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Magnesium in PDB 5xa8: Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-ALF4-Adp-2CA2+ Crystals

Enzymatic activity of Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-ALF4-Adp-2CA2+ Crystals

All present enzymatic activity of Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-ALF4-Adp-2CA2+ Crystals:
3.6.3.8;

Protein crystallography data

The structure of Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-ALF4-Adp-2CA2+ Crystals, PDB code: 5xa8 was solved by Y.Norimatsu, K.Hasegawa, N.Shimizu, C.Toyoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.64 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.970, 75.020, 152.240, 90.00, 109.31, 90.00
R / Rfree (%) 21.3 / 24.1

Other elements in 5xa8:

The structure of Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-ALF4-Adp-2CA2+ Crystals also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Aluminium (Al) 1 atom
Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-ALF4-Adp-2CA2+ Crystals (pdb code 5xa8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-ALF4-Adp-2CA2+ Crystals, PDB code: 5xa8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5xa8

Go back to Magnesium Binding Sites List in 5xa8
Magnesium binding site 1 out of 2 in the Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-ALF4-Adp-2CA2+ Crystals


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-ALF4-Adp-2CA2+ Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:22.0
occ:1.00
 O3B A:ADP1006 2.0 27.2 1.0
O1A A:ADP1006 2.6 34.0 1.0
O3A A:ADP1006 2.7 35.3 1.0
PB A:ADP1006 2.8 37.1 1.0
F2 A:ALF1004 2.9 51.2 1.0
O A:HOH1127 2.9 40.2 1.0
O A:HOH1141 2.9 33.8 1.0
O A:HOH1211 2.9 37.8 1.0
F4 A:ALF1004 3.0 27.9 1.0
PA A:ADP1006 3.2 28.0 1.0
O1B A:ADP1006 3.4 49.0 1.0
AL A:ALF1004 3.4 31.8 1.0
O5' A:ADP1006 3.8 55.9 1.0
NH2 A:ARG560 4.0 27.2 1.0
O2B A:ADP1006 4.2 39.1 1.0
MG A:MG1005 4.3 28.2 1.0
O A:HOH1122 4.3 26.7 1.0
CB A:THR353 4.4 39.9 1.0
CG2 A:THR353 4.5 32.0 1.0
ND2 A:ASN706 4.6 48.9 1.0
F3 A:ALF1004 4.6 34.5 1.0
O2A A:ADP1006 4.6 30.3 1.0
F1 A:ALF1004 4.6 38.2 1.0
NH2 A:ARG489 4.7 26.9 1.0
NH1 A:ARG560 4.8 26.0 1.0
CZ A:ARG560 4.9 29.0 1.0
OE2 A:GLU439 4.9 0.1 1.0
OG1 A:THR353 4.9 36.3 1.0

Magnesium binding site 2 out of 2 in 5xa8

Go back to Magnesium Binding Sites List in 5xa8
Magnesium binding site 2 out of 2 in the Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-ALF4-Adp-2CA2+ Crystals


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Complete Structure Factors and An Atomic Model of the Calcium Pump (SERCA1A) and Associated Phospholipids in the E1-ALF4-Adp-2CA2+ Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1005

b:28.2
occ:1.00
 OD1 A:ASP703 2.1 49.2 1.0
O A:THR353 2.1 32.3 1.0
O A:HOH1122 2.1 26.7 1.0
F4 A:ALF1004 2.2 27.9 1.0
O A:HOH1211 2.3 37.8 1.0
CG A:ASP703 2.7 41.4 1.0
OD2 A:ASP703 2.7 47.1 1.0
OD2 A:ASP351 2.7 18.4 1.0
C A:THR353 3.3 28.0 1.0
AL A:ALF1004 3.7 31.8 1.0
CG A:ASP351 3.8 30.0 1.0
F2 A:ALF1004 4.0 51.2 1.0
N A:GLY704 4.1 29.9 1.0
CA A:GLY354 4.1 37.1 1.0
N A:GLY354 4.1 30.9 1.0
CB A:ASP703 4.2 24.4 1.0
CB A:THR353 4.3 39.9 1.0
CA A:THR353 4.3 46.6 1.0
OD1 A:ASP351 4.3 35.6 1.0
MG A:MG1003 4.3 22.0 1.0
F1 A:ALF1004 4.3 38.2 1.0
O A:HOH1141 4.4 33.8 1.0
CG2 A:THR353 4.5 32.0 1.0
OD2 A:ASP707 4.6 25.1 1.0
CA A:GLY704 4.6 27.5 1.0
OG1 A:THR355 4.6 34.3 1.0
N A:THR353 4.7 38.8 1.0
C A:GLY354 4.7 48.8 1.0
N A:ASP703 4.7 32.2 1.0
N A:THR355 4.7 39.3 1.0
C A:ASP703 4.7 35.9 1.0
CA A:ASP703 4.8 33.5 1.0
CB A:ASP351 4.9 17.4 1.0

Reference:

Y.Norimatsu, K.Hasegawa, N.Shimizu, C.Toyoshima. Protein-Phospholipid Interplay Revealed with Crystals of A Calcium Pump. Nature V. 545 193 2017.
ISSN: ESSN 1476-4687
PubMed: 28467821
DOI: 10.1038/NATURE22357
Page generated: Mon Sep 30 09:14:05 2024

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