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Magnesium in PDB 3kfe: Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis

Protein crystallography data

The structure of Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis, PDB code: 3kfe was solved by J.H.Pereira, C.Y.Ralston, N.Douglas, D.Meyer, K.M.Knee, D.R.Goulet, J.A.King, J.Frydman, P.D.Adams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.49 / 3.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 261.450, 161.920, 147.370, 90.00, 124.12, 90.00
R / Rfree (%) 23.2 / 26.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis (pdb code 3kfe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis, PDB code: 3kfe:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3kfe

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Magnesium binding site 1 out of 8 in the Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg544

b:65.4
occ:1.00
 OD1 A:ASP91 2.5 58.4 1.0
O2 A:SO4546 2.6 81.3 1.0
O2A A:ADP545 2.8 55.1 1.0
O A:SER157 3.1 64.4 1.0
CG A:ASP91 3.3 63.6 1.0
O1B A:ADP545 3.4 43.6 1.0
OD2 A:ASP386 3.5 93.8 1.0
OD2 A:ASP91 3.6 63.1 1.0
NZ A:LYS161 3.7 73.5 1.0
S A:SO4546 3.8 0.8 1.0
O4 A:SO4546 3.8 0.3 1.0
CG A:LYS161 4.0 71.1 1.0
PA A:ADP545 4.1 68.1 1.0
C A:SER157 4.2 53.1 1.0
CG A:ASP386 4.2 98.5 1.0
CB A:ASP386 4.3 69.5 1.0
OG A:SER157 4.3 65.1 1.0
O A:THR159 4.5 66.9 1.0
O1 A:SO4546 4.5 83.5 1.0
O3A A:ADP545 4.6 77.3 1.0
PB A:ADP545 4.6 56.0 1.0
CB A:ASP91 4.7 53.7 1.0
N A:LYS161 4.7 84.8 1.0
O1A A:ADP545 4.7 57.1 1.0
CA A:SER157 4.7 59.2 1.0
CE A:LYS161 4.7 56.9 1.0
O3 A:SO4546 4.8 76.3 1.0
C A:GLY160 4.9 93.4 1.0
CB A:LYS161 4.9 68.6 1.0
CD A:LYS161 5.0 72.1 1.0

Magnesium binding site 2 out of 8 in 3kfe

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Magnesium binding site 2 out of 8 in the Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg544

b:58.4
occ:1.00
 OD1 B:ASP91 2.4 64.5 1.0
O2 B:SO4546 2.5 59.9 1.0
O2A B:ADP545 2.6 54.1 1.0
O B:SER157 3.1 84.8 1.0
O1B B:ADP545 3.3 49.5 1.0
CG B:ASP91 3.3 65.2 1.0
OD2 B:ASP91 3.5 57.2 1.0
OD2 B:ASP386 3.6 0.5 1.0
NZ B:LYS161 3.7 67.6 1.0
S B:SO4546 3.7 88.9 1.0
O4 B:SO4546 3.8 0.6 1.0
PA B:ADP545 4.0 65.0 1.0
CG B:LYS161 4.0 61.1 1.0
C B:SER157 4.2 70.2 1.0
CG B:ASP386 4.3 0.7 1.0
OG B:SER157 4.4 77.0 1.0
CB B:ASP386 4.4 84.4 1.0
O B:THR159 4.4 87.5 1.0
O3A B:ADP545 4.5 76.2 1.0
O1 B:SO4546 4.5 71.9 1.0
PB B:ADP545 4.5 57.7 1.0
O1A B:ADP545 4.6 63.1 1.0
CB B:ASP91 4.6 53.6 1.0
N B:LYS161 4.7 79.2 1.0
CA B:SER157 4.7 71.3 1.0
O3 B:SO4546 4.7 74.1 1.0
CE B:LYS161 4.7 51.5 1.0
C B:GLY160 4.8 0.2 1.0
CB B:LYS161 4.9 61.1 1.0
CD B:LYS161 5.0 65.1 1.0

Magnesium binding site 3 out of 8 in 3kfe

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Magnesium binding site 3 out of 8 in the Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg544

b:58.0
occ:1.00
 OD1 C:ASP91 2.5 62.5 1.0
O2 C:SO4546 2.6 71.1 1.0
O2A C:ADP545 2.7 46.0 1.0
O C:SER157 3.0 89.7 1.0
CG C:ASP91 3.2 62.1 1.0
O1B C:ADP545 3.3 51.2 1.0
OD2 C:ASP91 3.4 66.7 1.0
OD2 C:ASP386 3.7 93.4 1.0
S C:SO4546 3.8 0.3 1.0
NZ C:LYS161 3.9 78.8 1.0
O4 C:SO4546 3.9 0.7 1.0
PA C:ADP545 4.0 62.4 1.0
CG C:LYS161 4.1 79.4 1.0
C C:SER157 4.1 73.9 1.0
OG C:SER157 4.2 68.8 1.0
CG C:ASP386 4.3 98.8 1.0
CB C:ASP386 4.4 82.2 1.0
O C:THR159 4.4 77.4 1.0
O3A C:ADP545 4.5 77.8 1.0
PB C:ADP545 4.5 64.5 1.0
O1 C:SO4546 4.6 78.2 1.0
CB C:ASP91 4.6 50.6 1.0
CA C:SER157 4.6 74.4 1.0
O1A C:ADP545 4.7 68.2 1.0
N C:LYS161 4.7 89.2 1.0
O3 C:SO4546 4.9 81.8 1.0
C C:GLY160 4.9 0.2 1.0
CE C:LYS161 4.9 60.5 1.0
CB C:LYS161 5.0 80.0 1.0

Magnesium binding site 4 out of 8 in 3kfe

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Magnesium binding site 4 out of 8 in the Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg544

b:92.8
occ:1.00
 OD1 D:ASP91 2.4 74.6 1.0
O2 D:SO4546 2.5 71.1 1.0
O2A D:ADP545 2.8 71.7 1.0
O D:SER157 3.2 0.9 1.0
CG D:ASP91 3.3 73.9 1.0
O1B D:ADP545 3.4 73.0 1.0
OD2 D:ASP386 3.4 0.1 1.0
OD2 D:ASP91 3.6 74.3 1.0
NZ D:LYS161 3.6 87.9 1.0
S D:SO4546 3.7 89.0 1.0
O4 D:SO4546 3.7 0.3 1.0
CG D:LYS161 4.0 81.3 1.0
PA D:ADP545 4.0 99.2 1.0
CG D:ASP386 4.1 0.2 1.0
C D:SER157 4.2 0.7 1.0
CB D:ASP386 4.3 99.0 1.0
OG D:SER157 4.3 0.4 1.0
O1 D:SO4546 4.5 66.7 1.0
O3A D:ADP545 4.5 0.2 1.0
O D:THR159 4.6 0.9 1.0
PB D:ADP545 4.6 95.1 1.0
CB D:ASP91 4.6 67.7 1.0
O1A D:ADP545 4.7 86.0 1.0
CE D:LYS161 4.7 72.4 1.0
N D:LYS161 4.7 97.3 1.0
O3 D:SO4546 4.8 73.8 1.0
CA D:SER157 4.8 0.2 1.0
CB D:LYS161 4.9 82.5 1.0
C D:GLY160 4.9 0.7 1.0
CD D:LYS161 5.0 81.0 1.0

Magnesium binding site 5 out of 8 in 3kfe

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Magnesium binding site 5 out of 8 in the Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg544

b:55.2
occ:1.00
 OD1 E:ASP91 2.4 62.1 1.0
O2 E:SO4546 2.5 77.3 1.0
O2A E:ADP545 2.7 58.3 1.0
O E:SER157 3.2 94.6 1.0
CG E:ASP91 3.3 71.2 1.0
O1B E:ADP545 3.4 62.2 1.0
OD2 E:ASP386 3.5 0.8 1.0
OD2 E:ASP91 3.5 82.0 1.0
NZ E:LYS161 3.6 88.9 1.0
S E:SO4546 3.7 0.3 1.0
O4 E:SO4546 3.7 99.8 1.0
CG E:LYS161 4.0 76.1 1.0
PA E:ADP545 4.0 75.4 1.0
CG E:ASP386 4.2 0.3 1.0
C E:SER157 4.2 79.2 1.0
OG E:SER157 4.3 88.7 1.0
CB E:ASP386 4.3 86.8 1.0
O1 E:SO4546 4.5 65.2 1.0
O3A E:ADP545 4.5 76.1 1.0
O E:THR159 4.5 91.0 1.0
PB E:ADP545 4.6 64.7 1.0
CB E:ASP91 4.6 65.0 1.0
O1A E:ADP545 4.7 69.7 1.0
CE E:LYS161 4.7 71.3 1.0
N E:LYS161 4.7 81.8 1.0
CA E:SER157 4.8 84.9 1.0
O3 E:SO4546 4.8 72.7 1.0
C E:GLY160 4.9 96.4 1.0
CB E:LYS161 4.9 71.3 1.0
CD E:LYS161 5.0 79.2 1.0

Magnesium binding site 6 out of 8 in 3kfe

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Magnesium binding site 6 out of 8 in the Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg544

b:83.2
occ:1.00
 OD1 F:ASP91 2.4 62.6 1.0
O2 F:SO4546 2.5 0.4 1.0
O2A F:ADP545 2.7 57.4 1.0
O F:SER157 3.2 88.3 1.0
CG F:ASP91 3.3 71.0 1.0
O1B F:ADP545 3.3 58.8 1.0
OD2 F:ASP91 3.5 78.0 1.0
OD2 F:ASP386 3.5 0.3 1.0
NZ F:LYS161 3.6 87.7 1.0
S F:SO4546 3.7 1.0 1.0
O4 F:SO4546 3.7 0.0 1.0
PA F:ADP545 4.0 74.8 1.0
CG F:LYS161 4.0 76.6 1.0
C F:SER157 4.2 77.5 1.0
CG F:ASP386 4.2 0.9 1.0
OG F:SER157 4.3 89.9 1.0
CB F:ASP386 4.3 0.8 1.0
O1 F:SO4546 4.5 0.4 1.0
O F:THR159 4.5 85.4 1.0
O3A F:ADP545 4.5 83.5 1.0
PB F:ADP545 4.5 79.6 1.0
CB F:ASP91 4.6 65.6 1.0
O1A F:ADP545 4.7 60.1 1.0
N F:LYS161 4.7 92.9 1.0
CE F:LYS161 4.7 72.3 1.0
CA F:SER157 4.7 85.9 1.0
O3 F:SO4546 4.7 0.6 1.0
C F:GLY160 4.9 0.1 1.0
CB F:LYS161 4.9 71.8 1.0
CD F:LYS161 5.0 84.8 1.0

Magnesium binding site 7 out of 8 in 3kfe

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Magnesium binding site 7 out of 8 in the Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg544

b:0.7
occ:1.00
 OD1 G:ASP91 2.4 82.2 1.0
O2 G:SO4546 2.6 91.9 1.0
O2A G:ADP545 2.7 83.7 1.0
O G:SER157 3.1 0.2 1.0
CG G:ASP91 3.2 93.0 1.0
O1B G:ADP545 3.3 71.8 1.0
OD2 G:ASP91 3.5 89.0 1.0
OD2 G:ASP386 3.7 0.2 1.0
S G:SO4546 3.8 0.0 1.0
NZ G:LYS161 3.8 0.6 1.0
O4 G:SO4546 3.9 0.4 1.0
PA G:ADP545 4.0 0.5 1.0
CG G:LYS161 4.1 0.8 1.0
C G:SER157 4.1 89.7 1.0
OG G:SER157 4.2 86.0 1.0
CG G:ASP386 4.3 0.9 1.0
CB G:ASP386 4.4 0.7 1.0
O G:THR159 4.4 0.9 1.0
PB G:ADP545 4.5 97.2 1.0
O3A G:ADP545 4.5 0.6 1.0
O1 G:SO4546 4.6 75.2 1.0
CB G:ASP91 4.6 93.1 1.0
CA G:SER157 4.6 89.5 1.0
N G:LYS161 4.7 0.9 1.0
O1A G:ADP545 4.7 95.3 1.0
O3 G:SO4546 4.8 90.9 1.0
C G:GLY160 4.9 0.3 1.0
CE G:LYS161 4.9 0.1 1.0
CB G:LYS161 5.0 0.8 1.0
C5' G:ADP545 5.0 0.3 1.0

Magnesium binding site 8 out of 8 in 3kfe

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Magnesium binding site 8 out of 8 in the Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structures of A Group II Chaperonin From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg544

b:0.1
occ:1.00
 OD1 H:ASP91 2.4 94.0 1.0
O2 H:SO4546 2.6 0.5 1.0
O2A H:ADP545 2.7 88.5 1.0
O H:SER157 3.1 0.8 1.0
CG H:ASP91 3.3 96.0 1.0
O1B H:ADP545 3.4 73.0 1.0
OD2 H:ASP91 3.6 88.1 1.0
OD2 H:ASP386 3.6 0.2 1.0
NZ H:LYS161 3.8 0.1 1.0
S H:SO4546 3.8 0.0 1.0
O4 H:SO4546 3.9 0.3 1.0
PA H:ADP545 4.0 0.8 1.0
CG H:LYS161 4.0 0.1 1.0
C H:SER157 4.1 0.7 1.0
CG H:ASP386 4.3 0.7 1.0
OG H:SER157 4.3 0.7 1.0
CB H:ASP386 4.3 0.3 1.0
O H:THR159 4.4 0.1 1.0
O3A H:ADP545 4.5 0.7 1.0
PB H:ADP545 4.6 0.9 1.0
O1 H:SO4546 4.6 96.4 1.0
N H:LYS161 4.6 0.1 1.0
CB H:ASP91 4.6 94.0 1.0
CA H:SER157 4.7 0.8 1.0
O1A H:ADP545 4.7 84.2 1.0
CE H:LYS161 4.8 0.4 1.0
C H:GLY160 4.8 0.1 1.0
O3 H:SO4546 4.9 0.4 1.0
CB H:LYS161 4.9 0.1 1.0

Reference:

J.H.Pereira, C.Y.Ralston, N.R.Douglas, D.Meyer, K.M.Knee, D.R.Goulet, J.A.King, J.Frydman, P.D.Adams. Crystal Structures of A Group II Chaperonin Reveal the Open and Closed States Associated with the Protein Folding Cycle. J.Biol.Chem. V. 285 27958 2010.
ISSN: ISSN 0021-9258
PubMed: 20573955
DOI: 10.1074/JBC.M110.125344
Page generated: Wed Aug 14 18:06:13 2024

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