Atomistry » Magnesium » PDB 6d9m-6dlu » 6def
Atomistry »
  Magnesium »
    PDB 6d9m-6dlu »
      6def »

Magnesium in PDB 6def: VPS1 Gtpase-Bse Fusion Complexed with Gmppcp

Protein crystallography data

The structure of VPS1 Gtpase-Bse Fusion Complexed with Gmppcp, PDB code: 6def was solved by M.G.J.Ford, N.V.Varlakhanova, T.M.Brady, J.S.Chappie, C.J.Hosford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.79 / 2.26
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.659, 118.740, 84.140, 90.00, 99.30, 90.00
R / Rfree (%) 19.3 / 22.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the VPS1 Gtpase-Bse Fusion Complexed with Gmppcp (pdb code 6def). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the VPS1 Gtpase-Bse Fusion Complexed with Gmppcp, PDB code: 6def:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6def

Go back to Magnesium Binding Sites List in 6def
Magnesium binding site 1 out of 4 in the VPS1 Gtpase-Bse Fusion Complexed with Gmppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of VPS1 Gtpase-Bse Fusion Complexed with Gmppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:28.3
occ:1.00
HOB2 A:GCP1001 1.0 33.0 1.0
O2B A:GCP1001 2.0 27.5 1.0
OG A:SER57 2.1 38.0 1.0
OG1 A:THR77 2.1 45.7 1.0
O A:HOH1111 2.1 27.7 1.0
O1G A:GCP1001 2.1 36.6 1.0
O A:HOH1130 2.2 28.8 1.0
HB A:THR77 2.9 49.7 1.0
CB A:THR77 3.0 41.4 1.0
H A:SER57 3.1 36.6 1.0
HB2 A:SER57 3.2 40.3 1.0
CB A:SER57 3.2 33.6 1.0
PG A:GCP1001 3.3 35.3 1.0
PB A:GCP1001 3.3 29.6 1.0
H A:THR77 3.3 45.1 1.0
HOA2 A:GCP1001 3.4 38.8 1.0
C3B A:GCP1001 3.5 30.9 1.0
H3B2 A:GCP1001 3.6 37.0 1.0
N A:SER57 3.7 30.5 1.0
HG21 A:THR77 3.8 51.9 1.0
HB2 A:LYS56 3.9 41.9 1.0
HB3 A:SER57 3.9 40.3 1.0
HB A:VAL76 4.0 45.1 1.0
OD2 A:ASP170 4.0 34.6 1.0
N A:THR77 4.0 37.6 1.0
CA A:SER57 4.0 29.9 1.0
CG2 A:THR77 4.0 43.2 1.0
OD1 A:ASP170 4.1 33.8 1.0
CA A:THR77 4.1 37.8 1.0
O1B A:GCP1001 4.1 33.9 1.0
HE2 A:LYS56 4.2 38.7 1.0
O A:HOH1113 4.2 31.5 1.0
O2G A:GCP1001 4.2 34.8 1.0
O2A A:GCP1001 4.3 32.3 1.0
HA A:SER57 4.3 35.9 1.0
O3A A:GCP1001 4.4 30.6 1.0
HZ2 A:LYS56 4.4 40.0 1.0
O3G A:GCP1001 4.4 38.5 1.0
CG A:ASP170 4.5 33.6 1.0
O A:LEU171 4.5 27.9 1.0
HG23 A:THR77 4.5 51.9 1.0
HOG2 A:GCP1001 4.6 41.7 1.0
H3B1 A:GCP1001 4.6 37.0 1.0
HG12 A:VAL76 4.6 45.7 1.0
HA A:THR77 4.6 45.4 1.0
O A:PRO70 4.6 33.9 1.0
HZ3 A:LYS56 4.7 40.0 1.0
HG22 A:THR77 4.7 51.9 1.0
H A:LYS56 4.8 38.0 1.0
CB A:LYS56 4.8 34.9 1.0
PA A:GCP1001 4.8 31.4 1.0
C A:LYS56 4.8 32.8 1.0
NZ A:LYS56 4.9 33.3 1.0
CB A:VAL76 4.9 37.6 1.0
CE A:LYS56 5.0 32.2 1.0
HA A:PRO172 5.0 36.6 1.0

Magnesium binding site 2 out of 4 in 6def

Go back to Magnesium Binding Sites List in 6def
Magnesium binding site 2 out of 4 in the VPS1 Gtpase-Bse Fusion Complexed with Gmppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of VPS1 Gtpase-Bse Fusion Complexed with Gmppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:21.1
occ:1.00
HOB2 B:GCP1001 1.1 31.9 1.0
O1G B:GCP1001 2.0 25.9 1.0
OG1 B:THR77 2.0 36.8 1.0
OG B:SER57 2.0 35.7 1.0
O B:HOH1112 2.1 20.7 1.0
O2B B:GCP1001 2.1 26.6 1.0
O B:HOH1167 2.2 21.6 1.0
HB B:THR77 2.9 39.0 1.0
CB B:THR77 3.0 32.5 1.0
H B:SER57 3.1 37.0 1.0
CB B:SER57 3.2 30.6 1.0
HB2 B:SER57 3.2 36.7 1.0
PG B:GCP1001 3.2 29.1 1.0
H B:THR77 3.4 39.1 1.0
PB B:GCP1001 3.4 27.5 1.0
C3B B:GCP1001 3.6 29.8 1.0
H3B2 B:GCP1001 3.7 35.7 1.0
N B:SER57 3.7 30.9 1.0
HG21 B:THR77 3.8 41.5 1.0
OD2 B:ASP170 3.8 31.1 1.0
HB2 B:LYS56 3.8 32.6 1.0
HB3 B:SER57 3.9 36.7 1.0
O B:HOH1105 3.9 31.5 1.0
OD1 B:ASP170 3.9 31.4 1.0
HB B:VAL76 4.0 42.9 1.0
CA B:SER57 4.0 30.4 1.0
CG2 B:THR77 4.0 34.6 1.0
N B:THR77 4.0 32.6 1.0
HE2 B:LYS56 4.1 31.9 1.0
CA B:THR77 4.1 32.6 1.0
O2G B:GCP1001 4.2 24.6 1.0
O1B B:GCP1001 4.2 25.1 1.0
HA B:SER57 4.2 36.4 1.0
CG B:ASP170 4.3 30.9 1.0
O2A B:GCP1001 4.3 34.9 1.0
O3G B:GCP1001 4.3 37.6 1.0
O B:LEU171 4.4 34.0 1.0
HG23 B:THR77 4.5 41.5 1.0
O3A B:GCP1001 4.5 29.5 1.0
HZ3 B:LYS56 4.6 34.9 1.0
HA B:THR77 4.6 39.1 1.0
HOG2 B:GCP1001 4.6 29.5 1.0
O B:PRO70 4.6 28.0 1.0
HG12 B:VAL76 4.6 42.3 1.0
H3B1 B:GCP1001 4.7 35.7 1.0
HZ1 B:LYS56 4.7 34.9 1.0
HOA2 B:GCP1001 4.7 41.9 1.0
HG22 B:THR77 4.7 41.5 1.0
CB B:LYS56 4.7 27.1 1.0
H B:LYS56 4.8 35.2 1.0
C B:LYS56 4.8 29.9 1.0
CB B:VAL76 4.9 35.8 1.0
PA B:GCP1001 4.9 30.0 1.0
CE B:LYS56 4.9 26.6 1.0
NZ B:LYS56 4.9 29.1 1.0

Magnesium binding site 3 out of 4 in 6def

Go back to Magnesium Binding Sites List in 6def
Magnesium binding site 3 out of 4 in the VPS1 Gtpase-Bse Fusion Complexed with Gmppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of VPS1 Gtpase-Bse Fusion Complexed with Gmppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:25.5
occ:1.00
HOB2 C:GCP1001 1.1 41.2 1.0
O1G C:GCP1001 2.0 31.4 1.0
O2B C:GCP1001 2.0 34.3 1.0
OG1 C:THR77 2.1 45.0 1.0
O C:HOH1135 2.1 28.2 1.0
OG C:SER57 2.1 42.2 1.0
O C:HOH1126 2.2 29.7 1.0
HB C:THR77 2.9 47.3 1.0
CB C:THR77 3.0 39.4 1.0
PG C:GCP1001 3.2 31.0 1.0
H C:SER57 3.2 36.9 1.0
CB C:SER57 3.2 35.4 1.0
HB2 C:SER57 3.2 42.5 1.0
H C:THR77 3.3 44.2 1.0
PB C:GCP1001 3.3 33.0 1.0
C3B C:GCP1001 3.4 32.3 1.0
H3B2 C:GCP1001 3.5 38.8 1.0
HOA2 C:GCP1001 3.5 44.0 1.0
HB C:VAL76 3.8 50.3 1.0
N C:SER57 3.9 30.7 1.0
N C:THR77 3.9 36.9 1.0
HG21 C:THR77 3.9 46.9 1.0
HB3 C:SER57 3.9 42.5 1.0
OD2 C:ASP170 3.9 39.6 1.0
HB2 C:LYS56 4.0 44.8 1.0
CA C:THR77 4.1 36.9 1.0
CG2 C:THR77 4.1 39.1 1.0
CA C:SER57 4.1 30.6 1.0
O1B C:GCP1001 4.1 32.7 1.0
OD1 C:ASP170 4.2 39.3 1.0
O2G C:GCP1001 4.2 26.5 1.0
O C:HOH1152 4.2 35.2 1.0
O2A C:GCP1001 4.2 36.7 1.0
O3G C:GCP1001 4.2 34.4 1.0
HE2 C:LYS56 4.3 47.9 1.0
HA C:SER57 4.3 36.8 1.0
O3A C:GCP1001 4.4 32.8 1.0
HOG2 C:GCP1001 4.4 31.8 1.0
CG C:ASP170 4.5 38.9 1.0
HG12 C:VAL76 4.5 49.8 1.0
HZ3 C:LYS56 4.5 50.0 1.0
O C:LEU171 4.5 33.0 1.0
H3B1 C:GCP1001 4.5 38.8 1.0
HA C:THR77 4.5 44.3 1.0
HG23 C:THR77 4.6 46.9 1.0
O C:PRO70 4.6 32.6 1.0
HZ1 C:LYS56 4.7 50.0 1.0
CB C:VAL76 4.7 41.9 1.0
HG22 C:THR77 4.8 46.9 1.0
PA C:GCP1001 4.8 32.9 1.0
H C:LYS56 4.9 42.0 1.0
NZ C:LYS56 4.9 41.6 1.0
CB C:LYS56 4.9 37.3 1.0
HA C:PRO172 4.9 45.5 1.0
CG1 C:VAL76 5.0 41.5 1.0
C C:LYS56 5.0 35.1 1.0
HG11 C:VAL76 5.0 49.8 1.0

Magnesium binding site 4 out of 4 in 6def

Go back to Magnesium Binding Sites List in 6def
Magnesium binding site 4 out of 4 in the VPS1 Gtpase-Bse Fusion Complexed with Gmppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of VPS1 Gtpase-Bse Fusion Complexed with Gmppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1002

b:22.4
occ:1.00
HOB2 D:GCP1001 1.1 32.6 1.0
O1G D:GCP1001 1.9 30.3 1.0
O D:HOH1117 2.0 26.3 1.0
OG1 D:THR77 2.1 33.0 1.0
OG D:SER57 2.1 30.1 1.0
O2B D:GCP1001 2.1 27.1 1.0
O D:HOH1129 2.2 23.7 1.0
HB D:THR77 2.9 33.7 1.0
CB D:THR77 3.1 28.1 1.0
PG D:GCP1001 3.1 29.9 1.0
H D:SER57 3.2 30.9 1.0
CB D:SER57 3.2 24.4 1.0
HB2 D:SER57 3.2 29.3 1.0
H D:THR77 3.3 33.4 1.0
PB D:GCP1001 3.3 29.6 1.0
C3B D:GCP1001 3.5 30.4 1.0
H3B2 D:GCP1001 3.6 36.5 1.0
N D:SER57 3.8 25.8 1.0
HB D:VAL76 3.9 42.2 1.0
HG21 D:THR77 3.9 37.4 1.0
OD2 D:ASP170 3.9 32.2 1.0
HB3 D:SER57 3.9 29.3 1.0
HB2 D:LYS56 3.9 36.2 1.0
N D:THR77 4.0 27.9 1.0
CA D:SER57 4.0 23.1 1.0
OD1 D:ASP170 4.0 30.6 1.0
CG2 D:THR77 4.1 31.2 1.0
CA D:THR77 4.1 26.1 1.0
O D:HOH1146 4.1 32.9 1.0
O2G D:GCP1001 4.1 28.5 1.0
HE2 D:LYS56 4.1 39.3 1.0
O3G D:GCP1001 4.2 31.8 1.0
O1B D:GCP1001 4.2 32.3 1.0
HA D:SER57 4.3 27.7 1.0
O2A D:GCP1001 4.3 25.8 1.0
HZ3 D:LYS56 4.4 38.7 1.0
CG D:ASP170 4.4 32.6 1.0
HG12 D:VAL76 4.5 42.3 1.0
O3A D:GCP1001 4.5 29.1 1.0
O D:LEU171 4.5 30.4 1.0
HOA2 D:GCP1001 4.5 30.9 1.0
HOG2 D:GCP1001 4.5 34.2 1.0
HG23 D:THR77 4.5 37.4 1.0
O D:PRO70 4.5 28.9 1.0
HZ1 D:LYS56 4.6 38.7 1.0
H3B1 D:GCP1001 4.6 36.5 1.0
HA D:THR77 4.6 31.3 1.0
CB D:VAL76 4.8 35.2 1.0
NZ D:LYS56 4.8 32.2 1.0
HG22 D:THR77 4.8 37.4 1.0
CB D:LYS56 4.8 30.2 1.0
H D:LYS56 4.9 35.8 1.0
PA D:GCP1001 4.9 27.3 1.0
C D:LYS56 4.9 28.8 1.0
HA D:PRO172 4.9 34.6 1.0
CE D:LYS56 4.9 32.7 1.0
CG1 D:VAL76 5.0 35.3 1.0

Reference:

N.V.Varlakhanova, F.J.D.Alvarez, T.M.Brady, B.A.Tornabene, C.J.Hosford, J.S.Chappie, P.Zhang, M.G.J.Ford. Structures of the Fungal Dynamin-Related Protein VPS1 Reveal A Unique, Open Helical Architecture. J. Cell Biol. V. 217 3608 2018.
ISSN: ESSN 1540-8140
PubMed: 30087125
DOI: 10.1083/JCB.201712021
Page generated: Mon Sep 30 23:07:57 2024

Last articles

Mg in 8CGZ
Mg in 8CGR
Mg in 8CGJ
Mg in 8CAH
Mg in 8CGI
Mg in 8CEP
Mg in 8CF8
Mg in 8CF1
Mg in 8CGA
Mg in 8CAZ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy