Magnesium in PDB 6yso: Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing
Enzymatic activity of Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing
All present enzymatic activity of Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing:
7.2.2.10;
Protein crystallography data
The structure of Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing, PDB code: 6yso
was solved by
K.El Omari,
N.Mohamad,
K.Bountra,
R.Duman,
M.Romano,
K.Schlegel,
H.Kwong,
V.Mykhaylyk,
C.E.Olesen,
J.V.Moller,
M.Bublitz,
K.Beis,
A.Wagner,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
64.59 /
3.13
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
131.140,
94.390,
135.110,
90.00,
107.05,
90.00
|
R / Rfree (%)
|
20.1 /
25.9
|
Other elements in 6yso:
The structure of Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing
(pdb code 6yso). 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) CA2+-Atpase Solved By Vanadium Sad Phasing, PDB code: 6yso:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6yso
Go back to
Magnesium Binding Sites List in 6yso
Magnesium binding site 1 out
of 4 in the Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing
![](/pictures/MG/pdb/ys/6yso-MG-sphere_01.jpg) Mono view
![](/pictures/MG/pdb/ys/6yso-MG-sphere_01_stereo.jpg) 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) CA2+-Atpase Solved By Vanadium Sad Phasing within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1003
b:98.7
occ:1.00
|
O
|
A:HOH1104
|
1.9
|
0.1
|
1.0
|
OD2
|
A:ASP351
|
2.0
|
0.7
|
1.0
|
O
|
A:HOH1102
|
2.0
|
87.2
|
1.0
|
O
|
A:THR353
|
2.0
|
66.3
|
1.0
|
OD1
|
A:ASP703
|
2.1
|
78.0
|
1.0
|
O3
|
A:VN41002
|
2.3
|
0.1
|
1.0
|
CG
|
A:ASP703
|
3.1
|
77.1
|
1.0
|
CG
|
A:ASP351
|
3.2
|
91.6
|
1.0
|
C
|
A:THR353
|
3.2
|
82.1
|
1.0
|
OD2
|
A:ASP703
|
3.6
|
85.3
|
1.0
|
V
|
A:VN41002
|
3.7
|
0.0
|
1.0
|
OG1
|
A:THR353
|
3.7
|
0.4
|
1.0
|
OD1
|
A:ASP351
|
3.8
|
0.0
|
1.0
|
N
|
A:GLY354
|
4.1
|
80.2
|
1.0
|
CA
|
A:GLY354
|
4.1
|
73.3
|
1.0
|
O
|
A:GLY182
|
4.2
|
82.0
|
1.0
|
N
|
A:GLY704
|
4.2
|
83.2
|
1.0
|
CA
|
A:THR353
|
4.3
|
85.0
|
1.0
|
OD2
|
A:ASP707
|
4.3
|
95.6
|
1.0
|
N
|
A:THR353
|
4.3
|
85.7
|
1.0
|
CB
|
A:ASP351
|
4.3
|
70.8
|
1.0
|
CB
|
A:ASP703
|
4.4
|
73.3
|
1.0
|
O1
|
A:VN41002
|
4.6
|
92.0
|
1.0
|
OG1
|
A:THR355
|
4.6
|
65.2
|
1.0
|
CB
|
A:THR353
|
4.6
|
78.3
|
1.0
|
C
|
A:GLY354
|
4.6
|
64.8
|
1.0
|
N
|
A:ASP703
|
4.6
|
75.2
|
1.0
|
N
|
A:THR355
|
4.7
|
65.5
|
1.0
|
CA
|
A:GLY704
|
4.8
|
97.8
|
1.0
|
C
|
A:ASP703
|
4.8
|
82.0
|
1.0
|
CA
|
A:GLY182
|
4.9
|
77.4
|
1.0
|
O2
|
A:VN41002
|
4.9
|
0.2
|
1.0
|
CA
|
A:ASP703
|
4.9
|
77.4
|
1.0
|
C
|
A:GLY182
|
5.0
|
80.2
|
1.0
|
C
|
A:LYS352
|
5.0
|
86.5
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6yso
Go back to
Magnesium Binding Sites List in 6yso
Magnesium binding site 2 out
of 4 in the Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing
![](/pictures/MG/pdb/ys/6yso-MG-sphere_02.jpg) Mono view
![](/pictures/MG/pdb/ys/6yso-MG-sphere_02_stereo.jpg) 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) CA2+-Atpase Solved By Vanadium Sad Phasing within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1004
b:0.9
occ:1.00
|
OD1
|
A:ASN628
|
1.9
|
0.3
|
1.0
|
O
|
A:HOH1103
|
2.0
|
0.6
|
1.0
|
O3G
|
A:1281000
|
2.0
|
0.6
|
1.0
|
O1B
|
A:1281000
|
2.9
|
0.2
|
1.0
|
CG
|
A:ASN628
|
3.1
|
0.9
|
1.0
|
PG
|
A:1281000
|
3.3
|
0.1
|
1.0
|
ND2
|
A:ASN628
|
3.8
|
0.8
|
1.0
|
PB
|
A:1281000
|
3.9
|
0.2
|
1.0
|
O1G
|
A:1281000
|
4.0
|
0.7
|
1.0
|
NH2
|
A:ARG560
|
4.0
|
95.4
|
1.0
|
O3B
|
A:1281000
|
4.1
|
0.8
|
1.0
|
N7
|
A:1281000
|
4.2
|
0.8
|
1.0
|
CB
|
A:ASN628
|
4.3
|
0.3
|
1.0
|
O2B
|
A:1281000
|
4.4
|
0.8
|
1.0
|
O2G
|
A:1281000
|
4.5
|
0.3
|
1.0
|
C8
|
A:1281000
|
4.8
|
0.7
|
1.0
|
N6
|
A:1281000
|
5.0
|
99.5
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6yso
Go back to
Magnesium Binding Sites List in 6yso
Magnesium binding site 3 out
of 4 in the Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing
![](/pictures/MG/pdb/ys/6yso-MG-sphere_03.jpg) Mono view
![](/pictures/MG/pdb/ys/6yso-MG-sphere_03_stereo.jpg) 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) CA2+-Atpase Solved By Vanadium Sad Phasing within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg2003
b:93.2
occ:1.00
|
O
|
B:HOH2102
|
2.0
|
74.6
|
1.0
|
OD1
|
B:ASP703
|
2.0
|
88.5
|
1.0
|
OD2
|
B:ASP351
|
2.0
|
94.5
|
1.0
|
O
|
B:THR353
|
2.1
|
96.6
|
1.0
|
O
|
B:HOH2104
|
2.3
|
0.9
|
1.0
|
O3
|
B:VN42002
|
2.4
|
0.7
|
1.0
|
CG
|
B:ASP703
|
2.9
|
92.6
|
1.0
|
OD2
|
B:ASP703
|
3.0
|
62.6
|
1.0
|
CG
|
B:ASP351
|
3.2
|
79.6
|
1.0
|
C
|
B:THR353
|
3.3
|
87.4
|
1.0
|
V
|
B:VN42002
|
3.8
|
99.5
|
1.0
|
OD1
|
B:ASP351
|
3.9
|
81.8
|
1.0
|
OD2
|
B:ASP707
|
4.0
|
0.8
|
1.0
|
O
|
B:GLY182
|
4.1
|
76.2
|
1.0
|
N
|
B:GLY354
|
4.2
|
86.2
|
1.0
|
CA
|
B:GLY354
|
4.2
|
98.9
|
1.0
|
CA
|
B:THR353
|
4.2
|
81.2
|
1.0
|
CB
|
B:THR353
|
4.3
|
74.6
|
1.0
|
N
|
B:GLY704
|
4.3
|
82.5
|
1.0
|
CB
|
B:ASP703
|
4.3
|
89.3
|
1.0
|
CB
|
B:ASP351
|
4.3
|
70.5
|
1.0
|
OG1
|
B:THR355
|
4.4
|
0.7
|
1.0
|
N
|
B:THR353
|
4.4
|
77.6
|
1.0
|
CG2
|
B:THR353
|
4.5
|
76.5
|
1.0
|
N
|
B:ASP703
|
4.6
|
97.7
|
1.0
|
N
|
B:THR355
|
4.6
|
98.4
|
1.0
|
CA
|
B:GLY182
|
4.7
|
66.2
|
1.0
|
O2
|
B:VN42002
|
4.7
|
0.5
|
1.0
|
CA
|
B:GLY704
|
4.7
|
84.3
|
1.0
|
C
|
B:GLY354
|
4.8
|
92.8
|
1.0
|
CA
|
B:ASP703
|
4.9
|
90.0
|
1.0
|
C
|
B:GLY182
|
4.9
|
73.2
|
1.0
|
O1
|
B:VN42002
|
4.9
|
96.7
|
1.0
|
C
|
B:ASP703
|
4.9
|
80.0
|
1.0
|
CG
|
B:ASP707
|
5.0
|
97.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6yso
Go back to
Magnesium Binding Sites List in 6yso
Magnesium binding site 4 out
of 4 in the Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing
![](/pictures/MG/pdb/ys/6yso-MG-sphere_04.jpg) Mono view
![](/pictures/MG/pdb/ys/6yso-MG-sphere_04_stereo.jpg) 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) CA2+-Atpase Solved By Vanadium Sad Phasing within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg2004
b:0.2
occ:1.00
|
OD1
|
B:ASN628
|
1.9
|
0.9
|
1.0
|
O
|
B:HOH2103
|
2.2
|
0.4
|
1.0
|
O3G
|
B:1282000
|
2.2
|
0.5
|
1.0
|
O2B
|
B:1282000
|
2.6
|
0.1
|
1.0
|
CG
|
B:ASN628
|
2.9
|
0.5
|
1.0
|
PG
|
B:1282000
|
3.1
|
0.7
|
1.0
|
ND2
|
B:ASN628
|
3.3
|
0.2
|
1.0
|
O1G
|
B:1282000
|
3.3
|
0.1
|
1.0
|
O3B
|
B:1282000
|
3.7
|
0.2
|
1.0
|
PB
|
B:1282000
|
3.7
|
0.8
|
1.0
|
N7
|
B:1282000
|
4.2
|
0.8
|
1.0
|
CB
|
B:ASN628
|
4.3
|
0.7
|
1.0
|
O2G
|
B:1282000
|
4.6
|
0.2
|
1.0
|
C8
|
B:1282000
|
4.6
|
0.2
|
1.0
|
O1B
|
B:1282000
|
4.7
|
0.6
|
1.0
|
OD1
|
B:ASP627
|
4.8
|
0.1
|
1.0
|
NH2
|
B:ARG560
|
4.8
|
0.2
|
1.0
|
NH1
|
B:ARG678
|
4.9
|
93.6
|
1.0
|
O3A
|
B:1282000
|
4.9
|
0.4
|
1.0
|
|
Reference:
K.El Omari,
N.Mohamad,
K.Bountra,
R.Duman,
M.Romano,
K.Schlegel,
H.S.Kwong,
V.Mykhaylyk,
C.Olesen,
J.V.Moller,
M.Bublitz,
K.Beis,
A.Wagner.
Experimental Phasing with Vanadium and Application to Nucleotide-Binding Membrane Proteins. Iucrj V. 7 1092 2020.
ISSN: ESSN 2052-2525
PubMed: 33209320
DOI: 10.1107/S2052252520012312
Page generated: Tue Dec 15 02:27:53 2020
|