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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

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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

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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

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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

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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

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