Atomistry » Magnesium » PDB 2cw0-2dkg » 2d7c
Atomistry »
  Magnesium »
    PDB 2cw0-2dkg »
      2d7c »

Magnesium in PDB 2d7c: Crystal Structure of Human RAB11 in Complex with FIP3 Rab- Binding Domain

Protein crystallography data

The structure of Crystal Structure of Human RAB11 in Complex with FIP3 Rab- Binding Domain, PDB code: 2d7c was solved by T.Shiba, H.Koga, H.W.Shin, M.Kawasaki, R.Kato, K.Nakayama, S.Wakatsuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.75
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 108.717, 120.565, 36.249, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 22.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human RAB11 in Complex with FIP3 Rab- Binding Domain (pdb code 2d7c). 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 Human RAB11 in Complex with FIP3 Rab- Binding Domain, PDB code: 2d7c:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2d7c

Go back to Magnesium Binding Sites List in 2d7c
Magnesium binding site 1 out of 2 in the Crystal Structure of Human RAB11 in Complex with FIP3 Rab- Binding Domain


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 Human RAB11 in Complex with FIP3 Rab- Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:12.0
occ:1.00
O2G A:GTP1001 2.0 9.5 1.0
O2B A:GTP1001 2.1 8.7 1.0
OG A:SER25 2.1 10.1 1.0
OG1 A:THR43 2.1 9.7 1.0
O A:HOH1031 2.2 10.8 1.0
O A:HOH1036 2.3 14.8 1.0
CB A:SER25 3.2 10.8 1.0
CB A:THR43 3.2 10.8 1.0
PG A:GTP1001 3.3 11.1 1.0
PB A:GTP1001 3.3 9.9 1.0
O3B A:GTP1001 3.5 8.6 1.0
N A:THR43 3.7 11.8 1.0
OD1 A:ASP66 3.9 11.1 1.0
N A:SER25 3.9 9.5 1.0
O A:HOH1033 4.0 15.2 1.0
O3G A:GTP1001 4.0 13.1 1.0
CA A:THR43 4.0 11.6 1.0
O2A A:GTP1001 4.0 10.1 1.0
CA A:SER25 4.1 9.5 1.0
OD2 A:ASP66 4.2 12.4 1.0
O1B A:GTP1001 4.3 10.1 1.0
O3A A:GTP1001 4.4 11.0 1.0
O1G A:GTP1001 4.4 10.9 1.0
CG2 A:THR43 4.4 10.7 1.0
CG A:ASP66 4.5 10.7 1.0
O A:LYS41 4.6 16.3 1.0
PA A:GTP1001 4.6 10.7 1.0
C A:SER42 4.7 15.2 1.0
O1A A:GTP1001 4.7 9.3 1.0
O A:HOH1038 4.8 28.8 1.0
O A:THR67 4.8 12.2 1.0
CA A:SER42 4.9 16.0 1.0

Magnesium binding site 2 out of 2 in 2d7c

Go back to Magnesium Binding Sites List in 2d7c
Magnesium binding site 2 out of 2 in the Crystal Structure of Human RAB11 in Complex with FIP3 Rab- Binding Domain


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 Human RAB11 in Complex with FIP3 Rab- Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1102

b:11.6
occ:1.00
O2G B:GTP1101 2.0 9.2 1.0
O2B B:GTP1101 2.0 10.2 1.0
OG1 B:THR43 2.1 11.3 1.0
OG B:SER25 2.1 9.3 1.0
O B:HOH1138 2.2 8.4 1.0
O B:HOH1139 2.2 11.5 1.0
CB B:SER25 3.2 10.3 1.0
CB B:THR43 3.2 13.0 1.0
PG B:GTP1101 3.2 11.0 1.0
PB B:GTP1101 3.3 9.4 1.0
O3B B:GTP1101 3.5 9.7 1.0
N B:THR43 3.7 13.7 1.0
OD1 B:ASP66 3.9 12.0 1.0
O3G B:GTP1101 3.9 11.1 1.0
N B:SER25 3.9 11.2 1.0
O B:HOH1135 4.0 15.8 1.0
CA B:THR43 4.0 12.4 1.0
CA B:SER25 4.1 10.3 1.0
O2A B:GTP1101 4.2 7.6 1.0
OD2 B:ASP66 4.2 11.6 1.0
O1B B:GTP1101 4.3 9.9 1.0
CG2 B:THR43 4.3 12.8 1.0
O3A B:GTP1101 4.3 6.8 1.0
O1G B:GTP1101 4.3 11.2 1.0
CG B:ASP66 4.5 11.8 1.0
PA B:GTP1101 4.6 9.0 1.0
O B:LYS41 4.6 16.1 1.0
C B:SER42 4.7 15.3 1.0
O1A B:GTP1101 4.8 8.2 1.0
O B:THR67 4.8 12.7 1.0
O B:HOH1137 4.8 28.7 1.0
CA B:SER42 5.0 15.3 1.0
CB B:LYS24 5.0 10.6 1.0

Reference:

T.Shiba, H.Koga, H.W.Shin, M.Kawasaki, R.Kato, K.Nakayama, S.Wakatsuki. Structural Basis For RAB11-Dependent Membrane Recruitment of A Family of RAB11-Interacting Protein 3 (FIP3)/Arfophilin-1. Proc.Natl.Acad.Sci.Usa V. 103 15416 2006.
ISSN: ISSN 0027-8424
PubMed: 17030804
DOI: 10.1073/PNAS.0605357103
Page generated: Mon Dec 14 07:20:04 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy