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Magnesium in PDB 3kfb: Crystal Structure of A Group II Chaperonin From Methanococcus Maripaludis

Protein crystallography data

The structure of Crystal Structure of A Group II Chaperonin From Methanococcus Maripaludis, PDB code: 3kfb 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) 48.84 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 260.694, 162.220, 184.733, 90.00, 135.05, 90.00
R / Rfree (%) 21 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Group II Chaperonin From Methanococcus Maripaludis (pdb code 3kfb). 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 Structure of A Group II Chaperonin From Methanococcus Maripaludis, PDB code: 3kfb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3kfb

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Magnesium binding site 1 out of 8 in the Crystal Structure 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 Structure of A Group II Chaperonin From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg545

b:61.9
occ:1.00
 OD1 A:ASP91 2.3 71.1 1.0
O3G A:ANP544 2.7 97.3 1.0
O A:SER157 2.9 93.6 1.0
CG A:ASP91 3.1 87.0 1.0
O1B A:ANP544 3.1 46.0 1.0
O2A A:ANP544 3.2 79.2 1.0
OD2 A:ASP91 3.2 89.7 1.0
OG A:SER157 3.8 82.5 1.0
OD2 A:ASP386 3.9 0.4 1.0
C A:SER157 3.9 70.4 1.0
PG A:ANP544 4.0 85.9 1.0
CA A:SER157 4.2 60.0 1.0
NZ A:LYS161 4.2 0.9 1.0
O A:THR159 4.3 91.3 1.0
PB A:ANP544 4.3 69.2 1.0
CB A:ASP91 4.4 81.5 1.0
PA A:ANP544 4.5 73.2 1.0
CE A:LYS161 4.5 97.1 1.0
CG A:LYS161 4.5 74.4 1.0
O2G A:ANP544 4.5 59.4 1.0
N3B A:ANP544 4.6 53.3 1.0
CB A:ASP386 4.6 0.8 1.0
CB A:SER157 4.6 69.0 1.0
O3A A:ANP544 4.7 82.2 1.0
CG A:ASP386 4.7 0.0 1.0
N A:LYS161 4.8 58.2 1.0
C5' A:ANP544 4.9 55.8 1.0

Magnesium binding site 2 out of 8 in 3kfb

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Magnesium binding site 2 out of 8 in the Crystal Structure 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 Structure of A Group II Chaperonin From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg545

b:75.0
occ:1.00
 O3G B:ANP544 2.2 89.8 1.0
OD1 B:ASP91 2.5 70.4 1.0
O2A B:ANP544 2.8 89.8 1.0
O1B B:ANP544 3.1 59.1 1.0
O B:SER157 3.2 90.8 1.0
CG B:ASP91 3.4 85.1 1.0
OD2 B:ASP91 3.7 85.2 1.0
PG B:ANP544 3.7 94.6 1.0
NZ B:LYS161 3.8 0.2 1.0
OD2 B:ASP386 3.9 0.7 1.0
PA B:ANP544 4.1 67.2 1.0
PB B:ANP544 4.1 88.6 1.0
CG B:LYS161 4.1 75.6 1.0
CE B:LYS161 4.2 93.8 1.0
C B:SER157 4.2 71.6 1.0
N3B B:ANP544 4.3 51.7 1.0
O2G B:ANP544 4.3 39.3 1.0
OG B:SER157 4.3 87.0 1.0
O B:THR159 4.4 86.7 1.0
O3A B:ANP544 4.4 93.6 1.0
N B:LYS161 4.5 62.8 1.0
O1G B:ANP544 4.6 93.2 1.0
CA B:SER157 4.6 56.4 1.0
C B:GLY160 4.7 92.5 1.0
C5' B:ANP544 4.8 52.0 1.0
CB B:ASP91 4.8 80.3 1.0
CG B:ASP386 4.8 1.0 1.0
CB B:ASP386 4.8 0.7 1.0
CD B:LYS161 4.9 67.3 1.0
CA B:GLY160 4.9 90.1 1.0
O5' B:ANP544 4.9 0.7 1.0

Magnesium binding site 3 out of 8 in 3kfb

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Magnesium binding site 3 out of 8 in the Crystal Structure 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 Structure of A Group II Chaperonin From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg545

b:52.0
occ:1.00
 O3G C:ANP544 2.2 78.3 1.0
OD1 C:ASP91 2.3 70.4 1.0
O1B C:ANP544 2.8 41.3 1.0
O2A C:ANP544 2.8 73.2 1.0
CG C:ASP91 3.2 82.9 1.0
O C:SER157 3.4 90.4 1.0
OD2 C:ASP91 3.4 84.5 1.0
PG C:ANP544 3.6 77.6 1.0
PB C:ANP544 3.9 84.9 1.0
OD2 C:ASP386 3.9 0.0 1.0
NZ C:LYS161 4.0 0.6 1.0
PA C:ANP544 4.1 60.3 1.0
N3B C:ANP544 4.1 58.0 1.0
O2G C:ANP544 4.2 47.6 1.0
O3A C:ANP544 4.2 72.5 1.0
OG C:SER157 4.3 91.4 1.0
C C:SER157 4.4 72.1 1.0
CG C:LYS161 4.5 77.2 1.0
CE C:LYS161 4.5 98.2 1.0
O C:THR159 4.5 94.5 1.0
CB C:ASP91 4.6 87.0 1.0
C5' C:ANP544 4.6 67.3 1.0
O1G C:ANP544 4.6 68.6 1.0
CA C:SER157 4.7 58.9 1.0
N C:LYS161 4.8 58.1 1.0
O5' C:ANP544 4.8 82.1 1.0
CG C:ASP386 4.9 1.0 1.0
CB C:ASP386 4.9 0.1 1.0
C C:GLY160 4.9 90.8 1.0

Magnesium binding site 4 out of 8 in 3kfb

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Magnesium binding site 4 out of 8 in the Crystal Structure 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 Structure of A Group II Chaperonin From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg545

b:76.0
occ:1.00
 OD1 D:ASP91 2.5 77.5 1.0
O3G D:ANP544 2.6 99.1 1.0
O2A D:ANP544 2.9 85.0 1.0
O D:SER157 3.0 95.2 1.0
O1B D:ANP544 3.1 45.5 1.0
CG D:ASP91 3.3 88.4 1.0
OD2 D:ASP91 3.4 90.1 1.0
PG D:ANP544 4.0 92.5 1.0
C D:SER157 4.0 73.0 1.0
OD2 D:ASP386 4.1 0.6 1.0
OG D:SER157 4.1 83.9 1.0
O D:THR159 4.1 92.1 1.0
NZ D:LYS161 4.2 0.1 1.0
PB D:ANP544 4.2 89.9 1.0
PA D:ANP544 4.2 74.4 1.0
CA D:SER157 4.3 63.8 1.0
CG D:LYS161 4.4 75.9 1.0
CE D:LYS161 4.5 95.4 1.0
N3B D:ANP544 4.5 64.5 1.0
O3A D:ANP544 4.5 1.0 1.0
O2G D:ANP544 4.6 72.3 1.0
N D:LYS161 4.7 63.6 1.0
C5' D:ANP544 4.7 81.3 1.0
CB D:ASP91 4.7 80.5 1.0
C D:GLY160 4.8 91.4 1.0
CB D:SER157 4.8 71.2 1.0
CB D:ASP386 4.9 0.1 1.0
CA D:GLY160 4.9 87.9 1.0
O5' D:ANP544 4.9 73.5 1.0
CG D:ASP386 4.9 0.2 1.0
O1G D:ANP544 5.0 65.5 1.0

Magnesium binding site 5 out of 8 in 3kfb

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Magnesium binding site 5 out of 8 in the Crystal Structure 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 Structure of A Group II Chaperonin From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg545

b:65.6
occ:1.00
 OD1 E:ASP91 2.4 69.5 1.0
O3G E:ANP544 2.5 93.3 1.0
O2A E:ANP544 3.0 82.2 1.0
O E:SER157 3.0 98.7 1.0
O1B E:ANP544 3.0 44.4 1.0
CG E:ASP91 3.2 86.2 1.0
OD2 E:ASP91 3.3 93.6 1.0
PG E:ANP544 3.9 82.8 1.0
OD2 E:ASP386 3.9 0.7 1.0
C E:SER157 4.1 73.6 1.0
OG E:SER157 4.1 84.9 1.0
NZ E:LYS161 4.1 0.1 1.0
PB E:ANP544 4.2 68.0 1.0
PA E:ANP544 4.3 59.3 1.0
O E:THR159 4.3 93.4 1.0
CA E:SER157 4.4 59.2 1.0
CG E:LYS161 4.4 73.8 1.0
CE E:LYS161 4.4 96.2 1.0
O2G E:ANP544 4.4 51.7 1.0
N3B E:ANP544 4.4 51.1 1.0
O3A E:ANP544 4.5 77.3 1.0
CB E:ASP91 4.6 86.1 1.0
CB E:ASP386 4.7 0.1 1.0
C5' E:ANP544 4.8 47.9 1.0
N E:LYS161 4.8 58.9 1.0
CG E:ASP386 4.8 0.2 1.0
CB E:SER157 4.8 68.9 1.0
C E:GLY160 4.9 90.2 1.0
O1G E:ANP544 4.9 82.1 1.0
CA E:GLY160 5.0 83.6 1.0
O5' E:ANP544 5.0 70.0 1.0

Magnesium binding site 6 out of 8 in 3kfb

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Magnesium binding site 6 out of 8 in the Crystal Structure 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 Structure of A Group II Chaperonin From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg545

b:64.0
occ:1.00
 O3G F:ANP544 2.1 83.1 1.0
OD1 F:ASP91 2.6 73.8 1.0
O2A F:ANP544 2.9 87.1 1.0
O1B F:ANP544 3.2 56.1 1.0
O F:SER157 3.2 82.3 1.0
CG F:ASP91 3.5 84.5 1.0
NZ F:LYS161 3.6 0.1 1.0
PG F:ANP544 3.6 81.2 1.0
OD2 F:ASP386 3.7 0.1 1.0
OD2 F:ASP91 3.8 84.3 1.0
CG F:LYS161 3.9 76.1 1.0
CE F:LYS161 4.0 91.3 1.0
O2G F:ANP544 4.2 38.5 1.0
PB F:ANP544 4.2 83.0 1.0
PA F:ANP544 4.2 80.1 1.0
N3B F:ANP544 4.3 65.8 1.0
C F:SER157 4.3 70.9 1.0
OG F:SER157 4.3 86.9 1.0
O3A F:ANP544 4.4 75.8 1.0
O1G F:ANP544 4.5 79.9 1.0
O F:THR159 4.5 90.9 1.0
N F:LYS161 4.5 58.0 1.0
CG F:ASP386 4.6 0.7 1.0
CD F:LYS161 4.6 66.2 1.0
CB F:ASP386 4.7 0.5 1.0
C F:GLY160 4.7 91.5 1.0
CA F:SER157 4.8 64.0 1.0
CB F:ASP91 4.8 82.0 1.0
C5' F:ANP544 5.0 53.3 1.0
CB F:LYS161 5.0 69.0 1.0
CA F:GLY160 5.0 89.8 1.0

Magnesium binding site 7 out of 8 in 3kfb

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Magnesium binding site 7 out of 8 in the Crystal Structure 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 Structure of A Group II Chaperonin From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg545

b:38.9
occ:1.00
 O3G G:ANP544 2.2 76.5 1.0
OD1 G:ASP91 2.3 69.1 1.0
O1B G:ANP544 2.8 49.1 1.0
O2A G:ANP544 2.9 88.3 1.0
CG G:ASP91 3.2 81.0 1.0
O G:SER157 3.3 94.0 1.0
OD2 G:ASP91 3.4 80.6 1.0
PG G:ANP544 3.6 63.8 1.0
OD2 G:ASP386 3.9 0.5 1.0
PB G:ANP544 3.9 77.8 1.0
NZ G:LYS161 4.0 0.7 1.0
PA G:ANP544 4.1 60.9 1.0
N3B G:ANP544 4.2 41.8 1.0
O2G G:ANP544 4.2 52.4 1.0
OG G:SER157 4.3 88.8 1.0
O3A G:ANP544 4.3 69.2 1.0
C G:SER157 4.3 75.3 1.0
CG G:LYS161 4.4 81.6 1.0
CE G:LYS161 4.4 94.7 1.0
O G:THR159 4.5 96.2 1.0
CB G:ASP91 4.6 88.4 1.0
CA G:SER157 4.6 66.3 1.0
O1G G:ANP544 4.6 66.8 1.0
C5' G:ANP544 4.7 73.2 1.0
N G:LYS161 4.8 62.8 1.0
CG G:ASP386 4.8 0.5 1.0
CB G:ASP386 4.8 0.9 1.0
O5' G:ANP544 4.9 74.1 1.0
C G:GLY160 4.9 93.1 1.0

Magnesium binding site 8 out of 8 in 3kfb

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Magnesium binding site 8 out of 8 in the Crystal Structure 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 Structure of A Group II Chaperonin From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg545

b:57.6
occ:1.00
 OD1 H:ASP91 2.4 76.8 1.0
O3G H:ANP544 2.7 95.6 1.0
O1B H:ANP544 2.8 47.7 1.0
O2A H:ANP544 2.9 90.8 1.0
CG H:ASP91 3.1 87.1 1.0
OD2 H:ASP91 3.1 85.9 1.0
O H:SER157 3.1 95.4 1.0
PB H:ANP544 4.0 91.4 1.0
C H:SER157 4.1 69.7 1.0
OG H:SER157 4.1 83.8 1.0
PG H:ANP544 4.1 95.3 1.0
O H:THR159 4.2 93.1 1.0
PA H:ANP544 4.2 77.3 1.0
CA H:SER157 4.2 58.3 1.0
OD2 H:ASP386 4.3 0.9 1.0
C5' H:ANP544 4.4 79.9 1.0
O3A H:ANP544 4.4 0.6 1.0
N3B H:ANP544 4.5 70.8 1.0
NZ H:LYS161 4.5 0.1 1.0
CB H:ASP91 4.5 84.4 1.0
O2G H:ANP544 4.6 58.1 1.0
O5' H:ANP544 4.7 78.3 1.0
CG H:LYS161 4.8 70.6 1.0
CB H:SER157 4.8 69.0 1.0
CE H:LYS161 4.8 96.9 1.0
N H:LYS161 4.9 65.9 1.0
CA H:GLY160 4.9 92.2 1.0
O H:THR156 4.9 87.4 1.0
C H:GLY160 4.9 95.7 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 18:05:32 2024

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