Atomistry » Magnesium » PDB 6mlq-6mxc » 6mqk
Atomistry »
  Magnesium »
    PDB 6mlq-6mxc »
      6mqk »

Magnesium in PDB 6mqk: Crystal Structure of Gtpase Domain of Human Septin 12 in Complex with Gdp

Protein crystallography data

The structure of Crystal Structure of Gtpase Domain of Human Septin 12 in Complex with Gdp, PDB code: 6mqk was solved by D.K.S.V.Castro, H.M.Pereira, J.Brandao-Neto, A.P.U.Ulian, R.C.Garratt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.59 / 2.19
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.960, 69.250, 88.230, 75.45, 89.46, 76.43
R / Rfree (%) 18.4 / 22.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Gtpase Domain of Human Septin 12 in Complex with Gdp (pdb code 6mqk). 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 Gtpase Domain of Human Septin 12 in Complex with Gdp, PDB code: 6mqk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6mqk

Go back to Magnesium Binding Sites List in 6mqk
Magnesium binding site 1 out of 4 in the Crystal Structure of Gtpase Domain of Human Septin 12 in Complex with Gdp


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 Gtpase Domain of Human Septin 12 in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:44.4
occ:1.00
OG A:SER63 2.0 40.0 1.0
O1B A:GDP401 2.0 40.6 1.0
O A:HOH506 2.1 36.6 1.0
O A:HOH508 2.1 47.1 1.0
O A:HOH516 2.4 35.8 1.0
OG1 A:THR89 2.5 84.0 1.0
CG2 A:THR89 3.1 85.2 1.0
CB A:SER63 3.1 37.6 1.0
CB A:THR89 3.3 85.5 1.0
PB A:GDP401 3.5 39.2 1.0
N A:THR89 3.6 84.7 1.0
OD2 A:ASP112 3.8 47.6 1.0
O3B A:GDP401 3.8 37.3 1.0
N A:SER63 3.9 35.6 1.0
CA A:SER63 4.1 36.3 1.0
O A:PRO87 4.1 85.6 1.0
CA A:THR89 4.1 86.5 1.0
O2A A:GDP401 4.2 38.0 1.0
O2B A:GDP401 4.2 41.3 1.0
OD1 A:ASP112 4.2 49.8 1.0
CG A:ASP112 4.4 48.0 1.0
O3A A:GDP401 4.6 41.7 1.0
C A:GLN88 4.7 85.5 1.0
O A:THR113 4.8 53.0 1.0
PA A:GDP401 4.8 43.1 1.0
CA A:GLN88 4.9 85.8 1.0
NZ A:LYS62 5.0 36.6 1.0
O1A A:GDP401 5.0 45.7 1.0

Magnesium binding site 2 out of 4 in 6mqk

Go back to Magnesium Binding Sites List in 6mqk
Magnesium binding site 2 out of 4 in the Crystal Structure of Gtpase Domain of Human Septin 12 in Complex with Gdp


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 Gtpase Domain of Human Septin 12 in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:33.3
occ:1.00
O1B B:GDP401 2.0 29.8 1.0
OG B:SER63 2.0 49.7 1.0
O B:HOH509 2.1 33.1 1.0
O B:HOH517 2.1 33.7 1.0
OG1 B:THR89 2.1 56.6 1.0
O B:HOH513 2.1 38.5 1.0
CB B:SER63 3.2 41.9 1.0
CB B:THR89 3.2 55.6 1.0
PB B:GDP401 3.3 38.6 1.0
O2B B:GDP401 3.5 33.4 1.0
N B:THR89 3.8 61.2 1.0
N B:SER63 3.8 36.5 1.0
OD2 B:ASP112 3.9 42.5 1.0
O2A B:GDP401 4.0 35.8 1.0
O B:HOH520 4.0 42.6 1.0
CA B:SER63 4.0 38.1 1.0
OD1 B:ASP112 4.1 42.8 1.0
CA B:THR89 4.1 57.5 1.0
O B:PRO87 4.2 70.2 1.0
O3B B:GDP401 4.2 28.5 1.0
CG2 B:THR89 4.3 50.5 1.0
O3A B:GDP401 4.4 38.0 1.0
CG B:ASP112 4.4 41.2 1.0
PA B:GDP401 4.6 39.2 1.0
C B:GLN88 4.8 62.9 1.0
O1A B:GDP401 4.8 35.1 1.0
O B:THR113 4.8 39.0 1.0
C B:LYS62 4.9 36.0 1.0
CB B:LYS62 5.0 33.7 1.0
NZ B:LYS62 5.0 41.8 1.0

Magnesium binding site 3 out of 4 in 6mqk

Go back to Magnesium Binding Sites List in 6mqk
Magnesium binding site 3 out of 4 in the Crystal Structure of Gtpase Domain of Human Septin 12 in Complex with Gdp


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 Gtpase Domain of Human Septin 12 in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:47.8
occ:1.00
O C:HOH514 2.0 38.7 1.0
OG1 C:THR89 2.1 85.5 1.0
O C:HOH518 2.2 41.5 1.0
O C:HOH512 2.2 36.5 1.0
OG C:SER63 2.3 39.3 1.0
O3B C:GDP401 2.6 38.5 1.0
CB C:THR89 3.0 88.1 1.0
N C:THR89 3.2 95.3 1.0
CB C:SER63 3.6 38.0 1.0
O1B C:GDP401 3.7 39.9 1.0
CA C:THR89 3.7 92.4 1.0
PB C:GDP401 3.7 37.4 1.0
O C:PRO87 4.0 95.9 1.0
OD2 C:ASP112 4.0 40.6 1.0
CG2 C:THR89 4.2 87.0 1.0
C C:GLN88 4.3 98.2 1.0
OD1 C:ASP112 4.3 39.1 1.0
N C:SER63 4.3 33.2 1.0
O2A C:GDP401 4.4 34.5 1.0
CA C:GLN88 4.5 98.4 1.0
CG C:ASP112 4.5 40.0 1.0
CA C:SER63 4.5 37.1 1.0
O2B C:GDP401 4.6 34.3 1.0
O C:THR113 4.7 53.2 1.0
C C:THR89 4.9 93.5 1.0
O3A C:GDP401 5.0 40.1 1.0

Magnesium binding site 4 out of 4 in 6mqk

Go back to Magnesium Binding Sites List in 6mqk
Magnesium binding site 4 out of 4 in the Crystal Structure of Gtpase Domain of Human Septin 12 in Complex with Gdp


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 Gtpase Domain of Human Septin 12 in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:42.7
occ:1.00
O D:HOH517 2.0 47.0 1.0
O D:HOH522 2.0 35.8 1.0
OG D:SER63 2.1 40.4 1.0
O D:HOH506 2.3 40.9 1.0
O3B D:GDP401 2.3 36.8 1.0
CB D:SER63 3.1 37.6 1.0
PB D:GDP401 3.5 33.5 1.0
O1B D:GDP401 3.5 34.3 1.0
OD2 D:ASP112 4.0 44.4 1.0
N D:SER63 4.0 34.7 1.0
O2A D:GDP401 4.0 34.3 1.0
O D:THR86 4.1 67.2 1.0
CA D:SER63 4.2 37.9 1.0
O D:PRO87 4.3 60.4 1.0
OD1 D:ASP112 4.5 41.6 1.0
O3A D:GDP401 4.5 35.5 1.0
O2B D:GDP401 4.5 27.9 1.0
PA D:GDP401 4.5 37.0 1.0
CG2 D:THR86 4.6 69.8 1.0
CG D:ASP112 4.6 43.7 1.0
O1A D:GDP401 4.7 35.8 1.0
NE2 A:HIS170 4.8 43.6 1.0
CB D:THR86 4.8 69.1 1.0
O D:HOH541 4.9 45.7 1.0
C D:PRO87 4.9 66.0 1.0
CE1 A:HIS170 4.9 44.5 1.0
C D:THR86 5.0 68.4 1.0

Reference:

D.K.S.V.Castro, H.M.Pereira, J.Brandao-Neto, A.P.U.Ulian, R.C.Garratt. Crystal Structure of Gtpase Domain of Human Septin 12 To Be Published.
Page generated: Tue Oct 1 11:56:55 2024

Last articles

Na in 5ICF
Na in 5IBC
Na in 5IAJ
Na in 5IAR
Na in 5IAK
Na in 5IAN
Na in 5IAS
Na in 5IBW
Na in 5I8F
Na in 5I96
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy