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Magnesium in PDB 3d2l: Crystal Structure of Sam-Dependent Methyltransferase (ZP_00538691.1) From Exiguobacterium Sp. 255-15 at 1.90 A Resolution

Protein crystallography data

The structure of Crystal Structure of Sam-Dependent Methyltransferase (ZP_00538691.1) From Exiguobacterium Sp. 255-15 at 1.90 A Resolution, PDB code: 3d2l was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.37 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 67.830, 70.920, 77.190, 116.57, 104.63, 102.32
R / Rfree (%) 18.7 / 22.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Sam-Dependent Methyltransferase (ZP_00538691.1) From Exiguobacterium Sp. 255-15 at 1.90 A Resolution (pdb code 3d2l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Sam-Dependent Methyltransferase (ZP_00538691.1) From Exiguobacterium Sp. 255-15 at 1.90 A Resolution, PDB code: 3d2l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3d2l

Go back to Magnesium Binding Sites List in 3d2l
Magnesium binding site 1 out of 6 in the Crystal Structure of Sam-Dependent Methyltransferase (ZP_00538691.1) From Exiguobacterium Sp. 255-15 at 1.90 A Resolution


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 Sam-Dependent Methyltransferase (ZP_00538691.1) From Exiguobacterium Sp. 255-15 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg243

b:40.4
occ:1.00
 O A:HOH416 1.9 58.7 1.0
O A:HOH415 1.9 35.1 1.0
O A:HOH417 2.0 31.9 1.0
O A:HOH418 2.1 32.7 1.0
O A:HOH419 2.1 33.4 1.0
OD1 A:ASP128 2.3 45.9 1.0
CG A:ASP128 3.3 43.9 1.0
OD2 A:ASP128 3.5 52.0 1.0
O A:ILE242 4.1 36.1 1.0
OE2 A:GLU240 4.1 38.0 1.0
O A:LYS241 4.3 27.7 1.0
N A:GLY129 4.3 35.4 1.0
O A:HOH345 4.6 53.5 1.0
CB A:ASP128 4.7 37.8 1.0
CA A:GLY129 4.8 32.3 1.0
C A:ASP128 4.8 35.1 1.0
C A:ILE242 4.9 36.4 1.0
CA A:ILE242 4.9 30.4 1.0

Magnesium binding site 2 out of 6 in 3d2l

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Magnesium binding site 2 out of 6 in the Crystal Structure of Sam-Dependent Methyltransferase (ZP_00538691.1) From Exiguobacterium Sp. 255-15 at 1.90 A Resolution


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 Sam-Dependent Methyltransferase (ZP_00538691.1) From Exiguobacterium Sp. 255-15 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg243

b:49.8
occ:1.00
 O B:HOH372 1.8 60.1 1.0
O B:HOH370 2.1 35.7 1.0
O B:HOH369 2.2 40.2 1.0
OD1 B:ASP128 2.2 41.8 1.0
O B:HOH373 2.2 43.2 1.0
O B:HOH371 2.2 42.5 1.0
CG B:ASP128 3.2 40.1 1.0
OD2 B:ASP128 3.5 46.0 1.0
OXT B:ILE242 4.0 37.6 1.0
OE2 B:GLU240 4.0 38.6 1.0
N B:GLY129 4.3 34.6 1.0
O B:LYS241 4.3 28.1 1.0
CB B:ASP128 4.6 38.7 1.0
CA B:GLY129 4.7 33.7 1.0
C B:ASP128 4.7 34.9 1.0
C B:ILE242 4.9 35.5 1.0
CA B:ILE242 4.9 31.9 1.0
CA B:ASP128 4.9 37.5 1.0

Magnesium binding site 3 out of 6 in 3d2l

Go back to Magnesium Binding Sites List in 3d2l
Magnesium binding site 3 out of 6 in the Crystal Structure of Sam-Dependent Methyltransferase (ZP_00538691.1) From Exiguobacterium Sp. 255-15 at 1.90 A Resolution


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 Sam-Dependent Methyltransferase (ZP_00538691.1) From Exiguobacterium Sp. 255-15 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg244

b:42.8
occ:1.00
 O B:HOH362 1.9 31.6 1.0
O B:HOH374 2.0 35.0 1.0
O B:HOH376 2.1 34.7 1.0
O B:HOH375 2.1 37.8 1.0
O D:HOH308 2.1 43.3 1.0
O B:HOH377 2.2 45.4 1.0
O B:HOH361 4.1 38.6 1.0
OE1 B:GLU211 4.2 26.9 1.0
O B:HOH295 4.2 31.0 1.0
CB B:GLU211 4.2 25.6 1.0
O B:HOH293 4.2 37.1 1.0
OD2 B:ASP120 4.3 34.7 1.0
O B:HOH365 4.3 54.9 1.0
OD1 D:ASP16 4.4 50.3 1.0
OD1 B:ASP120 4.4 38.6 1.0
CD B:LYS116 4.6 33.9 1.0
O B:GLU211 4.8 29.0 1.0
CD B:GLU211 4.8 27.0 1.0
CG B:ASP120 4.8 33.1 1.0
CG B:GLU211 5.0 24.9 1.0
CB B:LYS116 5.0 30.4 1.0
C B:GLU211 5.0 27.0 1.0

Magnesium binding site 4 out of 6 in 3d2l

Go back to Magnesium Binding Sites List in 3d2l
Magnesium binding site 4 out of 6 in the Crystal Structure of Sam-Dependent Methyltransferase (ZP_00538691.1) From Exiguobacterium Sp. 255-15 at 1.90 A Resolution


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 Sam-Dependent Methyltransferase (ZP_00538691.1) From Exiguobacterium Sp. 255-15 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg243

b:53.5
occ:1.00
 O C:HOH338 1.8 40.8 1.0
O C:HOH336 1.9 41.3 1.0
O C:HOH339 2.1 49.9 1.0
OD1 C:ASP128 2.2 37.9 1.0
O C:HOH340 2.2 44.1 1.0
O C:HOH337 2.2 40.1 1.0
CG C:ASP128 3.2 43.8 1.0
OD2 C:ASP128 3.5 46.6 1.0
OXT C:ILE242 4.0 38.9 1.0
N C:GLY129 4.1 34.1 1.0
OE2 C:GLU240 4.1 42.3 1.0
O C:LYS241 4.2 33.1 1.0
CA C:GLY129 4.5 33.2 1.0
CB C:ASP128 4.5 37.4 1.0
C C:ASP128 4.6 35.1 1.0
C C:ILE242 4.8 37.4 1.0
CA C:ASP128 4.8 37.3 1.0
CA C:ILE242 4.8 34.6 1.0
O C:HOH304 4.8 53.9 1.0

Magnesium binding site 5 out of 6 in 3d2l

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Magnesium binding site 5 out of 6 in the Crystal Structure of Sam-Dependent Methyltransferase (ZP_00538691.1) From Exiguobacterium Sp. 255-15 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Sam-Dependent Methyltransferase (ZP_00538691.1) From Exiguobacterium Sp. 255-15 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg243

b:28.3
occ:1.00
 O A:HOH420 1.9 41.1 1.0
O D:HOH343 2.0 34.1 1.0
O D:HOH344 2.0 36.0 1.0
O D:HOH342 2.2 38.3 1.0
O A:HOH422 2.2 40.5 1.0
O A:HOH421 2.2 38.3 1.0
O D:ALA212 4.1 27.9 1.0
O A:HOH317 4.2 20.4 1.0
OD1 D:ASP120 4.2 33.9 1.0
O D:HOH248 4.2 23.2 1.0
OD1 A:ASP120 4.3 26.6 1.0
C D:ALA212 4.3 29.0 1.0
O D:GLU211 4.3 30.5 1.0
O A:GLU211 4.4 26.0 1.0
O A:ALA212 4.4 25.9 1.0
CA D:ALA212 4.6 30.0 1.0
C A:ALA212 4.6 27.6 1.0
O D:HOH306 4.6 33.5 1.0
CA A:ALA212 4.8 28.4 1.0
CG D:ASP120 4.8 29.9 1.0
CG A:ASP120 4.9 27.2 1.0
N D:GLY213 4.9 30.4 1.0

Magnesium binding site 6 out of 6 in 3d2l

Go back to Magnesium Binding Sites List in 3d2l
Magnesium binding site 6 out of 6 in the Crystal Structure of Sam-Dependent Methyltransferase (ZP_00538691.1) From Exiguobacterium Sp. 255-15 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Sam-Dependent Methyltransferase (ZP_00538691.1) From Exiguobacterium Sp. 255-15 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg244

b:58.0
occ:1.00
 O A:HOH424 1.9 47.0 1.0
OD1 D:ASP114 2.1 32.9 1.0
O A:HOH425 2.1 43.1 1.0
O D:HOH345 2.4 40.1 1.0
O A:HOH423 2.4 41.6 1.0
O D:HOH346 2.6 48.8 1.0
CG D:ASP114 3.0 28.5 1.0
OD2 D:ASP114 3.2 36.6 1.0
OG1 D:THR111 3.8 29.6 1.0
OE2 A:GLU91 3.9 43.5 1.0
OE1 A:GLU91 3.9 53.3 1.0
CD A:GLU91 4.3 47.1 1.0
CB D:ASP114 4.4 22.7 1.0
CD D:ARG88 4.6 35.6 1.0
N D:ASP114 4.7 24.7 1.0
CA D:ASP114 4.8 24.0 1.0
O D:HOH289 4.8 44.9 1.0
CG2 D:THR111 4.8 30.9 1.0
CB D:THR111 4.9 28.1 1.0
NE2 D:GLN117 4.9 39.3 1.0
NE D:ARG88 5.0 45.2 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Wed Aug 14 12:20:00 2024

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