Atomistry » Magnesium » PDB 4rcy-4rke » 4ret
Atomistry »
  Magnesium »
    PDB 4rcy-4rke »
      4ret »

Magnesium in PDB 4ret: Crystal Structure of the Na,K-Atpase E2P-Digoxin Complex with Bound Magnesium

Enzymatic activity of Crystal Structure of the Na,K-Atpase E2P-Digoxin Complex with Bound Magnesium

All present enzymatic activity of Crystal Structure of the Na,K-Atpase E2P-Digoxin Complex with Bound Magnesium:
3.6.3.9;

Protein crystallography data

The structure of Crystal Structure of the Na,K-Atpase E2P-Digoxin Complex with Bound Magnesium, PDB code: 4ret was solved by J.L.Gregersen, M.Laursen, L.Yatime, P.Nissen, N.U.Fedosova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.41 / 4.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 118.240, 118.350, 494.090, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 25.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Na,K-Atpase E2P-Digoxin Complex with Bound Magnesium (pdb code 4ret). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the Na,K-Atpase E2P-Digoxin Complex with Bound Magnesium, PDB code: 4ret:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4ret

Go back to Magnesium Binding Sites List in 4ret
Magnesium binding site 1 out of 6 in the Crystal Structure of the Na,K-Atpase E2P-Digoxin Complex with Bound Magnesium


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 Na,K-Atpase E2P-Digoxin Complex with Bound Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:0.8
occ:1.00
 OD2 A:PHD369 2.0 0.1 1.0
OP3 A:PHD369 2.0 0.9 1.0
O A:THR371 2.0 0.0 1.0
OD2 A:ASP710 2.2 0.9 1.0
OD1 A:ASP710 2.2 0.4 1.0
OG1 A:THR371 2.2 1.0 1.0
CG A:ASP710 2.4 0.5 1.0
OP1 A:PHD369 2.7 0.6 1.0
P A:PHD369 2.8 0.1 1.0
C A:THR371 3.0 0.8 1.0
CG A:PHD369 3.0 0.1 1.0
CB A:THR371 3.3 0.4 1.0
OD1 A:PHD369 3.3 0.6 1.0
CA A:THR371 3.4 0.4 1.0
N A:THR371 3.5 0.1 1.0
CB A:ASP710 3.9 0.1 1.0
OP2 A:PHD369 4.1 0.7 1.0
N A:GLY372 4.2 0.3 1.0
CB A:PHD369 4.3 0.9 1.0
C A:LYS370 4.4 0.7 1.0
CG2 A:THR371 4.5 0.2 1.0
N A:GLY711 4.5 0.5 1.0
O A:SER209 4.6 0.7 1.0
N A:LYS370 4.6 0.0 1.0
CA A:GLY372 4.7 0.0 1.0
OG1 A:THR373 4.7 0.7 1.0
OD2 A:ASP714 4.7 0.8 1.0
N A:ASP710 4.9 0.6 1.0
CA A:ASP710 4.9 0.9 1.0
N A:THR373 4.9 0.3 1.0
OD1 A:ASN713 5.0 0.7 1.0
ND2 A:ASN713 5.0 0.5 1.0

Magnesium binding site 2 out of 6 in 4ret

Go back to Magnesium Binding Sites List in 4ret
Magnesium binding site 2 out of 6 in the Crystal Structure of the Na,K-Atpase E2P-Digoxin Complex with Bound Magnesium


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 Na,K-Atpase E2P-Digoxin Complex with Bound Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:0.3
occ:1.00
 OD2 A:ASP740 2.1 0.7 1.0
OD1 A:ASP740 2.1 0.2 1.0
CG A:ASP740 2.4 1.0 1.0
O A:LYS719 3.6 0.5 1.0
CB A:ASP740 3.9 0.9 1.0
O A:ALA721 4.1 0.5 1.0
O A:GLY272 4.4 0.2 1.0
CA A:GLY272 4.4 0.0 1.0
O A:ALA738 4.4 0.8 1.0
O A:SER718 4.4 0.3 1.0
C A:LYS719 4.5 0.7 1.0
CA A:LYS719 4.7 1.0 1.0
N A:ASP740 4.8 0.3 1.0
CA A:ASP740 4.8 0.7 1.0
C A:GLY272 4.8 0.5 1.0
O A:ASP722 4.8 0.9 1.0
CD A:LYS719 4.9 1.0 1.0

Magnesium binding site 3 out of 6 in 4ret

Go back to Magnesium Binding Sites List in 4ret
Magnesium binding site 3 out of 6 in the Crystal Structure of the Na,K-Atpase E2P-Digoxin Complex with Bound Magnesium


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 Na,K-Atpase E2P-Digoxin Complex with Bound Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:0.8
occ:1.00
 O A:HOH1203 2.1 0.6 1.0
OE2 A:GLU779 2.1 0.4 1.0
O A:HOH1201 2.1 0.3 1.0
O A:HOH1202 2.1 0.6 1.0
OD1 A:ASP804 2.2 0.6 1.0
OD1 A:ASN776 2.3 0.1 1.0
OD2 A:ASP804 2.5 0.5 1.0
CG A:ASP804 2.7 0.7 1.0
CD A:GLU779 3.0 0.4 1.0
CG A:ASN776 3.3 0.8 1.0
OE1 A:GLU779 3.3 0.2 1.0
ND2 A:ASN776 3.9 0.6 1.0
OG A:SER775 4.0 0.6 1.0
OE1 A:GLU327 4.2 0.8 1.0
CB A:ASP804 4.2 0.3 1.0
CG A:GLU779 4.4 0.0 1.0
CB A:ASN776 4.5 0.7 1.0
CA A:ASN776 4.5 0.4 1.0
O A:VAL325 4.6 0.8 1.0
CB A:GLU779 4.7 0.5 1.0
O A:ALA323 4.8 0.4 1.0
N A:ASN776 4.8 0.6 1.0
C A:SER775 5.0 0.1 1.0
CA A:ASP804 5.0 0.9 1.0
CA A:PRO326 5.0 0.6 1.0

Magnesium binding site 4 out of 6 in 4ret

Go back to Magnesium Binding Sites List in 4ret
Magnesium binding site 4 out of 6 in the Crystal Structure of the Na,K-Atpase E2P-Digoxin Complex with Bound Magnesium


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 Na,K-Atpase E2P-Digoxin Complex with Bound Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2001

b:0.3
occ:1.00
 O C:THR371 2.0 0.1 1.0
OD2 C:PHD369 2.0 0.0 1.0
OP3 C:PHD369 2.1 0.8 1.0
OD2 C:ASP710 2.1 0.2 1.0
OD1 C:ASP710 2.2 0.3 1.0
OG1 C:THR371 2.2 0.2 1.0
CG C:ASP710 2.4 0.4 1.0
OP1 C:PHD369 2.7 0.5 1.0
P C:PHD369 2.8 0.1 1.0
C C:THR371 3.0 0.7 1.0
CG C:PHD369 3.0 0.1 1.0
CB C:THR371 3.3 0.6 1.0
OD1 C:PHD369 3.3 0.0 1.0
CA C:THR371 3.4 0.8 1.0
N C:THR371 3.5 0.7 1.0
CB C:ASP710 3.9 0.8 1.0
N C:GLY372 4.1 0.6 1.0
OP2 C:PHD369 4.2 0.2 1.0
CB C:PHD369 4.3 0.3 1.0
C C:LYS370 4.4 0.1 1.0
O C:SER209 4.4 0.6 1.0
CG2 C:THR371 4.5 0.1 1.0
N C:GLY711 4.5 0.2 1.0
N C:LYS370 4.6 0.5 1.0
CA C:GLY372 4.6 0.9 1.0
OG1 C:THR373 4.7 0.5 1.0
OD2 C:ASP714 4.7 0.8 1.0
N C:ASP710 4.9 0.6 1.0
CA C:ASP710 4.9 1.0 1.0
N C:THR373 4.9 0.7 1.0
OD1 C:ASN713 5.0 0.7 1.0
CA C:GLY213 5.0 0.3 1.0

Magnesium binding site 5 out of 6 in 4ret

Go back to Magnesium Binding Sites List in 4ret
Magnesium binding site 5 out of 6 in the Crystal Structure of the Na,K-Atpase E2P-Digoxin Complex with Bound Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Na,K-Atpase E2P-Digoxin Complex with Bound Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2002

b:0.8
occ:1.00
 OD2 C:ASP740 2.1 0.3 1.0
OD1 C:ASP740 2.1 0.1 1.0
CG C:ASP740 2.4 0.9 1.0
O C:LYS719 3.6 0.7 1.0
CB C:ASP740 3.9 0.5 1.0
O C:ALA721 4.1 0.5 1.0
O C:ALA738 4.4 0.7 1.0
O C:SER718 4.4 0.8 1.0
C C:LYS719 4.5 0.2 1.0
CA C:GLY272 4.7 0.1 1.0
CA C:LYS719 4.7 0.9 1.0
N C:ASP740 4.8 0.7 1.0
CA C:ASP740 4.8 0.4 1.0
O C:ASP722 4.9 0.6 1.0
CD C:LYS719 4.9 0.8 1.0
O C:GLY272 4.9 0.1 1.0

Magnesium binding site 6 out of 6 in 4ret

Go back to Magnesium Binding Sites List in 4ret
Magnesium binding site 6 out of 6 in the Crystal Structure of the Na,K-Atpase E2P-Digoxin Complex with Bound Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Na,K-Atpase E2P-Digoxin Complex with Bound Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2003

b:0.2
occ:1.00
 OE2 C:GLU779 2.0 0.8 1.0
O C:HOH2103 2.1 0.4 1.0
O C:HOH2101 2.1 1.0 1.0
O C:HOH2102 2.1 0.1 1.0
OD2 C:ASP804 2.2 0.7 1.0
OD1 C:ASP804 2.3 0.6 1.0
OD1 C:ASN776 2.4 0.7 1.0
CG C:ASP804 2.6 0.8 1.0
CD C:GLU779 3.0 0.4 1.0
OE1 C:GLU779 3.3 0.7 1.0
CG C:ASN776 3.5 0.1 1.0
OE1 C:GLU327 4.0 0.8 1.0
CB C:ASP804 4.1 0.3 1.0
ND2 C:ASN776 4.1 0.3 1.0
OG C:SER775 4.2 0.7 1.0
CG C:GLU779 4.3 0.6 1.0
O C:VAL325 4.6 0.9 1.0
CB C:GLU779 4.6 0.8 1.0
O C:ALA323 4.7 0.3 1.0
CA C:ASN776 4.7 0.3 1.0
CB C:ASN776 4.7 0.4 1.0
CG2 C:ILE800 4.9 0.8 1.0
CA C:ASP804 4.9 0.4 1.0

Reference:

M.Laursen, J.L.Gregersen, L.Yatime, P.Nissen, N.U.Fedosova. Structures and Characterization of Digoxin- and Bufalin-Bound Na+,K+-Atpase Compared with the Ouabain-Bound Complex. Proc.Natl.Acad.Sci.Usa 2015.
ISSN: ESSN 1091-6490
PubMed: 25624492
DOI: 10.1073/PNAS.1422997112
Page generated: Tue Aug 20 03:03:21 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy