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Magnesium in PDB 6mqt: Hras Mutant Structure in Complex with Gdp

Protein crystallography data

The structure of Hras Mutant Structure in Complex with Gdp, PDB code: 6mqt was solved by A.K.Bera, K.D.Westover, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.45 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 122.808, 79.773, 134.062, 90.00, 101.94, 90.00
R / Rfree (%) 15.7 / 19.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Hras Mutant Structure in Complex with Gdp (pdb code 6mqt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Hras Mutant Structure in Complex with Gdp, PDB code: 6mqt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6mqt

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Magnesium binding site 1 out of 8 in the Hras Mutant Structure in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hras Mutant Structure in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:12.2
occ:1.00
HOB3 A:GDP201 1.7 14.1 1.0
O A:HOH326 2.0 12.2 1.0
O3B A:GDP201 2.0 11.8 1.0
O A:HOH347 2.1 13.1 1.0
OG A:SER17 2.1 11.4 1.0
O A:HOH379 2.1 12.4 1.0
O A:HOH332 2.2 11.7 1.0
HB2 A:SER17 3.1 12.1 1.0
CB A:SER17 3.2 10.1 1.0
H A:SER17 3.2 12.3 1.0
PB A:GDP201 3.3 11.8 1.0
HOA2 A:GDP201 3.5 15.8 1.0
O1B A:GDP201 3.6 13.0 1.0
HA A:PRO34 3.6 19.1 1.0
HB3 A:SER17 3.8 12.1 1.0
N A:SER17 3.8 10.3 1.0
HD2 A:TYR32 3.9 17.4 1.0
HB2 A:LYS16 3.9 13.0 1.0
CA A:SER17 4.1 10.3 1.0
HE2 A:LYS16 4.1 18.3 1.0
OD2 A:ASP57 4.1 15.4 1.0
O2A A:GDP201 4.2 13.2 1.0
O A:ASP33 4.2 15.4 1.0
OD1 A:ASP57 4.2 13.9 1.0
O2B A:GDP201 4.3 14.6 1.0
O3A A:GDP201 4.3 12.5 1.0
O A:PRO34 4.3 16.0 1.0
HA A:SER17 4.4 12.3 1.0
O A:THR58 4.4 15.9 1.0
CA A:PRO34 4.4 15.9 1.0
CG A:ASP57 4.5 14.0 1.0
PA A:GDP201 4.6 11.7 1.0
O A:ILE36 4.6 15.7 1.0
O1A A:GDP201 4.6 12.1 1.0
C A:PRO34 4.6 15.7 1.0
HZ3 A:LYS16 4.7 17.0 1.0
CD2 A:TYR32 4.8 14.5 1.0
HZ2 A:LYS16 4.8 17.0 1.0
HB2 A:ALA59 4.8 22.0 1.0
CB A:LYS16 4.9 10.9 1.0
O A:HOH346 4.9 18.6 1.0
HE2 A:TYR32 4.9 19.6 1.0
CE A:LYS16 4.9 15.2 1.0
C A:LYS16 4.9 10.3 1.0

Magnesium binding site 2 out of 8 in 6mqt

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Magnesium binding site 2 out of 8 in the Hras Mutant Structure in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hras Mutant Structure in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:16.2
occ:1.00
HOB3 B:GDP201 1.7 18.5 1.0
O3B B:GDP201 2.1 15.4 1.0
OG B:SER17 2.1 16.1 1.0
O B:HOH318 2.1 15.8 1.0
O B:HOH326 2.1 15.6 1.0
O B:HOH343 2.1 16.2 1.0
O B:HOH309 2.1 15.3 1.0
HB2 B:SER17 3.1 17.7 1.0
CB B:SER17 3.2 14.8 1.0
PB B:GDP201 3.3 15.7 1.0
H B:SER17 3.3 17.7 1.0
HA B:PRO34 3.5 21.6 1.0
O1B B:GDP201 3.5 15.9 1.0
HD2 B:TYR32 3.7 27.6 1.0
HB3 B:SER17 3.8 17.7 1.0
HOA2 B:GDP201 3.9 21.7 1.0
N B:SER17 3.9 14.7 1.0
HB2 B:LYS16 4.0 16.7 1.0
CA B:SER17 4.1 14.5 1.0
HE2 B:LYS16 4.1 23.9 1.0
OD2 B:ASP57 4.1 18.4 1.0
O2A B:GDP201 4.1 18.1 1.0
O B:ASP33 4.2 17.9 1.0
OD1 B:ASP57 4.2 17.8 1.0
O B:PRO34 4.3 19.7 1.0
O3A B:GDP201 4.3 15.2 1.0
O2B B:GDP201 4.3 18.8 1.0
HB2 B:ALA59 4.4 28.6 1.0
CA B:PRO34 4.4 18.0 1.0
HA B:SER17 4.4 17.4 1.0
O B:THR58 4.5 18.4 1.0
O B:ILE36 4.5 21.8 1.0
PA B:GDP201 4.6 16.1 1.0
CG B:ASP57 4.6 17.3 1.0
C B:PRO34 4.6 18.8 1.0
CD2 B:TYR32 4.6 23.0 1.0
O1A B:GDP201 4.7 16.3 1.0
HZ2 B:LYS16 4.7 21.6 1.0
HE2 B:TYR32 4.8 31.3 1.0
HZ1 B:LYS16 4.8 21.6 1.0
CB B:LYS16 4.9 14.0 1.0
HB3 B:TYR32 4.9 24.9 1.0
HA B:ALA59 4.9 25.8 1.0
O B:HOH345 5.0 22.1 1.0
CE B:LYS16 5.0 19.9 1.0
C B:LYS16 5.0 15.6 1.0
O B:TYR32 5.0 18.3 1.0

Magnesium binding site 3 out of 8 in 6mqt

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Magnesium binding site 3 out of 8 in the Hras Mutant Structure in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hras Mutant Structure in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:14.2
occ:1.00
HOB3 C:GDP201 1.7 18.7 1.0
O C:HOH315 2.1 15.9 1.0
O3B C:GDP201 2.1 15.6 1.0
O C:HOH307 2.1 15.7 1.0
OG C:SER17 2.1 14.5 1.0
O C:HOH306 2.1 15.6 1.0
O C:HOH332 2.1 15.4 1.0
HB2 C:SER17 3.1 15.4 1.0
CB C:SER17 3.2 12.8 1.0
PB C:GDP201 3.3 15.0 1.0
H C:SER17 3.4 16.9 1.0
HA C:PRO34 3.5 18.9 1.0
O1B C:GDP201 3.5 16.2 1.0
HD2 C:TYR32 3.7 25.8 1.0
HOA2 C:GDP201 3.7 21.9 1.0
HB3 C:SER17 3.8 15.4 1.0
N C:SER17 3.9 14.1 1.0
HB2 C:LYS16 4.0 16.1 1.0
CA C:SER17 4.1 12.8 1.0
OD2 C:ASP57 4.1 16.9 1.0
O2A C:GDP201 4.1 18.2 1.0
HE2 C:LYS16 4.2 20.9 1.0
O C:ASP33 4.2 19.1 1.0
OD1 C:ASP57 4.2 16.8 1.0
O3A C:GDP201 4.3 14.9 1.0
O C:PRO34 4.3 17.6 1.0
O2B C:GDP201 4.3 18.4 1.0
CA C:PRO34 4.4 15.8 1.0
HA C:SER17 4.4 15.3 1.0
O C:THR58 4.4 16.9 1.0
PA C:GDP201 4.5 15.3 1.0
HB2 C:ALA59 4.6 29.7 1.0
O C:ILE36 4.6 20.2 1.0
CG C:ASP57 4.6 14.8 1.0
CD2 C:TYR32 4.6 21.5 1.0
C C:PRO34 4.6 17.3 1.0
HZ2 C:LYS16 4.7 19.8 1.0
O1A C:GDP201 4.7 16.7 1.0
HZ1 C:LYS16 4.7 19.8 1.0
HE2 C:TYR32 4.8 28.5 1.0
HB3 C:TYR32 4.8 21.6 1.0
HA C:ALA59 4.8 26.1 1.0
O C:TYR32 4.9 17.8 1.0
O C:HOH333 4.9 21.8 1.0
CB C:LYS16 5.0 13.4 1.0
NZ C:LYS16 5.0 16.5 1.0

Magnesium binding site 4 out of 8 in 6mqt

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Magnesium binding site 4 out of 8 in the Hras Mutant Structure in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Hras Mutant Structure in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:14.0
occ:1.00
HOB3 D:GDP201 1.7 16.2 1.0
O3B D:GDP201 2.0 13.5 1.0
O D:HOH332 2.1 13.3 1.0
O D:HOH350 2.1 15.6 1.0
OG D:SER17 2.1 12.8 1.0
O D:HOH359 2.1 14.3 1.0
O D:HOH337 2.2 13.4 1.0
HB2 D:SER17 3.1 14.5 1.0
CB D:SER17 3.2 12.1 1.0
H D:SER17 3.2 13.4 1.0
PB D:GDP201 3.3 13.3 1.0
HA D:PRO34 3.5 22.4 1.0
O1B D:GDP201 3.6 14.5 1.0
HOA2 D:GDP201 3.6 17.9 1.0
HD2 D:TYR32 3.8 22.2 1.0
N D:SER17 3.8 11.1 1.0
HB3 D:SER17 3.8 14.5 1.0
HB2 D:LYS16 3.9 13.2 1.0
CA D:SER17 4.1 12.2 1.0
OD2 D:ASP57 4.1 15.6 1.0
HE2 D:LYS16 4.1 20.2 1.0
O2A D:GDP201 4.1 14.9 1.0
OD1 D:ASP57 4.2 15.5 1.0
O D:ASP33 4.2 18.8 1.0
O3A D:GDP201 4.3 13.9 1.0
O2B D:GDP201 4.3 18.1 1.0
O D:PRO34 4.3 19.1 1.0
HA D:SER17 4.4 14.7 1.0
CA D:PRO34 4.4 18.7 1.0
O D:THR58 4.5 15.5 1.0
CG D:ASP57 4.5 14.6 1.0
PA D:GDP201 4.5 13.9 1.0
HZ2 D:LYS16 4.6 18.4 1.0
C D:PRO34 4.6 18.4 1.0
O D:ILE36 4.6 17.0 1.0
O1A D:GDP201 4.7 14.0 1.0
CD2 D:TYR32 4.7 18.5 1.0
HZ1 D:LYS16 4.7 18.4 1.0
HE2 D:TYR32 4.9 23.1 1.0
CB D:LYS16 4.9 11.0 1.0
HB2 D:ALA59 4.9 27.8 1.0
O D:HOH347 4.9 18.9 1.0
C D:LYS16 4.9 10.8 1.0
HG22 D:ILE36 4.9 29.3 1.0
CE D:LYS16 4.9 16.8 1.0
NZ D:LYS16 5.0 15.3 1.0

Magnesium binding site 5 out of 8 in 6mqt

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Magnesium binding site 5 out of 8 in the Hras Mutant Structure in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Hras Mutant Structure in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:14.0
occ:1.00
HOB3 E:GDP201 1.7 15.3 1.0
O3B E:GDP201 2.0 12.8 1.0
O E:HOH325 2.0 13.1 1.0
O E:HOH335 2.1 14.1 1.0
OG E:SER17 2.1 12.7 1.0
O E:HOH366 2.1 14.1 1.0
O E:HOH336 2.2 13.8 1.0
HB2 E:SER17 3.1 14.0 1.0
CB E:SER17 3.2 11.7 1.0
H E:SER17 3.2 13.9 1.0
PB E:GDP201 3.3 13.4 1.0
HA E:PRO34 3.5 19.7 1.0
O1B E:GDP201 3.5 14.6 1.0
HOA2 E:GDP201 3.6 17.8 1.0
HD2 E:TYR32 3.8 22.2 1.0
HB3 E:SER17 3.8 14.0 1.0
N E:SER17 3.9 11.6 1.0
HB2 E:LYS16 4.0 14.3 1.0
CA E:SER17 4.1 11.9 1.0
HE2 E:LYS16 4.1 18.8 1.0
OD2 E:ASP57 4.1 16.3 1.0
O2A E:GDP201 4.1 14.8 1.0
OD1 E:ASP57 4.2 14.5 1.0
O E:ASP33 4.2 17.4 1.0
O3A E:GDP201 4.3 12.9 1.0
O2B E:GDP201 4.3 17.8 1.0
O E:PRO34 4.3 17.8 1.0
HA E:SER17 4.4 14.3 1.0
CA E:PRO34 4.4 16.4 1.0
O E:THR58 4.4 15.7 1.0
CG E:ASP57 4.5 14.4 1.0
PA E:GDP201 4.5 14.3 1.0
C E:PRO34 4.6 17.1 1.0
O E:ILE36 4.6 15.6 1.0
O1A E:GDP201 4.6 13.9 1.0
HZ3 E:LYS16 4.7 17.3 1.0
CD2 E:TYR32 4.7 18.6 1.0
HZ2 E:LYS16 4.8 17.3 1.0
HG22 E:ILE36 4.8 29.4 1.0
CB E:LYS16 4.9 11.9 1.0
HB2 E:ALA59 4.9 23.8 1.0
HB3 E:TYR32 4.9 20.6 1.0
HE2 E:TYR32 4.9 22.8 1.0
CE E:LYS16 4.9 15.7 1.0
O E:HOH345 5.0 19.9 1.0
C E:LYS16 5.0 10.4 1.0

Magnesium binding site 6 out of 8 in 6mqt

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Magnesium binding site 6 out of 8 in the Hras Mutant Structure in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Hras Mutant Structure in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:11.9
occ:1.00
HOB3 F:GDP201 1.7 14.5 1.0
O3B F:GDP201 2.0 12.1 1.0
O F:HOH322 2.1 11.4 1.0
OG F:SER17 2.1 10.9 1.0
O F:HOH346 2.1 12.6 1.0
O F:HOH362 2.1 12.3 1.0
O F:HOH336 2.1 11.0 1.0
HB2 F:SER17 3.1 11.7 1.0
CB F:SER17 3.2 9.8 1.0
H F:SER17 3.2 12.1 1.0
PB F:GDP201 3.3 10.9 1.0
HOA2 F:GDP201 3.5 16.1 1.0
O1B F:GDP201 3.6 12.2 1.0
HA F:PRO34 3.6 17.1 1.0
HB3 F:SER17 3.8 11.7 1.0
HD2 F:TYR32 3.8 16.8 1.0
N F:SER17 3.9 10.1 1.0
HB2 F:LYS16 3.9 10.9 1.0
HE2 F:LYS16 4.1 17.5 1.0
CA F:SER17 4.1 9.7 1.0
OD2 F:ASP57 4.1 13.8 1.0
O F:ASP33 4.1 13.9 1.0
O2A F:GDP201 4.2 13.4 1.0
OD1 F:ASP57 4.2 13.6 1.0
O2B F:GDP201 4.3 13.6 1.0
O3A F:GDP201 4.3 11.6 1.0
O F:PRO34 4.3 14.3 1.0
HA F:SER17 4.4 11.6 1.0
O F:THR58 4.5 14.5 1.0
CA F:PRO34 4.5 14.3 1.0
CG F:ASP57 4.5 13.1 1.0
PA F:GDP201 4.6 11.6 1.0
O F:ILE36 4.6 14.2 1.0
O1A F:GDP201 4.6 12.1 1.0
C F:PRO34 4.6 13.8 1.0
HZ2 F:LYS16 4.7 17.1 1.0
CD2 F:TYR32 4.7 14.0 1.0
HZ1 F:LYS16 4.8 17.1 1.0
HB2 F:ALA59 4.8 21.6 1.0
HE2 F:TYR32 4.8 19.0 1.0
O F:HOH351 4.9 17.0 1.0
CB F:LYS16 4.9 9.1 1.0
CE F:LYS16 4.9 14.6 1.0
C F:LYS16 5.0 9.1 1.0

Magnesium binding site 7 out of 8 in 6mqt

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Magnesium binding site 7 out of 8 in the Hras Mutant Structure in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Hras Mutant Structure in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg202

b:17.8
occ:1.00
HOB3 G:GDP201 1.8 18.9 1.0
OG G:SER17 2.1 16.7 1.0
O3B G:GDP201 2.1 15.7 1.0
O G:HOH327 2.1 17.2 1.0
O G:HOH351 2.1 20.5 1.0
O G:HOH336 2.1 17.8 1.0
O G:HOH337 2.1 17.1 1.0
HB2 G:SER17 3.1 19.0 1.0
CB G:SER17 3.2 15.8 1.0
PB G:GDP201 3.3 16.9 1.0
H G:SER17 3.3 17.4 1.0
HA G:PRO34 3.5 27.9 1.0
HD2 G:TYR32 3.6 37.2 1.0
O1B G:GDP201 3.6 18.3 1.0
HB3 G:SER17 3.8 19.0 1.0
N G:SER17 3.9 14.5 1.0
HB2 G:LYS16 4.0 18.1 1.0
OD2 G:ASP57 4.0 20.4 1.0
CA G:SER17 4.1 13.7 1.0
O2A G:GDP201 4.1 20.1 1.0
HE2 G:LYS16 4.2 23.1 1.0
HOA2 G:GDP201 4.2 24.1 1.0
OD1 G:ASP57 4.2 18.9 1.0
O G:ASP33 4.3 26.4 1.0
O G:PRO34 4.3 23.2 1.0
O3A G:GDP201 4.3 16.7 1.0
O2B G:GDP201 4.4 21.9 1.0
CA G:PRO34 4.4 23.3 1.0
HA G:SER17 4.4 16.5 1.0
CD2 G:TYR32 4.5 31.0 1.0
O G:THR58 4.5 19.2 1.0
CG G:ASP57 4.5 18.2 1.0
O G:ILE36 4.6 24.4 1.0
PA G:GDP201 4.6 17.6 1.0
HE2 G:TYR32 4.6 40.8 1.0
C G:PRO34 4.6 23.5 1.0
HA G:ALA59 4.7 33.0 1.0
O1A G:GDP201 4.7 19.5 1.0
HZ1 G:LYS16 4.8 23.4 1.0
HB3 G:TYR32 4.8 37.5 1.0
HZ3 G:LYS16 4.9 23.4 1.0
O G:TYR32 4.9 27.1 1.0
CB G:LYS16 4.9 15.1 1.0
CE2 G:TYR32 5.0 34.0 1.0

Magnesium binding site 8 out of 8 in 6mqt

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Magnesium binding site 8 out of 8 in the Hras Mutant Structure in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Hras Mutant Structure in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg202

b:19.0
occ:1.00
HOB3 H:GDP201 1.7 19.6 1.0
O3B H:GDP201 2.0 16.3 1.0
OG H:SER17 2.0 16.8 1.0
O H:HOH616 2.1 21.6 1.0
O H:HOH614 2.1 18.2 1.0
O H:HOH617 2.1 18.4 1.0
O H:HOH628 2.2 18.6 1.0
HB2 H:SER17 3.1 18.1 1.0
CB H:SER17 3.1 15.1 1.0
H H:SER17 3.3 18.0 1.0
PB H:GDP201 3.3 17.7 1.0
HA H:PRO34 3.5 26.2 1.0
O1B H:GDP201 3.6 19.4 1.0
HD2 H:TYR32 3.6 31.7 1.0
HB3 H:SER17 3.8 18.1 1.0
N H:SER17 3.9 15.0 1.0
HB2 H:LYS16 3.9 18.8 1.0
OD2 H:ASP57 4.0 21.2 1.0
HE2 H:LYS16 4.0 24.0 1.0
CA H:SER17 4.1 14.2 1.0
HOA2 H:GDP201 4.1 23.2 1.0
O2A H:GDP201 4.1 19.3 1.0
OD1 H:ASP57 4.2 19.5 1.0
O H:ASP33 4.3 23.6 1.0
O3A H:GDP201 4.3 16.8 1.0
O H:PRO34 4.3 25.0 1.0
O2B H:GDP201 4.3 21.7 1.0
CA H:PRO34 4.4 21.8 1.0
HA H:SER17 4.4 17.0 1.0
CD2 H:TYR32 4.5 26.4 1.0
O H:THR58 4.5 20.6 1.0
CG H:ASP57 4.5 17.7 1.0
PA H:GDP201 4.5 17.3 1.0
O1A H:GDP201 4.6 19.4 1.0
O H:ILE36 4.6 25.5 1.0
C H:PRO34 4.6 23.5 1.0
HB3 H:TYR32 4.7 31.3 1.0
HA H:ALA59 4.7 35.6 1.0
HE2 H:TYR32 4.7 35.3 1.0
HZ2 H:LYS16 4.7 24.3 1.0
HZ1 H:LYS16 4.8 24.3 1.0
O H:TYR32 4.8 22.6 1.0
CB H:LYS16 4.9 15.6 1.0
CE H:LYS16 4.9 20.0 1.0
C H:LYS16 5.0 13.8 1.0
O H:HOH639 5.0 22.3 1.0

Reference:

A.K.Bera, K.D.Westover. Hras Mutant Structure in Complex with Gdp To Be Published.
Page generated: Tue Oct 1 11:58:07 2024

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