Magnesium in PDB 8b24: Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+

Protein crystallography data

The structure of Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+, PDB code: 8b24 was solved by J.Strauss, K.Vidilaseris, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 99.74 / 4.53
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.108, 111.068, 105.419, 90, 108.9, 90
R / Rfree (%) 32.6 / 36.1

Other elements in 8b24:

The structure of Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+ also contains other interesting chemical elements:

Potassium (K) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+ (pdb code 8b24). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+, PDB code: 8b24:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 8b24

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Magnesium binding site 1 out of 10 in the Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:474.9
occ:1.00
 OD2 A:ASP202 1.9 408.4 1.0
OD2 A:ASP692 2.0 450.4 1.0
O5 A:DPO801 2.1 436.2 1.0
OD1 A:ASP692 2.4 442.3 1.0
CG A:ASP692 2.4 439.5 1.0
CG A:ASP202 2.7 413.4 1.0
MG A:MG803 2.7 472.8 1.0
OD1 A:ASP202 3.2 424.5 1.0
P2 A:DPO801 3.4 436.2 1.0
O4 A:DPO801 3.6 436.2 1.0
NZ A:LYS199 3.6 414.4 1.0
O2 A:DPO801 3.7 436.2 1.0
OD2 A:ASP688 3.8 452.4 1.0
CB A:ASP202 3.8 409.9 1.0
CB A:ASP692 3.8 418.2 1.0
OD1 A:ASP688 3.9 433.4 1.0
P1 A:DPO801 4.1 436.2 1.0
OD2 A:ASP206 4.1 451.0 1.0
CG A:ASP688 4.2 441.1 1.0
O1 A:DPO801 4.2 436.2 1.0
NZ A:LYS695 4.3 474.5 1.0
O7 A:DPO801 4.3 436.2 1.0
O6 A:DPO801 4.4 436.2 1.0
O A:ASP688 4.7 427.1 1.0
CE A:LYS199 4.8 406.6 1.0
CA A:ASP692 4.8 412.9 1.0
CD A:LYS199 4.9 410.3 1.0
MG A:MG805 4.9 450.9 1.0
OD1 A:ASP660 4.9 423.0 1.0
CA A:ASP202 5.0 412.4 1.0

Magnesium binding site 2 out of 10 in 8b24

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Magnesium binding site 2 out of 10 in the Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:472.8
occ:1.00
 O1 A:DPO801 2.1 436.2 1.0
O2 A:DPO801 2.4 436.2 1.0
OD2 A:ASP688 2.6 452.4 1.0
P1 A:DPO801 2.6 436.2 1.0
OD2 A:ASP206 2.7 451.0 1.0
MG A:MG802 2.7 474.9 1.0
NZ A:LYS663 2.8 474.9 1.0
O4 A:DPO801 3.4 436.2 1.0
OD1 A:ASP202 3.4 424.5 1.0
OD2 A:ASP202 3.5 408.4 1.0
OD1 A:ASP660 3.6 423.0 1.0
CG A:ASP688 3.7 441.1 1.0
CG A:ASP206 3.7 455.4 1.0
O5 A:DPO801 3.7 436.2 1.0
CG A:ASP202 3.8 413.4 1.0
O3 A:DPO801 4.0 436.2 1.0
OD2 A:ASP692 4.0 450.4 1.0
OD1 A:ASP688 4.1 433.4 1.0
OD1 A:ASP206 4.1 456.7 1.0
P2 A:DPO801 4.2 436.2 1.0
CE A:LYS663 4.2 466.6 1.0
MG A:MG804 4.5 440.4 1.0
OD1 A:ASP692 4.5 442.3 1.0
CG A:ASP660 4.7 414.2 1.0
MG A:MG805 4.7 450.9 1.0
CG A:ASP692 4.7 439.5 1.0
NZ A:LYS664 4.7 449.2 1.0
NZ A:LYS210 4.8 481.8 1.0
OE2 A:GLU217 4.8 408.0 1.0
MG A:MG806 4.8 404.4 1.0
O6 A:DPO801 4.9 436.2 1.0
CD A:GLU217 4.9 408.4 1.0
CB A:ASP688 4.9 435.3 1.0

Magnesium binding site 3 out of 10 in 8b24

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Magnesium binding site 3 out of 10 in the Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:440.4
occ:1.00
 O2 A:DPO801 2.2 436.2 1.0
MG A:MG805 2.5 450.9 1.0
O3 A:DPO801 2.7 436.2 1.0
OD2 A:ASP218 2.8 451.7 1.0
OD1 A:ASP218 2.9 460.7 1.0
P1 A:DPO801 3.0 436.2 1.0
OD1 A:ASP465 3.1 432.9 1.0
OD2 A:ASP228 3.1 403.6 1.0
CG A:ASP218 3.3 459.1 1.0
OE2 A:GLU217 3.3 408.0 1.0
OD2 A:ASP465 3.8 419.1 1.0
CG A:ASP465 3.9 431.4 1.0
O4 A:DPO801 4.1 436.2 1.0
CG A:ASP228 4.2 405.0 1.0
O1 A:DPO801 4.2 436.2 1.0
CD A:GLU217 4.2 408.4 1.0
OD2 A:ASP232 4.2 430.7 1.0
CG A:GLU217 4.4 411.4 1.0
OD1 A:ASP202 4.5 424.5 1.0
MG A:MG803 4.5 472.8 1.0
OD1 A:ASP228 4.6 406.2 1.0
OD1 A:ASN229 4.6 418.9 1.0
CB A:ASP218 4.8 473.0 1.0
OD2 A:ASP202 4.8 408.4 1.0
CG A:ASP202 4.9 413.4 1.0

Magnesium binding site 4 out of 10 in 8b24

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Magnesium binding site 4 out of 10 in the Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg805

b:450.9
occ:1.00
 OD2 A:ASP465 2.3 419.1 1.0
MG A:MG804 2.5 440.4 1.0
O2 A:DPO801 2.6 436.2 1.0
O4 A:DPO801 2.8 436.2 1.0
P1 A:DPO801 2.9 436.2 1.0
OD2 A:ASP232 3.0 430.7 1.0
O3 A:DPO801 3.1 436.2 1.0
CG A:ASP465 3.1 431.4 1.0
OD1 A:ASP232 3.1 417.3 1.0
OD1 A:ASP465 3.2 432.9 1.0
CG A:ASP232 3.4 423.2 1.0
OD2 A:ASP228 3.4 403.6 1.0
OD1 A:ASP228 3.6 406.2 1.0
OD2 A:ASP202 3.6 408.4 1.0
O7 A:DPO801 3.9 436.2 1.0
CG A:ASP228 3.9 405.0 1.0
P2 A:DPO801 4.0 436.2 1.0
CG A:ASP202 4.1 413.4 1.0
OD1 A:ASP202 4.4 424.5 1.0
O1 A:DPO801 4.4 436.2 1.0
CB A:ASP465 4.5 428.7 1.0
O5 A:DPO801 4.6 436.2 1.0
MG A:MG806 4.7 404.4 1.0
MG A:MG803 4.7 472.8 1.0
CB A:ASP232 4.8 416.9 1.0
MG A:MG802 4.9 474.9 1.0
OD2 A:ASP236 4.9 415.8 1.0
OD2 A:ASP218 5.0 451.7 1.0

Magnesium binding site 5 out of 10 in 8b24

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Magnesium binding site 5 out of 10 in the Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg806

b:404.4
occ:1.00
 O4 A:DPO801 2.5 436.2 1.0
O3 A:DPO801 2.8 436.2 1.0
O6 A:DPO801 2.8 436.2 1.0
OD2 A:ASP488 2.8 387.8 1.0
ND2 A:ASN492 2.9 397.4 1.0
OD2 A:ASP660 2.9 423.7 1.0
P1 A:DPO801 2.9 436.2 1.0
OD1 A:ASN492 3.0 405.7 1.0
O1 A:DPO801 3.0 436.2 1.0
OD1 A:ASP488 3.1 386.8 1.0
P2 A:DPO801 3.2 436.2 1.0
CG A:ASP488 3.2 389.1 1.0
CG A:ASN492 3.3 397.4 1.0
CG A:ASP660 3.8 414.2 1.0
OD1 A:ASP660 4.0 423.0 1.0
OD2 A:ASP465 4.0 419.1 1.0
NZ A:LYS664 4.0 449.2 1.0
O7 A:DPO801 4.0 436.2 1.0
CG A:ASP465 4.3 431.4 1.0
O2 A:DPO801 4.4 436.2 1.0
O5 A:DPO801 4.5 436.2 1.0
O A:ASP488 4.5 376.9 1.0
CE A:LYS664 4.5 451.6 1.0
OD1 A:ASP465 4.6 432.9 1.0
CB A:ASP488 4.6 394.2 1.0
MG A:MG805 4.7 450.9 1.0
K A:K807 4.7 331.8 1.0
CB A:ASN492 4.8 384.0 1.0
MG A:MG803 4.8 472.8 1.0
C A:ASP488 5.0 378.2 1.0
CB A:ASP465 5.0 428.7 1.0

Magnesium binding site 6 out of 10 in 8b24

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Magnesium binding site 6 out of 10 in the Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:352.8
occ:1.00
 OD1 B:ASN229 2.5 375.2 1.0
OD2 B:ASP232 2.6 425.3 1.0
O1 B:PO4802 2.7 406.6 1.0
OD1 B:ASP465 3.2 474.6 1.0
O B:ASP465 3.5 504.6 1.0
CG B:ASN229 3.5 373.2 1.0
CG B:ASP465 3.6 463.1 1.0
OD1 B:ASP218 3.8 420.9 1.0
CG B:ASP232 3.8 412.2 1.0
C B:ASP465 4.0 496.9 1.0
OD2 B:ASP465 4.0 450.2 1.0
CA B:ASN229 4.0 360.2 1.0
P B:PO4802 4.0 406.6 1.0
CB B:ASN229 4.2 365.4 1.0
OD2 B:ASP228 4.3 403.0 1.0
OD1 B:ASN466 4.3 368.6 1.0
N B:ASN466 4.4 380.6 1.0
N B:ASN229 4.4 361.3 1.0
O4 B:PO4802 4.4 406.6 1.0
CA B:ASN466 4.4 395.8 1.0
ND2 B:ASN229 4.4 378.2 1.0
CA B:GLY469 4.5 386.0 1.0
CB B:ASP465 4.5 465.7 1.0
CG B:ASP228 4.6 391.8 1.0
O3 B:PO4802 4.6 406.6 1.0
OD1 B:ASP232 4.7 404.6 1.0
CB B:ASP232 4.7 406.4 1.0
CG B:ASP218 4.7 428.6 1.0
N B:GLY469 4.7 381.8 1.0
C B:ASP228 4.7 381.2 1.0
O B:ASP228 4.8 371.5 1.0
CA B:ASP465 4.8 482.8 1.0
OD1 B:ASP228 4.9 379.8 1.0

Magnesium binding site 7 out of 10 in 8b24

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Magnesium binding site 7 out of 10 in the Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg804

b:379.7
occ:1.00
 O4 B:PO4801 2.2 389.0 1.0
O2 B:PO4801 2.4 389.0 1.0
NZ B:LYS199 2.6 403.3 1.0
OD1 B:ASP232 2.6 404.6 1.0
P B:PO4801 2.7 389.0 1.0
MG B:MG807 3.0 381.4 1.0
O1 B:PO4801 3.5 389.0 1.0
OD2 B:ASP696 3.5 360.3 1.0
OD2 B:ASP202 3.6 403.0 1.0
CG B:ASP232 3.8 412.2 1.0
CE B:LYS199 3.8 391.4 1.0
O3 B:PO4801 4.0 389.0 1.0
OD2 B:ASP465 4.1 450.2 1.0
CG B:ASP202 4.5 404.4 1.0
OD1 B:ASP228 4.5 379.8 1.0
OD2 B:ASP232 4.5 425.3 1.0
CG B:ASP696 4.6 349.7 1.0
CB B:ASP232 4.6 406.4 1.0
CA B:ASP232 4.7 391.4 1.0
CB B:ASP202 4.9 397.9 1.0

Magnesium binding site 8 out of 10 in 8b24

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Magnesium binding site 8 out of 10 in the Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg805

b:368.6
occ:1.00
 O3 B:PO4801 2.8 389.0 1.0
OD2 B:ASP692 3.1 374.5 1.0
OD1 B:ASP202 3.2 411.4 1.0
O2 B:PO4802 3.2 406.6 1.0
OD2 B:ASP688 3.5 389.8 1.0
OD2 B:ASP202 3.7 403.0 1.0
CG B:ASP202 3.8 404.4 1.0
NZ B:LYS663 4.1 470.1 1.0
CG B:ASP692 4.1 361.5 1.0
P B:PO4801 4.3 389.0 1.0
MG B:MG806 4.3 387.4 1.0
OD1 B:ASP206 4.3 430.0 1.0
CG B:ASP688 4.4 377.6 1.0
OD1 B:ASP692 4.4 356.3 1.0
P B:PO4802 4.5 406.6 1.0
O3 B:PO4802 4.6 406.6 1.0
CG B:ASP206 4.7 425.5 1.0
CB B:ASP206 4.7 413.4 1.0
OD1 B:ASP688 4.7 365.8 1.0
O4 B:PO4801 4.7 389.0 1.0
OE2 B:GLU217 4.8 404.7 1.0

Magnesium binding site 9 out of 10 in 8b24

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Magnesium binding site 9 out of 10 in the Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg806

b:387.4
occ:1.00
 O1 B:PO4801 2.5 389.0 1.0
O3 B:PO4801 2.6 389.0 1.0
OD1 B:ASP660 2.8 432.4 1.0
OD2 B:ASP660 2.9 426.0 1.0
P B:PO4801 3.0 389.0 1.0
CG B:ASP660 3.1 423.6 1.0
NZ B:LYS664 3.3 393.2 1.0
O3 B:PO4802 3.7 406.6 1.0
O2 B:PO4801 3.8 389.0 1.0
NZ B:LYS695 4.3 369.6 1.0
O4 B:PO4801 4.3 389.0 1.0
MG B:MG805 4.3 368.6 1.0
CB B:ASP660 4.4 410.5 1.0
OD2 B:ASP688 4.5 389.8 1.0
CE B:LYS664 4.6 404.1 1.0
O2 B:PO4802 4.9 406.6 1.0
OD1 B:ASP688 4.9 365.8 1.0
NZ B:LYS663 4.9 470.1 1.0
P B:PO4802 4.9 406.6 1.0
OD1 B:ASP692 4.9 356.3 1.0

Magnesium binding site 10 out of 10 in 8b24

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Magnesium binding site 10 out of 10 in the Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Time-Resolved Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima 3600-Seconds Post Reaction Initiation with Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg807

b:381.4
occ:1.00
 OD1 B:ASP228 2.3 379.8 1.0
OD1 B:ASP232 2.8 404.6 1.0
CB B:ASP202 3.0 397.9 1.0
NZ B:LYS199 3.0 403.3 1.0
MG B:MG804 3.0 379.7 1.0
O B:THR198 3.1 408.3 1.0
CG B:ASP202 3.4 404.4 1.0
OD2 B:ASP202 3.4 403.0 1.0
O B:ASP228 3.6 371.5 1.0
CE B:LYS199 3.6 391.4 1.0
O4 B:PO4801 3.6 389.0 1.0
CG B:ASP228 3.6 391.8 1.0
C B:THR198 3.8 396.1 1.0
CG B:ASP232 3.9 412.2 1.0
CA B:ASP202 3.9 400.9 1.0
N B:ASP202 4.1 394.2 1.0
CB B:THR198 4.1 383.9 1.0
N B:ASP232 4.2 390.5 1.0
CA B:THR198 4.3 389.4 1.0
OD1 B:ASP202 4.3 411.4 1.0
C B:ASP228 4.4 381.2 1.0
OD2 B:ASP228 4.4 403.0 1.0
CA B:ASP228 4.4 382.1 1.0
OD2 B:ASP232 4.4 425.3 1.0
CB B:ASP228 4.5 393.9 1.0
C B:GLY231 4.6 373.3 1.0
CA B:ASP232 4.7 391.4 1.0
O2 B:PO4801 4.7 389.0 1.0
N B:LYS199 4.7 381.1 1.0
P B:PO4801 4.8 389.0 1.0
CD B:LYS199 4.8 389.2 1.0
OG1 B:THR198 4.9 375.6 1.0
CB B:ASP232 4.9 406.4 1.0
CA B:GLY231 4.9 374.2 1.0

Reference:

J.Strauss, K.Vidilaseris, A.Goldman. The Structure of Tmppase After 3600 Second Soaking with Sodium Ion To Be Published.
Page generated: Thu Oct 3 19:07:57 2024

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