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Magnesium in PDB 1q3q: Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Two-Point Mutant Complexed with Amp-Pnp)

Enzymatic activity of Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Two-Point Mutant Complexed with Amp-Pnp)

All present enzymatic activity of Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Two-Point Mutant Complexed with Amp-Pnp):
3.6.4.9;

Protein crystallography data

The structure of Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Two-Point Mutant Complexed with Amp-Pnp), PDB code: 1q3q 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) 41.97 / 2.30
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 210.829, 210.829, 156.421, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 25

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Two-Point Mutant Complexed with Amp-Pnp) (pdb code 1q3q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Two-Point Mutant Complexed with Amp-Pnp), PDB code: 1q3q:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1q3q

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Magnesium binding site 1 out of 4 in the Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Two-Point Mutant Complexed with Amp-Pnp)


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 (Two-Point Mutant Complexed with Amp-Pnp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1527

b:71.4
occ:1.00
 O2A A:ANP1528 2.1 50.6 1.0
O3G A:ANP1528 2.1 57.9 1.0
O1B A:ANP1528 2.8 43.3 1.0
OD2 A:ASP95 3.0 32.0 1.0
CG A:ASP95 3.2 27.0 1.0
OD1 A:ASP95 3.3 29.7 1.0
PA A:ANP1528 3.4 48.2 1.0
PG A:ANP1528 3.6 58.4 1.0
PB A:ANP1528 3.8 43.6 1.0
O3A A:ANP1528 3.8 46.9 1.0
NZ A:LYS165 3.9 29.6 1.0
CE A:LYS165 4.0 29.8 1.0
O A:SER161 4.0 19.9 1.0
N3B A:ANP1528 4.1 51.4 1.0
CB A:ASP95 4.1 23.3 1.0
C5' A:ANP1528 4.3 49.5 1.0
O5' A:ANP1528 4.3 50.0 1.0
O1G A:ANP1528 4.4 56.2 1.0
O2G A:ANP1528 4.4 56.1 1.0
O1A A:ANP1528 4.6 48.8 1.0
CA A:ASP95 4.7 21.3 1.0
N A:GLY96 4.7 17.9 1.0
OG A:SER161 4.8 22.9 1.0
C A:SER161 4.9 21.0 1.0
CA A:SER161 4.9 20.1 1.0

Magnesium binding site 2 out of 4 in 1q3q

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Magnesium binding site 2 out of 4 in the Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Two-Point Mutant Complexed with Amp-Pnp)


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 (Two-Point Mutant Complexed with Amp-Pnp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2527

b:39.4
occ:1.00
 O3G B:ANP2528 2.2 66.6 1.0
O2A B:ANP2528 2.2 58.7 1.0
OD2 B:ASP95 2.5 32.0 1.0
CG B:ASP95 3.1 28.1 1.0
O1B B:ANP2528 3.1 52.4 1.0
NZ B:LYS165 3.1 33.2 1.0
OD1 B:ASP95 3.5 32.0 1.0
PA B:ANP2528 3.5 58.5 1.0
PG B:ANP2528 3.6 66.6 1.0
O B:SER161 3.8 17.8 1.0
PB B:ANP2528 4.0 50.5 1.0
O3A B:ANP2528 4.0 55.0 1.0
CB B:ASP95 4.1 24.7 1.0
O1G B:ANP2528 4.2 65.3 1.0
N3B B:ANP2528 4.2 58.5 1.0
CE B:LYS165 4.4 32.0 1.0
CA B:SER161 4.4 19.3 1.0
O5' B:ANP2528 4.4 60.0 1.0
C5' B:ANP2528 4.5 60.6 1.0
CB B:SER161 4.5 19.8 1.0
C B:SER161 4.6 19.1 1.0
CA B:ASP95 4.6 21.0 1.0
O2G B:ANP2528 4.6 64.3 1.0
O1A B:ANP2528 4.6 58.6 1.0
O B:HOH2143 4.7 47.6 1.0
N B:GLY96 4.8 18.2 1.0
OD2 B:ASP393 4.9 29.8 1.0

Magnesium binding site 3 out of 4 in 1q3q

Go back to Magnesium Binding Sites List in 1q3q
Magnesium binding site 3 out of 4 in the Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Two-Point Mutant Complexed with Amp-Pnp)


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 (Two-Point Mutant Complexed with Amp-Pnp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3527

b:85.2
occ:1.00
 O3G C:ANP3528 2.1 62.9 1.0
O2A C:ANP3528 2.2 57.8 1.0
OD2 C:ASP95 3.0 28.3 1.0
O1B C:ANP3528 3.2 48.9 1.0
CE C:LYS165 3.3 26.3 1.0
NZ C:LYS165 3.3 29.6 1.0
CG C:ASP95 3.5 22.4 1.0
PA C:ANP3528 3.5 57.1 1.0
PG C:ANP3528 3.6 62.9 1.0
O C:SER161 3.8 16.3 1.0
OD1 C:ASP95 3.8 25.1 1.0
O C:HOH3120 3.8 37.3 1.0
O3A C:ANP3528 4.0 52.4 1.0
PB C:ANP3528 4.0 46.2 1.0
O2G C:ANP3528 4.2 59.9 1.0
N3B C:ANP3528 4.2 55.5 1.0
CB C:ASP95 4.4 18.9 1.0
O1G C:ANP3528 4.5 60.5 1.0
O1A C:ANP3528 4.5 55.8 1.0
OD2 C:ASP393 4.5 26.5 1.0
O5' C:ANP3528 4.5 58.1 1.0
C5' C:ANP3528 4.7 58.2 1.0
CD C:LYS165 4.8 26.0 1.0
OG C:SER161 4.8 18.9 1.0
C C:SER161 4.8 16.4 1.0
CA C:ASP95 4.9 15.7 1.0
O C:HOH3042 4.9 29.2 1.0

Magnesium binding site 4 out of 4 in 1q3q

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Magnesium binding site 4 out of 4 in the Crystal Structure of the Chaperonin From Thermococcus Strain Ks-1 (Two-Point Mutant Complexed with Amp-Pnp)


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 (Two-Point Mutant Complexed with Amp-Pnp) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg4527

b:57.2
occ:1.00
 O2A D:ANP4528 2.2 54.2 1.0
O3G D:ANP4528 2.2 60.0 1.0
OD2 D:ASP95 2.6 36.0 1.0
O1B D:ANP4528 3.1 47.7 1.0
CG D:ASP95 3.2 30.4 1.0
NZ D:LYS165 3.4 37.0 1.0
CE D:LYS165 3.5 34.2 1.0
OD1 D:ASP95 3.6 31.4 1.0
PA D:ANP4528 3.6 53.0 1.0
PG D:ANP4528 3.7 59.8 1.0
O D:SER161 3.7 21.5 1.0
PB D:ANP4528 4.0 46.6 1.0
O3A D:ANP4528 4.0 51.0 1.0
N3B D:ANP4528 4.3 54.0 1.0
CB D:ASP95 4.3 25.9 1.0
O2G D:ANP4528 4.3 57.3 1.0
O5' D:ANP4528 4.5 55.2 1.0
C5' D:ANP4528 4.6 56.3 1.0
O1G D:ANP4528 4.6 57.6 1.0
OG D:SER161 4.6 20.9 1.0
O1A D:ANP4528 4.6 53.0 1.0
C D:SER161 4.7 20.9 1.0
CA D:ASP95 4.7 23.2 1.0
OD2 D:ASP393 4.8 27.8 1.0
CA D:SER161 4.9 19.8 1.0
N D:GLY96 5.0 18.2 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 02:27:54 2025

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