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Magnesium in PDB 1q3s: Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp)

Enzymatic activity of Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp)

All present enzymatic activity of Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp):
3.6.4.9;

Protein crystallography data

The structure of Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp), PDB code: 1q3s was solved by Y.Shomura, T.Yoshida, R.Iizuka, T.Maruyama, M.Yohda, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.62 / 3.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 207.425, 236.230, 234.106, 90.00, 90.00, 90.00
R / Rfree (%) 25.1 / 28.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp) (pdb code 1q3s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp), PDB code: 1q3s:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 1q3s

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Magnesium binding site 1 out of 7 in the Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp)


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 Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1527

b:15.9
occ:1.00
 OD2 A:ASP95 2.4 30.1 1.0
O1A A:ADP1528 2.5 30.4 1.0
O3B A:ADP1528 2.5 22.1 1.0
CG A:ASP95 3.1 28.1 1.0
OD1 A:ASP95 3.1 28.6 1.0
NZ A:LYS165 3.2 65.9 1.0
PB A:ADP1528 3.7 23.3 1.0
PA A:ADP1528 3.8 29.5 1.0
O2B A:ADP1528 4.0 21.5 1.0
O3A A:ADP1528 4.0 26.2 1.0
O A:SER161 4.1 33.0 1.0
OG A:SER161 4.4 28.8 1.0
OD2 A:ASP393 4.4 40.7 1.0
CE A:LYS165 4.5 65.7 1.0
CB A:ASP95 4.6 25.8 1.0
C5' A:ADP1528 4.7 30.0 1.0
O5' A:ADP1528 4.7 30.0 1.0
N A:GLY96 4.8 22.8 1.0
CB A:ASP393 4.8 32.2 1.0
O2A A:ADP1528 4.8 28.2 1.0
CG A:ASP393 4.9 38.0 1.0
CG A:LYS165 4.9 65.5 1.0
C A:SER161 5.0 32.1 1.0

Magnesium binding site 2 out of 7 in 1q3s

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Magnesium binding site 2 out of 7 in the Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp)


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 Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2527

b:10.7
occ:1.00
 OD2 B:ASP95 2.4 21.6 1.0
O3B B:ADP2528 2.5 20.1 1.0
O1A B:ADP2528 2.5 25.6 1.0
CG B:ASP95 3.1 21.4 1.0
OD1 B:ASP95 3.2 22.5 1.0
PA B:ADP2528 3.8 26.1 1.0
NZ B:LYS165 3.8 61.5 1.0
PB B:ADP2528 3.9 18.3 1.0
O B:SER161 4.0 25.6 1.0
OG B:SER161 4.1 24.4 1.0
O3A B:ADP2528 4.2 21.9 1.0
C5' B:ADP2528 4.4 28.2 1.0
O2B B:ADP2528 4.4 18.3 1.0
N B:GLY96 4.5 19.6 1.0
O5' B:ADP2528 4.5 26.1 1.0
CB B:ASP95 4.6 20.6 1.0
OD2 B:ASP393 4.7 36.6 1.0
C B:SER161 4.8 25.9 1.0
CA B:SER161 4.8 25.7 1.0
O2A B:ADP2528 4.9 25.6 1.0

Magnesium binding site 3 out of 7 in 1q3s

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Magnesium binding site 3 out of 7 in the Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp)


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 Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3527

b:18.8
occ:1.00
 OD2 C:ASP95 2.3 39.5 1.0
O1A C:ADP3528 2.5 36.8 1.0
O3B C:ADP3528 2.5 36.3 1.0
CG C:ASP95 3.0 38.9 1.0
OD1 C:ASP95 3.1 38.4 1.0
NZ C:LYS165 3.5 72.9 1.0
PA C:ADP3528 3.7 35.9 1.0
PB C:ADP3528 3.7 32.9 1.0
O C:SER161 3.9 51.0 1.0
O3A C:ADP3528 4.0 34.4 1.0
O2B C:ADP3528 4.0 34.0 1.0
C5' C:ADP3528 4.4 36.6 1.0
OG C:SER161 4.5 50.7 1.0
N C:GLY96 4.5 38.1 1.0
CB C:ASP95 4.5 39.2 1.0
O5' C:ADP3528 4.5 36.2 1.0
OD2 C:ASP393 4.6 51.7 1.0
CE C:LYS165 4.6 73.4 1.0
O2A C:ADP3528 4.8 36.4 1.0
C C:SER161 4.9 50.8 1.0
CA C:ASP95 5.0 39.6 1.0
CA C:SER161 5.0 49.1 1.0

Magnesium binding site 4 out of 7 in 1q3s

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Magnesium binding site 4 out of 7 in the Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp)


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 Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg4527

b:17.5
occ:1.00
 OD2 D:ASP95 2.1 39.6 1.0
O1A D:ADP4528 2.5 35.8 1.0
O3B D:ADP4528 2.5 35.2 1.0
CG D:ASP95 3.1 38.5 1.0
OD1 D:ASP95 3.3 39.9 1.0
PB D:ADP4528 3.6 32.5 1.0
NZ D:LYS165 3.7 63.2 1.0
PA D:ADP4528 3.7 36.1 1.0
O2B D:ADP4528 3.8 32.8 1.0
O3A D:ADP4528 3.9 34.2 1.0
OD2 D:ASP393 4.1 47.4 1.0
O D:SER161 4.4 45.1 1.0
CB D:ASP95 4.4 35.6 1.0
N D:GLY96 4.5 33.9 1.0
OG D:SER161 4.6 41.7 1.0
C5' D:ADP4528 4.6 37.8 1.0
CG D:ASP393 4.6 46.5 1.0
O5' D:ADP4528 4.7 36.4 1.0
O2A D:ADP4528 4.8 36.1 1.0
CA D:ASP95 4.8 34.2 1.0
CE D:LYS165 4.9 63.5 1.0
CB D:ASP393 4.9 43.5 1.0
O1B D:ADP4528 5.0 32.1 1.0

Magnesium binding site 5 out of 7 in 1q3s

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Magnesium binding site 5 out of 7 in the Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp)


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 Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg5527

b:14.7
occ:1.00
 OD2 E:ASP95 2.2 37.1 1.0
O3B E:ADP5528 2.6 33.1 1.0
O1A E:ADP5528 2.6 35.4 1.0
CG E:ASP95 3.2 36.0 1.0
OD1 E:ASP95 3.4 36.6 1.0
NZ E:LYS165 3.6 66.6 1.0
PB E:ADP5528 3.7 33.5 1.0
PA E:ADP5528 3.8 36.1 1.0
O2B E:ADP5528 3.9 33.7 1.0
O3A E:ADP5528 3.9 33.9 1.0
O E:SER161 4.3 44.6 1.0
OG E:SER161 4.4 42.1 1.0
N E:GLY96 4.5 35.6 1.0
CB E:ASP95 4.6 34.9 1.0
C5' E:ADP5528 4.7 34.4 1.0
OD2 E:ASP393 4.7 53.7 1.0
O5' E:ADP5528 4.7 34.8 1.0
CG E:ASP393 4.9 50.9 1.0
O2A E:ADP5528 4.9 35.9 1.0
CB E:ASP393 4.9 46.8 1.0
CA E:ASP95 4.9 34.8 1.0
CE E:LYS165 5.0 64.9 1.0

Magnesium binding site 6 out of 7 in 1q3s

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Magnesium binding site 6 out of 7 in the Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp)


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 Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg6527

b:16.9
occ:1.00
 OD2 G:ASP95 2.2 25.9 1.0
O1A G:ADP7528 2.5 34.4 1.0
O3B G:ADP7528 2.5 34.7 1.0
OD1 G:ASP95 2.8 27.5 1.0
CG G:ASP95 2.8 25.9 1.0
PA G:ADP7528 3.8 34.0 1.0
O G:SER161 3.8 40.5 1.0
PB G:ADP7528 4.0 30.2 1.0
OG G:SER161 4.1 35.6 1.0
O3A G:ADP7528 4.2 31.4 1.0
C5' G:ADP7528 4.3 38.3 1.0
N G:GLY96 4.3 27.2 1.0
CB G:ASP95 4.3 26.0 1.0
NZ G:LYS165 4.4 64.3 1.0
O5' G:ADP7528 4.4 35.8 1.0
O2B G:ADP7528 4.5 30.2 1.0
C G:SER161 4.7 40.2 1.0
OD2 G:ASP393 4.7 43.7 1.0
CA G:SER161 4.7 38.0 1.0
CA G:ASP95 4.9 26.6 1.0
O2A G:ADP7528 4.9 34.0 1.0
CB G:SER161 5.0 37.4 1.0

Magnesium binding site 7 out of 7 in 1q3s

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Magnesium binding site 7 out of 7 in the Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp)


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 Chaperonin From Thermococcus Strain Ks-1 (Formiii Crystal Complexed with Adp) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg8527

b:25.1
occ:1.00
 OD2 H:ASP95 2.2 26.7 1.0
O1A H:ADP8528 2.5 27.0 1.0
O3B H:ADP8528 2.5 29.3 1.0
CG H:ASP95 3.1 24.8 1.0
OD1 H:ASP95 3.3 24.8 1.0
NZ H:LYS165 3.5 64.8 1.0
PB H:ADP8528 3.6 27.6 1.0
PA H:ADP8528 3.8 26.5 1.0
O2B H:ADP8528 3.8 29.7 1.0
O3A H:ADP8528 3.9 26.7 1.0
O H:SER161 4.1 24.2 1.0
CB H:ASP95 4.5 23.1 1.0
OD2 H:ASP393 4.5 38.3 1.0
OG H:SER161 4.6 20.3 1.0
N H:GLY96 4.6 24.7 1.0
C5' H:ADP8528 4.7 27.1 1.0
O5' H:ADP8528 4.7 27.4 1.0
CE H:LYS165 4.7 63.2 1.0
O2A H:ADP8528 4.8 28.9 1.0
CG H:ASP393 4.9 36.5 1.0
CA H:ASP95 4.9 24.0 1.0
CB H:ASP393 4.9 32.8 1.0
O1B H:ADP8528 5.0 27.6 1.0

Reference:

Y.Shomura, T.Yoshida, R.Iizuka, T.Maruyama, M.Yohda, K.Miki. Crystal Structures of the Group II Chaperonin From Thermococcus Strain Ks-1: Steric Hindrance By the Substituted Amino Acid, and Inter-Subunit Rearrangement Between Two Crystal Forms. J.Mol.Biol. V. 335 1265 2004.
ISSN: ISSN 0022-2836
PubMed: 14729342
DOI: 10.1016/J.JMB.2003.11.028
Page generated: Sun Aug 10 02:28:16 2025

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