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Magnesium in PDB 2pk0: Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution

Enzymatic activity of Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution

All present enzymatic activity of Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution:
3.1.3.16;

Protein crystallography data

The structure of Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution, PDB code: 2pk0 was solved by M.K.Rantanen, L.Lehtio, L.Rajagopal, C.E.Rubens, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.65 / 2.65
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 139.400, 92.100, 86.900, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 27.1

Other elements in 2pk0:

The structure of Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution (pdb code 2pk0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution, PDB code: 2pk0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 2pk0

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Magnesium binding site 1 out of 10 in the Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:27.1
occ:1.00
O A:HOH580 1.8 17.4 1.0
OD1 A:ASP36 1.9 27.2 1.0
O A:GLY37 2.0 39.4 1.0
O A:HOH579 2.1 29.9 1.0
O A:HOH583 2.2 11.3 1.0
O A:HOH578 2.3 23.9 1.0
CG A:ASP36 3.2 28.3 1.0
C A:GLY37 3.2 40.0 1.0
O A:HOH508 3.7 25.3 1.0
OD2 A:ASP36 3.7 27.6 1.0
N A:GLY37 3.8 33.0 1.0
O A:HOH556 3.9 35.2 1.0
C A:ASP36 4.0 32.1 1.0
MG A:MG502 4.0 28.8 1.0
CA A:GLY37 4.0 37.2 1.0
OD1 A:ASP18 4.1 30.8 1.0
N A:MET38 4.2 42.3 1.0
O A:HOH582 4.2 23.8 1.0
O A:HOH581 4.2 29.2 1.0
OE1 A:GLN17 4.3 36.7 1.0
CB A:GLN17 4.3 36.2 1.0
O A:ASP36 4.3 32.6 1.0
CA A:MET38 4.4 45.6 1.0
CB A:ASP36 4.4 27.8 1.0
CA A:ASP36 4.5 28.4 1.0
O A:GLN17 4.6 34.2 1.0
OD1 A:ASN232 4.7 29.9 1.0
CB A:MET38 4.7 46.0 1.0
C A:GLN17 4.8 36.0 1.0
OD1 A:ASP231 4.8 34.3 1.0
NH1 A:ARG13 5.0 54.8 1.0

Magnesium binding site 2 out of 10 in 2pk0

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Magnesium binding site 2 out of 10 in the Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:28.8
occ:1.00
OD1 A:ASP192 2.1 29.9 1.0
OD2 A:ASP231 2.1 34.2 1.0
O A:HOH582 2.2 23.8 1.0
O A:HOH581 2.2 29.2 1.0
O A:HOH583 2.2 11.3 1.0
OD2 A:ASP36 2.3 27.6 1.0
CG A:ASP192 3.0 30.5 1.0
CG A:ASP231 3.1 32.4 1.0
CG A:ASP36 3.2 28.3 1.0
OD1 A:ASP231 3.3 34.3 1.0
OD2 A:ASP192 3.3 30.6 1.0
OD1 A:ASP36 3.5 27.2 1.0
O A:HOH556 3.8 35.2 1.0
O A:HOH584 3.9 45.7 1.0
MG A:MG501 4.0 27.1 1.0
O A:HOH530 4.1 33.0 1.0
O A:HOH578 4.1 23.9 1.0
O A:HOH526 4.2 36.7 1.0
O A:HOH579 4.2 29.9 1.0
N A:ASP192 4.4 29.0 1.0
CB A:ASP231 4.4 30.2 1.0
CB A:ASP192 4.4 29.8 1.0
N A:GLY193 4.5 26.2 1.0
O A:ASN232 4.5 31.1 1.0
OD1 A:ASP18 4.5 30.8 1.0
CB A:ASP36 4.6 27.8 1.0
CA A:ASP192 4.8 28.1 1.0
CB A:SER191 4.9 27.3 1.0
O A:HOH580 5.0 17.4 1.0
C A:ASP192 5.0 29.1 1.0

Magnesium binding site 3 out of 10 in 2pk0

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Magnesium binding site 3 out of 10 in the Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:39.7
occ:1.00
O B:HOH684 1.8 36.0 1.0
O B:HOH680 2.0 23.0 1.0
O B:GLY37 2.1 39.7 1.0
OD1 B:ASP36 2.2 28.0 1.0
O B:HOH685 2.2 23.3 1.0
O B:HOH609 2.3 22.8 1.0
CG B:ASP36 3.3 30.0 1.0
C B:GLY37 3.3 39.3 1.0
MG B:MG510 3.7 42.5 1.0
OD2 B:ASP36 3.8 28.8 1.0
CB B:GLN17 3.8 35.5 1.0
O B:HOH651 3.9 18.3 1.0
N B:GLY37 4.0 33.4 1.0
O B:HOH681 4.1 19.2 1.0
OD1 B:ASP18 4.1 32.0 1.0
CA B:GLY37 4.2 38.0 1.0
C B:ASP36 4.2 32.4 1.0
O B:HOH667 4.2 32.7 1.0
O B:HOH682 4.3 26.0 1.0
N B:MET38 4.3 42.3 1.0
OE1 B:GLN17 4.3 39.0 1.0
NH1 B:ARG13 4.3 57.1 1.0
O B:ASP36 4.4 33.9 1.0
CG B:GLN17 4.4 37.5 1.0
CA B:MET38 4.5 47.0 1.0
OD1 B:ASP231 4.5 38.3 1.0
OD1 B:ASN232 4.5 25.8 1.0
CB B:ASP36 4.6 30.6 1.0
C B:GLN17 4.7 35.8 1.0
CA B:ASP36 4.8 28.9 1.0
O B:GLN17 4.8 35.4 1.0
CD B:GLN17 4.8 38.5 1.0
CA B:GLN17 4.9 34.8 1.0
CB B:MET38 5.0 47.5 1.0

Magnesium binding site 4 out of 10 in 2pk0

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Magnesium binding site 4 out of 10 in the Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg510

b:42.5
occ:1.00
O B:HOH685 1.9 23.3 1.0
O B:HOH682 2.0 26.0 1.0
OD2 B:ASP36 2.1 28.8 1.0
O B:HOH681 2.2 19.2 1.0
OD2 B:ASP231 2.2 34.5 1.0
OD1 B:ASP192 2.2 30.5 1.0
CG B:ASP36 3.0 30.0 1.0
CG B:ASP231 3.1 36.1 1.0
CG B:ASP192 3.2 31.8 1.0
OD1 B:ASP36 3.2 28.0 1.0
OD1 B:ASP231 3.3 38.3 1.0
OD2 B:ASP192 3.5 31.5 1.0
O B:HOH687 3.7 35.7 1.0
MG B:MG503 3.7 39.7 1.0
O B:HOH651 3.7 18.3 1.0
O B:HOH680 3.8 23.0 1.0
O B:HOH609 4.0 22.8 1.0
O B:HOH679 4.2 38.7 1.0
O B:HOH686 4.3 37.0 1.0
OD1 B:ASP18 4.3 32.0 1.0
CB B:ASP36 4.4 30.6 1.0
O B:ASN232 4.5 30.3 1.0
CB B:ASP231 4.5 31.9 1.0
N B:GLY193 4.5 28.9 1.0
N B:ASP192 4.6 28.2 1.0
CB B:ASP192 4.6 31.5 1.0
OG B:SER191 4.8 29.2 1.0
CB B:SER191 4.9 28.2 1.0
CA B:ASP192 5.0 28.4 1.0

Magnesium binding site 5 out of 10 in 2pk0

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Magnesium binding site 5 out of 10 in the Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg504

b:16.8
occ:1.00
O C:HOH562 1.9 19.9 1.0
O C:HOH565 2.0 22.2 1.0
O C:HOH561 2.0 13.8 1.0
OD1 C:ASP36 2.1 32.7 1.0
O C:HOH560 2.2 20.6 1.0
O C:GLY37 2.3 32.2 1.0
CG C:ASP36 3.2 31.9 1.0
C C:GLY37 3.5 34.6 1.0
MG C:MG508 3.5 27.4 1.0
O C:HOH532 3.6 29.2 1.0
OD2 C:ASP36 3.7 27.5 1.0
O C:HOH569 4.0 25.1 1.0
N C:GLY37 4.0 36.0 1.0
OD1 C:ASP18 4.1 32.6 1.0
O C:HOH564 4.1 39.2 1.0
OE1 C:GLN17 4.1 37.6 1.0
O C:HOH533 4.2 23.8 1.0
C C:ASP36 4.2 32.9 1.0
CB C:GLN17 4.2 33.8 1.0
CA C:GLY37 4.4 33.2 1.0
OD1 C:ASN232 4.5 35.3 1.0
CB C:ASP36 4.5 31.5 1.0
N C:MET38 4.5 35.5 1.0
OD2 C:ASP231 4.5 38.5 1.0
O C:ASP36 4.5 35.1 1.0
CA C:MET38 4.6 36.9 1.0
CA C:ASP36 4.6 32.4 1.0
C C:GLN17 4.9 33.4 1.0
CB C:MET38 4.9 37.4 1.0
O C:GLN17 4.9 32.7 1.0
OD1 C:ASP231 5.0 38.3 1.0

Magnesium binding site 6 out of 10 in 2pk0

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Magnesium binding site 6 out of 10 in the Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg505

b:22.8
occ:1.00
O C:HOH567 1.8 35.1 1.0
O C:HOH566 2.0 36.8 1.0
O C:HOH568 2.1 28.0 1.0
OD2 C:ASP118 2.2 37.0 1.0
O C:HOH563 2.3 24.5 1.0
OD2 C:ASP192 2.4 30.9 1.0
CG C:ASP118 3.4 37.0 1.0
CG C:ASP192 3.5 32.1 1.0
CB C:ASP192 3.9 31.8 1.0
CB C:ASP118 4.2 34.8 1.0
ND2 C:ASN196 4.2 38.6 1.0
O C:ASN160 4.2 38.7 1.0
O C:HOH570 4.3 26.5 1.0
O C:HOH569 4.3 25.1 1.0
OD1 C:ASP118 4.3 38.1 1.0
O A:HOH534 4.3 28.6 1.0
ND2 C:ASN160 4.3 38.2 1.0
OD1 C:ASP192 4.5 31.4 1.0
CA C:ASN160 4.7 34.7 1.0
O C:HOH516 4.7 19.9 1.0
C C:ASN160 4.9 36.5 1.0
CG2 C:ILE162 4.9 33.6 1.0

Magnesium binding site 7 out of 10 in 2pk0

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Magnesium binding site 7 out of 10 in the Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg508

b:27.4
occ:1.00
O C:HOH569 2.0 25.1 1.0
O C:HOH564 2.1 39.2 1.0
O C:HOH565 2.1 22.2 1.0
OD2 C:ASP36 2.2 27.5 1.0
OD1 C:ASP231 2.2 38.3 1.0
OD1 C:ASP192 2.3 31.4 1.0
CG C:ASP36 3.1 31.9 1.0
CG C:ASP231 3.1 39.4 1.0
OD1 C:ASP36 3.2 32.7 1.0
CG C:ASP192 3.3 32.1 1.0
OD2 C:ASP231 3.4 38.5 1.0
MG C:MG504 3.5 16.8 1.0
OD2 C:ASP192 3.7 30.9 1.0
O C:HOH561 4.1 13.8 1.0
O C:HOH513 4.2 24.2 1.0
O C:HOH560 4.2 20.6 1.0
O C:HOH570 4.3 26.5 1.0
OD1 C:ASP18 4.3 32.6 1.0
CB C:ASP36 4.4 31.5 1.0
CB C:ASP231 4.5 37.5 1.0
O C:ASN232 4.5 33.0 1.0
N C:GLY193 4.6 32.0 1.0
CB C:ASP192 4.7 31.8 1.0
N C:ASP192 4.8 32.4 1.0
O A:HOH534 5.0 28.6 1.0

Magnesium binding site 8 out of 10 in 2pk0

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Magnesium binding site 8 out of 10 in the Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg506

b:33.2
occ:1.00
O D:HOH765 2.0 24.4 1.0
OD1 D:ASP36 2.0 35.2 1.0
O D:HOH758 2.0 38.9 1.0
O D:GLY37 2.1 31.3 1.0
O D:HOH759 2.2 40.5 1.0
O D:HOH760 2.4 16.0 1.0
CG D:ASP36 3.2 33.4 1.0
C D:GLY37 3.3 33.7 1.0
O D:HOH726 3.7 23.5 1.0
OD2 D:ASP36 3.8 31.8 1.0
O D:HOH764 3.8 25.2 1.0
N D:GLY37 3.8 36.5 1.0
O D:HOH763 3.9 26.8 1.0
C D:ASP36 3.9 34.6 1.0
OE1 D:GLN17 4.0 37.9 1.0
MG D:MG507 4.0 29.4 1.0
O D:HOH719 4.2 20.4 1.0
CA D:GLY37 4.2 34.6 1.0
O D:ASP36 4.2 35.0 1.0
N D:MET38 4.2 34.5 1.0
CB D:GLN17 4.3 35.2 1.0
CA D:MET38 4.3 36.6 1.0
CB D:ASP36 4.4 31.6 1.0
O D:HOH762 4.4 30.4 1.0
OD1 D:ASP18 4.4 35.0 1.0
CA D:ASP36 4.5 33.9 1.0
CB D:MET38 4.5 36.8 1.0
OD1 D:ASN232 4.8 36.9 1.0
OD2 D:ASP231 4.8 39.9 1.0
O D:GLN17 4.9 36.0 1.0

Magnesium binding site 9 out of 10 in 2pk0

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Magnesium binding site 9 out of 10 in the Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg507

b:29.4
occ:1.00
O D:HOH762 2.1 30.4 1.0
OD1 D:ASP192 2.2 32.3 1.0
O D:HOH763 2.2 26.8 1.0
OD2 D:ASP36 2.2 31.8 1.0
OD1 D:ASP231 2.2 37.2 1.0
O D:HOH760 2.2 16.0 1.0
CG D:ASP231 3.0 38.1 1.0
CG D:ASP36 3.1 33.4 1.0
CG D:ASP192 3.2 32.3 1.0
OD2 D:ASP231 3.3 39.9 1.0
OD1 D:ASP36 3.4 35.2 1.0
OD2 D:ASP192 3.6 31.7 1.0
MG D:MG506 4.0 33.2 1.0
O D:ASN232 4.0 37.0 1.0
N D:GLY193 4.1 33.1 1.0
O D:HOH759 4.1 40.5 1.0
O D:HOH703 4.3 29.8 1.0
OD1 D:ASP18 4.4 35.0 1.0
CB D:ASP231 4.4 36.7 1.0
N D:ASP192 4.4 31.8 1.0
CB D:ASP36 4.4 31.6 1.0
CB D:ASP192 4.5 31.8 1.0
O D:HOH758 4.6 38.9 1.0
CB D:SER191 4.7 31.8 1.0
O D:HOH725 4.8 20.7 1.0
N D:ASN232 4.8 35.1 1.0
CA D:ASP192 4.8 31.1 1.0
CA D:GLY193 4.8 33.6 1.0
C D:ASP192 4.8 31.6 1.0
OD2 D:ASP18 4.9 32.7 1.0
O D:HOH765 5.0 24.4 1.0
CB D:ASN232 5.0 32.7 1.0
C D:ASN232 5.0 35.8 1.0

Magnesium binding site 10 out of 10 in 2pk0

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Magnesium binding site 10 out of 10 in the Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the S. Agalactiae Serine/Threonine Phosphatase at 2.65 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg509

b:30.2
occ:1.00
O D:HOH761 1.9 31.4 1.0
O D:HOH766 2.0 33.4 1.0
OD2 D:ASP118 2.1 37.2 1.0
O D:HOH728 2.2 30.5 1.0
OD2 D:ASP192 2.3 31.7 1.0
O D:HOH727 2.5 24.0 1.0
CG D:ASP192 3.2 32.3 1.0
CG D:ASP118 3.3 36.1 1.0
CB D:ASP192 3.4 31.8 1.0
ND2 D:ASN196 3.8 37.3 1.0
O D:HOH743 3.9 27.2 1.0
CB D:ASP118 4.1 32.1 1.0
OD1 D:ASP118 4.3 35.8 1.0
OD1 D:ASP192 4.4 32.3 1.0
O D:HOH725 4.4 20.7 1.0
ND2 D:ASN160 4.5 35.3 1.0
O D:HOH763 4.5 26.8 1.0
O D:ASN160 4.6 38.6 1.0
OD1 D:ASN196 4.7 39.4 1.0
CG D:ASN196 4.7 39.5 1.0
CA D:ASN160 4.9 36.1 1.0
CA D:ASP192 4.9 31.1 1.0

Reference:

M.K.Rantanen, L.Lehtio, L.Rajagopal, C.E.Rubens, A.Goldman. Structure of Streptococcus Agalactiae Serine/Threonine Phosphatase. the Subdomain Conformation Is Coupled to the Binding of A Third Metal Ion Febs J. V. 274 3128 2007.
ISSN: ISSN 1742-464X
PubMed: 17521332
DOI: 10.1111/J.1742-4658.2007.05845.X
Page generated: Mon Dec 14 07:34:38 2020

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