Magnesium in PDB 6afu: Proton Pyrophosphatase-L555M Mutant

Enzymatic activity of Proton Pyrophosphatase-L555M Mutant

All present enzymatic activity of Proton Pyrophosphatase-L555M Mutant:
3.6.1.1;

Protein crystallography data

The structure of Proton Pyrophosphatase-L555M Mutant, PDB code: 6afu 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) 26.07 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 221.185, 88.393, 159.741, 90.00, 125.72, 90.00
R / Rfree (%) 18.2 / 22.9

Other elements in 6afu:

The structure of Proton Pyrophosphatase-L555M Mutant also contains other interesting chemical elements:

Potassium (K) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Proton Pyrophosphatase-L555M Mutant (pdb code 6afu). 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-L555M Mutant, PDB code: 6afu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 6afu

Go back to Magnesium Binding Sites List in 6afu
Magnesium binding site 1 out of 10 in the Proton Pyrophosphatase-L555M 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-L555M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:17.2
occ:1.00
OD2 A:ASP257 2.1 16.3 1.0
O A:HOH1118 2.2 10.1 1.0
O A:HOH1106 2.2 14.6 1.0
O A:HOH1111 2.2 11.0 1.0
O2 A:PO41002 2.3 13.6 1.0
OD1 A:ASP253 2.4 19.4 1.0
O3 A:PO41002 3.0 16.9 1.0
CG A:ASP257 3.1 12.5 1.0
P A:PO41002 3.1 18.3 1.0
OD1 A:ASP257 3.3 12.8 1.0
CG A:ASP253 3.4 13.3 1.0
MG A:MG1005 3.6 14.3 1.0
OD2 A:ASP253 3.7 14.3 1.0
O A:HOH1121 3.7 10.4 1.0
OE1 A:GLU268 3.7 15.3 1.0
O A:HOH1180 3.7 14.3 1.0
O4 A:PO41002 4.0 15.0 1.0
CD A:GLU268 4.2 18.7 1.0
OD2 A:ASP723 4.2 14.6 1.0
O A:HOH1108 4.3 11.4 1.0
O1 A:PO41002 4.3 20.1 1.0
O A:HOH1122 4.4 13.1 1.0
CB A:ASP257 4.4 11.9 1.0
OD2 A:ASP279 4.5 16.1 1.0
OE2 A:GLU268 4.6 18.5 1.0
MG A:MG1004 4.7 22.8 1.0
O A:ASP253 4.7 9.7 1.0
CB A:ASP253 4.8 12.9 1.0
CG A:GLU268 4.8 17.6 1.0
OD2 A:ASP727 4.8 15.0 1.0
O A:HOH1115 4.9 21.9 1.0
OD1 A:ASP727 5.0 13.3 1.0

Magnesium binding site 2 out of 10 in 6afu

Go back to Magnesium Binding Sites List in 6afu
Magnesium binding site 2 out of 10 in the Proton Pyrophosphatase-L555M 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-L555M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1004

b:22.8
occ:1.00
O A:HOH1119 1.9 16.5 1.0
O A:HOH1180 1.9 14.3 1.0
O A:HOH1124 2.0 14.9 1.0
OD1 A:ASP507 2.2 16.8 1.0
O4 A:PO41002 2.3 15.0 1.0
O A:HOH1115 2.4 21.9 1.0
CG A:ASP507 3.1 16.0 1.0
O3 A:PO41002 3.2 16.9 1.0
P A:PO41002 3.3 18.3 1.0
OD2 A:ASP507 3.4 16.3 1.0
MG A:MG1006 3.4 15.8 1.0
OD2 A:ASP269 3.8 21.0 1.0
O A:HOH1192 3.8 17.6 1.0
OD1 A:ASP279 4.1 19.3 1.0
OE2 A:GLU268 4.1 18.5 1.0
O A:HOH1118 4.2 10.1 1.0
O2 A:PO41002 4.2 13.6 1.0
O A:HOH1108 4.2 11.4 1.0
OD1 A:ASP269 4.3 18.2 1.0
O A:ASP507 4.3 13.0 1.0
O1 A:PO41002 4.4 20.1 1.0
OD2 A:ASP283 4.4 15.9 1.0
CB A:ASP507 4.5 13.6 1.0
CG A:ASP269 4.5 20.5 1.0
MG A:MG1003 4.7 17.2 1.0
O2 A:PO41001 4.7 17.6 1.0
C A:ASP507 4.8 18.3 1.0
CD A:GLU268 4.8 18.7 1.0
CA A:ASP507 4.8 14.1 1.0
OD2 A:ASP530 4.9 15.6 1.0
ND2 A:ASN280 4.9 16.5 1.0

Magnesium binding site 3 out of 10 in 6afu

Go back to Magnesium Binding Sites List in 6afu
Magnesium binding site 3 out of 10 in the Proton Pyrophosphatase-L555M 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-L555M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1005

b:14.3
occ:1.00
OD1 A:ASP727 1.8 13.3 1.0
O A:HOH1122 2.0 13.1 1.0
O4 A:PO41001 2.2 13.2 1.0
O2 A:PO41002 2.2 13.6 1.0
O A:HOH1111 2.3 11.0 1.0
OD2 A:ASP253 2.5 14.3 1.0
CG A:ASP727 2.8 12.7 1.0
CG A:ASP253 3.2 13.3 1.0
OD2 A:ASP727 3.2 15.0 1.0
OD1 A:ASP253 3.4 19.4 1.0
P A:PO41002 3.4 18.3 1.0
O1 A:PO41002 3.5 20.1 1.0
NZ A:LYS730 3.5 8.4 1.0
MG A:MG1003 3.6 17.2 1.0
P A:PO41001 3.6 37.8 1.0
OD1 A:ASP723 3.9 8.2 1.0
O A:HOH1106 3.9 14.6 1.0
CE A:LYS250 4.0 8.8 1.0
OD2 A:ASP723 4.1 14.6 1.0
CB A:ASP727 4.2 9.0 1.0
O A:HOH1108 4.2 11.4 1.0
O2 A:PO41001 4.2 17.6 1.0
NZ A:LYS250 4.3 8.5 1.0
O3 A:PO41001 4.3 15.0 1.0
O3 A:PO41002 4.4 16.9 1.0
OD2 A:ASP691 4.4 8.7 1.0
CG A:ASP723 4.4 9.4 1.0
O4 A:PO41002 4.4 15.0 1.0
CB A:ASP253 4.5 12.9 1.0
O1 A:PO41001 4.6 26.0 1.0
O A:HOH1152 4.7 8.5 1.0
CA A:ASP727 4.7 11.6 1.0
OD2 A:ASP257 4.8 16.3 1.0
CE A:LYS730 4.9 9.3 1.0
OD2 A:ASP731 4.9 11.3 1.0
O A:ASP723 4.9 11.3 1.0
MG A:MG1007 5.0 11.3 1.0

Magnesium binding site 4 out of 10 in 6afu

Go back to Magnesium Binding Sites List in 6afu
Magnesium binding site 4 out of 10 in the Proton Pyrophosphatase-L555M 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-L555M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1006

b:15.8
occ:1.00
OD1 A:ASP283 2.0 18.3 1.0
O A:HOH1124 2.0 14.9 1.0
O A:HOH1108 2.1 11.4 1.0
OD2 A:ASP507 2.3 16.3 1.0
O2 A:PO41001 2.3 17.6 1.0
O4 A:PO41002 2.4 15.0 1.0
CG A:ASP283 2.7 15.8 1.0
OD2 A:ASP283 2.7 15.9 1.0
CG A:ASP507 3.2 16.0 1.0
MG A:MG1004 3.4 22.8 1.0
OD1 A:ASP507 3.6 16.8 1.0
P A:PO41002 3.7 18.3 1.0
P A:PO41001 3.8 37.8 1.0
O A:HOH1102 3.8 10.8 1.0
O A:HOH1131 3.8 14.6 1.0
OD1 A:ASP279 3.9 19.3 1.0
O A:HOH1178 3.9 10.7 1.0
O2 A:PO41002 4.0 13.6 1.0
CB A:ASP283 4.1 14.0 1.0
O1 A:PO41002 4.3 20.1 1.0
O A:HOH1180 4.3 14.3 1.0
CB A:ASP507 4.3 13.6 1.0
O4 A:PO41001 4.4 13.2 1.0
OD2 A:ASP253 4.4 14.3 1.0
NZ A:LYS250 4.5 8.5 1.0
O1 A:PO41001 4.5 26.0 1.0
O A:ASP279 4.5 15.8 1.0
O A:HOH1119 4.6 16.5 1.0
O3 A:PO41001 4.6 15.0 1.0
O A:HOH1129 4.7 12.0 1.0
CG A:ASP279 4.8 17.1 1.0
O3 A:PO41002 4.8 16.9 1.0
CA A:ASP283 4.9 11.5 1.0

Magnesium binding site 5 out of 10 in 6afu

Go back to Magnesium Binding Sites List in 6afu
Magnesium binding site 5 out of 10 in the Proton Pyrophosphatase-L555M 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-L555M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1007

b:11.3
occ:1.00
O3 A:PO41001 1.9 15.0 1.0
OD1 A:ASN534 2.0 17.4 1.0
O1 A:PO41002 2.2 20.1 1.0
OD2 A:ASP691 2.2 8.7 1.0
O A:HOH1129 2.3 12.0 1.0
O A:HOH1105 2.3 7.3 1.0
CG A:ASN534 2.8 12.9 1.0
ND2 A:ASN534 3.1 13.7 1.0
CG A:ASP691 3.3 10.6 1.0
P A:PO41001 3.3 37.8 1.0
P A:PO41002 3.6 18.3 1.0
O A:HOH1188 3.7 11.2 1.0
OD1 A:ASP691 3.7 15.7 1.0
K A:K1008 3.8 16.8 1.0
O4 A:PO41001 3.8 13.2 1.0
O2 A:PO41001 3.9 17.6 1.0
O A:HOH1122 3.9 13.1 1.0
OD2 A:ASP530 4.2 15.6 1.0
O4 A:PO41002 4.2 15.0 1.0
CB A:ASN534 4.2 11.8 1.0
O3 A:PO41002 4.3 16.9 1.0
O1 A:PO41001 4.4 26.0 1.0
OD1 A:ASP530 4.4 17.7 1.0
CB A:ASP691 4.5 11.2 1.0
O2 A:PO41002 4.5 13.6 1.0
OD2 A:ASP507 4.6 16.3 1.0
CG A:ASP530 4.6 14.4 1.0
CA A:ASN534 4.7 11.1 1.0
O A:HOH1131 4.9 14.6 1.0
O A:HOH1161 4.9 9.7 1.0
CE A:LYS730 4.9 9.3 1.0
O A:ASP530 4.9 13.9 1.0
NZ A:LYS730 4.9 8.4 1.0
MG A:MG1005 5.0 14.3 1.0

Magnesium binding site 6 out of 10 in 6afu

Go back to Magnesium Binding Sites List in 6afu
Magnesium binding site 6 out of 10 in the Proton Pyrophosphatase-L555M 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-L555M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:23.2
occ:1.00
OD2 B:ASP257 2.0 26.4 1.0
O B:HOH1108 2.2 20.7 1.0
OD1 B:ASP253 2.2 23.7 1.0
O B:HOH1124 2.3 22.5 1.0
O2 B:PO41002 2.5 18.6 1.0
O B:HOH1114 2.6 26.2 1.0
CG B:ASP257 2.9 21.1 1.0
OD1 B:ASP257 3.1 20.8 1.0
CG B:ASP253 3.2 20.0 1.0
O4 B:PO41002 3.3 24.2 1.0
P B:PO41002 3.4 23.2 1.0
OD2 B:ASP253 3.5 20.2 1.0
MG B:MG1005 3.7 18.2 1.0
O B:HOH1151 4.1 18.4 1.0
O3 B:PO41002 4.2 17.7 1.0
CB B:ASP257 4.2 17.8 1.0
OD2 B:ASP723 4.2 21.6 1.0
OE2 B:GLU268 4.2 28.4 1.0
OD2 B:ASP279 4.3 21.1 1.0
O B:ASP253 4.3 20.4 1.0
O B:HOH1146 4.4 23.0 1.0
CD B:GLU268 4.5 28.3 1.0
CB B:ASP253 4.5 17.3 1.0
O1 B:PO41002 4.6 27.3 1.0
O B:HOH1126 4.6 17.9 1.0
CA B:ASP253 4.8 20.7 1.0
C B:ASP253 4.8 21.1 1.0
MG B:MG1004 4.8 21.7 1.0
OD2 B:ASP727 4.8 16.6 1.0
OE1 B:GLU268 4.9 25.2 1.0
OD1 B:ASP727 4.9 15.5 1.0
NZ B:LYS694 5.0 19.0 1.0

Magnesium binding site 7 out of 10 in 6afu

Go back to Magnesium Binding Sites List in 6afu
Magnesium binding site 7 out of 10 in the Proton Pyrophosphatase-L555M 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-L555M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1004

b:21.7
occ:1.00
O B:HOH1105 1.9 23.1 1.0
O B:HOH1104 2.0 20.9 1.0
O B:HOH1101 2.4 25.6 1.0
OD1 B:ASP507 2.6 27.8 1.0
O3 B:PO41002 2.8 17.7 1.0
O4 B:PO41002 3.3 24.2 1.0
CG B:ASP507 3.5 23.1 1.0
O B:HOH1124 3.6 22.5 1.0
OD2 B:ASP269 3.6 29.7 1.0
P B:PO41002 3.7 23.2 1.0
OD1 B:ASP269 3.7 28.7 1.0
OD2 B:ASP507 3.7 23.0 1.0
OD1 B:ASP279 3.7 24.8 1.0
OE1 B:GLU268 3.9 25.2 1.0
CG B:ASP269 4.1 30.7 1.0
O B:HOH1151 4.4 18.4 1.0
MG B:MG1006 4.4 27.6 1.0
ND2 B:ASN280 4.4 23.5 1.0
O B:ASP507 4.5 24.5 1.0
O2 B:PO41002 4.5 18.6 1.0
CG B:ASP279 4.6 28.0 1.0
CD B:GLU268 4.6 28.3 1.0
OD2 B:ASP279 4.7 21.1 1.0
OD2 B:ASP283 4.7 29.4 1.0
MG B:MG1003 4.8 23.2 1.0
O1 B:PO41002 4.8 27.3 1.0
CB B:ASP507 4.9 23.9 1.0

Magnesium binding site 8 out of 10 in 6afu

Go back to Magnesium Binding Sites List in 6afu
Magnesium binding site 8 out of 10 in the Proton Pyrophosphatase-L555M 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-L555M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1005

b:18.2
occ:1.00
O B:HOH1126 2.0 17.9 1.0
OD1 B:ASP727 2.0 15.5 1.0
O2 B:PO41001 2.1 26.7 1.0
O2 B:PO41002 2.1 18.6 1.0
O B:HOH1108 2.2 20.7 1.0
OD2 B:ASP253 2.2 20.2 1.0
CG B:ASP727 3.1 18.1 1.0
CG B:ASP253 3.2 20.0 1.0
P B:PO41002 3.4 23.2 1.0
NZ B:LYS730 3.4 13.1 1.0
O1 B:PO41002 3.5 27.3 1.0
OD1 B:ASP253 3.5 23.7 1.0
P B:PO41001 3.5 50.2 1.0
OD2 B:ASP727 3.6 16.6 1.0
MG B:MG1003 3.7 23.2 1.0
CE B:LYS250 3.9 12.6 1.0
O3 B:PO41001 4.1 24.1 1.0
OD1 B:ASP723 4.2 18.3 1.0
O B:HOH1151 4.2 18.4 1.0
O4 B:PO41001 4.2 26.5 1.0
OD2 B:ASP723 4.3 21.6 1.0
NZ B:LYS250 4.3 12.7 1.0
O3 B:PO41002 4.3 17.7 1.0
CB B:ASP727 4.3 15.2 1.0
O4 B:PO41002 4.4 24.2 1.0
O B:HOH1114 4.5 26.2 1.0
O B:HOH1147 4.5 12.6 1.0
CB B:ASP253 4.5 17.3 1.0
O1 B:PO41001 4.5 36.3 1.0
CE B:LYS730 4.6 13.1 1.0
OD2 B:ASP691 4.6 15.2 1.0
CG B:ASP723 4.6 19.1 1.0
CA B:ASP727 4.7 14.6 1.0
OD2 B:ASP731 4.7 19.2 1.0
CG B:ASP691 5.0 16.5 1.0
MG B:MG1006 5.0 27.6 1.0
OD2 B:ASP257 5.0 26.4 1.0

Magnesium binding site 9 out of 10 in 6afu

Go back to Magnesium Binding Sites List in 6afu
Magnesium binding site 9 out of 10 in the Proton Pyrophosphatase-L555M 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-L555M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1006

b:27.6
occ:1.00
OD1 B:ASP283 1.9 29.9 1.0
O4 B:PO41001 2.0 26.5 1.0
O B:HOH1151 2.2 18.4 1.0
O B:HOH1101 2.4 25.6 1.0
OD2 B:ASP507 2.6 23.0 1.0
O3 B:PO41002 2.6 17.7 1.0
CG B:ASP283 3.1 29.5 1.0
O B:HOH1111 3.1 17.2 1.0
P B:PO41001 3.3 50.2 1.0
OD2 B:ASP283 3.6 29.4 1.0
NZ B:LYS250 3.6 12.7 1.0
O2 B:PO41001 3.7 26.7 1.0
O B:HOH1158 3.7 18.3 1.0
CG B:ASP507 3.8 23.1 1.0
P B:PO41002 3.8 23.2 1.0
O B:HOH1171 3.9 23.2 1.0
O1 B:PO41001 4.0 36.3 1.0
O2 B:PO41002 4.0 18.6 1.0
CB B:ASP283 4.3 22.4 1.0
OD2 B:ASP253 4.3 20.2 1.0
OD1 B:ASP507 4.3 27.8 1.0
OD1 B:ASP279 4.3 24.8 1.0
O1 B:PO41002 4.4 27.3 1.0
MG B:MG1004 4.4 21.7 1.0
O3 B:PO41001 4.4 24.1 1.0
O B:ASP279 4.5 24.1 1.0
OG1 B:THR249 4.5 20.4 1.0
CA B:ASP283 4.6 22.2 1.0
OD2 B:ASP287 4.7 23.0 1.0
O B:HOH1136 4.9 18.6 1.0
N B:ASP283 4.9 25.3 1.0
CE B:LYS250 4.9 12.6 1.0
CB B:ASP507 5.0 23.9 1.0
MG B:MG1005 5.0 18.2 1.0
CG B:ASP253 5.0 20.0 1.0

Magnesium binding site 10 out of 10 in 6afu

Go back to Magnesium Binding Sites List in 6afu
Magnesium binding site 10 out of 10 in the Proton Pyrophosphatase-L555M 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-L555M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1007

b:13.7
occ:1.00
OD1 B:ASN534 1.9 25.3 1.0
O3 B:PO41001 2.0 24.1 1.0
O B:HOH1136 2.1 18.6 1.0
O1 B:PO41002 2.2 27.3 1.0
OD2 B:ASP691 2.4 15.2 1.0
O B:HOH1137 2.5 23.1 1.0
CG B:ASN534 2.8 21.1 1.0
ND2 B:ASN534 3.1 28.8 1.0
P B:PO41001 3.4 50.2 1.0
K B:K1008 3.5 30.0 1.0
O B:HOH1145 3.5 15.4 1.0
CG B:ASP691 3.5 16.5 1.0
P B:PO41002 3.7 23.2 1.0
O4 B:PO41001 3.8 26.5 1.0
OD1 B:ASP691 4.0 25.2 1.0
O2 B:PO41001 4.1 26.7 1.0
CB B:ASN534 4.1 16.9 1.0
OD2 B:ASP530 4.2 23.6 1.0
O3 B:PO41002 4.2 17.7 1.0
OD1 B:ASP530 4.3 28.2 1.0
O B:HOH1126 4.3 17.9 1.0
O4 B:PO41002 4.3 24.2 1.0
O1 B:PO41001 4.4 36.3 1.0
CG B:ASP530 4.6 24.3 1.0
O2 B:PO41002 4.6 18.6 1.0
O B:HOH1153 4.6 16.9 1.0
CA B:ASN534 4.6 21.1 1.0
CB B:ASP691 4.8 14.8 1.0
O B:ASP530 4.9 27.2 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 22:20:11 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