Magnesium in PDB 7qtv: Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)
Enzymatic activity of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)
All present enzymatic activity of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx):
7.2.2.13;
Protein crystallography data
The structure of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx), PDB code: 7qtv
was solved by
M.U.Fruergaard,
I.Dach,
J.L.Andersen,
M.Ozol,
A.Shahsavar,
E.M.Quistgaard,
H.Poulsen,
N.U.Fedosova,
P.Nissen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.67 /
4.05
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
117.47,
118.08,
494.66,
90,
90,
90
|
R / Rfree (%)
|
24.7 /
28.1
|
Other elements in 7qtv:
The structure of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)
(pdb code 7qtv). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx), PDB code: 7qtv:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 7qtv
Go back to
Magnesium Binding Sites List in 7qtv
Magnesium binding site 1 out
of 6 in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1105
b:160.4
occ:1.00
|
OE1
|
A:GLU779
|
1.9
|
145.0
|
1.0
|
OD1
|
A:ASN776
|
2.0
|
128.2
|
1.0
|
O
|
A:HOH1203
|
2.1
|
156.7
|
1.0
|
OD2
|
A:ASP804
|
2.2
|
154.3
|
1.0
|
O
|
A:HOH1204
|
2.3
|
127.4
|
1.0
|
OD1
|
A:ASP804
|
2.5
|
156.2
|
1.0
|
CG
|
A:ASP804
|
2.6
|
143.3
|
1.0
|
OE2
|
A:GLU327
|
2.6
|
151.8
|
1.0
|
O
|
A:HOH1201
|
2.6
|
168.1
|
1.0
|
CD
|
A:GLU779
|
2.7
|
138.5
|
1.0
|
OE2
|
A:GLU779
|
2.8
|
135.2
|
1.0
|
CG
|
A:ASN776
|
3.2
|
114.2
|
1.0
|
CD
|
A:GLU327
|
3.5
|
131.6
|
1.0
|
OE1
|
A:GLU327
|
3.7
|
126.1
|
1.0
|
O
|
A:ALA323
|
4.0
|
127.1
|
1.0
|
ND2
|
A:ASN776
|
4.0
|
121.1
|
1.0
|
CB
|
A:ASP804
|
4.0
|
126.8
|
1.0
|
CG
|
A:GLU779
|
4.1
|
129.2
|
1.0
|
CB
|
A:ASN776
|
4.3
|
94.1
|
1.0
|
O
|
A:VAL325
|
4.4
|
130.4
|
1.0
|
CA
|
A:ASN776
|
4.4
|
101.4
|
1.0
|
OG
|
A:SER775
|
4.4
|
124.1
|
1.0
|
CB
|
A:GLU779
|
4.5
|
124.5
|
1.0
|
CG2
|
A:ILE800
|
4.7
|
120.0
|
1.0
|
N
|
A:ASN776
|
4.9
|
108.6
|
1.0
|
CG
|
A:GLU327
|
4.9
|
121.7
|
1.0
|
N
|
A:GLU327
|
5.0
|
123.5
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 7qtv
Go back to
Magnesium Binding Sites List in 7qtv
Magnesium binding site 2 out
of 6 in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1106
b:145.6
occ:1.00
|
F2
|
A:BEF1101
|
1.9
|
192.9
|
1.0
|
OD1
|
A:ASP710
|
1.9
|
142.2
|
1.0
|
OD2
|
A:ASP369
|
2.1
|
148.4
|
1.0
|
O
|
A:THR371
|
2.1
|
146.9
|
1.0
|
CG
|
A:ASP369
|
2.5
|
146.2
|
1.0
|
BE
|
A:BEF1101
|
2.6
|
197.0
|
1.0
|
CG
|
A:ASP710
|
2.8
|
146.9
|
1.0
|
OD1
|
A:ASP369
|
2.8
|
158.9
|
1.0
|
OG1
|
A:THR371
|
2.9
|
159.7
|
1.0
|
C
|
A:THR371
|
3.1
|
153.8
|
1.0
|
F3
|
A:BEF1101
|
3.2
|
208.0
|
1.0
|
OD2
|
A:ASP710
|
3.3
|
151.2
|
1.0
|
N
|
A:THR371
|
3.4
|
140.3
|
1.0
|
CB
|
A:ASP369
|
3.5
|
130.7
|
1.0
|
CA
|
A:THR371
|
3.6
|
142.5
|
1.0
|
F1
|
A:BEF1101
|
3.8
|
191.6
|
1.0
|
CB
|
A:THR371
|
3.8
|
142.7
|
1.0
|
CB
|
A:ASP710
|
3.9
|
145.7
|
1.0
|
OG1
|
A:THR373
|
4.0
|
128.0
|
1.0
|
N
|
A:LYS370
|
4.1
|
140.6
|
1.0
|
C
|
A:LYS370
|
4.1
|
136.7
|
1.0
|
OD2
|
A:ASP714
|
4.1
|
180.8
|
1.0
|
N
|
A:GLY372
|
4.2
|
219.6
|
1.0
|
C
|
A:ASP369
|
4.4
|
129.6
|
1.0
|
N
|
A:ASP710
|
4.4
|
129.2
|
1.0
|
N
|
A:THR373
|
4.5
|
151.6
|
1.0
|
ND2
|
A:ASN713
|
4.5
|
151.4
|
1.0
|
CA
|
A:ASP369
|
4.6
|
122.7
|
1.0
|
N
|
A:GLY711
|
4.6
|
137.9
|
1.0
|
CA
|
A:ASP710
|
4.7
|
134.4
|
1.0
|
O
|
A:LYS370
|
4.7
|
159.0
|
1.0
|
CA
|
A:GLY372
|
4.7
|
217.9
|
1.0
|
CA
|
A:LYS370
|
4.7
|
133.8
|
1.0
|
OD1
|
A:ASP714
|
4.8
|
173.5
|
1.0
|
CB
|
A:THR373
|
4.8
|
122.3
|
1.0
|
CG
|
A:ASP714
|
4.9
|
172.2
|
1.0
|
OD1
|
A:ASN713
|
4.9
|
145.8
|
1.0
|
O
|
A:ASP369
|
5.0
|
124.4
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 7qtv
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Magnesium Binding Sites List in 7qtv
Magnesium binding site 3 out
of 6 in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1107
b:116.0
occ:1.00
|
O
|
A:HOH1205
|
2.0
|
135.0
|
1.0
|
O
|
A:HOH1202
|
2.0
|
117.2
|
1.0
|
OD2
|
A:ASP740
|
2.0
|
111.0
|
1.0
|
OD1
|
A:ASP740
|
2.2
|
132.4
|
1.0
|
CG
|
A:ASP740
|
2.3
|
124.9
|
1.0
|
CB
|
A:ASP740
|
3.7
|
120.1
|
1.0
|
O
|
A:ASP722
|
3.7
|
116.9
|
1.0
|
O
|
A:ALA721
|
3.8
|
127.8
|
1.0
|
O
|
A:LYS719
|
3.9
|
121.7
|
1.0
|
O
|
A:GLY272
|
3.9
|
120.8
|
1.0
|
CA
|
A:ILE723
|
4.1
|
112.6
|
1.0
|
C
|
A:ASP722
|
4.3
|
113.6
|
1.0
|
O
|
A:SER718
|
4.4
|
145.1
|
1.0
|
N
|
A:ILE723
|
4.5
|
105.0
|
1.0
|
N
|
A:GLY724
|
4.5
|
125.3
|
1.0
|
N
|
A:ASP740
|
4.6
|
121.1
|
1.0
|
CA
|
A:ASP740
|
4.7
|
112.7
|
1.0
|
C
|
A:ILE723
|
4.8
|
103.8
|
1.0
|
O
|
A:ALA738
|
4.8
|
121.1
|
1.0
|
C
|
A:LYS719
|
4.9
|
116.2
|
1.0
|
C
|
A:GLY272
|
4.9
|
134.3
|
1.0
|
C
|
A:ALA721
|
4.9
|
121.3
|
1.0
|
CA
|
A:GLY272
|
4.9
|
146.5
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 7qtv
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Magnesium Binding Sites List in 7qtv
Magnesium binding site 4 out
of 6 in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1103
b:187.3
occ:1.00
|
OE1
|
C:GLU779
|
1.8
|
175.9
|
1.0
|
O
|
C:HOH1202
|
1.9
|
252.5
|
1.0
|
OD2
|
C:ASP804
|
1.9
|
192.6
|
1.0
|
OD1
|
C:ASN776
|
2.2
|
156.2
|
1.0
|
O
|
C:HOH1203
|
2.3
|
149.4
|
1.0
|
O
|
C:HOH1201
|
2.7
|
159.0
|
1.0
|
CD
|
C:GLU779
|
2.7
|
164.2
|
1.0
|
CG
|
C:ASP804
|
2.8
|
168.3
|
1.0
|
OE1
|
C:GLU327
|
2.8
|
174.8
|
1.0
|
OE2
|
C:GLU779
|
3.0
|
170.9
|
1.0
|
OD1
|
C:ASP804
|
3.0
|
174.9
|
1.0
|
CG
|
C:ASN776
|
3.4
|
141.4
|
1.0
|
OE2
|
C:GLU327
|
3.5
|
154.3
|
1.0
|
CD
|
C:GLU327
|
3.5
|
162.0
|
1.0
|
O
|
C:ALA323
|
3.9
|
114.6
|
1.0
|
CG
|
C:GLU779
|
4.1
|
148.7
|
1.0
|
CB
|
C:ASP804
|
4.2
|
144.9
|
1.0
|
ND2
|
C:ASN776
|
4.3
|
135.1
|
1.0
|
CG2
|
C:ILE800
|
4.4
|
169.2
|
1.0
|
CB
|
C:ASN776
|
4.5
|
133.9
|
1.0
|
O
|
C:VAL325
|
4.5
|
132.5
|
1.0
|
CB
|
C:GLU779
|
4.5
|
146.0
|
1.0
|
CA
|
C:ASN776
|
4.6
|
130.6
|
1.0
|
OG
|
C:SER775
|
4.7
|
130.6
|
1.0
|
CG
|
C:GLU327
|
4.9
|
147.1
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 7qtv
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Magnesium Binding Sites List in 7qtv
Magnesium binding site 5 out
of 6 in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1104
b:144.6
occ:1.00
|
O
|
C:HOH1204
|
2.0
|
154.9
|
1.0
|
OD2
|
C:ASP740
|
2.1
|
159.4
|
1.0
|
OD1
|
C:ASP740
|
2.2
|
136.8
|
1.0
|
CG
|
C:ASP740
|
2.4
|
145.4
|
1.0
|
O
|
C:LYS719
|
3.4
|
126.3
|
1.0
|
CB
|
C:ASP740
|
3.9
|
141.2
|
1.0
|
O
|
C:SER718
|
3.9
|
139.6
|
1.0
|
O
|
C:GLY272
|
3.9
|
173.7
|
1.0
|
O
|
C:ALA721
|
4.0
|
131.3
|
1.0
|
C
|
C:LYS719
|
4.3
|
125.9
|
1.0
|
O
|
C:ALA738
|
4.3
|
143.3
|
1.0
|
CA
|
C:LYS719
|
4.4
|
121.8
|
1.0
|
O
|
C:ASP722
|
4.5
|
138.8
|
1.0
|
CA
|
C:GLY272
|
4.5
|
178.9
|
1.0
|
N
|
C:ASP740
|
4.7
|
154.0
|
1.0
|
C
|
C:GLY272
|
4.7
|
181.8
|
1.0
|
CA
|
C:ILE723
|
4.7
|
134.7
|
1.0
|
N
|
C:GLY724
|
4.8
|
170.3
|
1.0
|
CA
|
C:ASP740
|
4.8
|
142.2
|
1.0
|
C
|
C:ASP722
|
4.9
|
128.2
|
1.0
|
C
|
C:SER718
|
4.9
|
133.8
|
1.0
|
CD
|
C:LYS719
|
5.0
|
148.3
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 7qtv
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Magnesium Binding Sites List in 7qtv
Magnesium binding site 6 out
of 6 in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1105
b:163.3
occ:1.00
|
O
|
C:THR371
|
1.7
|
177.8
|
1.0
|
OD1
|
C:ASP710
|
1.7
|
170.5
|
1.0
|
OD2
|
C:ASP369
|
1.8
|
155.7
|
1.0
|
CG
|
C:ASP710
|
2.6
|
178.5
|
1.0
|
CG2
|
C:THR371
|
2.6
|
173.6
|
1.0
|
C
|
C:THR371
|
2.6
|
177.4
|
1.0
|
CG
|
C:ASP369
|
2.8
|
157.4
|
1.0
|
F1
|
C:BEF1101
|
3.1
|
155.8
|
1.0
|
CB
|
C:ASP369
|
3.2
|
150.0
|
1.0
|
CA
|
C:THR371
|
3.3
|
169.2
|
1.0
|
OD2
|
C:ASP710
|
3.3
|
182.1
|
1.0
|
N
|
C:THR371
|
3.3
|
161.2
|
1.0
|
CB
|
C:ASP710
|
3.4
|
174.0
|
1.0
|
CB
|
C:THR371
|
3.5
|
172.6
|
1.0
|
BE
|
C:BEF1101
|
3.5
|
165.0
|
1.0
|
OG1
|
C:THR373
|
3.7
|
151.6
|
1.0
|
OD2
|
C:ASP714
|
3.7
|
163.8
|
1.0
|
N
|
C:GLY372
|
3.7
|
184.2
|
1.0
|
N
|
C:THR373
|
3.8
|
164.1
|
1.0
|
O
|
C:ASP369
|
3.8
|
161.2
|
1.0
|
OD1
|
C:ASP369
|
3.9
|
161.5
|
1.0
|
F2
|
C:BEF1101
|
3.9
|
173.8
|
1.0
|
C
|
C:ASP369
|
4.0
|
159.5
|
1.0
|
N
|
C:ASP710
|
4.0
|
165.1
|
1.0
|
CA
|
C:GLY372
|
4.2
|
168.9
|
1.0
|
C
|
C:LYS370
|
4.2
|
164.5
|
1.0
|
CA
|
C:ASP369
|
4.2
|
151.2
|
1.0
|
CA
|
C:ASP710
|
4.2
|
169.6
|
1.0
|
OG1
|
C:THR371
|
4.2
|
179.9
|
1.0
|
C
|
C:GLY372
|
4.5
|
160.3
|
1.0
|
N
|
C:LYS370
|
4.5
|
165.2
|
1.0
|
CB
|
C:THR373
|
4.5
|
148.9
|
1.0
|
N
|
C:GLY711
|
4.7
|
158.5
|
1.0
|
CG
|
C:ASP714
|
4.7
|
164.9
|
1.0
|
O
|
C:LYS370
|
4.7
|
170.2
|
1.0
|
C
|
C:ASP710
|
4.7
|
167.9
|
1.0
|
F3
|
C:BEF1101
|
4.8
|
175.0
|
1.0
|
CA
|
C:THR373
|
4.8
|
155.4
|
1.0
|
OD1
|
C:ASP714
|
4.9
|
166.1
|
1.0
|
|
Reference:
M.U.Fruergaard,
I.Dach,
J.L.Andersen,
M.Ozol,
A.Shahsavar,
E.M.Quistgaard,
H.Poulsen,
N.U.Fedosova,
P.Nissen.
The Na + ,K + -Atpase in Complex with Beryllium Fluoride Mimics An Atpase Phosphorylated State. J.Biol.Chem. V. 298 02317 2022.
ISSN: ESSN 1083-351X
PubMed: 35926706
DOI: 10.1016/J.JBC.2022.102317
Page generated: Thu Oct 3 07:01:25 2024
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