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Magnesium in PDB 1wpg: Crystal Structure of the Sr CA2+-Atpase with MGF4

Enzymatic activity of Crystal Structure of the Sr CA2+-Atpase with MGF4

All present enzymatic activity of Crystal Structure of the Sr CA2+-Atpase with MGF4:
3.6.3.8;

Protein crystallography data

The structure of Crystal Structure of the Sr CA2+-Atpase with MGF4, PDB code: 1wpg was solved by C.Toyoshima, H.Nomura, T.Tsuda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 102.210, 275.394, 109.945, 90.00, 90.01, 90.00
R / Rfree (%) 22.3 / 24.5

Other elements in 1wpg:

The structure of Crystal Structure of the Sr CA2+-Atpase with MGF4 also contains other interesting chemical elements:

Fluorine (F) 16 atoms
Sodium (Na) 4 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Sr CA2+-Atpase with MGF4 (pdb code 1wpg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of the Sr CA2+-Atpase with MGF4, PDB code: 1wpg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 1wpg

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Magnesium binding site 1 out of 12 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


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 Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg997

b:25.5
occ:1.00
O A:HOH2100 1.9 25.3 1.0
F4 A:MF4998 2.0 22.3 1.0
OD1 A:ASP703 2.0 27.5 1.0
O A:THR353 2.1 25.9 1.0
O A:HOH2105 2.2 30.1 1.0
OD1 A:ASP351 2.2 22.4 1.0
CG A:ASP703 3.0 25.6 1.0
CG A:ASP351 3.2 26.2 1.0
C A:THR353 3.2 28.8 1.0
OD2 A:ASP703 3.3 32.2 1.0
OD2 A:ASP351 3.5 22.8 1.0
MG A:MF4998 3.7 31.2 1.0
CA A:THR353 4.0 28.1 1.0
CB A:THR353 4.0 27.7 1.0
OD2 A:ASP707 4.2 27.8 1.0
O A:GLY182 4.2 21.5 1.0
N A:GLY704 4.2 31.5 1.0
N A:THR353 4.3 28.1 1.0
N A:GLY354 4.3 28.8 1.0
OG1 A:THR355 4.3 26.3 1.0
CB A:ASP703 4.4 30.5 1.0
F3 A:MF4998 4.4 25.4 1.0
CA A:GLY182 4.5 23.1 1.0
CB A:ASP351 4.5 22.1 1.0
CA A:GLY354 4.5 32.0 1.0
CG2 A:THR353 4.6 28.4 1.0
F1 A:MF4998 4.6 26.7 1.0
N A:ASP703 4.6 32.5 1.0
C A:GLY182 4.8 25.5 1.0
CA A:GLY704 4.8 30.5 1.0
OD1 A:ASN706 4.8 30.2 1.0
F2 A:MF4998 4.8 32.7 1.0
N A:THR355 4.8 33.8 1.0
C A:ASP703 4.8 29.1 1.0
CA A:ASP703 4.9 31.6 1.0
C A:LYS352 4.9 28.5 1.0
C A:GLY354 5.0 33.9 1.0

Magnesium binding site 2 out of 12 in 1wpg

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Magnesium binding site 2 out of 12 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


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 Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:86.0
occ:1.00
O1A A:ADP1002 2.2 97.3 1.0
O1B A:ADP1002 2.7 0.7 1.0
O3A A:ADP1002 2.9 99.5 1.0
PA A:ADP1002 3.0 98.9 1.0
PB A:ADP1002 3.1 0.0 1.0
O2B A:ADP1002 3.4 99.0 1.0
NZ A:LYS205 3.5 54.8 1.0
O5' A:ADP1002 3.8 93.2 1.0
O2A A:ADP1002 4.2 97.2 1.0
O3B A:ADP1002 4.6 99.7 1.0

Magnesium binding site 3 out of 12 in 1wpg

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Magnesium binding site 3 out of 12 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


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 Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg998

b:31.2
occ:1.00
MG A:MF4998 0.0 31.2 1.0
F4 A:MF4998 1.8 22.3 1.0
F3 A:MF4998 1.8 25.4 1.0
F1 A:MF4998 1.8 26.7 1.0
F2 A:MF4998 1.8 32.7 1.0
OD2 A:ASP351 2.5 22.8 1.0
OG1 A:THR625 3.3 24.6 1.0
CG A:ASP351 3.5 26.2 1.0
N A:GLY626 3.7 22.9 1.0
O A:THR181 3.7 24.8 1.0
MG A:MG997 3.7 25.5 1.0
OD1 A:ASP351 3.9 22.4 1.0
N A:THR353 3.9 28.1 1.0
CB A:THR353 3.9 27.7 1.0
O A:HOH2105 4.0 30.1 1.0
CB A:THR625 4.1 21.9 1.0
CA A:THR625 4.1 22.6 1.0
OG1 A:THR353 4.1 31.9 1.0
OE1 A:GLU183 4.2 38.3 1.0
NZ A:LYS684 4.2 22.7 1.0
CA A:GLY182 4.2 23.1 1.0
N A:LYS352 4.2 26.8 1.0
ND2 A:ASN706 4.3 22.5 1.0
C A:THR625 4.4 21.4 1.0
CA A:THR353 4.4 28.1 1.0
O A:THR353 4.5 25.9 1.0
C A:GLY182 4.5 25.5 1.0
CA A:GLY626 4.6 25.1 1.0
C A:THR181 4.6 25.8 1.0
O A:GLY182 4.7 21.5 1.0
O A:HOH2100 4.7 25.3 1.0
N A:ASP627 4.8 23.7 1.0
C A:LYS352 4.8 28.5 1.0
CB A:ASP351 4.8 22.1 1.0
CA A:LYS352 4.9 27.5 1.0
N A:GLY182 4.9 24.8 1.0
O A:ILE624 4.9 25.2 1.0
CB A:LYS352 5.0 24.6 1.0
C A:THR353 5.0 28.8 1.0

Magnesium binding site 4 out of 12 in 1wpg

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Magnesium binding site 4 out of 12 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


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 Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg997

b:22.6
occ:1.00
F4 B:MF41098 2.0 22.4 1.0
OD1 B:ASP351 2.1 14.0 1.0
O B:THR353 2.1 25.4 1.0
OD1 B:ASP703 2.1 29.1 1.0
O B:HOH3100 2.1 22.0 1.0
O B:HOH3105 2.2 20.1 1.0
CG B:ASP351 3.0 16.6 1.0
CG B:ASP703 3.2 30.7 1.0
C B:THR353 3.3 21.9 1.0
OD2 B:ASP351 3.3 16.8 1.0
OD2 B:ASP703 3.5 32.1 1.0
MG B:MF41098 3.7 27.1 1.0
CA B:THR353 4.0 20.9 1.0
OD2 B:ASP707 4.1 22.8 1.0
CB B:THR353 4.1 20.1 1.0
OG1 B:THR355 4.1 24.1 1.0
N B:GLY704 4.2 26.8 1.0
N B:THR353 4.2 18.9 1.0
O B:GLY182 4.3 25.1 1.0
N B:GLY354 4.3 21.1 1.0
CB B:ASP351 4.3 18.8 1.0
F1 B:MF41098 4.4 20.7 1.0
N B:ASP703 4.5 26.4 1.0
CB B:ASP703 4.5 25.4 1.0
CA B:GLY182 4.5 21.5 1.0
F2 B:MF41098 4.5 23.8 1.0
CA B:GLY354 4.6 21.7 1.0
CA B:GLY704 4.7 25.2 1.0
CG2 B:THR353 4.7 16.4 1.0
C B:ASP703 4.8 26.1 1.0
N B:THR355 4.8 21.9 1.0
OD1 B:ASN706 4.8 25.9 1.0
C B:GLY182 4.8 24.8 1.0
CA B:ASP703 4.8 26.4 1.0
C B:GLY354 4.9 21.1 1.0
C B:LYS352 4.9 20.3 1.0
F3 B:MF41098 4.9 25.7 1.0

Magnesium binding site 5 out of 12 in 1wpg

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Magnesium binding site 5 out of 12 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


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 Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1101

b:72.3
occ:1.00
O1B B:ADP1102 2.2 90.4 1.0
O1A B:ADP1102 2.9 87.6 1.0
PB B:ADP1102 3.4 92.1 1.0
O5' B:ADP1102 3.5 81.5 1.0
PA B:ADP1102 3.6 87.7 1.0
O3A B:ADP1102 3.8 88.8 1.0
O2B B:ADP1102 4.1 90.2 1.0
O3B B:ADP1102 4.6 89.1 1.0
C5' B:ADP1102 4.7 70.8 1.0
O3' B:ADP1102 4.9 65.8 1.0

Magnesium binding site 6 out of 12 in 1wpg

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Magnesium binding site 6 out of 12 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


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 Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1098

b:27.1
occ:1.00
MG B:MF41098 0.0 27.1 1.0
F2 B:MF41098 1.7 23.8 1.0
F1 B:MF41098 1.8 20.7 1.0
F4 B:MF41098 1.8 22.4 1.0
F3 B:MF41098 1.8 25.7 1.0
OD2 B:ASP351 2.4 16.8 1.0
OG1 B:THR625 3.4 21.4 1.0
CG B:ASP351 3.5 16.6 1.0
O B:THR181 3.7 17.4 1.0
MG B:MG997 3.7 22.6 1.0
N B:GLY626 3.7 23.2 1.0
N B:THR353 3.8 18.9 1.0
CB B:THR353 3.9 20.1 1.0
OD1 B:ASP351 3.9 14.0 1.0
O B:HOH3105 4.0 20.1 1.0
OE1 B:GLU183 4.0 23.7 1.0
OG1 B:THR353 4.1 22.4 1.0
CA B:GLY182 4.1 21.5 1.0
CA B:THR625 4.2 22.3 1.0
N B:LYS352 4.2 17.6 1.0
CB B:THR625 4.2 22.1 1.0
NZ B:LYS684 4.3 17.4 1.0
ND2 B:ASN706 4.3 18.3 1.0
CA B:THR353 4.4 20.9 1.0
C B:GLY182 4.5 24.8 1.0
C B:THR625 4.5 20.5 1.0
O B:THR353 4.5 25.4 1.0
O B:HOH3100 4.6 22.0 1.0
C B:THR181 4.6 18.9 1.0
CA B:GLY626 4.6 17.3 1.0
C B:LYS352 4.8 20.3 1.0
CB B:ASP351 4.8 18.8 1.0
N B:ASP627 4.8 20.5 1.0
O B:GLY182 4.8 25.1 1.0
N B:GLY182 4.9 20.1 1.0
CA B:LYS352 4.9 18.3 1.0
C B:THR353 4.9 21.9 1.0
O B:ILE624 5.0 24.1 1.0
CB B:LYS352 5.0 15.5 1.0

Magnesium binding site 7 out of 12 in 1wpg

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Magnesium binding site 7 out of 12 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


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 the Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg997

b:21.1
occ:1.00
O C:THR353 2.0 24.7 1.0
F4 C:MF41198 2.1 22.3 1.0
OD1 C:ASP351 2.1 16.3 1.0
OD1 C:ASP703 2.1 29.2 1.0
O C:HOH4100 2.2 21.9 1.0
O C:HOH4105 2.2 18.7 1.0
CG C:ASP351 3.0 17.9 1.0
CG C:ASP703 3.1 29.9 1.0
C C:THR353 3.2 22.6 1.0
OD2 C:ASP351 3.3 15.5 1.0
OD2 C:ASP703 3.4 30.9 1.0
MG C:MF41198 3.8 27.7 1.0
CA C:THR353 4.0 21.6 1.0
CB C:THR353 4.1 20.8 1.0
OG1 C:THR355 4.1 22.1 1.0
OD2 C:ASP707 4.1 25.2 1.0
N C:GLY704 4.2 26.9 1.0
N C:THR353 4.2 20.4 1.0
N C:GLY354 4.3 21.6 1.0
O C:GLY182 4.3 28.9 1.0
CB C:ASP351 4.4 19.9 1.0
F1 C:MF41198 4.5 20.6 1.0
CB C:ASP703 4.5 25.7 1.0
N C:ASP703 4.5 28.2 1.0
CA C:GLY354 4.5 23.2 1.0
CA C:GLY182 4.5 22.1 1.0
F2 C:MF41198 4.6 24.7 1.0
CG2 C:THR353 4.7 16.4 1.0
CA C:GLY704 4.8 26.8 1.0
N C:THR355 4.8 21.8 1.0
C C:GLY354 4.8 22.0 1.0
C C:ASP703 4.8 26.6 1.0
CA C:ASP703 4.8 27.3 1.0
C C:GLY182 4.8 26.1 1.0
C C:LYS352 4.9 21.0 1.0
OD1 C:ASN706 4.9 24.2 1.0
F3 C:MF41198 5.0 25.4 1.0

Magnesium binding site 8 out of 12 in 1wpg

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Magnesium binding site 8 out of 12 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


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 the Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1201

b:72.8
occ:1.00
O1B C:ADP1202 2.2 90.5 1.0
O1A C:ADP1202 2.9 87.6 1.0
PB C:ADP1202 3.4 92.0 1.0
O5' C:ADP1202 3.4 81.7 1.0
PA C:ADP1202 3.6 87.9 1.0
O3A C:ADP1202 3.8 88.7 1.0
O2B C:ADP1202 4.1 90.0 1.0
O3B C:ADP1202 4.6 89.2 1.0
C5' C:ADP1202 4.6 70.6 1.0
O3' C:ADP1202 4.8 65.3 1.0
CE C:LYS492 5.0 52.0 1.0
O2A C:ADP1202 5.0 88.0 1.0

Magnesium binding site 9 out of 12 in 1wpg

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Magnesium binding site 9 out of 12 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1198

b:27.7
occ:1.00
MG C:MF41198 0.0 27.7 1.0
F2 C:MF41198 1.7 24.7 1.0
F4 C:MF41198 1.8 22.3 1.0
F1 C:MF41198 1.8 20.6 1.0
F3 C:MF41198 1.8 25.4 1.0
OD2 C:ASP351 2.4 15.5 1.0
OG1 C:THR625 3.5 22.3 1.0
CG C:ASP351 3.5 17.9 1.0
O C:THR181 3.7 14.7 1.0
N C:GLY626 3.7 22.6 1.0
MG C:MG997 3.8 21.1 1.0
N C:THR353 3.8 20.4 1.0
CB C:THR353 3.9 20.8 1.0
OD1 C:ASP351 3.9 16.3 1.0
O C:HOH4105 4.0 18.7 1.0
OG1 C:THR353 4.0 22.5 1.0
OE1 C:GLU183 4.0 23.2 1.0
CA C:GLY182 4.1 22.1 1.0
CA C:THR625 4.2 23.1 1.0
N C:LYS352 4.3 19.1 1.0
CB C:THR625 4.3 23.7 1.0
ND2 C:ASN706 4.3 18.5 1.0
NZ C:LYS684 4.3 20.3 1.0
CA C:THR353 4.3 21.6 1.0
C C:THR625 4.5 21.7 1.0
C C:GLY182 4.5 26.1 1.0
O C:THR353 4.5 24.7 1.0
O C:HOH4100 4.6 21.9 1.0
CA C:GLY626 4.6 18.8 1.0
C C:THR181 4.6 17.4 1.0
C C:LYS352 4.8 21.0 1.0
N C:ASP627 4.8 21.3 1.0
CB C:ASP351 4.8 19.9 1.0
O C:GLY182 4.8 28.9 1.0
N C:GLY182 4.8 20.3 1.0
CA C:LYS352 4.9 19.1 1.0
C C:THR353 4.9 22.6 1.0

Magnesium binding site 10 out of 12 in 1wpg

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Magnesium binding site 10 out of 12 in the Crystal Structure of the Sr CA2+-Atpase with MGF4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Sr CA2+-Atpase with MGF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg997

b:26.5
occ:1.00
O D:HOH5100 1.9 26.7 1.0
O D:THR353 2.0 26.9 1.0
OD1 D:ASP703 2.0 26.7 1.0
F4 D:MF41298 2.0 21.9 1.0
O D:HOH5105 2.2 27.3 1.0
OD1 D:ASP351 2.2 22.4 1.0
CG D:ASP703 3.0 26.0 1.0
CG D:ASP351 3.1 26.0 1.0
C D:THR353 3.2 28.8 1.0
OD2 D:ASP703 3.3 30.8 1.0
OD2 D:ASP351 3.4 20.5 1.0
MG D:MF41298 3.7 31.7 1.0
CA D:THR353 4.0 27.8 1.0
CB D:THR353 4.0 27.5 1.0
OD2 D:ASP707 4.2 28.0 1.0
O D:GLY182 4.2 23.0 1.0
N D:GLY704 4.2 32.1 1.0
N D:THR353 4.3 28.5 1.0
N D:GLY354 4.3 29.3 1.0
OG1 D:THR355 4.3 25.0 1.0
CB D:ASP703 4.4 29.8 1.0
F3 D:MF41298 4.4 26.6 1.0
CB D:ASP351 4.5 22.4 1.0
CA D:GLY182 4.5 24.2 1.0
CA D:GLY354 4.5 31.8 1.0
CG2 D:THR353 4.6 27.4 1.0
F1 D:MF41298 4.6 26.6 1.0
N D:ASP703 4.6 32.6 1.0
C D:GLY182 4.8 26.6 1.0
N D:THR355 4.8 32.7 1.0
CA D:GLY704 4.8 30.7 1.0
OD1 D:ASN706 4.8 31.7 1.0
C D:LYS352 4.8 29.2 1.0
C D:ASP703 4.9 30.1 1.0
F2 D:MF41298 4.9 32.9 1.0
CA D:ASP703 4.9 32.1 1.0
C D:GLY354 4.9 34.0 1.0

Reference:

C.Toyoshima, H.Nomura, T.Tsuda. Lumenal Gating Mechanism Revealed in Calcium Pump Crystal Structures with Phosphate Analogues Nature V. 432 361 2004.
ISSN: ISSN 0028-0836
PubMed: 15448704
DOI: 10.1038/NATURE02981
Page generated: Mon Dec 14 07:02:17 2020

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