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Magnesium in PDB 3wvl: Crystal Structure of the Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli

Enzymatic activity of Crystal Structure of the Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli

All present enzymatic activity of Crystal Structure of the Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli:
3.6.4.9;

Protein crystallography data

The structure of Crystal Structure of the Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli, PDB code: 3wvl was solved by A.Koike-Takeshita, T.Arakawa, H.Taguchi, T.Shimamura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.56 / 3.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 160.280, 217.117, 198.481, 90.00, 98.02, 90.00
R / Rfree (%) 21.1 / 25

Other elements in 3wvl:

The structure of Crystal Structure of the Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli also contains other interesting chemical elements:

Potassium (K) 14 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli (pdb code 3wvl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Crystal Structure of the Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli, PDB code: 3wvl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 3wvl

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Magnesium binding site 1 out of 14 in the Crystal Structure of the Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli


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 Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:76.2
occ:1.00
 O3G A:ATP601 2.4 1.0 1.0
O1B A:ATP601 2.5 74.2 1.0
O2A A:ATP601 2.5 0.1 1.0
OD1 A:ASP87 2.8 0.1 1.0
OD2 A:ASP87 3.3 80.5 1.0
O A:SER151 3.4 0.9 1.0
CG A:ASP87 3.4 0.4 1.0
PB A:ATP601 3.5 89.9 1.0
O3A A:ATP601 3.7 1.0 1.0
PA A:ATP601 3.7 0.1 1.0
PG A:ATP601 3.8 0.0 1.0
O3B A:ATP601 4.1 0.5 1.0
C A:SER151 4.1 84.1 1.0
CA A:SER151 4.3 88.5 1.0
K A:K603 4.4 0.4 1.0
O2G A:ATP601 4.5 0.6 1.0
OG A:SER151 4.5 0.1 1.0
O1A A:ATP601 4.7 0.2 1.0
O A:ILE150 4.8 0.7 1.0
C5' A:ATP601 4.8 1.0 1.0
O5' A:ATP601 4.8 77.6 1.0
O1G A:ATP601 4.8 78.3 1.0
O2B A:ATP601 4.9 94.1 1.0
CB A:ASP87 4.9 0.6 1.0

Magnesium binding site 2 out of 14 in 3wvl

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Magnesium binding site 2 out of 14 in the Crystal Structure of the Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli


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 Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:69.0
occ:1.00
 O1B B:ATP601 2.1 0.1 1.0
O2A B:ATP601 2.1 0.6 1.0
OD1 B:ASP87 2.7 0.8 1.0
O3G B:ATP601 2.8 0.8 1.0
OD2 B:ASP87 3.3 85.4 1.0
PB B:ATP601 3.3 86.6 1.0
PA B:ATP601 3.3 0.5 1.0
CG B:ASP87 3.3 0.4 1.0
O3A B:ATP601 3.4 0.7 1.0
O B:SER151 3.5 0.4 1.0
PG B:ATP601 4.1 0.7 1.0
O3B B:ATP601 4.2 0.9 1.0
C5' B:ATP601 4.2 0.7 1.0
K B:K603 4.2 0.5 1.0
CA B:SER151 4.2 0.8 1.0
C B:SER151 4.2 86.2 1.0
OG B:SER151 4.2 0.2 1.0
O5' B:ATP601 4.3 98.5 1.0
O1A B:ATP601 4.5 1.0 1.0
O2B B:ATP601 4.6 81.6 1.0
CB B:SER151 4.8 0.6 1.0
O2G B:ATP601 4.8 0.4 1.0
CB B:ASP87 4.8 0.5 1.0
O B:ILE150 4.8 0.5 1.0

Magnesium binding site 3 out of 14 in 3wvl

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Magnesium binding site 3 out of 14 in the Crystal Structure of the Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli


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 Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:71.8
occ:1.00
 OD1 C:ASP87 2.2 0.3 1.0
O3G C:ATP601 2.2 0.9 1.0
O1B C:ATP601 2.7 0.9 1.0
O2A C:ATP601 2.7 71.1 1.0
CG C:ASP87 3.1 0.6 1.0
OD2 C:ASP87 3.2 80.8 1.0
O C:SER151 3.5 0.5 1.0
K C:K603 3.5 0.6 1.0
PG C:ATP601 3.7 0.7 1.0
PB C:ATP601 3.7 0.3 1.0
O3A C:ATP601 3.7 0.2 1.0
PA C:ATP601 3.8 0.3 1.0
O3B C:ATP601 4.1 65.2 1.0
C C:SER151 4.3 91.9 1.0
OG C:SER151 4.4 0.8 1.0
CA C:SER151 4.5 0.5 1.0
CB C:ASP87 4.5 0.8 1.0
O2G C:ATP601 4.5 0.7 1.0
O1G C:ATP601 4.6 0.4 1.0
N C:GLY88 4.8 0.0 1.0
O1A C:ATP601 4.9 0.0 1.0
C5' C:ATP601 4.9 0.5 1.0
O5' C:ATP601 4.9 0.3 1.0
CA C:ASP87 5.0 80.7 1.0

Magnesium binding site 4 out of 14 in 3wvl

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Magnesium binding site 4 out of 14 in the Crystal Structure of the Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli


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 Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:87.2
occ:1.00
 O3G D:ATP601 2.0 0.3 1.0
O2A D:ATP601 2.1 0.3 1.0
O1B D:ATP601 2.2 0.8 1.0
OD1 D:ASP87 2.8 0.1 1.0
OD2 D:ASP87 3.1 98.9 1.0
CG D:ASP87 3.3 0.0 1.0
PB D:ATP601 3.3 78.2 1.0
PA D:ATP601 3.3 0.3 1.0
PG D:ATP601 3.4 0.7 1.0
O3A D:ATP601 3.6 97.3 1.0
O3B D:ATP601 3.7 69.0 1.0
C5' D:ATP601 3.8 90.2 1.0
O D:SER151 3.8 0.4 1.0
CA D:SER151 4.0 97.2 1.0
O5' D:ATP601 4.0 0.6 1.0
O1G D:ATP601 4.2 0.7 1.0
OG D:SER151 4.2 0.3 1.0
C D:SER151 4.3 77.1 1.0
O2G D:ATP601 4.4 1.0 1.0
O D:ILE150 4.5 0.8 1.0
CB D:SER151 4.6 0.3 1.0
O1A D:ATP601 4.6 0.2 1.0
O2B D:ATP601 4.7 68.0 1.0
CB D:ASP87 4.8 0.3 1.0
N D:GLY88 4.9 0.2 1.0
N D:SER151 5.0 82.5 1.0

Magnesium binding site 5 out of 14 in 3wvl

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Magnesium binding site 5 out of 14 in the Crystal Structure of the Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli


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 Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg602

b:94.8
occ:1.00
 O1B E:ATP601 2.3 66.0 1.0
O2A E:ATP601 2.4 0.0 1.0
O3G E:ATP601 2.6 0.8 1.0
OD1 E:ASP87 2.7 0.4 1.0
OD2 E:ASP87 3.0 78.2 1.0
CG E:ASP87 3.2 0.2 1.0
O E:SER151 3.3 1.0 1.0
PB E:ATP601 3.5 82.7 1.0
PA E:ATP601 3.6 0.8 1.0
O3A E:ATP601 3.7 0.3 1.0
PG E:ATP601 3.9 0.6 1.0
C E:SER151 4.0 97.7 1.0
CA E:SER151 4.0 0.4 1.0
ND2 E:ASN153 4.1 0.5 1.0
O3B E:ATP601 4.2 61.0 1.0
O E:ILE150 4.3 0.2 1.0
C5' E:ATP601 4.3 92.5 1.0
OG E:SER151 4.4 0.5 1.0
O5' E:ATP601 4.5 67.3 1.0
O2G E:ATP601 4.6 0.2 1.0
CB E:ASP87 4.7 89.9 1.0
O1A E:ATP601 4.8 0.6 1.0
CB E:SER151 4.8 0.3 1.0
O2B E:ATP601 4.8 0.8 1.0

Magnesium binding site 6 out of 14 in 3wvl

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Magnesium binding site 6 out of 14 in the Crystal Structure of the Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli


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 Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg602

b:77.9
occ:1.00
 O1B F:ATP601 2.0 82.5 1.0
O2A F:ATP601 2.1 0.9 1.0
O3G F:ATP601 2.2 0.8 1.0
OD1 F:ASP87 2.8 0.5 1.0
PB F:ATP601 3.1 76.6 1.0
PA F:ATP601 3.1 0.8 1.0
O3A F:ATP601 3.1 0.1 1.0
OD2 F:ASP87 3.5 98.9 1.0
CG F:ASP87 3.5 0.9 1.0
PG F:ATP601 3.5 1.0 1.0
O3B F:ATP601 3.8 87.1 1.0
O F:SER151 3.9 0.9 1.0
O5' F:ATP601 4.2 0.0 1.0
C5' F:ATP601 4.2 0.1 1.0
O2G F:ATP601 4.3 0.1 1.0
O1A F:ATP601 4.3 91.0 1.0
O2B F:ATP601 4.4 0.9 1.0
K F:K603 4.6 0.6 1.0
C F:SER151 4.6 98.4 1.0
CA F:SER151 4.6 0.7 1.0
O1G F:ATP601 4.7 89.5 1.0
O F:ILE150 4.9 1.0 1.0
OG F:SER151 4.9 0.4 1.0
N F:GLY88 4.9 0.9 1.0
CB F:ASP87 5.0 0.7 1.0

Magnesium binding site 7 out of 14 in 3wvl

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Magnesium binding site 7 out of 14 in the Crystal Structure of the Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli


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 Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg602

b:88.2
occ:1.00
 O1B G:ATP601 2.1 87.4 1.0
O2A G:ATP601 2.3 0.7 1.0
OD1 G:ASP87 2.5 0.9 1.0
O3G G:ATP601 2.6 0.9 1.0
OD2 G:ASP87 2.8 97.7 1.0
CG G:ASP87 3.0 0.1 1.0
PB G:ATP601 3.3 90.8 1.0
O G:SER151 3.4 0.3 1.0
PA G:ATP601 3.5 0.3 1.0
O3A G:ATP601 3.5 100.0 1.0
PG G:ATP601 3.9 0.8 1.0
O3B G:ATP601 4.0 69.8 1.0
C5' G:ATP601 4.1 0.9 1.0
OG G:SER151 4.1 0.6 1.0
CA G:SER151 4.2 97.3 1.0
C G:SER151 4.2 89.3 1.0
O5' G:ATP601 4.3 69.0 1.0
K G:K603 4.3 0.8 1.0
O2G G:ATP601 4.5 0.4 1.0
CB G:ASP87 4.5 0.9 1.0
O2B G:ATP601 4.6 0.4 1.0
O1A G:ATP601 4.7 0.6 1.0
CB G:SER151 4.7 0.8 1.0
N G:GLY88 4.8 0.1 1.0
O G:ILE150 4.8 98.9 1.0

Magnesium binding site 8 out of 14 in 3wvl

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Magnesium binding site 8 out of 14 in the Crystal Structure of the Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli


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 Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg602

b:74.5
occ:1.00
 O1B H:ATP601 2.5 67.8 1.0
OD1 H:ASP87 2.5 0.3 1.0
O2A H:ATP601 2.5 0.9 1.0
O3G H:ATP601 2.5 91.8 1.0
OD2 H:ASP87 3.0 83.9 1.0
CG H:ASP87 3.1 0.2 1.0
O H:SER151 3.2 0.4 1.0
PB H:ATP601 3.6 85.7 1.0
PA H:ATP601 3.8 0.7 1.0
PG H:ATP601 3.8 0.4 1.0
O3A H:ATP601 3.8 0.3 1.0
C H:SER151 4.0 87.8 1.0
CA H:SER151 4.0 0.1 1.0
OG H:SER151 4.1 0.9 1.0
O3B H:ATP601 4.2 98.0 1.0
O2G H:ATP601 4.2 0.5 1.0
O H:ILE150 4.6 0.9 1.0
CB H:ASP87 4.6 0.8 1.0
CB H:SER151 4.7 0.3 1.0
C5' H:ATP601 4.8 0.2 1.0
O1A H:ATP601 4.8 0.7 1.0
O5' H:ATP601 4.8 67.4 1.0
K H:K603 4.8 0.2 1.0
N H:GLY88 4.9 0.1 1.0
O2B H:ATP601 5.0 76.8 1.0

Magnesium binding site 9 out of 14 in 3wvl

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Magnesium binding site 9 out of 14 in the Crystal Structure of the Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli


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 Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg602

b:0.9
occ:1.00
 O3G I:ATP601 2.0 0.1 1.0
O2A I:ATP601 2.1 0.4 1.0
OD1 I:ASP87 2.7 0.2 1.0
O1B I:ATP601 3.2 0.5 1.0
PA I:ATP601 3.4 0.1 1.0
O I:SER151 3.4 0.0 1.0
PG I:ATP601 3.5 0.5 1.0
CG I:ASP87 3.6 0.3 1.0
OD2 I:ASP87 3.7 92.5 1.0
O3A I:ATP601 3.7 0.8 1.0
PB I:ATP601 3.9 0.3 1.0
O2G I:ATP601 4.1 0.7 1.0
O1A I:ATP601 4.1 0.8 1.0
O3B I:ATP601 4.2 58.1 1.0
C I:SER151 4.3 0.5 1.0
O1G I:ATP601 4.5 0.5 1.0
CA I:SER151 4.5 0.3 1.0
OG I:SER151 4.5 0.6 1.0
K I:K603 4.6 0.5 1.0
O5' I:ATP601 4.6 0.9 1.0
C5' I:ATP601 4.8 0.9 1.0

Magnesium binding site 10 out of 14 in 3wvl

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Magnesium binding site 10 out of 14 in the Crystal Structure of the Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli


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 Football-Shaped Groel-Groes Complex (Groel: GROES2:ATP14) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg602

b:1.0
occ:1.00
 O1B J:ATP601 2.1 92.1 1.0
O2A J:ATP601 2.3 0.2 1.0
OD1 J:ASP87 2.3 0.9 1.0
O3G J:ATP601 2.5 0.4 1.0
OD2 J:ASP87 3.0 90.4 1.0
CG J:ASP87 3.0 0.3 1.0
PB J:ATP601 3.3 0.1 1.0
PA J:ATP601 3.4 0.4 1.0
O3A J:ATP601 3.5 0.1 1.0
O J:SER151 3.6 96.0 1.0
PG J:ATP601 3.8 0.1 1.0
O3B J:ATP601 4.0 0.9 1.0
C5' J:ATP601 4.1 0.7 1.0
CA J:SER151 4.2 96.5 1.0
OG J:SER151 4.2 0.9 1.0
C J:SER151 4.3 77.4 1.0
O5' J:ATP601 4.3 0.9 1.0
K J:K603 4.4 0.6 1.0
CB J:ASP87 4.5 0.8 1.0
N J:GLY88 4.5 0.6 1.0
O2G J:ATP601 4.6 0.4 1.0
O2B J:ATP601 4.6 0.4 1.0
O1A J:ATP601 4.7 0.0 1.0
CB J:SER151 4.8 0.3 1.0
O J:ILE150 4.8 0.8 1.0
O1G J:ATP601 4.9 0.9 1.0

Reference:

A.Koike-Takeshita, T.Arakawa, H.Taguchi, T.Shimamura. Crystal Structure of A Symmetric Football-Shaped Groel:GROES2 Complex Determined at 3.8 Angstrom Reveals Rearrangement Between Two Groel Rings. J.Mol.Biol. 2014.
ISSN: ESSN 1089-8638
PubMed: 25174333
DOI: 10.1016/J.JMB.2014.08.017
Page generated: Mon Dec 14 09:02:08 2020

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