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 Dec 14 21:26:55 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy