Magnesium in PDB 6afw: Proton Pyrophosphatase-T228D Mutant

Enzymatic activity of Proton Pyrophosphatase-T228D Mutant

All present enzymatic activity of Proton Pyrophosphatase-T228D Mutant:
3.6.1.1;

Protein crystallography data

The structure of Proton Pyrophosphatase-T228D Mutant, PDB code: 6afw was solved by J.-Y.Tsai, K.-M.Li, Y.-J.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.62 / 2.19
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 212.672, 88.101, 156.686, 90.00, 124.54, 90.00
R / Rfree (%) 19.9 / 23.5

Other elements in 6afw:

The structure of Proton Pyrophosphatase-T228D Mutant also contains other interesting chemical elements:

Potassium (K) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Proton Pyrophosphatase-T228D Mutant (pdb code 6afw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Proton Pyrophosphatase-T228D Mutant, PDB code: 6afw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 6afw

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Magnesium binding site 1 out of 10 in the Proton Pyrophosphatase-T228D Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:32.9
occ:1.00
O A:HOH1114 2.1 27.8 1.0
OD2 A:ASP257 2.1 31.4 1.0
OD1 A:ASP253 2.1 30.5 1.0
O A:HOH1196 2.1 28.7 1.0
O2 A:PO41002 2.2 31.5 1.0
O A:HOH1142 2.3 27.2 1.0
CG A:ASP257 3.0 31.9 1.0
CG A:ASP253 3.1 31.8 1.0
MG A:MG1005 3.3 28.9 1.0
OD1 A:ASP257 3.3 30.6 1.0
P A:PO41002 3.3 34.7 1.0
O3 A:PO41002 3.4 31.5 1.0
OD2 A:ASP253 3.4 33.7 1.0
O A:HOH1130 3.8 28.7 1.0
O A:HOH1232 4.1 31.0 1.0
O4 A:PO41002 4.1 29.6 1.0
OD2 A:ASP723 4.1 31.9 1.0
O A:HOH1167 4.1 27.1 1.0
OE1 A:GLU268 4.1 30.0 1.0
OD2 A:ASP279 4.2 31.6 1.0
O A:ASP253 4.3 29.9 1.0
CB A:ASP257 4.3 32.3 1.0
O1 A:PO41002 4.4 36.5 1.0
OD2 A:ASP727 4.5 29.0 1.0
O A:HOH1115 4.5 26.8 1.0
CB A:ASP253 4.5 32.2 1.0
CD A:GLU268 4.5 35.0 1.0
NZ A:LYS694 4.7 31.2 1.0
C A:ASP253 4.8 28.9 1.0
CA A:ASP253 4.8 31.3 1.0
OD1 A:ASP727 4.9 28.1 1.0
O4 A:PO41001 5.0 27.8 1.0
OE2 A:GLU268 5.0 36.0 1.0

Magnesium binding site 2 out of 10 in 6afw

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Magnesium binding site 2 out of 10 in the Proton Pyrophosphatase-T228D Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1004

b:35.4
occ:1.00
OD1 A:ASP507 2.0 34.7 1.0
O A:HOH1133 2.0 34.5 1.0
O A:HOH1232 2.1 31.0 1.0
O A:HOH1107 2.2 31.2 1.0
O A:HOH1162 2.2 33.8 1.0
O4 A:PO41002 2.3 29.6 1.0
CG A:ASP507 2.9 33.3 1.0
OD2 A:ASP507 3.2 32.6 1.0
MG A:MG1006 3.4 34.1 1.0
P A:PO41002 3.5 34.7 1.0
O3 A:PO41002 3.6 31.5 1.0
O A:HOH1279 3.7 35.3 1.0
OD2 A:ASP269 4.0 31.6 1.0
OD1 A:ASP279 4.0 32.0 1.0
OD2 A:ASP283 4.1 32.2 1.0
O A:ASP507 4.1 35.2 1.0
O A:HOH1196 4.2 28.7 1.0
O A:HOH1167 4.3 27.1 1.0
CB A:ASP507 4.3 32.9 1.0
OD1 A:ASP269 4.4 33.9 1.0
O2 A:PO41002 4.4 31.5 1.0
OE2 A:GLU268 4.4 36.0 1.0
C A:ASP507 4.5 33.7 1.0
ND2 A:ASN280 4.6 34.9 1.0
O1 A:PO41002 4.6 36.5 1.0
CG A:ASP269 4.6 36.5 1.0
CA A:ASP507 4.6 36.3 1.0
O2 A:PO41001 4.7 30.0 1.0
O A:HOH1146 4.8 30.9 1.0
CG A:ASP283 4.9 35.5 1.0
OD2 A:ASP530 4.9 35.2 1.0
OD1 A:ASP283 4.9 37.1 1.0
CG A:ASP279 4.9 32.7 1.0
OD2 A:ASP279 5.0 31.6 1.0

Magnesium binding site 3 out of 10 in 6afw

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Magnesium binding site 3 out of 10 in the Proton Pyrophosphatase-T228D Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1005

b:28.9
occ:1.00
O2 A:PO41002 2.1 31.5 1.0
OD1 A:ASP727 2.1 28.1 1.0
O A:HOH1142 2.2 27.2 1.0
O A:HOH1115 2.2 26.8 1.0
O4 A:PO41001 2.2 27.8 1.0
OD2 A:ASP253 2.3 33.7 1.0
CG A:ASP727 3.0 30.1 1.0
CG A:ASP253 3.2 31.8 1.0
O1 A:PO41002 3.2 36.5 1.0
P A:PO41002 3.2 34.7 1.0
MG A:MG1003 3.3 32.9 1.0
OD2 A:ASP727 3.3 29.0 1.0
OD1 A:ASP253 3.4 30.5 1.0
NZ A:LYS730 3.7 26.6 1.0
P A:PO41001 3.7 48.8 1.0
OD2 A:ASP723 4.0 31.9 1.0
O A:HOH1167 4.0 27.1 1.0
OD1 A:ASP723 4.1 28.1 1.0
O3 A:PO41002 4.1 31.5 1.0
O A:HOH1114 4.2 27.8 1.0
O2 A:PO41001 4.3 30.0 1.0
NZ A:LYS250 4.3 28.7 1.0
CE A:LYS250 4.3 25.4 1.0
O4 A:PO41002 4.3 29.6 1.0
O3 A:PO41001 4.4 35.0 1.0
CB A:ASP727 4.4 27.4 1.0
CG A:ASP723 4.4 28.2 1.0
OD2 A:ASP691 4.5 30.9 1.0
CB A:ASP253 4.5 32.2 1.0
O1 A:PO41001 4.7 34.0 1.0
CE A:LYS730 4.8 30.2 1.0
OD2 A:ASP257 4.8 31.4 1.0
O A:HOH1137 4.8 29.9 1.0
O A:ASP723 4.9 24.9 1.0
OD2 A:ASP731 4.9 28.5 1.0
CA A:ASP727 5.0 29.2 1.0
MG A:MG1006 5.0 34.1 1.0
CG A:ASP691 5.0 31.1 1.0

Magnesium binding site 4 out of 10 in 6afw

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Magnesium binding site 4 out of 10 in the Proton Pyrophosphatase-T228D Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1006

b:34.1
occ:1.00
O A:HOH1167 2.1 27.1 1.0
OD1 A:ASP283 2.1 37.1 1.0
O2 A:PO41001 2.2 30.0 1.0
O A:HOH1107 2.2 31.2 1.0
OD2 A:ASP507 2.2 32.6 1.0
O4 A:PO41002 2.3 29.6 1.0
CG A:ASP283 2.8 35.5 1.0
OD2 A:ASP283 2.9 32.2 1.0
CG A:ASP507 3.3 33.3 1.0
MG A:MG1004 3.4 35.4 1.0
P A:PO41002 3.4 34.7 1.0
O A:HOH1135 3.5 29.1 1.0
P A:PO41001 3.6 48.8 1.0
OD1 A:ASP507 3.7 34.7 1.0
O2 A:PO41002 3.7 31.5 1.0
O1 A:PO41002 3.9 36.5 1.0
O A:HOH1219 3.9 29.9 1.0
O4 A:PO41001 3.9 27.8 1.0
OD1 A:ASP279 4.0 32.0 1.0
O A:HOH1247 4.1 35.9 1.0
CB A:ASP283 4.3 29.3 1.0
O A:HOH1146 4.3 30.9 1.0
OD2 A:ASP253 4.4 33.7 1.0
O A:HOH1232 4.4 31.0 1.0
O1 A:PO41001 4.4 34.0 1.0
CB A:ASP507 4.5 32.9 1.0
NZ A:LYS250 4.6 28.7 1.0
O3 A:PO41001 4.6 35.0 1.0
O3 A:PO41002 4.7 31.5 1.0
CG A:ASP279 4.8 32.7 1.0
O A:ASP279 4.8 32.4 1.0
OD2 A:ASP279 4.9 31.6 1.0
CA A:ASP283 4.9 32.9 1.0
CG A:ASP253 4.9 31.8 1.0
MG A:MG1005 5.0 28.9 1.0
O A:HOH1133 5.0 34.5 1.0

Magnesium binding site 5 out of 10 in 6afw

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Magnesium binding site 5 out of 10 in the Proton Pyrophosphatase-T228D Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1007

b:34.9
occ:1.00
O A:HOH1146 2.0 30.9 1.0
O A:HOH1152 2.1 29.5 1.0
OD1 A:ASN534 2.1 33.6 1.0
O3 A:PO41001 2.1 35.0 1.0
OD2 A:ASP691 2.2 30.9 1.0
O1 A:PO41002 2.2 36.5 1.0
CG A:ASN534 3.0 32.6 1.0
CG A:ASP691 3.2 31.1 1.0
ND2 A:ASN534 3.3 29.4 1.0
P A:PO41001 3.4 48.8 1.0
P A:PO41002 3.6 34.7 1.0
OD1 A:ASP691 3.6 30.6 1.0
O2 A:PO41001 3.8 30.0 1.0
K A:K1008 3.8 45.5 1.0
O3 A:PO41002 3.9 31.5 1.0
OD1 A:ASP530 3.9 36.3 1.0
O A:HOH1115 4.0 26.8 1.0
O4 A:PO41001 4.0 27.8 1.0
O A:HOH1281 4.1 28.8 1.0
OD2 A:ASP530 4.1 35.2 1.0
O4 A:PO41002 4.2 29.6 1.0
CB A:ASN534 4.4 31.8 1.0
CG A:ASP530 4.4 36.6 1.0
CB A:ASP691 4.5 27.0 1.0
O1 A:PO41001 4.6 34.0 1.0
O2 A:PO41002 4.7 31.5 1.0
OD2 A:ASP507 4.8 32.6 1.0
O A:HOH1218 4.8 31.1 1.0
O A:ASP530 4.8 35.9 1.0
CA A:ASN534 4.8 32.6 1.0
O A:HOH1247 4.9 35.9 1.0
CE A:LYS730 4.9 30.2 1.0

Magnesium binding site 6 out of 10 in 6afw

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Magnesium binding site 6 out of 10 in the Proton Pyrophosphatase-T228D Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:40.7
occ:1.00
OD2 B:ASP257 2.0 38.9 1.0
OD1 B:ASP253 2.0 38.1 1.0
O B:HOH1110 2.1 38.7 1.0
O B:HOH1141 2.3 38.1 1.0
O2 B:PO41002 2.3 34.8 1.0
O B:HOH1131 2.4 36.8 1.0
CG B:ASP253 3.0 39.0 1.0
CG B:ASP257 3.0 38.9 1.0
OD2 B:ASP253 3.3 39.0 1.0
MG B:MG1005 3.4 37.6 1.0
P B:PO41002 3.4 39.8 1.0
OD1 B:ASP257 3.5 36.4 1.0
O4 B:PO41002 3.6 37.6 1.0
O B:HOH1162 3.9 36.1 1.0
O3 B:PO41002 4.0 37.6 1.0
OD2 B:ASP723 4.0 36.6 1.0
O B:HOH1220 4.1 37.7 1.0
OE1 B:GLU268 4.2 39.8 1.0
OD2 B:ASP279 4.2 38.4 1.0
O B:HOH1234 4.2 32.1 1.0
CB B:ASP257 4.3 39.1 1.0
CB B:ASP253 4.4 34.5 1.0
OD2 B:ASP727 4.4 34.4 1.0
O B:ASP253 4.4 38.2 1.0
O B:HOH1128 4.5 28.8 1.0
O1 B:PO41002 4.7 41.0 1.0
CA B:ASP253 4.7 39.4 1.0
CD B:GLU268 4.7 40.0 1.0
C B:ASP253 4.7 40.2 1.0
NZ B:LYS694 4.8 36.9 1.0
OD1 B:ASP727 4.8 32.9 1.0
O2 B:PO41001 4.9 32.3 1.0

Magnesium binding site 7 out of 10 in 6afw

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Magnesium binding site 7 out of 10 in the Proton Pyrophosphatase-T228D Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1004

b:43.7
occ:1.00
O B:HOH1220 1.9 37.7 1.0
OD1 B:ASP507 2.0 40.6 1.0
O B:HOH1163 2.1 40.0 1.0
O B:HOH1119 2.1 34.5 1.0
O B:HOH1112 2.2 42.2 1.0
O3 B:PO41002 2.2 37.6 1.0
CG B:ASP507 3.0 43.4 1.0
OD2 B:ASP507 3.3 38.4 1.0
P B:PO41002 3.4 39.8 1.0
MG B:MG1006 3.4 37.3 1.0
O4 B:PO41002 3.4 37.6 1.0
O B:HOH1235 3.9 42.0 1.0
OD2 B:ASP269 4.1 42.6 1.0
O B:HOH1131 4.1 36.8 1.0
OD1 B:ASP279 4.1 38.9 1.0
OD1 B:ASP269 4.2 40.0 1.0
O B:ASP507 4.2 44.9 1.0
OE2 B:GLU268 4.2 41.1 1.0
O1 B:PO41002 4.3 41.0 1.0
O2 B:PO41002 4.4 34.8 1.0
CB B:ASP507 4.4 40.5 1.0
O B:HOH1234 4.4 32.1 1.0
OD2 B:ASP283 4.4 43.3 1.0
ND2 B:ASN280 4.6 43.6 1.0
CG B:ASP269 4.6 44.0 1.0
C B:ASP507 4.6 43.8 1.0
CA B:ASP507 4.7 41.1 1.0
CD B:GLU268 4.8 40.0 1.0
O B:HOH1152 4.8 43.2 1.0
O B:HOH1110 4.9 38.7 1.0
O4 B:PO41001 4.9 36.6 1.0
OD1 B:ASP283 4.9 42.2 1.0
OD2 B:ASP530 4.9 46.7 1.0

Magnesium binding site 8 out of 10 in 6afw

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Magnesium binding site 8 out of 10 in the Proton Pyrophosphatase-T228D Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1005

b:37.6
occ:1.00
O B:HOH1128 2.0 28.8 1.0
O B:HOH1141 2.1 38.1 1.0
OD1 B:ASP727 2.1 32.9 1.0
O2 B:PO41002 2.1 34.8 1.0
O2 B:PO41001 2.2 32.3 1.0
OD2 B:ASP253 2.3 39.0 1.0
CG B:ASP727 3.0 34.5 1.0
CG B:ASP253 3.3 39.0 1.0
OD2 B:ASP727 3.3 34.4 1.0
P B:PO41002 3.4 39.8 1.0
MG B:MG1003 3.4 40.7 1.0
NZ B:LYS730 3.5 31.7 1.0
O1 B:PO41002 3.5 41.0 1.0
OD1 B:ASP253 3.6 38.1 1.0
P B:PO41001 3.6 54.2 1.0
OD2 B:ASP723 4.0 36.6 1.0
OD1 B:ASP723 4.0 37.2 1.0
NZ B:LYS250 4.1 35.9 1.0
O B:HOH1234 4.2 32.1 1.0
CE B:LYS250 4.2 33.5 1.0
O4 B:PO41001 4.3 36.6 1.0
O3 B:PO41001 4.3 40.1 1.0
O4 B:PO41002 4.3 37.6 1.0
O3 B:PO41002 4.3 37.6 1.0
OD2 B:ASP691 4.4 39.6 1.0
CB B:ASP727 4.4 33.6 1.0
O B:HOH1110 4.4 38.7 1.0
CG B:ASP723 4.4 36.5 1.0
CB B:ASP253 4.6 34.5 1.0
CE B:LYS730 4.6 31.7 1.0
O1 B:PO41001 4.6 41.9 1.0
OD2 B:ASP731 4.7 34.5 1.0
O B:HOH1199 4.8 30.6 1.0
O B:ASP723 4.8 31.9 1.0
CA B:ASP727 4.9 34.4 1.0
CG B:ASP691 4.9 38.2 1.0
OD2 B:ASP257 4.9 38.9 1.0

Magnesium binding site 9 out of 10 in 6afw

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Magnesium binding site 9 out of 10 in the Proton Pyrophosphatase-T228D Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1006

b:37.3
occ:1.00
O B:HOH1234 2.1 32.1 1.0
OD1 B:ASP283 2.1 42.2 1.0
O3 B:PO41002 2.1 37.6 1.0
OD2 B:ASP507 2.1 38.4 1.0
O4 B:PO41001 2.3 36.6 1.0
O B:HOH1112 2.3 42.2 1.0
CG B:ASP283 3.0 43.3 1.0
CG B:ASP507 3.2 43.4 1.0
OD2 B:ASP283 3.2 43.3 1.0
P B:PO41002 3.3 39.8 1.0
MG B:MG1004 3.4 43.7 1.0
OD1 B:ASP507 3.5 40.6 1.0
P B:PO41001 3.7 54.2 1.0
O1 B:PO41002 3.7 41.0 1.0
O B:HOH1142 3.7 34.4 1.0
O2 B:PO41002 3.8 34.8 1.0
OD1 B:ASP279 3.9 38.9 1.0
O B:HOH1217 4.0 36.4 1.0
O2 B:PO41001 4.0 32.3 1.0
O B:HOH1242 4.2 44.4 1.0
O B:HOH1152 4.3 43.2 1.0
O B:HOH1220 4.3 37.7 1.0
CB B:ASP283 4.3 41.7 1.0
CB B:ASP507 4.5 40.5 1.0
O1 B:PO41001 4.6 41.9 1.0
O4 B:PO41002 4.6 37.6 1.0
O3 B:PO41001 4.6 40.1 1.0
OD2 B:ASP253 4.6 39.0 1.0
NZ B:LYS250 4.6 35.9 1.0
O B:ASP279 4.8 41.6 1.0
CG B:ASP279 4.8 40.5 1.0
O B:HOH1119 4.9 34.5 1.0
CA B:ASP283 5.0 41.8 1.0
O B:HOH1163 5.0 40.0 1.0

Magnesium binding site 10 out of 10 in 6afw

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Magnesium binding site 10 out of 10 in the Proton Pyrophosphatase-T228D Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Proton Pyrophosphatase-T228D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1007

b:43.7
occ:1.00
OD1 B:ASN534 2.0 37.8 1.0
O B:HOH1152 2.1 43.2 1.0
O1 B:PO41002 2.2 41.0 1.0
O B:HOH1167 2.2 37.8 1.0
O3 B:PO41001 2.2 40.1 1.0
OD2 B:ASP691 2.4 39.6 1.0
CG B:ASN534 2.9 42.3 1.0
ND2 B:ASN534 3.2 42.5 1.0
CG B:ASP691 3.3 38.2 1.0
P B:PO41001 3.5 54.2 1.0
P B:PO41002 3.6 39.8 1.0
K B:K1008 3.7 56.1 1.0
OD1 B:ASP691 3.7 39.9 1.0
O4 B:PO41001 3.9 36.6 1.0
O4 B:PO41002 3.9 37.6 1.0
O B:HOH1231 3.9 40.1 1.0
OD2 B:ASP530 4.0 46.7 1.0
O2 B:PO41001 4.0 32.3 1.0
OD1 B:ASP530 4.1 47.4 1.0
O B:HOH1128 4.1 28.8 1.0
CB B:ASN534 4.2 40.0 1.0
CG B:ASP530 4.4 46.7 1.0
O3 B:PO41002 4.4 37.6 1.0
O2 B:PO41002 4.6 34.8 1.0
O B:HOH1219 4.6 38.2 1.0
CB B:ASP691 4.6 34.6 1.0
O1 B:PO41001 4.7 41.9 1.0
CA B:ASN534 4.8 41.3 1.0
OD2 B:ASP507 4.9 38.4 1.0
O B:ASP530 4.9 45.0 1.0
CE B:LYS730 4.9 31.7 1.0

Reference:

J.Y.Tsai, K.Z.Tang, K.M.Li, B.L.Hsu, Y.W.Chiang, A.Goldman, Y.J.Sun. Roles of the Hydrophobic Gate and Exit Channel in Vigna Radiata Pyrophosphatase Ion Translocation. J. Mol. Biol. V. 431 1619 2019.
ISSN: ESSN 1089-8638
PubMed: 30878480
DOI: 10.1016/J.JMB.2019.03.009
Page generated: Mon Dec 14 22:20:16 2020

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