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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:

Potassium (K) 2 atoms
Vanadium (V) 2 atoms
Chlorine (Cl) 2 atoms

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

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