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Magnesium in PDB 5gpj: Crystal Structure of Proton-Pumping Pyrophosphatase

Enzymatic activity of Crystal Structure of Proton-Pumping Pyrophosphatase

All present enzymatic activity of Crystal Structure of Proton-Pumping Pyrophosphatase:
3.6.1.1;

Protein crystallography data

The structure of Crystal Structure of Proton-Pumping Pyrophosphatase, PDB code: 5gpj was solved by K.M.Li, J.Y.Tsai, Y.J.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 225.703, 81.637, 264.845, 90.00, 92.87, 90.00
R / Rfree (%) 22.6 / 30.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Proton-Pumping Pyrophosphatase (pdb code 5gpj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Proton-Pumping Pyrophosphatase, PDB code: 5gpj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5gpj

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Magnesium binding site 1 out of 8 in the Crystal Structure of Proton-Pumping Pyrophosphatase


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 Proton-Pumping Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:51.5
occ:1.00
 O3 A:PO41001 2.5 0.6 1.0
O2 A:PO41001 2.6 0.6 1.0
O4 A:PO41001 2.8 0.9 1.0
P A:PO41001 2.8 0.2 1.0
OD2 A:ASP507 3.0 84.2 1.0
OD1 A:ASP507 3.4 0.2 1.0
CG A:ASP507 3.6 91.4 1.0
OD2 A:ASP279 4.3 77.2 1.0
O1 A:PO41001 4.4 0.8 1.0
OD2 A:ASP283 4.5 88.0 1.0
MG A:MG1003 4.6 0.4 1.0
OD1 A:ASP283 4.6 87.4 1.0

Magnesium binding site 2 out of 8 in 5gpj

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Magnesium binding site 2 out of 8 in the Crystal Structure of Proton-Pumping Pyrophosphatase


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 Proton-Pumping Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:0.4
occ:1.00
 O4 A:PO41001 1.8 0.9 1.0
OD1 A:ASP727 2.2 88.9 1.0
P A:PO41001 2.8 0.2 1.0
O1 A:PO41001 3.0 0.8 1.0
OD2 A:ASP253 3.0 0.1 1.0
CG A:ASP727 3.1 88.2 1.0
NZ A:LYS730 3.2 83.1 1.0
OD2 A:ASP727 3.4 82.3 1.0
OD2 A:ASP723 3.7 67.3 1.0
O2 A:PO41001 3.7 0.6 1.0
NZ A:LYS250 3.8 0.1 1.0
OD1 A:ASP723 3.9 67.2 1.0
O3 A:PO41001 4.0 0.6 1.0
CG A:ASP253 4.1 96.3 1.0
CG A:ASP723 4.2 69.6 1.0
CE A:LYS730 4.3 92.2 1.0
OD1 A:ASP691 4.5 76.8 1.0
OD1 A:ASP253 4.5 0.7 1.0
MG A:MG1002 4.6 51.5 1.0
CB A:ASP727 4.6 89.3 1.0
CE A:LYS250 4.8 0.5 1.0
CG A:ASP691 4.9 75.3 1.0

Magnesium binding site 3 out of 8 in 5gpj

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Magnesium binding site 3 out of 8 in the Crystal Structure of Proton-Pumping Pyrophosphatase


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 Proton-Pumping Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:0.3
occ:1.00
 O2 B:PO41001 2.0 0.3 1.0
OD2 B:ASP507 2.5 0.6 1.0
OD1 B:ASP507 2.6 0.9 1.0
O3 B:PO41001 2.8 0.6 1.0
CG B:ASP507 2.9 0.7 1.0
P B:PO41001 3.0 0.5 1.0
OD2 B:ASP283 3.7 0.4 1.0
O1 B:PO41001 3.9 0.7 1.0
O4 B:PO41001 4.0 0.5 1.0
CB B:ASP507 4.5 0.6 1.0
CG B:ASP283 4.5 0.1 1.0
OD2 B:ASP279 4.6 0.1 1.0
OD1 B:ASP283 4.6 0.8 1.0
OD2 B:ASP530 4.9 0.3 1.0

Magnesium binding site 4 out of 8 in 5gpj

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Magnesium binding site 4 out of 8 in the Crystal Structure of Proton-Pumping Pyrophosphatase


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 Proton-Pumping Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:1.0
occ:1.00
 O4 B:PO41001 2.0 0.5 1.0
OD1 B:ASP727 2.2 99.1 1.0
OD2 B:ASP253 2.7 0.3 1.0
P B:PO41001 2.8 0.5 1.0
O1 B:PO41001 2.8 0.7 1.0
NZ B:LYS730 3.1 98.3 1.0
CG B:ASP727 3.1 0.7 1.0
CE B:LYS730 3.2 0.6 1.0
O3 B:PO41001 3.5 0.6 1.0
OD2 B:ASP727 3.5 0.1 1.0
NZ B:LYS250 3.8 0.3 1.0
OD1 B:ASP723 3.9 0.6 1.0
CG B:ASP253 3.9 0.2 1.0
OD2 B:ASP723 4.1 1.0 1.0
O2 B:PO41001 4.1 0.3 1.0
CE B:LYS250 4.1 0.6 1.0
CD B:LYS730 4.3 0.4 1.0
CB B:ASP727 4.4 0.1 1.0
CG B:ASP723 4.4 0.7 1.0
OD1 B:ASP253 4.5 0.2 1.0
CD B:LYS250 4.7 0.1 1.0
CA B:ASP727 4.8 0.5 1.0

Magnesium binding site 5 out of 8 in 5gpj

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Magnesium binding site 5 out of 8 in the Crystal Structure of Proton-Pumping Pyrophosphatase


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 Proton-Pumping Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:81.8
occ:1.00
 OD1 C:ASP507 2.7 0.6 1.0
O C:ASP507 3.7 0.3 1.0
OD1 C:ASN280 3.8 0.9 1.0
OD2 C:ASP279 3.9 0.8 1.0
CG C:ASP507 3.9 0.8 1.0
O1 C:PO41001 4.3 0.2 1.0
OD2 C:ASP283 4.4 0.2 1.0
OD2 C:ASP507 4.6 0.0 1.0
CA C:GLY511 4.6 0.8 1.0
CG C:ASN280 4.8 0.0 1.0
C C:ASP507 4.8 0.9 1.0
OD2 C:ASP530 4.8 0.8 1.0
ND2 C:ASN280 4.9 0.6 1.0

Magnesium binding site 6 out of 8 in 5gpj

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Magnesium binding site 6 out of 8 in the Crystal Structure of Proton-Pumping Pyrophosphatase


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 Proton-Pumping Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:0.5
occ:1.00
 O2 C:PO41001 1.9 0.4 1.0
OD2 C:ASP253 2.9 0.7 1.0
P C:PO41001 3.1 0.5 1.0
OD1 C:ASP727 3.2 0.2 1.0
OD2 C:ASP723 3.2 0.6 1.0
O1 C:PO41001 3.4 0.2 1.0
OD1 C:ASP691 3.5 0.5 1.0
OD1 C:ASP723 3.6 0.9 1.0
CG C:ASP253 3.8 0.7 1.0
O3 C:PO41001 3.8 0.3 1.0
CG C:ASP723 3.8 0.3 1.0
OD1 C:ASP253 3.9 0.7 1.0
OD2 C:ASP727 3.9 0.5 1.0
CG C:ASP727 3.9 0.5 1.0
NZ C:LYS730 4.2 0.3 1.0
O4 C:PO41001 4.3 0.5 1.0
CG C:ASP691 4.5 0.8 1.0
NZ C:LYS694 4.6 0.8 1.0
OD2 C:ASP691 4.9 0.8 1.0

Magnesium binding site 7 out of 8 in 5gpj

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Magnesium binding site 7 out of 8 in the Crystal Structure of Proton-Pumping Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Proton-Pumping Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1002

b:0.1
occ:1.00
 OD2 D:ASP507 2.1 0.6 1.0
O3 D:PO41001 2.1 0.3 1.0
O4 D:PO41001 2.2 0.7 1.0
OD1 D:ASP283 2.4 0.0 1.0
P D:PO41001 2.5 0.8 1.0
CG D:ASP283 3.2 0.9 1.0
CG D:ASP507 3.2 0.3 1.0
O1 D:PO41001 3.3 0.3 1.0
OD2 D:ASP283 3.3 0.1 1.0
OD2 D:ASP279 3.5 0.8 1.0
OD1 D:ASP507 3.8 0.5 1.0
OD2 D:ASP253 3.8 0.9 1.0
O2 D:PO41001 3.9 0.2 1.0
NZ D:LYS250 4.0 0.3 1.0
MG D:MG1003 4.1 0.1 1.0
CB D:ASP507 4.4 0.6 1.0
CG D:ASP279 4.4 0.5 1.0
OD1 D:ASP279 4.4 0.2 1.0
CB D:ASP283 4.6 0.5 1.0
CG D:ASP253 5.0 0.5 1.0

Magnesium binding site 8 out of 8 in 5gpj

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Magnesium binding site 8 out of 8 in the Crystal Structure of Proton-Pumping Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Proton-Pumping Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1003

b:0.1
occ:1.00
 O2 D:PO41001 1.7 0.2 1.0
OD1 D:ASP727 2.0 0.0 1.0
O3 D:PO41001 2.3 0.3 1.0
P D:PO41001 2.4 0.8 1.0
OD2 D:ASP253 2.4 0.9 1.0
CG D:ASP727 2.9 0.1 1.0
CG D:ASP253 3.1 0.5 1.0
OD2 D:ASP727 3.2 0.6 1.0
NZ D:LYS730 3.2 0.6 1.0
NZ D:LYS250 3.4 0.3 1.0
OD1 D:ASP253 3.4 0.7 1.0
O4 D:PO41001 3.5 0.7 1.0
O1 D:PO41001 3.5 0.3 1.0
CE D:LYS250 4.1 1.0 1.0
MG D:MG1002 4.1 0.1 1.0
CB D:ASP253 4.2 0.2 1.0
CB D:ASP727 4.3 0.9 1.0
OD1 D:ASP723 4.3 0.2 1.0
OD1 D:ASP691 4.4 0.5 1.0
CD D:LYS250 4.4 0.3 1.0
OD2 D:ASP723 4.5 0.2 1.0
CE D:LYS730 4.5 0.5 1.0
CG D:ASP723 4.8 0.6 1.0
CA D:ASP727 4.9 0.7 1.0

Reference:

K.M.Li, C.Wilkinson, J.Kellosalo, J.Y.Tsai, T.Kajander, L.J.Jeuken, Y.J.Sun, A.Goldman. Membrane Pyrophosphatases From Thermotoga Maritima and Vigna Radiata Suggest A Conserved Coupling Mechanism Nat Commun V. 7 13596 2016.
ISSN: ESSN 2041-1723
PubMed: 27922000
DOI: 10.1038/NCOMMS13596
Page generated: Tue Aug 12 10:22:29 2025

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