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Magnesium in PDB 7e1t: Crystal Structure of RAB9A-Gtp-NDE1

Protein crystallography data

The structure of Crystal Structure of RAB9A-Gtp-NDE1, PDB code: 7e1t was solved by Y.Zhang, T.Zhang, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.75 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.421, 67.646, 118.516, 90, 90, 90
R / Rfree (%) 19.4 / 24.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of RAB9A-Gtp-NDE1 (pdb code 7e1t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of RAB9A-Gtp-NDE1, PDB code: 7e1t:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7e1t

Go back to Magnesium Binding Sites List in 7e1t
Magnesium binding site 1 out of 2 in the Crystal Structure of RAB9A-Gtp-NDE1


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 RAB9A-Gtp-NDE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:25.4
occ:1.00
OG1 A:THR39 2.2 25.0 1.0
O2B A:GTP302 2.2 28.5 1.0
O A:HOH415 2.2 24.6 1.0
OG A:SER21 2.2 21.9 1.0
O3G A:GTP302 2.3 26.3 1.0
O A:HOH406 2.5 23.1 1.0
CB A:SER21 3.1 20.5 1.0
CB A:THR39 3.2 25.3 1.0
PG A:GTP302 3.5 29.3 1.0
PB A:GTP302 3.6 31.3 1.0
N A:THR39 3.6 28.2 1.0
OD2 A:ASP62 3.9 19.5 1.0
O3B A:GTP302 3.9 30.4 1.0
N A:SER21 4.0 21.0 1.0
CA A:THR39 4.0 27.9 1.0
O2G A:GTP302 4.0 25.4 1.0
CA A:SER21 4.1 21.1 1.0
O A:HOH418 4.1 34.1 1.0
O2A A:GTP302 4.1 30.3 1.0
OD1 A:ASP62 4.2 20.3 1.0
CG2 A:THR39 4.4 23.7 1.0
CG A:ASP62 4.5 18.3 1.0
O A:PHE37 4.5 34.0 1.0
O1B A:GTP302 4.6 23.3 1.0
O1A A:GTP302 4.6 27.4 1.0
C A:HIS38 4.6 30.7 1.0
O3A A:GTP302 4.6 28.6 1.0
PA A:GTP302 4.6 31.2 1.0
O A:THR63 4.7 27.4 1.0
O1G A:GTP302 4.8 27.1 1.0
CA A:HIS38 4.9 31.8 1.0
O A:HOH462 4.9 35.5 1.0

Magnesium binding site 2 out of 2 in 7e1t

Go back to Magnesium Binding Sites List in 7e1t
Magnesium binding site 2 out of 2 in the Crystal Structure of RAB9A-Gtp-NDE1


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 RAB9A-Gtp-NDE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:34.8
occ:1.00
O1B B:GTP302 2.2 31.8 1.0
O B:HOH401 2.2 33.0 1.0
OG1 B:THR39 2.2 30.4 1.0
O3G B:GTP302 2.2 30.3 1.0
OG B:SER21 2.3 24.4 1.0
O B:HOH411 2.4 28.6 1.0
CB B:SER21 3.1 24.4 1.0
CB B:THR39 3.2 30.1 1.0
PG B:GTP302 3.5 31.8 1.0
PB B:GTP302 3.5 29.7 1.0
N B:THR39 3.7 30.0 1.0
N B:SER21 3.7 26.2 1.0
O3B B:GTP302 3.8 35.7 1.0
OD2 B:ASP62 3.9 25.1 1.0
CA B:SER21 3.9 24.6 1.0
O2A B:GTP302 4.0 39.8 1.0
OD1 B:ASP62 4.0 26.2 1.0
O1G B:GTP302 4.1 28.6 1.0
CA B:THR39 4.1 28.8 1.0
O B:HOH407 4.2 27.1 1.0
CG B:ASP62 4.3 24.2 1.0
O1A B:GTP302 4.4 33.3 1.0
CG2 B:THR39 4.4 27.9 1.0
O B:THR63 4.4 27.2 1.0
PA B:GTP302 4.5 38.7 1.0
O3A B:GTP302 4.5 34.5 1.0
O2B B:GTP302 4.6 30.8 1.0
C B:HIS38 4.8 32.5 1.0
O2G B:GTP302 4.8 35.6 1.0
O B:PHE37 4.8 31.6 1.0
C B:LYS20 4.8 25.2 1.0
CB B:LYS20 4.8 24.4 1.0
O B:HOH402 4.9 26.3 1.0

Reference:

T.Zhang, J.Ding. Crystal Structure of RAB9A-Gtp-NDE1 To Be Published.
Page generated: Wed Oct 2 20:30:40 2024

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