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Magnesium in PDB 3d6a: Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate.

Protein crystallography data

The structure of Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate., PDB code: 3d6a was solved by Y.Chen, N.Carpino, N.Nassar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.95 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.205, 116.665, 121.471, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.7

Other elements in 3d6a:

The structure of Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate. also contains other interesting chemical elements:

Tungsten (W) 4 atoms
Sodium (Na) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate. (pdb code 3d6a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate., PDB code: 3d6a:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3d6a

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Magnesium binding site 1 out of 9 in the Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate.


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 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2

b:54.5
occ:1.00
 NH2 A:ARG437 3.6 39.4 1.0
NZ A:LYS465 4.1 44.2 1.0
NE A:ARG437 4.3 39.6 1.0
CE A:LYS465 4.3 41.5 1.0
CZ A:ARG437 4.4 40.0 1.0

Magnesium binding site 2 out of 9 in 3d6a

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Magnesium binding site 2 out of 9 in the Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate.


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 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3

b:44.9
occ:1.00
 N A:LEU492 3.5 38.0 1.0
CA A:THR491 3.8 38.5 1.0
CG A:LEU492 3.8 38.9 1.0
CB A:THR491 3.9 38.4 1.0
O A:HOH676 3.9 46.5 1.0
NH1 A:ARG512 3.9 48.6 1.0
CZ A:ARG512 4.0 48.1 1.0
C A:THR491 4.2 38.3 1.0
CG2 A:THR491 4.2 38.5 1.0
NE A:ARG512 4.2 48.2 1.0
CB A:LEU492 4.4 38.5 1.0
NH2 A:ARG512 4.4 47.0 1.0
CD2 A:LEU492 4.5 39.7 1.0
CD A:ARG512 4.5 44.9 1.0
CA A:LEU492 4.6 38.6 1.0
CD1 A:LEU492 4.7 39.4 1.0

Magnesium binding site 3 out of 9 in 3d6a

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Magnesium binding site 3 out of 9 in the Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate.


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 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5

b:44.5
occ:1.00
 N A:TYR521 3.7 36.1 1.0
CB A:SER520 3.7 36.7 1.0
CA A:SER520 3.8 36.7 1.0
CZ2 A:TRP477 4.3 31.7 1.0
C A:SER520 4.3 36.4 1.0
NZ A:LYS479 4.6 46.9 1.0
CB A:TYR521 4.6 35.3 1.0
CH2 A:TRP477 4.8 32.6 1.0
CA A:TYR521 4.8 35.6 1.0
OG A:SER520 5.0 37.0 1.0

Magnesium binding site 4 out of 9 in 3d6a

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Magnesium binding site 4 out of 9 in the Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate.


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 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg7

b:31.9
occ:1.00
 NZ D:LYS579 2.8 46.3 1.0
CZ3 A:TRP620 3.3 64.2 1.0
CZ2 B:TRP620 3.7 56.8 1.0
CH2 A:TRP620 4.0 64.8 1.0
CE3 A:TRP620 4.2 64.7 1.0
CG1 A:VAL614 4.3 41.4 1.0
CE D:LYS579 4.3 44.1 1.0
CG2 A:VAL614 4.4 41.4 1.0
N A:ASN616 4.4 46.7 1.0
CH2 B:TRP620 4.5 57.0 1.0
ND2 A:ASN619 4.5 60.1 1.0
N A:PHE615 4.5 43.2 1.0
MG B:MG9 4.6 62.8 1.0
CA A:PHE615 4.6 43.8 1.0
C A:VAL614 4.6 42.2 1.0
CE2 B:TRP620 4.7 57.0 1.0
O A:VAL614 4.7 42.4 1.0
C A:PHE615 4.7 45.3 1.0
CB A:VAL614 4.8 41.7 1.0
CB A:ASN616 4.9 48.3 1.0
NE1 B:TRP620 4.9 57.3 1.0
CD D:LYS579 4.9 40.9 1.0

Magnesium binding site 5 out of 9 in 3d6a

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Magnesium binding site 5 out of 9 in the Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate.


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 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg9

b:62.8
occ:1.00
 NE1 B:TRP620 3.4 57.3 1.0
ND2 B:ASN619 3.9 51.4 1.0
N B:ASN616 4.1 44.7 1.0
CD1 B:TRP620 4.1 57.0 1.0
CB B:ASN616 4.1 45.6 1.0
CB B:ASN619 4.5 52.7 1.0
CE2 B:TRP620 4.5 57.0 1.0
O B:VAL614 4.5 42.1 1.0
MG A:MG7 4.6 31.9 1.0
CA B:ASN616 4.7 45.4 1.0
CG B:ASN619 4.7 52.5 1.0
O B:ASN616 4.7 45.8 1.0
CZ2 B:TRP620 4.9 56.8 1.0

Magnesium binding site 6 out of 9 in 3d6a

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Magnesium binding site 6 out of 9 in the Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate.


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 the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg6

b:58.6
occ:1.00
 O C:HOH97 2.2 34.0 1.0
NH1 B:ARG578 3.7 46.9 1.0
N C:LYS376 3.8 34.4 1.0
CA C:GLY375 3.8 32.2 1.0
CD B:ARG578 3.9 46.9 1.0
CG C:LYS376 4.0 39.0 1.0
C C:GLY375 4.4 33.1 1.0
CG B:ARG578 4.5 46.5 1.0
CZ B:ARG578 4.5 46.2 1.0
NE B:ARG578 4.6 47.0 1.0
CD C:LYS376 4.6 43.8 1.0
CB C:LYS376 4.7 36.1 1.0
CE C:LYS376 4.7 45.6 1.0
CA C:LYS376 4.9 35.5 1.0

Magnesium binding site 7 out of 9 in 3d6a

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Magnesium binding site 7 out of 9 in the Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg8

b:64.1
occ:1.00
 NE1 C:TRP620 3.1 49.6 1.0
N C:ASN616 3.5 37.0 1.0
ND2 C:ASN619 3.6 47.3 1.0
CD1 C:TRP620 3.8 49.4 1.0
O C:VAL614 4.0 35.2 1.0
CA C:PHE615 4.1 36.1 1.0
CB C:ASN616 4.2 38.1 1.0
O C:ASN616 4.2 37.5 1.0
C C:PHE615 4.2 36.4 1.0
CB C:ASN619 4.3 45.5 1.0
CE2 C:TRP620 4.3 50.7 1.0
CA C:ASN616 4.3 37.8 1.0
CG C:ASN619 4.5 46.7 1.0
CD1 C:PHE615 4.6 33.2 1.0
C C:ASN616 4.7 37.6 1.0
C C:VAL614 4.7 35.5 1.0
N C:PHE615 4.8 35.7 1.0
CZ2 C:TRP620 4.8 50.1 1.0
ND2 D:ASN619 5.0 66.0 1.0

Magnesium binding site 8 out of 9 in 3d6a

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Magnesium binding site 8 out of 9 in the Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1

b:29.8
occ:1.00
 ND2 D:ASN619 3.9 66.0 1.0
CZ2 C:TRP620 3.9 50.1 1.0
N D:ASN616 4.1 53.2 1.0
CG1 D:VAL614 4.1 45.9 1.0
CG2 D:VAL614 4.2 45.7 1.0
N D:PHE615 4.3 48.3 1.0
NZ A:LYS579 4.3 47.2 1.0
ND2 D:ASN616 4.4 57.9 1.0
C D:PHE615 4.4 51.4 1.0
CA D:PHE615 4.4 50.0 1.0
C D:VAL614 4.5 46.7 1.0
O D:VAL614 4.6 46.8 1.0
CH2 C:TRP620 4.6 49.6 1.0
CB D:VAL614 4.7 45.7 1.0
CB D:ASN616 4.7 55.4 1.0
NZ B:LYS579 4.9 48.3 1.0
CE2 C:TRP620 4.9 50.7 1.0
CG D:ASN619 5.0 65.8 1.0
CD A:LYS579 5.0 42.1 1.0
CA D:ASN616 5.0 54.8 1.0

Magnesium binding site 9 out of 9 in 3d6a

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Magnesium binding site 9 out of 9 in the Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg4

b:44.9
occ:1.00
 N D:TYR521 3.9 38.4 1.0
CA D:SER520 3.9 38.1 1.0
CB D:SER520 4.1 37.6 1.0
NZ D:LYS479 4.2 45.5 1.0
O D:HOH656 4.3 40.6 1.0
CE D:LYS479 4.4 43.6 1.0
C D:SER520 4.5 38.1 1.0
CZ2 D:TRP477 4.5 32.8 1.0
CB D:TYR521 4.9 37.6 1.0

Reference:

Y.Chen, J.Jakoncic, N.Carpino, N.Nassar. Structural and Functional Characterization of the 2H-Phosphatase Domain of Sts-2 Reveals An Acid-Dependent Phosphatase Activity. Biochemistry V. 48 1681 2009.
ISSN: ISSN 0006-2960
PubMed: 19196006
DOI: 10.1021/BI802219N
Page generated: Wed Aug 14 12:24:09 2024

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