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Magnesium in PDB 1k5g: Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex

Protein crystallography data

The structure of Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex, PDB code: 1k5g was solved by M.J.Seewald, C.Koerner, A.Wittinghofer, I.R.Vetter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.00 / 3.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 99.930, 102.568, 118.850, 71.67, 79.09, 67.81
R / Rfree (%) 25 / 26.9

Other elements in 1k5g:

The structure of Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Aluminium (Al) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap Complex (pdb code 1k5g). 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 Ran-Gdp-Alfx-RANBP1-Rangap Complex, PDB code: 1k5g:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1k5g

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Magnesium binding site 1 out of 4 in the Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap 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 Ran-Gdp-Alfx-RANBP1-Rangap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1251

b:31.7
occ:1.00
O2B A:GDP1250 1.8 43.3 1.0
OG1 A:THR42 2.3 33.6 1.0
F1 A:AF31252 2.6 57.3 1.0
F3 A:AF31252 2.9 57.5 1.0
OG1 A:THR24 2.9 45.2 1.0
PB A:GDP1250 3.0 43.3 1.0
CB A:THR42 3.1 33.6 1.0
AL A:AF31252 3.2 57.4 1.0
O1B A:GDP1250 3.4 43.3 1.0
N A:THR42 3.7 34.6 1.0
O3B A:GDP1250 3.7 43.3 1.0
CG2 A:THR24 3.8 45.2 1.0
CB A:THR24 3.9 45.2 1.0
OD1 A:ASP65 4.0 28.8 1.0
CA A:THR42 4.0 34.6 1.0
O A:THR66 4.2 38.6 1.0
N A:THR24 4.2 36.8 1.0
CG2 A:THR42 4.2 33.6 1.0
O3A A:GDP1250 4.3 43.3 1.0
O2A A:GDP1250 4.4 43.3 1.0
CE A:LYS23 4.4 30.1 1.0
CB A:LYS23 4.7 30.1 1.0
PA A:GDP1250 4.7 43.3 1.0
CA A:THR24 4.7 36.8 1.0
C A:ALA41 4.8 24.4 1.0
NZ A:LYS23 4.8 30.1 1.0
O1A A:GDP1250 4.8 43.3 1.0
F2 A:AF31252 4.8 57.7 1.0
CG A:ASP65 4.9 28.8 1.0
OD2 A:ASP65 4.9 28.8 1.0
O A:VAL40 4.9 26.0 1.0
CA A:ALA41 5.0 24.4 1.0

Magnesium binding site 2 out of 4 in 1k5g

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Magnesium binding site 2 out of 4 in the Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap 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 Ran-Gdp-Alfx-RANBP1-Rangap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2251

b:45.2
occ:1.00
O2B D:GDP2250 1.7 32.0 1.0
F1 D:AF32252 2.0 57.3 1.0
OG1 D:THR42 2.3 2.1 1.0
OG1 D:THR24 2.9 24.1 1.0
PB D:GDP2250 3.0 32.0 1.0
AL D:AF32252 3.1 57.4 1.0
CB D:THR42 3.1 2.1 1.0
F3 D:AF32252 3.2 57.5 1.0
O1B D:GDP2250 3.4 32.0 1.0
O3B D:GDP2250 3.7 32.0 1.0
N D:THR42 3.7 25.1 1.0
CG2 D:THR24 3.8 24.1 1.0
CB D:THR24 3.9 24.1 1.0
OD1 D:ASP65 4.0 42.0 1.0
CA D:THR42 4.0 25.1 1.0
N D:THR24 4.2 31.9 1.0
O3A D:GDP2250 4.3 32.0 1.0
CG2 D:THR42 4.3 2.1 1.0
O D:THR66 4.3 23.3 1.0
O2A D:GDP2250 4.3 32.0 1.0
CE D:LYS23 4.4 26.3 1.0
PA D:GDP2250 4.6 32.0 1.0
CA D:THR24 4.7 31.9 1.0
F2 D:AF32252 4.7 57.7 1.0
CB D:LYS23 4.7 26.3 1.0
O1A D:GDP2250 4.7 32.0 1.0
C D:ALA41 4.7 27.9 1.0
NZ D:LYS23 4.8 26.3 1.0
CG D:ASP65 4.8 42.0 1.0
OD2 D:ASP65 4.9 42.0 1.0
O D:VAL40 4.9 19.9 1.0
CA D:ALA41 5.0 27.9 1.0

Magnesium binding site 3 out of 4 in 1k5g

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Magnesium binding site 3 out of 4 in the Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap 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 Ran-Gdp-Alfx-RANBP1-Rangap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg3251

b:44.9
occ:1.00
O2B G:GDP3250 1.8 35.4 1.0
OG1 G:THR42 2.3 46.2 1.0
F3 G:AF33252 2.8 57.5 1.0
F1 G:AF33252 2.9 57.3 1.0
OG1 G:THR24 2.9 27.7 1.0
PB G:GDP3250 3.0 35.4 1.0
AL G:AF33252 3.0 57.4 1.0
CB G:THR42 3.1 46.2 1.0
O1B G:GDP3250 3.4 35.4 1.0
N G:THR42 3.6 40.0 1.0
O3B G:GDP3250 3.7 35.4 1.0
CG2 G:THR24 3.8 27.7 1.0
CB G:THR24 3.9 27.7 1.0
CA G:THR42 4.0 40.0 1.0
OD1 G:ASP65 4.0 39.1 1.0
N G:THR24 4.2 39.5 1.0
CG2 G:THR42 4.3 46.2 1.0
O G:THR66 4.3 29.3 1.0
O3A G:GDP3250 4.3 35.4 1.0
O2A G:GDP3250 4.3 35.4 1.0
F2 G:AF33252 4.4 57.7 1.0
CE G:LYS23 4.4 26.7 1.0
PA G:GDP3250 4.6 35.4 1.0
C G:ALA41 4.7 14.8 1.0
CA G:THR24 4.7 39.5 1.0
CB G:LYS23 4.7 26.7 1.0
O1A G:GDP3250 4.7 35.4 1.0
NZ G:LYS23 4.9 26.7 1.0
O G:VAL40 4.9 17.6 1.0
CG G:ASP65 4.9 39.1 1.0
OD2 G:ASP65 4.9 39.1 1.0
CA G:ALA41 4.9 14.8 1.0

Magnesium binding site 4 out of 4 in 1k5g

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Magnesium binding site 4 out of 4 in the Crystal Structure of Ran-Gdp-Alfx-RANBP1-Rangap 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 Ran-Gdp-Alfx-RANBP1-Rangap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg4251

b:33.0
occ:1.00
O2B J:GDP4250 1.7 29.1 1.0
F1 J:AF34252 2.3 57.3 1.0
OG1 J:THR42 2.4 20.4 1.0
OG1 J:THR24 2.9 34.8 1.0
PB J:GDP4250 2.9 29.1 1.0
AL J:AF34252 3.0 57.4 1.0
F3 J:AF34252 3.0 57.5 1.0
CB J:THR42 3.2 20.4 1.0
O1B J:GDP4250 3.4 29.1 1.0
O3B J:GDP4250 3.6 29.1 1.0
N J:THR42 3.7 14.9 1.0
CG2 J:THR24 3.8 34.8 1.0
CB J:THR24 3.9 34.8 1.0
CA J:THR42 4.1 14.9 1.0
OD1 J:ASP65 4.1 27.7 1.0
N J:THR24 4.2 37.9 1.0
O3A J:GDP4250 4.2 29.1 1.0
O J:THR66 4.3 28.0 1.0
O2A J:GDP4250 4.3 29.1 1.0
CG2 J:THR42 4.4 20.4 1.0
CE J:LYS23 4.4 28.9 1.0
F2 J:AF34252 4.4 57.7 1.0
PA J:GDP4250 4.6 29.1 1.0
O1A J:GDP4250 4.7 29.1 1.0
CB J:LYS23 4.7 28.9 1.0
CA J:THR24 4.7 37.9 1.0
C J:ALA41 4.7 12.5 1.0
NZ J:LYS23 4.8 28.9 1.0
O J:VAL40 4.9 14.4 1.0
CG J:ASP65 4.9 27.7 1.0
CA J:ALA41 4.9 12.5 1.0
OD2 J:ASP65 5.0 27.7 1.0

Reference:

M.J.Seewald, C.Korner, A.Wittinghofer, I.R.Vetter. Rangap Mediates Gtp Hydrolysis Without An Arginine Finger. Nature V. 415 662 2002.
ISSN: ISSN 0028-0836
PubMed: 11832950
DOI: 10.1038/415662A
Page generated: Mon Dec 14 06:12:51 2020

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