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Magnesium in PDB 4qiw: Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis

Enzymatic activity of Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis

All present enzymatic activity of Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis, PDB code: 4qiw was solved by S.-H.Jun, K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.73 / 3.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 112.975, 206.606, 365.157, 90.00, 90.00, 90.00
R / Rfree (%) 27.7 / 31.6

Other elements in 4qiw:

The structure of Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis also contains other interesting chemical elements:

Zinc (Zn) 10 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis (pdb code 4qiw). 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 Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis, PDB code: 4qiw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4qiw

Go back to Magnesium Binding Sites List in 4qiw
Magnesium binding site 1 out of 4 in the Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis


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 Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:53.0
occ:1.00
 OD1 A:ASP461 1.8 0.8 1.0
OD1 A:ASP465 2.1 0.5 1.0
OD2 A:ASP465 2.2 0.7 1.0
CG A:ASP465 2.3 0.3 1.0
CG A:ASP461 2.6 0.7 1.0
OD2 A:ASP461 2.9 0.7 1.0
OD1 A:ASP463 3.0 0.4 1.0
OD2 A:ASP463 3.5 0.8 1.0
CG A:ASP463 3.6 0.6 1.0
CB A:ASP465 3.6 0.2 1.0
O A:HOH1101 4.0 64.3 1.0
CB A:ASP461 4.1 0.7 1.0
N A:ASP461 4.2 99.6 1.0
N A:ASP465 4.4 93.4 1.0
CA A:ASP465 4.5 93.1 1.0
CA A:ASP461 4.5 0.1 1.0
N A:PHE462 4.6 0.8 1.0
C A:ASP461 4.6 0.9 1.0
N A:ASP463 4.9 0.5 1.0
NH1 A:ARG426 4.9 0.5 1.0
CB A:ASP463 5.0 0.4 1.0

Magnesium binding site 2 out of 4 in 4qiw

Go back to Magnesium Binding Sites List in 4qiw
Magnesium binding site 2 out of 4 in the Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis


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 Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1004

b:58.8
occ:1.00
 OD2 A:ASP461 2.6 0.7 1.0
CB A:ASP461 2.9 0.7 1.0
CG A:ASP461 3.1 0.7 1.0
OE1 B:GLU737 3.6 0.6 1.0
CA A:ASP461 3.9 0.1 1.0
O A:HOH1101 4.1 64.3 1.0
N A:ASP461 4.1 99.6 1.0
O A:ALA460 4.3 85.7 1.0
OD1 A:ASP461 4.4 0.8 1.0
C A:ALA460 4.4 89.7 1.0
CD B:GLU737 4.8 0.2 1.0
OD2 B:ASP738 4.9 0.5 1.0
O A:ASN459 5.0 99.8 1.0

Magnesium binding site 3 out of 4 in 4qiw

Go back to Magnesium Binding Sites List in 4qiw
Magnesium binding site 3 out of 4 in the Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis


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 Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1101

b:0.1
occ:1.00
 OD1 I:ASP461 1.8 0.1 1.0
OD1 I:ASP465 1.9 0.1 1.0
OD2 I:ASP465 2.1 0.4 1.0
CG I:ASP465 2.1 1.0 1.0
CG I:ASP461 2.7 0.9 1.0
OD2 I:ASP461 3.0 0.5 1.0
OD1 I:ASP463 3.0 0.7 1.0
CB I:ASP465 3.5 0.4 1.0
OD2 I:ASP463 3.6 0.6 1.0
O I:HOH1201 3.6 78.6 1.0
CG I:ASP463 3.6 0.8 1.0
CB I:ASP461 4.1 0.2 1.0
N I:ASP461 4.1 0.8 1.0
N I:ASP465 4.3 0.3 1.0
CA I:ASP465 4.3 0.0 1.0
CA I:ASP461 4.5 0.9 1.0
N I:PHE462 4.6 0.3 1.0
C I:ASP461 4.6 0.5 1.0
NH1 I:ARG426 4.8 0.9 1.0
N I:ASP463 4.9 0.6 1.0
N I:GLY464 5.0 0.3 1.0

Magnesium binding site 4 out of 4 in 4qiw

Go back to Magnesium Binding Sites List in 4qiw
Magnesium binding site 4 out of 4 in the Crystal Structure of Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis


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 Euryarchaeal Rna Polymerase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1104

b:54.9
occ:1.00
 OD2 I:ASP461 3.2 0.5 1.0
CB I:ASP461 3.5 0.2 1.0
O I:HOH1201 3.8 78.6 1.0
CG I:ASP461 3.8 0.9 1.0
OE1 J:GLU737 4.0 0.4 1.0
CA I:ASP461 4.5 0.9 1.0
N I:ASP461 4.8 0.8 1.0
O I:ALA460 4.8 93.5 1.0
C I:ALA460 5.0 96.5 1.0

Reference:

S.-H.Jun, A.Hirata, T.Kanai, T.J.Santangelo, T.Imanaka, K.S.Murakami. The X-Ray Crystal Structure of the Euryarchaeal Rna Polymerase in An Open Clamp Configuration Nat.Commun. 2014.
Page generated: Tue Aug 20 02:00:30 2024

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