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Magnesium in PDB 4yqf: Gtpase Domain of Human Septin 9

Protein crystallography data

The structure of Gtpase Domain of Human Septin 9, PDB code: 4yqf was solved by S.O.Matos, D.A.Leonardo, J.N.Macedo, H.M.Pereira, A.P.U.Araujo, R.C.Garratt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.73 / 2.73
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.040, 77.523, 77.909, 90.00, 105.81, 90.00
R / Rfree (%) 20.8 / 24.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Gtpase Domain of Human Septin 9 (pdb code 4yqf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Gtpase Domain of Human Septin 9, PDB code: 4yqf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4yqf

Go back to Magnesium Binding Sites List in 4yqf
Magnesium binding site 1 out of 2 in the Gtpase Domain of Human Septin 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gtpase Domain of Human Septin 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:21.7
occ:1.00
OG B:SER37 2.0 33.0 1.0
O B:HOH442 2.0 43.9 1.0
OG1 B:THR64 2.2 34.7 1.0
O B:HOH441 2.2 32.6 1.0
O1B B:GDP301 2.6 28.7 1.0
O3B B:GDP301 2.8 28.7 1.0
CB B:THR64 3.1 35.1 1.0
CB B:SER37 3.2 33.5 1.0
PB B:GDP301 3.3 28.7 1.0
N B:THR64 3.5 39.7 1.0
CA B:THR64 3.9 38.1 1.0
N B:SER37 4.1 31.0 1.0
O2A B:GDP301 4.1 28.7 1.0
OD2 B:ASP87 4.2 42.0 1.0
OD1 B:ASP87 4.2 40.1 1.0
CA B:SER37 4.2 31.6 1.0
O2B B:GDP301 4.2 28.7 1.0
O B:PRO62 4.3 51.6 1.0
CG2 B:THR64 4.4 34.2 1.0
O3A B:GDP301 4.5 28.7 1.0
C B:LYS63 4.6 42.8 1.0
CG B:ASP87 4.6 40.5 1.0
PA B:GDP301 4.7 28.7 1.0
CA B:LYS63 4.8 44.6 1.0
O1A B:GDP301 4.9 28.7 1.0
NE2 A:HIS145 4.9 41.5 1.0
O B:THR88 5.0 37.8 1.0

Magnesium binding site 2 out of 2 in 4yqf

Go back to Magnesium Binding Sites List in 4yqf
Magnesium binding site 2 out of 2 in the Gtpase Domain of Human Septin 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Gtpase Domain of Human Septin 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:15.3
occ:1.00
O A:HOH438 2.0 30.6 1.0
O A:HOH437 2.1 12.2 1.0
OG A:SER37 2.2 24.4 1.0
O A:HOH439 2.2 20.6 1.0
O2B A:GDP301 2.3 19.3 1.0
OG1 A:THR64 2.3 28.3 1.0
CB A:THR64 3.0 27.8 1.0
O1B A:GDP301 3.4 19.3 1.0
PB A:GDP301 3.4 19.3 1.0
CB A:SER37 3.4 24.8 1.0
N A:THR64 3.5 28.4 1.0
O A:HOH436 3.7 26.7 1.0
CA A:THR64 3.9 28.9 1.0
OD1 A:ASP87 3.9 28.6 1.0
OD2 A:ASP87 4.1 29.2 1.0
O A:HOH410 4.1 22.6 1.0
N A:SER37 4.2 23.1 1.0
O1A A:GDP301 4.2 19.3 1.0
CG2 A:THR64 4.3 28.2 1.0
O3B A:GDP301 4.3 19.3 1.0
CA A:SER37 4.3 24.0 1.0
O A:PRO62 4.4 48.6 1.0
CG A:ASP87 4.4 29.4 1.0
O3A A:GDP301 4.5 19.3 1.0
C A:LYS63 4.6 46.3 1.0
O A:THR88 4.7 23.2 1.0
PA A:GDP301 4.7 19.3 1.0
CA A:LYS63 4.8 45.7 1.0
O2A A:GDP301 4.8 19.3 1.0
NZ A:LYS36 5.0 21.8 1.0

Reference:

S.O.Matos, D.A.Leonardo, J.N.Macedo, H.M.Pereira, A.P.U.Araujo, R.C.Garratt. Gtpase Domain of Human Septin 9 To Be Published.
Page generated: Mon Dec 14 19:55:21 2020

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