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Magnesium in PDB 5opd: Structure of Phosphorylated Ef-Tu in Complex with Gtp

Protein crystallography data

The structure of Structure of Phosphorylated Ef-Tu in Complex with Gtp, PDB code: 5opd was solved by A.Garcia-Pino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.37 / 2.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.840, 61.880, 65.480, 70.37, 75.83, 89.41
R / Rfree (%) 18.1 / 25.8

Other elements in 5opd:

The structure of Structure of Phosphorylated Ef-Tu in Complex with Gtp also contains other interesting chemical elements:

Iodine (I) 28 atoms
Sodium (Na) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Phosphorylated Ef-Tu in Complex with Gtp (pdb code 5opd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Phosphorylated Ef-Tu in Complex with Gtp, PDB code: 5opd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5opd

Go back to Magnesium Binding Sites List in 5opd
Magnesium binding site 1 out of 2 in the Structure of Phosphorylated Ef-Tu in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Phosphorylated Ef-Tu in Complex with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg515

b:9.3
occ:1.00
OG1 A:THR26 2.2 30.3 1.0
O A:HOH615 2.3 5.9 0.5
O1B A:GTP516 2.3 20.1 1.0
O A:HOH603 2.5 3.0 0.5
O A:HOH618 2.9 20.1 1.0
O1G A:GTP516 3.2 23.1 0.5
CB A:THR26 3.6 26.6 1.0
PB A:GTP516 3.6 19.7 1.0
O3B A:GTP516 3.9 23.9 1.0
OD1 A:ASP51 3.9 59.8 1.0
O A:CYS82 4.0 20.9 1.0
CA A:PRO83 4.0 17.6 1.0
PG A:GTP516 4.1 23.8 0.5
O A:PRO83 4.2 18.6 1.0
OD2 A:ASP81 4.2 38.8 1.0
CG2 A:THR26 4.3 23.8 1.0
N A:THR26 4.4 15.0 1.0
O2B A:GTP516 4.5 15.3 1.0
C A:PRO83 4.5 18.5 1.0
C A:CYS82 4.6 22.2 1.0
CA A:THR26 4.6 15.5 1.0
N A:PRO83 4.7 18.0 1.0
O2A A:GTP516 4.7 19.5 1.0
O3A A:GTP516 4.7 19.7 1.0
O3G A:GTP516 4.8 25.0 0.5
O A:HOH666 4.9 24.9 1.0
CG A:ASP51 4.9 59.6 1.0
CB A:PRO83 4.9 19.7 1.0

Magnesium binding site 2 out of 2 in 5opd

Go back to Magnesium Binding Sites List in 5opd
Magnesium binding site 2 out of 2 in the Structure of Phosphorylated Ef-Tu in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Phosphorylated Ef-Tu in Complex with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg515

b:3.0
occ:1.00
O1G B:GTP516 2.0 19.1 0.2
O2B B:GTP516 2.4 13.8 1.0
OG1 B:THR26 2.4 8.3 1.0
O2G B:GTP516 2.6 20.4 0.2
PG B:GTP516 2.6 19.7 0.2
O B:HOH645 3.1 17.9 1.0
O3B B:GTP516 3.2 18.2 1.0
PB B:GTP516 3.4 14.7 1.0
O B:CYS82 3.6 20.6 1.0
CB B:THR26 3.7 10.0 1.0
NZ B:LYS25 4.0 21.0 1.0
O B:PRO83 4.0 20.6 1.0
O3G B:GTP516 4.0 20.0 0.2
CA B:PRO83 4.1 17.1 1.0
N B:THR26 4.1 7.0 1.0
OD2 B:ASP81 4.2 34.9 1.0
OD1 B:ASP51 4.3 44.2 1.0
O1B B:GTP516 4.4 12.7 1.0
CA B:THR26 4.4 7.2 1.0
C B:CYS82 4.5 21.6 1.0
O3A B:GTP516 4.5 14.5 1.0
OD1 B:ASP81 4.5 31.8 1.0
C B:PRO83 4.5 20.1 1.0
CB B:LYS25 4.6 7.3 1.0
N B:PRO83 4.7 17.5 1.0
O B:HOH611 4.7 60.0 1.0
CG2 B:THR26 4.7 8.3 1.0
CG B:ASP81 4.8 30.0 1.0
CE B:LYS25 4.8 8.1 1.0
O2A B:GTP516 4.9 13.5 1.0

Reference:

A.Garcia-Pino, A.Garcia-Pino. N/A N/A.
Page generated: Mon Dec 14 21:00:39 2020

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