
4.5
|
0.0
|
1.0
|
N
|
B:ASP703
|
4.6
|
88.2
|
1.0
|
O1
|
B:VN41001
|
4.7
|
92.3
|
1.0
|
C
|
B:GLY354
|
4.8
|
88.3
|
1.0
|
CG2
|
B:THR353
|
4.8
|
87.8
|
1.0
|
C
|
B:ASP703
|
4.8
|
97.6
|
1.0
|
CA
|
B:GLY182
|
4.8
|
45.5
|
1.0
|
CA
|
B:GLY704
|
4.8
|
85.1
|
1.0
|
CA
|
B:ASP703
|
4.9
|
92.3
|
1.0
|
C
|
B:GLY182
|
4.9
|
47.9
|
1.0
|
CG
|
B:ASP707
|
5.0
|
91.0
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5a3s
Go back to
Magnesium Binding Sites List in 5a3s
Magnesium binding site 4 out
of 4 in the Crystal Structure of the (Sr) Calcium Atpase E2-Vanadate Complex Bound to Thapsigargin and Tnp-Atp
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of the (Sr) Calcium Atpase E2-Vanadate Complex Bound to Thapsigargin and Tnp-Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1004
b:0.3
occ:1.00
|
OD1
|
B:ASN628
|
2.1
|
1.0
|
1.0
|
O
|
B:HOH2004
|
2.2
|
0.0
|
1.0
|
O2B
|
B:1281002
|
2.3
|
0.1
|
1.0
|
O3G
|
B:1281002
|
3.0
|
0.6
|
1.0
|
CG
|
B:ASN628
|
3.0
|
0.8
|
1.0
|
ND2
|
B:ASN628
|
3.3
|
1.0
|
1.0
|
PB
|
B:1281002
|
3.4
|
0.2
|
1.0
|
N7
|
B:1281002
|
3.6
|
0.7
|
1.0
|
O3A
|
B:1281002
|
3.7
|
0.9
|
1.0
|
PG
|
B:1281002
|
3.7
|
0.2
|
1.0
|
O3B
|
B:1281002
|
3.9
|
0.2
|
1.0
|
O1G
|
B:1281002
|
4.0
|
0.2
|
1.0
|
C8
|
B:1281002
|
4.3
|
0.0
|
1.0
|
CB
|
B:ASN628
|
4.5
|
89.3
|
1.0
|
OD1
|
B:ASP627
|
4.5
|
0.7
|
1.0
|
C5
|
B:1281002
|
4.6
|
0.3
|
1.0
|
N6
|
B:1281002
|
4.6
|
0.6
|
1.0
|
O1B
|
B:1281002
|
4.8
|
0.3
|
1.0
|
NH1
|
B:ARG678
|
5.0
|
82.8
|
1.0
|
|
Reference:
J.D.Clausen,
M.Bublitz,
B.Arnou,
C.Olesen,
J.P.Andersen,
J.V.Moller,
P.Nissen.
Crystal Structure of the Vanadate-Inhibited Ca(2+)-Atpase. Structure V. 24 617 2016.
ISSN: ISSN 0969-2126
PubMed: 27050689
DOI: 10.1016/J.STR.2016.02.018
Page generated: Sun Sep 29 00:18:01 2024
|