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Magnesium in PDB 2e6b: Crystal Structure of the Stationary Phase Survival Protein Sure From Thermus Thermophilus HB8 in Complex with Magnesium and Tungstate

Enzymatic activity of Crystal Structure of the Stationary Phase Survival Protein Sure From Thermus Thermophilus HB8 in Complex with Magnesium and Tungstate

All present enzymatic activity of Crystal Structure of the Stationary Phase Survival Protein Sure From Thermus Thermophilus HB8 in Complex with Magnesium and Tungstate:
3.1.3.5;

Protein crystallography data

The structure of Crystal Structure of the Stationary Phase Survival Protein Sure From Thermus Thermophilus HB8 in Complex with Magnesium and Tungstate, PDB code: 2e6b was solved by W.Iwasaki, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.46 / 2.50
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 132.018, 132.018, 130.824, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 23

Other elements in 2e6b:

The structure of Crystal Structure of the Stationary Phase Survival Protein Sure From Thermus Thermophilus HB8 in Complex with Magnesium and Tungstate also contains other interesting chemical elements:

Tungsten (W) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Stationary Phase Survival Protein Sure From Thermus Thermophilus HB8 in Complex with Magnesium and Tungstate (pdb code 2e6b). 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 Stationary Phase Survival Protein Sure From Thermus Thermophilus HB8 in Complex with Magnesium and Tungstate, PDB code: 2e6b:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2e6b

Go back to Magnesium Binding Sites List in 2e6b
Magnesium binding site 1 out of 4 in the Crystal Structure of the Stationary Phase Survival Protein Sure From Thermus Thermophilus HB8 in Complex with Magnesium and Tungstate


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 Stationary Phase Survival Protein Sure From Thermus Thermophilus HB8 in Complex with Magnesium and Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:38.5
occ:1.00
 O3 A:WO4302 1.9 39.4 1.0
OD1 A:ASP9 2.1 30.2 1.0
OD2 A:ASP8 2.3 32.0 1.0
OD1 A:ASN96 2.4 33.2 1.0
CG A:ASP9 3.2 33.0 1.0
CG A:ASP8 3.3 28.4 1.0
CG A:ASN96 3.5 28.1 1.0
OD1 A:ASP8 3.6 28.6 1.0
W A:WO4302 3.6 41.7 1.0
OD2 A:ASP9 3.9 36.0 1.0
ND2 A:ASN96 4.0 27.9 1.0
O A:ASP8 4.2 26.8 1.0
C A:ASP8 4.2 27.1 1.0
N A:ASP9 4.3 27.9 1.0
CA A:ASP9 4.3 29.9 1.0
CB A:ASP9 4.3 30.3 1.0
O1 A:WO4302 4.4 48.5 1.0
O4 A:WO4302 4.5 47.0 1.0
O A:HOH512 4.6 27.5 1.0
CB A:ASP8 4.6 27.3 1.0
O2 A:WO4302 4.6 49.9 1.0
OG1 A:THR110 4.7 22.4 1.0
O A:LEU97 4.8 34.4 1.0
CB A:ASN96 4.8 29.7 1.0
CA A:ASP8 4.9 27.8 1.0
N A:LEU97 4.9 30.1 1.0

Magnesium binding site 2 out of 4 in 2e6b

Go back to Magnesium Binding Sites List in 2e6b
Magnesium binding site 2 out of 4 in the Crystal Structure of the Stationary Phase Survival Protein Sure From Thermus Thermophilus HB8 in Complex with Magnesium and Tungstate


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 Stationary Phase Survival Protein Sure From Thermus Thermophilus HB8 in Complex with Magnesium and Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1301

b:51.8
occ:1.00
 OD1 B:ASP9 1.9 36.4 1.0
O3 B:WO41302 2.1 42.0 1.0
OD1 B:ASN96 2.2 35.7 1.0
OD2 B:ASP8 2.5 33.7 1.0
CG B:ASP9 3.0 39.0 1.0
CG B:ASN96 3.4 32.8 1.0
CG B:ASP8 3.5 30.6 1.0
OD2 B:ASP9 3.6 40.7 1.0
W B:WO41302 3.8 48.4 1.0
OD1 B:ASP8 3.8 29.9 1.0
ND2 B:ASN96 3.9 34.7 1.0
CB B:ASP9 4.1 36.8 1.0
CA B:ASP9 4.2 32.8 1.0
O B:ASP8 4.2 32.2 1.0
N B:ASP9 4.2 30.3 1.0
C B:ASP8 4.3 30.4 1.0
O B:HOH1417 4.3 28.8 1.0
O B:LEU97 4.4 36.7 1.0
O1 B:WO41302 4.6 41.9 1.0
CB B:ASN96 4.6 31.0 1.0
N B:LEU97 4.6 30.6 1.0
O2 B:WO41302 4.6 55.4 1.0
O4 B:WO41302 4.8 45.4 1.0
OG1 B:THR110 4.8 31.6 1.0
CB B:ASP8 4.8 33.3 1.0

Magnesium binding site 3 out of 4 in 2e6b

Go back to Magnesium Binding Sites List in 2e6b
Magnesium binding site 3 out of 4 in the Crystal Structure of the Stationary Phase Survival Protein Sure From Thermus Thermophilus HB8 in Complex with Magnesium and Tungstate


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 Stationary Phase Survival Protein Sure From Thermus Thermophilus HB8 in Complex with Magnesium and Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2301

b:49.4
occ:1.00
 O3 C:WO42302 1.8 33.5 1.0
OD1 C:ASP9 2.2 40.8 1.0
OD1 C:ASN96 2.2 41.8 1.0
OD2 C:ASP8 2.3 40.9 1.0
CG C:ASP8 3.2 39.0 1.0
CG C:ASP9 3.2 41.8 1.0
CG C:ASN96 3.2 38.3 1.0
OD1 C:ASP8 3.3 40.1 1.0
W C:WO42302 3.5 50.8 1.0
OD2 C:ASP9 3.7 43.0 1.0
ND2 C:ASN96 3.7 39.3 1.0
O C:ASP8 4.2 31.8 1.0
O C:HOH2413 4.2 28.3 1.0
C C:ASP8 4.3 33.7 1.0
O1 C:WO42302 4.3 49.6 1.0
O4 C:WO42302 4.4 49.4 1.0
N C:ASP9 4.4 34.9 1.0
CB C:ASP9 4.4 38.6 1.0
CA C:ASP9 4.4 37.6 1.0
O2 C:WO42302 4.5 54.0 1.0
OG1 C:THR110 4.5 35.3 1.0
CB C:ASN96 4.5 33.3 1.0
CB C:ASP8 4.6 38.0 1.0
N C:LEU97 4.7 38.0 1.0
O C:LEU97 4.7 41.0 1.0
CA C:ASP8 4.9 33.1 1.0

Magnesium binding site 4 out of 4 in 2e6b

Go back to Magnesium Binding Sites List in 2e6b
Magnesium binding site 4 out of 4 in the Crystal Structure of the Stationary Phase Survival Protein Sure From Thermus Thermophilus HB8 in Complex with Magnesium and Tungstate


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 Stationary Phase Survival Protein Sure From Thermus Thermophilus HB8 in Complex with Magnesium and Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3301

b:43.4
occ:1.00
 OD1 D:ASP9 2.0 33.7 1.0
O3 D:WO43302 2.1 43.3 1.0
OD1 D:ASN96 2.2 37.5 1.0
OD2 D:ASP8 2.4 34.3 1.0
CG D:ASP9 3.0 35.8 1.0
CG D:ASN96 3.3 33.8 1.0
CG D:ASP8 3.4 31.9 1.0
OD2 D:ASP9 3.5 38.3 1.0
ND2 D:ASN96 3.8 34.2 1.0
W D:WO43302 3.8 48.0 1.0
OD1 D:ASP8 3.9 33.0 1.0
CB D:ASP9 4.1 35.7 1.0
N D:ASP9 4.1 32.9 1.0
O D:HOH3410 4.1 38.1 1.0
CA D:ASP9 4.2 34.6 1.0
C D:ASP8 4.3 30.7 1.0
O D:ASP8 4.4 31.1 1.0
CB D:ASN96 4.6 30.0 1.0
O1 D:WO43302 4.6 53.8 1.0
O2 D:WO43302 4.6 56.4 1.0
O D:LEU97 4.7 37.8 1.0
N D:LEU97 4.7 33.7 1.0
O4 D:WO43302 4.7 46.9 1.0
CB D:ASP8 4.7 32.2 1.0
OG1 D:THR110 4.8 29.3 1.0
CA D:ASP8 5.0 29.9 1.0

Reference:

W.Iwasaki, K.Miki. Crystal Structure of the Stationary Phase Survival Protein Sure with Metal Ion and Amp J.Mol.Biol. V. 371 123 2007.
ISSN: ISSN 0022-2836
PubMed: 17561111
DOI: 10.1016/J.JMB.2007.05.007
Page generated: Tue Aug 13 22:39:31 2024

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