Magnesium in PDB 4pj1: Crystal Structure of the Human Mitochondrial Chaperonin Symmetrical 'Football' Complex

Protein crystallography data

The structure of Crystal Structure of the Human Mitochondrial Chaperonin Symmetrical 'Football' Complex, PDB code: 4pj1 was solved by F.Frolow, A.Azem, S.Nisemblat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.78 / 3.15
Space group P 41 21 2 1
Cell size a, b, c (Å), α, β, γ (°) 199.100, 199.100, 627.390, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 27

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 Human Mitochondrial Chaperonin Symmetrical 'Football' Complex (pdb code 4pj1). 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 Human Mitochondrial Chaperonin Symmetrical 'Football' Complex, PDB code: 4pj1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 4pj1

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Magnesium binding site 1 out of 14 in the Crystal Structure of the Human Mitochondrial Chaperonin Symmetrical 'Football' Complex


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 Human Mitochondrial Chaperonin Symmetrical 'Football' Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:72.2
occ:1.00
 O2A A:ADP601 2.1 0.3 1.0
O2B A:ADP601 2.3 90.2 1.0
OD1 A:ASP87 2.6 0.2 1.0
OD2 A:ASP87 3.1 0.1 1.0
CG A:ASP87 3.2 0.8 1.0
PA A:ADP601 3.2 93.7 1.0
O3A A:ADP601 3.3 0.2 1.0
PB A:ADP601 3.3 0.9 1.0
O A:SER151 3.4 81.8 1.0
O3B A:ADP601 3.9 85.9 1.0
OG A:SER151 4.0 86.4 1.0
O5' A:ADP601 4.2 93.7 1.0
C5' A:ADP601 4.3 0.5 1.0
C A:SER151 4.3 89.0 1.0
CA A:SER151 4.4 93.0 1.0
O1A A:ADP601 4.4 0.8 1.0
OD2 A:ASP399 4.4 0.2 1.0
O1B A:ADP601 4.6 68.2 1.0
CB A:ASP399 4.7 97.3 1.0
CB A:ASP87 4.7 0.2 1.0
CB A:SER151 4.7 94.9 1.0
CG A:ASP399 4.9 0.7 1.0
N A:GLY88 4.9 89.7 1.0

Magnesium binding site 2 out of 14 in 4pj1

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Magnesium binding site 2 out of 14 in the Crystal Structure of the Human Mitochondrial Chaperonin Symmetrical 'Football' Complex


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 Human Mitochondrial Chaperonin Symmetrical 'Football' Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:74.1
occ:1.00
 O2A B:ADP601 2.2 0.8 1.0
OD1 B:ASP87 2.4 0.5 1.0
O1B B:ADP601 2.6 95.8 1.0
PA B:ADP601 3.2 0.4 1.0
PB B:ADP601 3.2 0.8 1.0
CG B:ASP87 3.3 0.3 1.0
O3A B:ADP601 3.3 96.2 1.0
O2B B:ADP601 3.3 76.2 1.0
OD2 B:ASP87 3.4 0.6 1.0
O B:SER151 3.9 0.0 1.0
OD2 B:ASP399 3.9 0.1 1.0
O1A B:ADP601 4.2 98.7 1.0
O5' B:ADP601 4.4 97.0 1.0
CG B:ASP399 4.4 0.5 1.0
CB B:ASP399 4.4 0.0 1.0
OG B:SER151 4.4 0.7 1.0
C5' B:ADP601 4.7 0.7 1.0
CB B:ASP87 4.7 99.9 1.0
O3B B:ADP601 4.7 74.1 1.0
C B:SER151 4.8 99.9 1.0
N B:GLY88 4.8 89.6 1.0
CA B:SER151 4.9 0.6 1.0

Magnesium binding site 3 out of 14 in 4pj1

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Magnesium binding site 3 out of 14 in the Crystal Structure of the Human Mitochondrial Chaperonin Symmetrical 'Football' Complex


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 Human Mitochondrial Chaperonin Symmetrical 'Football' Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:84.5
occ:1.00
 OD1 C:ASP87 2.3 99.6 1.0
O1B C:ADP601 2.3 90.5 1.0
O2A C:ADP601 2.4 98.1 1.0
CG C:ASP87 3.1 0.5 1.0
OD2 C:ASP87 3.2 0.8 1.0
PB C:ADP601 3.2 93.2 1.0
O3A C:ADP601 3.3 93.9 1.0
PA C:ADP601 3.4 92.9 1.0
O2B C:ADP601 3.5 85.4 1.0
O C:SER151 3.7 93.6 1.0
OD2 C:ASP399 4.0 91.2 1.0
OG C:SER151 4.3 0.7 1.0
CB C:ASP399 4.4 97.3 1.0
O5' C:ADP601 4.4 81.1 1.0
CG C:ASP399 4.4 94.4 1.0
CB C:ASP87 4.5 97.0 1.0
O1A C:ADP601 4.6 0.3 1.0
O3B C:ADP601 4.6 69.2 1.0
C5' C:ADP601 4.6 88.7 1.0
C C:SER151 4.7 85.1 1.0
N C:GLY88 4.7 95.2 1.0
CA C:SER151 4.8 91.3 1.0
CA C:ASP87 5.0 91.2 1.0

Magnesium binding site 4 out of 14 in 4pj1

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Magnesium binding site 4 out of 14 in the Crystal Structure of the Human Mitochondrial Chaperonin Symmetrical 'Football' Complex


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 Human Mitochondrial Chaperonin Symmetrical 'Football' Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:77.5
occ:1.00
 O2A D:ADP601 2.2 76.5 1.0
OD1 D:ASP87 2.5 87.8 1.0
O3B D:ADP601 2.7 76.2 1.0
CG D:ASP87 3.2 87.8 1.0
OD2 D:ASP87 3.2 94.6 1.0
O1B D:ADP601 3.2 67.2 1.0
PB D:ADP601 3.4 82.0 1.0
PA D:ADP601 3.4 81.2 1.0
O3A D:ADP601 3.7 82.0 1.0
O D:SER151 3.7 94.2 1.0
OG D:SER151 4.2 83.7 1.0
OD2 D:ASP399 4.3 95.5 1.0
O5' D:ADP601 4.5 79.9 1.0
O1A D:ADP601 4.5 81.3 1.0
C D:SER151 4.5 86.8 1.0
C5' D:ADP601 4.5 88.8 1.0
CB D:ASP399 4.6 0.7 1.0
CA D:SER151 4.6 91.0 1.0
CB D:ASP87 4.7 90.3 1.0
CG D:ASP399 4.7 0.5 1.0
O2B D:ADP601 4.8 62.1 1.0
N D:GLY88 4.9 87.3 1.0
CB D:SER151 5.0 89.3 1.0

Magnesium binding site 5 out of 14 in 4pj1

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Magnesium binding site 5 out of 14 in the Crystal Structure of the Human Mitochondrial Chaperonin Symmetrical 'Football' Complex


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 Human Mitochondrial Chaperonin Symmetrical 'Football' Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg602

b:63.0
occ:1.00
 OD1 E:ASP87 2.1 97.0 1.0
O2A E:ADP601 2.2 93.7 1.0
O1B E:ADP601 2.2 86.2 1.0
CG E:ASP87 2.8 0.1 1.0
OD2 E:ASP87 2.9 0.6 1.0
PB E:ADP601 3.2 89.1 1.0
O2B E:ADP601 3.4 69.2 1.0
PA E:ADP601 3.5 86.7 1.0
O3A E:ADP601 3.7 84.3 1.0
O E:SER151 3.9 83.9 1.0
OG E:SER151 4.0 0.4 1.0
O E:ASP87 4.1 0.9 1.0
CB E:ASP87 4.1 90.1 1.0
O5' E:ADP601 4.3 75.6 1.0
OD2 E:ASP399 4.4 91.2 1.0
C E:ASP87 4.5 87.5 1.0
C5' E:ADP601 4.5 80.0 1.0
CA E:ASP87 4.5 86.1 1.0
CA E:SER151 4.5 90.4 1.0
CB E:ASP399 4.6 99.6 1.0
O3B E:ADP601 4.6 75.0 1.0
C E:SER151 4.6 78.6 1.0
O1A E:ADP601 4.7 85.8 1.0
CG E:ASP399 4.7 96.1 1.0
CB E:SER151 4.8 94.1 1.0

Magnesium binding site 6 out of 14 in 4pj1

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Magnesium binding site 6 out of 14 in the Crystal Structure of the Human Mitochondrial Chaperonin Symmetrical 'Football' Complex


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 Human Mitochondrial Chaperonin Symmetrical 'Football' Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg602

b:66.5
occ:1.00
 O2A F:ADP601 2.0 79.3 1.0
OD1 F:ASP87 2.3 88.0 1.0
O3B F:ADP601 2.7 86.5 1.0
O1B F:ADP601 3.0 78.2 1.0
OD2 F:ASP87 3.0 1.0 1.0
CG F:ASP87 3.0 90.7 1.0
PB F:ADP601 3.2 86.3 1.0
PA F:ADP601 3.3 82.5 1.0
O3A F:ADP601 3.6 89.9 1.0
O F:SER151 3.8 82.2 1.0
O5' F:ADP601 4.2 74.2 1.0
OG F:SER151 4.3 99.5 1.0
OD2 F:ASP399 4.4 0.1 1.0
O1A F:ADP601 4.4 88.7 1.0
CB F:ASP87 4.4 85.7 1.0
C5' F:ADP601 4.6 84.8 1.0
N F:GLY88 4.6 78.0 1.0
C F:SER151 4.6 85.5 1.0
CB F:ASP399 4.7 0.1 1.0
CA F:SER151 4.7 97.8 1.0
O2B F:ADP601 4.7 62.0 1.0
CG F:ASP399 4.8 0.4 1.0
CA F:ASP87 5.0 83.8 1.0

Magnesium binding site 7 out of 14 in 4pj1

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Magnesium binding site 7 out of 14 in the Crystal Structure of the Human Mitochondrial Chaperonin Symmetrical 'Football' Complex


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 Human Mitochondrial Chaperonin Symmetrical 'Football' Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg602

b:67.3
occ:1.00
 OD1 G:ASP87 2.1 87.0 1.0
O2A G:ADP601 2.2 84.5 1.0
CG G:ASP87 2.8 90.5 1.0
OD2 G:ASP87 2.8 94.3 1.0
O1B G:ADP601 2.9 73.3 1.0
O3B G:ADP601 3.0 73.0 1.0
PB G:ADP601 3.4 80.9 1.0
PA G:ADP601 3.5 78.6 1.0
O G:SER151 3.8 80.8 1.0
O3A G:ADP601 3.8 75.7 1.0
OG G:SER151 4.1 81.6 1.0
CB G:ASP87 4.3 90.2 1.0
OD2 G:ASP399 4.3 94.8 1.0
O5' G:ADP601 4.5 76.9 1.0
CB G:ASP399 4.5 91.6 1.0
N G:GLY88 4.5 86.0 1.0
O1A G:ADP601 4.6 83.9 1.0
C G:SER151 4.6 83.0 1.0
CG G:ASP399 4.6 96.9 1.0
CA G:SER151 4.7 85.6 1.0
CA G:ASP87 4.8 88.2 1.0
O2B G:ADP601 4.8 65.9 1.0
CB G:SER151 4.9 85.5 1.0

Magnesium binding site 8 out of 14 in 4pj1

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Magnesium binding site 8 out of 14 in the Crystal Structure of the Human Mitochondrial Chaperonin Symmetrical 'Football' Complex


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 Human Mitochondrial Chaperonin Symmetrical 'Football' Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg602

b:73.3
occ:1.00
 O2A H:ADP601 2.1 89.9 1.0
OD1 H:ASP87 2.4 0.6 1.0
O2B H:ADP601 2.7 80.8 1.0
O1B H:ADP601 3.0 77.2 1.0
CG H:ASP87 3.2 0.3 1.0
OD2 H:ASP87 3.2 0.1 1.0
PB H:ADP601 3.3 86.6 1.0
PA H:ADP601 3.4 81.8 1.0
O H:SER151 3.8 88.9 1.0
O3A H:ADP601 3.8 79.6 1.0
OD2 H:ASP399 4.2 0.3 1.0
OG H:SER151 4.3 90.5 1.0
O1A H:ADP601 4.4 88.6 1.0
C5' H:ADP601 4.5 87.7 1.0
O5' H:ADP601 4.5 80.8 1.0
CB H:ASP399 4.6 98.7 1.0
CB H:ASP87 4.6 95.9 1.0
C H:SER151 4.7 83.9 1.0
CG H:ASP399 4.7 0.6 1.0
O3B H:ADP601 4.8 75.6 1.0
N H:GLY88 4.8 89.0 1.0
CA H:SER151 4.8 83.2 1.0

Magnesium binding site 9 out of 14 in 4pj1

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Magnesium binding site 9 out of 14 in the Crystal Structure of the Human Mitochondrial Chaperonin Symmetrical 'Football' Complex


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 Human Mitochondrial Chaperonin Symmetrical 'Football' Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg602

b:60.2
occ:1.00
 O2A I:ADP601 2.0 96.8 1.0
OD1 I:ASP87 2.1 90.9 1.0
CG I:ASP87 2.9 91.4 1.0
O3B I:ADP601 2.9 73.3 1.0
OD2 I:ASP87 2.9 97.7 1.0
O1B I:ADP601 3.2 66.9 1.0
PA I:ADP601 3.4 88.9 1.0
PB I:ADP601 3.5 77.7 1.0
O I:SER151 3.8 91.0 1.0
O3A I:ADP601 3.9 76.8 1.0
OD2 I:ASP399 4.2 0.5 1.0
OG I:SER151 4.2 82.2 1.0
O5' I:ADP601 4.3 90.8 1.0
CB I:ASP87 4.3 86.8 1.0
CB I:ASP399 4.5 93.7 1.0
CG I:ASP399 4.6 0.2 1.0
N I:GLY88 4.6 85.0 1.0
O1A I:ADP601 4.6 84.5 1.0
C I:SER151 4.7 83.2 1.0
CA I:SER151 4.7 86.1 1.0
CA I:ASP87 4.8 91.3 1.0
O2B I:ADP601 4.9 62.0 1.0
CB I:SER151 5.0 81.6 1.0

Magnesium binding site 10 out of 14 in 4pj1

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Magnesium binding site 10 out of 14 in the Crystal Structure of the Human Mitochondrial Chaperonin Symmetrical 'Football' Complex


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 Human Mitochondrial Chaperonin Symmetrical 'Football' Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg602

b:66.1
occ:1.00
 OD1 J:ASP87 2.1 0.4 1.0
O2A J:ADP601 2.2 94.3 1.0
O2B J:ADP601 2.5 85.6 1.0
CG J:ASP87 2.8 0.7 1.0
OD2 J:ASP87 2.9 98.7 1.0
O1B J:ADP601 3.1 76.0 1.0
PB J:ADP601 3.3 89.7 1.0
PA J:ADP601 3.5 86.9 1.0
O3A J:ADP601 3.8 88.3 1.0
O J:SER151 3.9 88.3 1.0
OG J:SER151 4.2 84.2 1.0
CB J:ASP87 4.3 91.1 1.0
OD2 J:ASP399 4.3 0.7 1.0
C5' J:ADP601 4.4 89.1 1.0
O5' J:ADP601 4.5 84.4 1.0
N J:GLY88 4.6 88.9 1.0
CB J:ASP399 4.6 97.7 1.0
O1A J:ADP601 4.6 89.5 1.0
CA J:SER151 4.7 88.2 1.0
CG J:ASP399 4.7 0.3 1.0
C J:SER151 4.7 78.5 1.0
O3B J:ADP601 4.7 70.0 1.0
CA J:ASP87 4.8 86.7 1.0
CB J:SER151 4.9 91.9 1.0

Reference:

S.Nisemblat, O.Yaniv, A.Parnas, F.Frolow, A.Azem. Crystal Structure of the Human Mitochondrial Chaperonin Symmetrical Football Complex. Proc.Natl.Acad.Sci.Usa V. 112 6044 2015.
ISSN: ESSN 1091-6490
PubMed: 25918392
DOI: 10.1073/PNAS.1411718112
Page generated: Mon Dec 14 19:20:07 2020

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