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Magnesium in PDB 2jft: Crystal Structure of the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Sulfate

Protein crystallography data

The structure of Crystal Structure of the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Sulfate, PDB code: 2jft was solved by M.Bellinzoni, A.Wehenkel, W.Shepard, P.M.Alzari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 1.08
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.547, 84.402, 33.609, 90.00, 90.00, 90.00
R / Rfree (%) 11.6 / 16

Other elements in 2jft:

The structure of Crystal Structure of the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Sulfate also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Sulfate (pdb code 2jft). 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 the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Sulfate, PDB code: 2jft:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 2jft

Go back to Magnesium Binding Sites List in 2jft
Magnesium binding site 1 out of 5 in the Crystal Structure of the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Sulfate


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 the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:10.3
occ:1.00
 OD1 A:ASP35 2.0 10.7 1.0
O A:GLY36 2.0 10.8 1.0
O A:HOH544 2.1 11.4 1.0
O A:HOH496 2.1 11.0 1.0
O A:HOH470 2.1 11.9 1.0
O A:HOH451 2.1 12.0 1.0
CG A:ASP35 3.2 9.6 1.0
C A:GLY36 3.2 10.3 1.0
OD2 A:ASP35 3.7 10.9 1.0
MN A:MN302 3.8 10.6 0.9
N A:GLY36 3.9 10.2 1.0
O2 A:SO4306 4.0 16.9 0.9
O A:HOH583 4.0 12.9 1.0
C A:ASP35 4.1 9.8 1.0
OD1 A:ASP22 4.1 11.3 1.0
N A:PHE37 4.2 11.3 1.0
CA A:GLY36 4.2 10.8 1.0
CB A:GLN21 4.2 10.9 1.0
O A:HOH568 4.3 11.0 1.0
OE1 A:GLN21 4.3 14.9 1.0
O4 A:SO4306 4.3 17.8 0.9
O A:HOH579 4.3 13.8 1.0
CA A:PHE37 4.3 11.5 1.0
O A:HOH604 4.4 12.4 1.0
CB A:ASP35 4.4 10.2 1.0
OD1 A:ASN224 4.4 10.9 1.0
O A:ASP35 4.4 10.3 1.0
CA A:ASP35 4.5 9.8 1.0
OD1 A:ASP223 4.5 11.3 1.0
CB A:PHE37 4.7 12.1 1.0
NH1 A:ARG17 4.8 14.4 1.0
S A:SO4306 4.8 16.2 0.9
C A:GLN21 4.8 10.4 1.0
O A:GLN21 4.8 10.7 1.0

Magnesium binding site 2 out of 5 in 2jft

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Magnesium binding site 2 out of 5 in the Crystal Structure of the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Sulfate


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 the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:13.2
occ:0.22
 O A:HOH464 1.6 19.2 1.0
O A:HOH579 1.7 13.8 1.0
OD2 A:ASP185 2.3 22.5 1.0
O A:HOH531 2.4 14.7 1.0
O A:HOH512 2.6 41.0 1.0
MG A:MG304 2.8 12.4 0.3
O A:HOH520 2.9 26.6 1.0
CG A:ASP185 3.2 12.3 1.0
OD2 A:ASP111 3.2 20.0 1.0
OD1 A:ASP185 3.5 11.4 1.0
MN A:MN302 3.6 10.6 0.9
O2 A:SO4306 4.1 16.9 0.9
CG A:ASP111 4.1 14.0 1.0
MG A:MG305 4.1 12.3 0.4
O1 A:SO4306 4.1 28.9 0.9
OD2 A:ASP35 4.1 10.9 1.0
OD1 A:ASP111 4.1 13.5 1.0
O A:HOH455 4.2 42.0 1.0
O A:HOH470 4.3 11.9 1.0
CB A:ASP185 4.4 12.5 1.0
O A:HOH559 4.4 20.1 1.0
O A:HOH457 4.4 33.6 1.0
O A:HOH428 4.5 27.2 1.0
S A:SO4306 4.5 16.2 0.9
O A:HOH583 4.5 12.9 1.0
OD2 A:ASP223 4.6 11.9 1.0
O4 A:SO4306 4.7 17.8 0.9
O A:HOH451 4.7 12.0 1.0
O A:HOH524 4.8 11.4 1.0
O A:HOH523 4.8 36.6 1.0
O A:HIS153 4.9 22.6 1.0
CA A:HIS153 4.9 14.4 1.0
CG A:ASP35 5.0 9.6 1.0

Magnesium binding site 3 out of 5 in 2jft

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Magnesium binding site 3 out of 5 in the Crystal Structure of the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Sulfate


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 the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:12.4
occ:0.32
 OD2 A:ASP111 1.8 20.0 1.0
O A:HOH428 1.9 27.2 1.0
O A:HOH464 2.1 19.2 1.0
O A:HOH523 2.2 36.6 1.0
OD2 A:ASP185 2.3 22.5 1.0
O A:HOH455 2.3 42.0 1.0
MG A:MG303 2.8 13.2 0.2
CG A:ASP111 3.0 14.0 1.0
O A:HOH512 3.2 41.0 1.0
CG A:ASP185 3.2 12.3 1.0
CB A:ASP185 3.5 12.5 1.0
MG A:MG305 3.5 12.3 0.4
O A:ARG152 3.8 17.9 1.0
OD1 A:ASP111 3.9 13.5 1.0
CB A:ASP111 3.9 13.0 1.0
O A:HOH531 4.1 14.7 1.0
OD1 A:ASP185 4.2 11.4 1.0
O A:HOH579 4.2 13.8 1.0
O A:HOH513 4.3 21.2 1.0
O A:HOH499 4.4 14.4 1.0
NE A:ARG152 4.4 22.6 0.3
CA A:HIS153 4.6 14.4 1.0
C A:ARG152 4.7 14.6 1.0
O A:HOH520 4.7 26.6 1.0
CZ A:ARG152 4.7 24.3 0.3
O A:HOH551 4.8 24.2 1.0
CD A:ARG152 4.8 22.3 0.3
O A:ASP111 4.9 12.0 1.0
NH2 A:ARG152 4.9 35.6 0.3
CG A:ARG152 4.9 19.2 0.3
CA A:ASP185 5.0 11.1 1.0
O A:HOH559 5.0 20.1 1.0

Magnesium binding site 4 out of 5 in 2jft

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Magnesium binding site 4 out of 5 in the Crystal Structure of the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Sulfate


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 the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:12.3
occ:0.39
 O A:HOH551 2.0 24.2 1.0
O A:HOH455 2.1 42.0 1.0
O A:HOH559 2.1 20.1 1.0
O A:HOH512 2.2 41.0 1.0
O A:HOH686 2.2 33.6 1.0
OD2 A:ASP185 2.6 22.5 1.0
CG A:ASP185 3.4 12.3 1.0
MG A:MG304 3.5 12.4 0.3
O A:HOH523 3.8 36.6 1.0
NH1 A:ARG152 3.8 26.3 0.3
CB A:ASP185 3.9 12.5 1.0
CD A:ARG152 4.0 22.3 0.3
CZ A:ARG152 4.1 24.3 0.3
MG A:MG303 4.1 13.2 0.2
O A:HOH711 4.1 32.9 1.0
NE A:ARG152 4.1 22.6 0.3
OD1 A:ASP185 4.1 11.4 1.0
O A:ASP185 4.2 13.6 1.0
O A:HOH585 4.2 26.3 1.0
O A:HOH457 4.2 33.6 1.0
O A:HOH431 4.3 39.8 1.0
O A:HOH464 4.3 19.2 1.0
O A:HOH401 4.3 40.6 0.7
O A:HOH579 4.5 13.8 1.0
OD2 A:ASP223 4.5 11.9 1.0
O A:HOH641 4.6 31.8 1.0
C A:ASP185 4.6 11.2 1.0
CG A:ARG152 4.7 19.2 0.3
O A:HOH428 4.7 27.2 1.0
NE A:ARG152 4.9 17.5 0.7
NH2 A:ARG152 4.9 35.6 0.3
CA A:ASP185 4.9 11.1 1.0
CB A:ALA189 5.0 16.1 1.0

Magnesium binding site 5 out of 5 in 2jft

Go back to Magnesium Binding Sites List in 2jft
Magnesium binding site 5 out of 5 in the Crystal Structure of the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Sulfate


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 the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg307

b:15.5
occ:0.27
 O A:HOH669 2.1 48.5 1.0
O A:HOH736 2.3 41.9 1.0
O A:HOH700 3.0 57.0 1.0
O A:HOH448 3.7 39.2 0.5
O A:HOH498 3.9 21.2 1.0
O A:HOH607 4.1 25.3 1.0
OE2 A:GLU193 4.6 55.6 1.0
CD2 A:HIS121 4.7 23.1 1.0
O A:HOH681 4.8 56.1 1.0

Reference:

M.Bellinzoni, A.Wehenkel, W.Shepard, P.M.Alzari. Insights Into the Mechanism of Ppm Ser/Thr Phosphatases From the Atomic Resolution Structures of A Mycobacterial Enzyme Structure V. 15 863 2007.
ISSN: ISSN 0969-2126
PubMed: 17637345
DOI: 10.1016/J.STR.2007.06.002
Page generated: Mon Dec 14 07:29:25 2020

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