Atomistry » Magnesium » PDB 3g8d-3gn6 » 3gj8
Atomistry »
  Magnesium »
    PDB 3g8d-3gn6 »
      3gj8 »

Magnesium in PDB 3gj8: Crystal Structure of Human Rangdp-NUP153ZNF34 Complex

Protein crystallography data

The structure of Crystal Structure of Human Rangdp-NUP153ZNF34 Complex, PDB code: 3gj8 was solved by J.R.Partridge, T.U.Schwartz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.75 / 1.82
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.257, 61.713, 70.635, 90.00, 112.31, 90.00
R / Rfree (%) 17 / 20.3

Other elements in 3gj8:

The structure of Crystal Structure of Human Rangdp-NUP153ZNF34 Complex also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Rangdp-NUP153ZNF34 Complex (pdb code 3gj8). 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 Human Rangdp-NUP153ZNF34 Complex, PDB code: 3gj8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3gj8

Go back to Magnesium Binding Sites List in 3gj8
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Rangdp-NUP153ZNF34 Complex


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 Rangdp-NUP153ZNF34 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:21.1
occ:1.00
O1B A:GDP302 2.1 20.6 1.0
OG1 A:THR24 2.2 17.0 1.0
O A:HOH479 2.2 18.1 1.0
O A:HOH482 2.2 17.1 1.0
O A:HOH481 2.3 20.7 1.0
O A:HOH480 2.3 18.4 1.0
CB A:THR24 3.2 21.4 1.0
PB A:GDP302 3.3 21.0 1.0
O2B A:GDP302 3.4 21.5 1.0
N A:THR24 3.9 16.1 1.0
CA A:THR24 4.1 18.7 1.0
O2A A:GDP302 4.2 20.2 1.0
O A:THR66 4.2 20.9 1.0
OD1 A:ASP65 4.2 20.5 1.0
OD2 A:ASP65 4.2 25.0 1.0
O3B A:GDP302 4.2 19.9 1.0
OG1 A:THR66 4.3 19.3 1.0
CG2 A:THR24 4.3 20.3 1.0
OE2 A:GLU70 4.4 23.2 1.0
O3A A:GDP302 4.4 21.1 1.0
O A:HOH572 4.6 59.8 1.0
PA A:GDP302 4.6 21.0 1.0
CG A:ASP65 4.6 20.9 1.0
O1A A:GDP302 4.7 20.0 1.0
N A:GLY68 4.8 20.6 1.0
CB A:LYS23 4.9 16.6 1.0
NZ A:LYS23 4.9 24.4 1.0
C A:LYS23 5.0 18.6 1.0

Magnesium binding site 2 out of 4 in 3gj8

Go back to Magnesium Binding Sites List in 3gj8
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Rangdp-NUP153ZNF34 Complex


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 Rangdp-NUP153ZNF34 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:28.0
occ:1.00
O A:HOH322 2.8 21.8 1.0
O A:HOH354 3.1 36.7 1.0
N A:ALA181 3.2 20.1 1.0
MG C:MG303 3.2 25.9 1.0
CA A:PRO180 3.6 26.0 1.0
O C:HOH483 3.6 33.4 1.0
CB A:PRO180 3.7 33.1 1.0
C A:PRO180 3.9 18.6 1.0
CB A:ALA181 4.1 16.2 1.0
CE1 A:HIS30 4.2 25.7 1.0
OG1 A:THR32 4.2 25.3 1.0
CA A:ALA181 4.2 21.0 1.0
NE2 A:HIS30 4.3 17.2 1.0
O A:HOH376 4.4 37.7 1.0
CB C:ALA181 4.4 18.0 1.0
O A:ALA181 4.6 17.8 1.0
O A:VAL51 4.8 17.6 1.0
CB A:THR32 4.8 26.1 1.0
N C:ALA181 4.9 20.8 1.0
OG1 C:THR32 4.9 25.4 1.0
CG A:PRO180 4.9 36.6 1.0
C A:ALA181 4.9 20.0 1.0
N A:PRO180 5.0 23.2 1.0
O C:HOH243 5.0 23.6 1.0

Magnesium binding site 3 out of 4 in 3gj8

Go back to Magnesium Binding Sites List in 3gj8
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Rangdp-NUP153ZNF34 Complex


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 Human Rangdp-NUP153ZNF34 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:25.9
occ:1.00
O C:HOH243 2.9 23.6 1.0
O C:HOH341 3.1 50.5 1.0
N C:ALA181 3.2 20.8 1.0
MG A:MG303 3.2 28.0 1.0
O C:HOH345 3.2 35.6 1.0
O A:HOH376 3.6 37.7 1.0
CA C:PRO180 3.6 25.5 1.0
CB C:PRO180 3.7 28.3 1.0
C C:PRO180 3.9 19.8 1.0
CB C:ALA181 4.1 18.0 1.0
CE1 C:HIS30 4.2 24.8 1.0
CA C:ALA181 4.2 22.2 1.0
OG1 C:THR32 4.2 25.4 1.0
NE2 C:HIS30 4.3 16.8 1.0
O C:HOH483 4.4 33.4 1.0
CB A:ALA181 4.4 16.2 1.0
O C:ALA181 4.7 16.8 1.0
O C:VAL51 4.8 18.5 1.0
CB C:THR32 4.8 25.4 1.0
N A:ALA181 4.8 20.1 1.0
OG1 A:THR32 4.9 25.3 1.0
O A:HOH322 4.9 21.8 1.0
C C:ALA181 5.0 21.1 1.0
CG C:PRO180 5.0 30.7 1.0
ND1 C:HIS30 5.0 18.5 1.0

Magnesium binding site 4 out of 4 in 3gj8

Go back to Magnesium Binding Sites List in 3gj8
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Rangdp-NUP153ZNF34 Complex


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 Human Rangdp-NUP153ZNF34 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:21.3
occ:1.00
OG1 C:THR24 2.2 16.9 1.0
O1B C:GDP302 2.2 20.5 1.0
O C:HOH475 2.2 18.3 1.0
O C:HOH476 2.3 18.2 1.0
O C:HOH478 2.3 19.7 1.0
O C:HOH477 2.3 19.1 1.0
CB C:THR24 3.2 21.9 1.0
PB C:GDP302 3.4 21.8 1.0
O2B C:GDP302 3.5 21.1 1.0
N C:THR24 3.9 17.1 1.0
CA C:THR24 4.1 20.1 1.0
OD2 C:ASP65 4.1 24.0 1.0
OD1 C:ASP65 4.2 22.4 1.0
O C:THR66 4.2 23.0 1.0
O2A C:GDP302 4.2 18.1 1.0
OG1 C:THR66 4.2 21.7 1.0
CG2 C:THR24 4.3 20.5 1.0
O3B C:GDP302 4.3 19.3 1.0
OE2 C:GLU70 4.4 23.5 1.0
O3A C:GDP302 4.5 22.0 1.0
CG C:ASP65 4.6 21.9 1.0
PA C:GDP302 4.7 20.8 1.0
N C:GLY68 4.8 24.1 1.0
O1A C:GDP302 4.8 20.5 1.0
CB C:LYS23 4.9 15.8 1.0
C C:THR66 4.9 22.6 1.0
NZ C:LYS23 5.0 24.8 1.0

Reference:

J.R.Partridge, T.U.Schwartz. Crystallographic and Biochemical Analysis of the Ran-Binding Zinc Finger Domain. J.Mol.Biol. V. 391 375 2009.
ISSN: ISSN 0022-2836
PubMed: 19505478
DOI: 10.1016/J.JMB.2009.06.011
Page generated: Wed Aug 14 14:48:28 2024

Last articles

Mg in 4Y52
Mg in 4Y30
Mg in 4Y2V
Mg in 4Y2X
Mg in 4Y2Y
Mg in 4Y2U
Mg in 4Y2T
Mg in 4Y2Q
Mg in 4Y2R
Mg in 4Y2S
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy