Atomistry » Magnesium » PDB 1q3b-1qc1 » 1q3q
Atomistry »
  Magnesium »
    PDB 1q3b-1qc1 »
      1q3q »

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

Go back to Magnesium Binding Sites List in 1q3q
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

Go back to Magnesium Binding Sites List in 1q3q
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

Go back to Magnesium Binding Sites List in 1q3q
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: Tue Aug 13 11:04:35 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy