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Magnesium in PDB 5cj2: Ran Gdp Y39A Mutant Triclinic Crystal Form

Protein crystallography data

The structure of Ran Gdp Y39A Mutant Triclinic Crystal Form, PDB code: 5cj2 was solved by I.R.Vetter, S.Brucker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.58 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.190, 80.730, 91.650, 97.66, 90.00, 90.01
R / Rfree (%) 19.7 / 23.9

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Ran Gdp Y39A Mutant Triclinic Crystal Form (pdb code 5cj2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Ran Gdp Y39A Mutant Triclinic Crystal Form, PDB code: 5cj2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 5cj2

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Magnesium binding site 1 out of 12 in the Ran Gdp Y39A Mutant Triclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ran Gdp Y39A Mutant Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:23.6
occ:1.00
 O A:HOH416 2.0 22.0 1.0
OG1 A:THR24 2.0 19.4 1.0
O1B A:GDP301 2.1 19.8 1.0
O A:HOH418 2.1 20.3 1.0
O A:HOH404 2.1 24.8 1.0
O A:HOH409 2.2 23.2 1.0
CB A:THR24 3.1 21.3 1.0
PB A:GDP301 3.4 22.1 1.0
O2B A:GDP301 3.5 20.7 1.0
N A:THR24 4.0 18.8 1.0
CG2 A:THR24 4.0 20.5 1.0
CA A:THR24 4.1 18.9 1.0
OD2 A:ASP65 4.2 24.2 1.0
O A:THR66 4.2 26.5 1.0
O1A A:GDP301 4.2 21.2 1.0
OD1 A:ASP65 4.2 21.2 1.0
OE2 A:GLU70 4.3 26.3 1.0
OG1 A:THR66 4.3 27.3 1.0
O3A A:GDP301 4.4 23.0 1.0
O3B A:GDP301 4.4 26.7 1.0
CG A:ASP65 4.6 23.6 1.0
PA A:GDP301 4.6 21.1 1.0
CB A:LYS23 4.8 19.8 1.0
N A:GLY68 4.9 21.7 1.0
O2A A:GDP301 4.9 23.5 1.0
O A:HOH405 4.9 31.4 1.0
NZ A:LYS23 5.0 23.8 1.0

Magnesium binding site 2 out of 12 in 5cj2

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Magnesium binding site 2 out of 12 in the Ran Gdp Y39A Mutant Triclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ran Gdp Y39A Mutant Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:15.4
occ:1.00
 O1B B:GDP301 2.0 14.9 1.0
O B:HOH452 2.0 16.7 1.0
OG1 B:THR24 2.0 12.5 1.0
O B:HOH442 2.0 16.8 1.0
O B:HOH430 2.1 14.8 1.0
O B:HOH408 2.2 17.4 1.0
CB B:THR24 3.1 13.3 1.0
PB B:GDP301 3.3 13.8 1.0
O2B B:GDP301 3.5 14.9 1.0
N B:THR24 3.9 12.9 1.0
CA B:THR24 4.1 13.6 1.0
OD2 B:ASP65 4.2 16.6 1.0
O B:THR66 4.2 16.8 1.0
CG2 B:THR24 4.2 15.4 1.0
OD1 B:ASP65 4.2 15.2 1.0
O1A B:GDP301 4.3 15.4 1.0
OE2 B:GLU70 4.3 16.8 1.0
O3B B:GDP301 4.3 13.9 1.0
O3A B:GDP301 4.4 13.2 1.0
O B:HOH481 4.4 29.9 1.0
OG1 B:THR66 4.4 19.5 1.0
CG B:ASP65 4.6 14.9 1.0
O B:HOH478 4.6 28.8 1.0
PA B:GDP301 4.7 15.3 1.0
O2A B:GDP301 4.8 14.9 1.0
CB B:LYS23 4.9 11.7 1.0
N B:GLY68 4.9 15.8 1.0
C B:LYS23 4.9 13.2 1.0
O B:HOH402 5.0 20.9 1.0

Magnesium binding site 3 out of 12 in 5cj2

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Magnesium binding site 3 out of 12 in the Ran Gdp Y39A Mutant Triclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ran Gdp Y39A Mutant Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:26.8
occ:1.00
 O2 B:PO4304 2.0 24.5 1.0
OE2 B:GLU175 2.1 22.0 1.0
O B:HOH471 2.1 23.9 1.0
O B:HOH429 2.2 23.2 1.0
CD B:GLU175 3.0 20.9 1.0
OE1 B:GLU175 3.3 22.3 1.0
P B:PO4304 3.3 28.3 1.0
O4 B:PO4304 3.7 28.8 1.0
O3 B:PO4304 3.7 27.7 1.0
NH1 B:ARG166 3.9 20.1 1.0
O B:HOH421 4.0 22.9 1.0
CG B:GLU175 4.3 18.2 1.0
O1 B:PO4304 4.5 25.1 1.0
MG B:MG305 4.8 25.4 1.0
CZ B:ARG166 5.0 23.1 1.0

Magnesium binding site 4 out of 12 in 5cj2

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Magnesium binding site 4 out of 12 in the Ran Gdp Y39A Mutant Triclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ran Gdp Y39A Mutant Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:25.4
occ:1.00
 O4 B:PO4304 2.0 28.8 1.0
O B:HOH424 2.0 26.7 1.0
O B:HOH421 2.1 22.9 1.0
P B:PO4304 3.2 28.3 1.0
O1 B:PO4304 3.5 25.1 1.0
O2 B:PO4304 3.8 24.5 1.0
OE2 B:GLU175 4.3 22.0 1.0
OD1 B:ASN173 4.4 24.9 1.0
O3 B:PO4304 4.4 27.7 1.0
O B:ASN173 4.5 20.8 1.0
CB B:ASN173 4.6 21.4 1.0
CA B:ASN173 4.7 20.7 1.0
MG B:MG303 4.8 26.8 1.0
NH1 B:ARG166 4.8 20.1 1.0
CG B:ASN173 4.9 24.3 1.0

Magnesium binding site 5 out of 12 in 5cj2

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Magnesium binding site 5 out of 12 in the Ran Gdp Y39A Mutant Triclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ran Gdp Y39A Mutant Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:19.8
occ:1.00
 O C:HOH440 2.0 18.8 1.0
O C:HOH421 2.0 21.7 1.0
O1B C:GDP301 2.0 18.4 1.0
OG1 C:THR24 2.0 19.4 1.0
O C:HOH407 2.2 21.3 1.0
O E:HOH410 2.2 24.6 1.0
CB C:THR24 3.1 17.8 1.0
PB C:GDP301 3.2 19.1 1.0
O2B C:GDP301 3.6 19.7 1.0
N C:THR24 3.8 16.6 1.0
OD2 C:ASP65 4.0 27.1 1.0
CA C:THR24 4.0 15.9 1.0
OD1 C:ASP65 4.1 32.2 1.0
O1A C:GDP301 4.2 20.4 1.0
OE2 E:GLU113 4.2 50.6 1.0
CG2 C:THR24 4.2 20.9 1.0
O3B C:GDP301 4.2 20.6 1.0
O3A C:GDP301 4.3 18.7 1.0
OE2 C:GLU70 4.4 26.3 1.0
OG1 C:THR66 4.4 32.5 1.0
CG C:ASP65 4.5 27.0 1.0
OE1 E:GLU113 4.5 57.3 1.0
O C:THR66 4.5 29.4 1.0
PA C:GDP301 4.6 21.2 1.0
O2A C:GDP301 4.7 20.2 1.0
CB C:LYS23 4.7 18.5 1.0
NZ C:LYS23 4.8 17.1 1.0
CD E:GLU113 4.8 49.5 1.0
N C:GLY68 4.8 37.9 1.0
C C:LYS23 4.9 16.8 1.0
CE C:LYS23 5.0 17.6 1.0

Magnesium binding site 6 out of 12 in 5cj2

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Magnesium binding site 6 out of 12 in the Ran Gdp Y39A Mutant Triclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ran Gdp Y39A Mutant Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:26.6
occ:1.00
 O2 C:PO4304 2.0 26.8 1.0
OE2 C:GLU175 2.1 24.3 1.0
O C:HOH445 2.2 21.5 1.0
O C:HOH406 2.3 20.9 1.0
CD C:GLU175 3.1 26.8 1.0
P C:PO4304 3.2 26.8 1.0
OE1 C:GLU175 3.4 26.7 1.0
O4 C:PO4304 3.6 25.6 1.0
O C:HOH413 3.7 25.4 1.0
O3 C:PO4304 3.8 23.7 1.0
NH1 C:ARG166 3.9 24.9 1.0
O C:HOH447 4.3 28.4 1.0
CG C:GLU175 4.4 22.4 1.0
O1 C:PO4304 4.4 27.0 1.0
MG C:MG305 4.7 25.8 1.0
CZ C:ARG166 5.0 25.0 1.0

Magnesium binding site 7 out of 12 in 5cj2

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Magnesium binding site 7 out of 12 in the Ran Gdp Y39A Mutant Triclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ran Gdp Y39A Mutant Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg305

b:25.8
occ:1.00
 O3 C:PO4304 2.0 23.7 1.0
O C:HOH419 2.1 35.8 1.0
O C:HOH413 2.1 25.4 1.0
P C:PO4304 3.3 26.8 1.0
O2 C:PO4304 3.7 26.8 1.0
O1 C:PO4304 3.7 27.0 1.0
OD1 C:ASN173 4.4 26.6 1.0
OE2 C:GLU175 4.5 24.3 1.0
O4 C:PO4304 4.5 25.6 1.0
CA C:ASN173 4.7 22.6 1.0
MG C:MG303 4.7 26.6 1.0
O C:ASN173 4.7 22.0 1.0
CB C:ASN173 4.7 25.1 1.0
NH1 C:ARG166 4.9 24.9 1.0
CG C:ASN173 4.9 29.9 1.0

Magnesium binding site 8 out of 12 in 5cj2

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Magnesium binding site 8 out of 12 in the Ran Gdp Y39A Mutant Triclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ran Gdp Y39A Mutant Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:14.2
occ:1.00
 O D:HOH441 2.0 14.9 1.0
O2B D:GDP301 2.0 14.5 1.0
O D:HOH432 2.0 16.0 1.0
OG1 D:THR24 2.0 12.7 1.0
O D:HOH431 2.1 13.7 1.0
O D:HOH413 2.2 16.8 1.0
CB D:THR24 3.1 14.1 1.0
PB D:GDP301 3.3 14.3 1.0
O3B D:GDP301 3.5 15.1 1.0
N D:THR24 3.9 12.5 1.0
O D:HOH474 4.0 32.7 1.0
CA D:THR24 4.1 14.1 1.0
O D:THR66 4.2 16.5 1.0
OD2 D:ASP65 4.2 16.6 1.0
CG2 D:THR24 4.2 15.7 1.0
OD1 D:ASP65 4.3 15.9 1.0
O2A D:GDP301 4.3 15.8 1.0
OE2 D:GLU70 4.3 18.0 1.0
O1B D:GDP301 4.3 12.9 1.0
OG1 D:THR66 4.4 18.5 1.0
O D:HOH479 4.4 30.4 1.0
O D:HOH477 4.4 31.1 1.0
O3A D:GDP301 4.4 14.1 1.0
CG D:ASP65 4.6 16.2 1.0
PA D:GDP301 4.7 16.0 1.0
O1A D:GDP301 4.8 14.0 1.0
CB D:LYS23 4.8 11.4 1.0
C D:LYS23 4.9 12.8 1.0
N D:GLY68 5.0 15.3 1.0

Magnesium binding site 9 out of 12 in 5cj2

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Magnesium binding site 9 out of 12 in the Ran Gdp Y39A Mutant Triclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Ran Gdp Y39A Mutant Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:20.1
occ:1.00
 O E:HOH438 2.0 19.4 1.0
OG1 E:THR24 2.0 18.5 1.0
O2B E:GDP301 2.1 17.3 1.0
O E:HOH420 2.2 21.1 1.0
CB E:THR24 3.1 17.2 1.0
PB E:GDP301 3.3 19.6 1.0
O3B E:GDP301 3.6 19.7 1.0
N E:THR24 3.8 17.9 1.0
OD2 E:ASP65 3.9 24.3 1.0
CA E:THR24 4.0 16.6 1.0
OD1 E:ASP65 4.1 34.1 1.0
CG2 E:THR24 4.2 21.2 1.0
O2A E:GDP301 4.2 21.7 1.0
O1B E:GDP301 4.3 19.9 1.0
OG1 E:THR66 4.3 30.3 1.0
O3A E:GDP301 4.3 18.5 1.0
CG E:ASP65 4.4 23.3 1.0
OE2 E:GLU70 4.4 25.9 1.0
O E:THR66 4.5 29.1 1.0
PA E:GDP301 4.7 20.5 1.0
CB E:LYS23 4.7 18.6 1.0
O1A E:GDP301 4.8 20.4 1.0
NZ E:LYS23 4.8 18.3 1.0
N E:GLY68 4.8 35.5 1.0
C E:LYS23 4.8 16.9 1.0
CE E:LYS23 5.0 16.8 1.0

Magnesium binding site 10 out of 12 in 5cj2

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Magnesium binding site 10 out of 12 in the Ran Gdp Y39A Mutant Triclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Ran Gdp Y39A Mutant Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:23.1
occ:1.00
 O F:HOH409 1.9 24.8 1.0
O1B F:GDP301 1.9 23.3 1.0
O F:HOH416 1.9 23.6 1.0
OG1 F:THR24 2.1 21.1 1.0
O F:HOH434 2.1 23.8 1.0
O F:HOH410 2.1 24.7 1.0
CB F:THR24 3.2 20.5 1.0
PB F:GDP301 3.2 23.3 1.0
O2B F:GDP301 3.4 30.2 1.0
N F:THR24 3.8 18.4 1.0
OD1 F:ASP65 4.1 25.4 1.0
CA F:THR24 4.1 19.2 1.0
O3B F:GDP301 4.1 22.8 1.0
O1A F:GDP301 4.2 24.9 1.0
OD2 F:ASP65 4.2 22.7 1.0
CG2 F:THR24 4.2 21.9 1.0
OG1 F:THR66 4.2 24.1 1.0
O3A F:GDP301 4.3 23.6 1.0
OE2 F:GLU70 4.3 33.5 1.0
CG F:ASP65 4.5 22.9 1.0
O F:THR66 4.5 35.6 1.0
PA F:GDP301 4.6 25.9 1.0
O2A F:GDP301 4.7 25.2 1.0
CB F:LYS23 4.8 20.0 1.0
NZ F:LYS23 4.8 28.5 1.0
CA F:GLY68 4.8 39.6 1.0
C F:LYS23 4.8 18.4 1.0
N F:GLY68 4.9 39.8 1.0

Reference:

T.Rudack, S.Jenrich, S.Brucker, I.R.Vetter, K.Gerwert, C.Kotting. Catalysis of Gtp Hydrolysis By Small Gtpases at Atomic Detail By Integration of X-Ray Crystallography, Experimental, and Theoretical Ir Spectroscopy. J.Biol.Chem. V. 290 24079 2015.
ISSN: ESSN 1083-351X
PubMed: 26272610
DOI: 10.1074/JBC.M115.648071
Page generated: Sun Sep 29 02:10:09 2024

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