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Magnesium in PDB 3m1y: Crystal Structure of A Phosphoserine Phosphatase (Serb) From Helicobacter Pylori

Protein crystallography data

The structure of Crystal Structure of A Phosphoserine Phosphatase (Serb) From Helicobacter Pylori, PDB code: 3m1y was solved by B.Syed Ibrahim, S.K.Burley, S.Swaminathan, New York Sgxresearch Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.07 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.607, 84.719, 204.826, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 27.1

Other elements in 3m1y:

The structure of Crystal Structure of A Phosphoserine Phosphatase (Serb) From Helicobacter Pylori also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Phosphoserine Phosphatase (Serb) From Helicobacter Pylori (pdb code 3m1y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of A Phosphoserine Phosphatase (Serb) From Helicobacter Pylori, PDB code: 3m1y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3m1y

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Magnesium binding site 1 out of 5 in the Crystal Structure of A Phosphoserine Phosphatase (Serb) From Helicobacter Pylori


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 A Phosphoserine Phosphatase (Serb) From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg300

b:31.9
occ:1.00
 O A:HOH323 2.1 35.1 1.0
O A:HOH319 2.1 24.9 1.0
O A:HOH321 2.2 36.4 1.0
OD2 A:ASP8 2.4 26.4 1.0
OD2 A:ASP164 2.4 24.1 1.0
O A:ASP10 2.4 22.4 1.0
CG A:ASP164 3.4 24.8 1.0
CG A:ASP8 3.4 25.8 1.0
C A:ASP10 3.5 22.9 1.0
OD1 A:ASP164 3.6 25.8 1.0
OD1 A:ASP8 3.8 26.2 1.0
OD1 A:ASN167 3.9 41.9 1.0
CB A:ASP10 4.1 22.6 1.0
CA A:ASP10 4.2 22.7 1.0
OE1 A:GLU17 4.3 37.4 1.0
CB A:SER11 4.3 24.2 1.0
N A:ASP10 4.4 23.3 1.0
OD2 A:ASP168 4.5 24.7 1.0
N A:GLY165 4.5 26.1 1.0
N A:SER11 4.5 21.3 1.0
OG1 A:THR12 4.6 25.8 1.0
CL A:CL302 4.6 38.5 1.0
CB A:ASP8 4.7 23.7 1.0
OE2 A:GLU17 4.7 33.8 1.0
CB A:ASP164 4.7 25.8 1.0
CA A:SER11 4.8 23.7 1.0
O A:HOH322 4.9 34.4 1.0
N A:ASP164 4.9 24.7 1.0
CD A:GLU17 4.9 33.0 1.0

Magnesium binding site 2 out of 5 in 3m1y

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Magnesium binding site 2 out of 5 in the Crystal Structure of A Phosphoserine Phosphatase (Serb) From Helicobacter Pylori


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 A Phosphoserine Phosphatase (Serb) From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg300

b:28.4
occ:1.00
 O B:ASP10 2.1 29.7 1.0
O B:HOH316 2.1 43.5 1.0
O B:HOH324 2.3 28.4 1.0
O B:HOH315 2.4 35.4 1.0
OD2 B:ASP164 2.5 46.8 1.0
OD2 B:ASP8 2.5 34.9 1.0
OD1 B:ASP164 2.8 43.8 1.0
CG B:ASP164 3.0 43.2 1.0
C B:ASP10 3.2 32.7 1.0
CG B:ASP8 3.5 34.3 1.0
CB B:SER11 3.9 34.4 1.0
OD1 B:ASP8 3.9 31.7 1.0
CA B:ASP10 4.1 31.4 1.0
CB B:ASP10 4.1 30.7 1.0
N B:SER11 4.2 33.2 1.0
N B:GLY165 4.4 40.2 1.0
OD2 B:ASP168 4.4 33.7 1.0
CB B:ASP164 4.4 43.0 1.0
ND2 B:ASN167 4.4 45.7 1.0
CA B:SER11 4.4 34.4 1.0
N B:ASP10 4.5 31.6 1.0
O B:HOH343 4.5 42.5 1.0
OE1 B:GLU17 4.5 48.3 1.0
OG B:SER11 4.5 33.6 1.0
OG1 B:THR12 4.5 32.7 1.0
C B:SER11 4.7 34.9 1.0
C B:ASP164 4.8 41.0 1.0
CB B:ASP8 4.8 31.3 1.0
OE2 B:GLU17 4.8 47.2 1.0
N B:ASP164 4.8 41.7 1.0
CA B:GLY165 4.8 41.8 1.0
CA B:ASP164 4.9 41.3 1.0
N B:THR12 5.0 35.3 1.0

Magnesium binding site 3 out of 5 in 3m1y

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Magnesium binding site 3 out of 5 in the Crystal Structure of A Phosphoserine Phosphatase (Serb) From Helicobacter Pylori


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 A Phosphoserine Phosphatase (Serb) From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg300

b:36.4
occ:1.00
 O C:HOH326 1.8 36.3 1.0
O C:HOH313 2.1 21.1 1.0
O C:ASP10 2.1 26.7 1.0
O C:HOH317 2.3 34.6 1.0
OD2 C:ASP164 2.3 26.7 1.0
OD2 C:ASP8 2.6 28.3 1.0
OD1 C:ASP164 2.9 30.6 1.0
CG C:ASP164 3.0 29.2 1.0
C C:ASP10 3.2 26.9 1.0
CG C:ASP8 3.6 24.2 1.0
CB C:ASP10 3.9 29.8 1.0
OD1 C:ASP8 4.0 24.7 1.0
CB C:SER11 4.0 26.1 1.0
O C:HOH366 4.0 44.3 1.0
CA C:ASP10 4.1 28.0 1.0
OE1 C:GLU17 4.2 44.4 1.0
N C:SER11 4.2 26.0 1.0
OE2 C:GLU17 4.5 40.8 1.0
N C:GLY165 4.5 33.4 1.0
CB C:ASP164 4.5 29.6 1.0
OD2 C:ASP168 4.5 33.6 1.0
CA C:SER11 4.5 25.2 1.0
N C:ASP10 4.5 27.9 1.0
OG1 C:THR12 4.6 25.3 1.0
OG C:SER11 4.7 30.9 1.0
C C:SER11 4.7 25.7 1.0
CD C:GLU17 4.8 40.8 1.0
CB C:ASP8 4.9 20.4 1.0
N C:ASP164 5.0 29.3 1.0

Magnesium binding site 4 out of 5 in 3m1y

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Magnesium binding site 4 out of 5 in the Crystal Structure of A Phosphoserine Phosphatase (Serb) From Helicobacter Pylori


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 A Phosphoserine Phosphatase (Serb) From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:45.2
occ:1.00
 O C:HOH312 2.3 30.2 1.0
OD2 C:ASP199 2.5 39.9 1.0
OD1 C:ASP199 2.9 36.4 1.0
CG C:ASP199 3.1 35.9 1.0
OE1 C:GLU80 4.0 41.5 1.0
OE2 C:GLU76 4.0 39.4 1.0
CB C:ALA201 4.1 26.6 1.0
CB C:GLU76 4.4 25.9 1.0
N C:GLY77 4.5 21.2 1.0
O C:HOH391 4.6 40.9 1.0
CB C:ASP199 4.6 31.1 1.0
CA C:GLY77 4.7 19.9 1.0
C C:GLU76 4.8 22.0 1.0

Magnesium binding site 5 out of 5 in 3m1y

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Magnesium binding site 5 out of 5 in the Crystal Structure of A Phosphoserine Phosphatase (Serb) From Helicobacter Pylori


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 A Phosphoserine Phosphatase (Serb) From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg300

b:44.4
occ:1.00
 OD2 D:ASP8 1.9 42.7 1.0
O D:ASP10 2.1 40.1 1.0
O D:HOH328 2.2 37.6 1.0
OD2 D:ASP164 2.3 57.7 1.0
CG D:ASP164 3.0 57.0 1.0
OD1 D:ASP164 3.0 58.3 1.0
CG D:ASP8 3.0 41.3 1.0
C D:ASP10 3.3 41.9 1.0
OD1 D:ASP8 3.5 43.0 1.0
OG1 D:THR12 4.0 47.7 1.0
OD2 D:ASP168 4.0 51.6 1.0
CA D:ASP10 4.1 41.8 1.0
CB D:SER11 4.1 42.9 1.0
CB D:ASP10 4.2 42.1 1.0
CB D:ASP8 4.3 40.6 1.0
N D:SER11 4.3 42.3 1.0
N D:GLY165 4.3 55.2 1.0
CB D:ASP164 4.4 55.5 1.0
N D:ASP10 4.4 40.2 1.0
ND2 D:ASN167 4.5 60.6 1.0
CA D:SER11 4.6 44.1 1.0
N D:ASP164 4.6 54.1 1.0
O D:HOH327 4.6 33.8 1.0
C D:SER11 4.6 45.4 1.0
O D:SER11 4.7 45.1 1.0
OD1 D:ASN167 4.8 58.4 1.0
OE2 D:GLU17 4.8 54.3 1.0
OE1 D:GLU17 4.8 53.8 1.0
OD1 D:ASP168 4.8 52.9 1.0
CG D:ASP168 4.9 51.6 1.0
CA D:ASP164 4.9 54.9 1.0
OG D:SER11 4.9 42.4 1.0
CL D:CL302 4.9 55.2 1.0
C D:PHE9 5.0 39.2 1.0

Reference:

B.Syed Ibrahim, S.K.Burley, S.Swaminathan. Crystal Structure of A Phosphoserine Phosphatase (Serb) From Helicobacter Pylori To Be Published.
Page generated: Wed Aug 14 19:06:56 2024

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