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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: Mon Dec 14 08:11:32 2020

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