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Magnesium in PDB 2q5e: Crystal Structure of Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2

Enzymatic activity of Crystal Structure of Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2

All present enzymatic activity of Crystal Structure of Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2:
3.1.3.16;

Protein crystallography data

The structure of Crystal Structure of Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2, PDB code: 2q5e was solved by J.B.Bonanno, M.Dickey, K.T.Bain, C.Lau, R.Romero, D.Smith, S.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 108.643, 117.637, 170.134, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 27.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2 (pdb code 2q5e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2, PDB code: 2q5e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2q5e

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Magnesium binding site 1 out of 8 in the Crystal Structure of Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2


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 Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1

b:38.7
occ:1.00
 OD2 A:ASP107 2.3 45.2 1.0
O A:ASP109 2.5 28.7 1.0
OD1 A:ASN218 2.6 30.4 1.0
CG A:ASP107 3.1 36.6 1.0
OD1 A:ASP107 3.2 34.9 1.0
C A:ASP109 3.7 29.3 1.0
CG A:ASN218 3.7 27.8 1.0
OG A:SER219 3.9 30.6 1.0
OG1 A:THR111 4.0 26.0 1.0
OD1 A:ASP217 4.0 47.2 1.0
ND2 A:ASN218 4.2 23.8 1.0
CB A:ASP107 4.4 31.9 1.0
CA A:ASP109 4.4 29.3 1.0
N A:ASP109 4.4 27.2 1.0
OE1 A:GLU110 4.5 28.7 1.0
CB A:ASP109 4.6 30.6 1.0
CB A:GLU110 4.7 27.7 1.0
N A:GLU110 4.7 28.8 1.0
N A:THR111 4.8 26.8 1.0
CG A:ASP217 4.9 37.0 1.0
N A:SER219 4.9 26.9 1.0
N A:ASN218 4.9 27.3 1.0
CB A:ASN218 4.9 27.0 1.0
C A:LEU108 5.0 25.6 1.0
CA A:GLU110 5.0 28.3 1.0
CB A:SER219 5.0 28.4 1.0

Magnesium binding site 2 out of 8 in 2q5e

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Magnesium binding site 2 out of 8 in the Crystal Structure of Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2


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 Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:40.4
occ:1.00
 OD2 B:ASP107 2.3 38.8 1.0
O B:HOH275 2.3 35.4 1.0
OD1 B:ASN218 2.4 33.4 1.0
O B:HOH280 2.5 35.1 1.0
O B:ASP109 2.5 30.4 1.0
CG B:ASN218 3.2 31.2 1.0
ND2 B:ASN218 3.4 25.7 1.0
CG B:ASP107 3.5 35.9 1.0
OG B:SER219 3.7 35.4 1.0
C B:ASP109 3.7 30.6 1.0
OD1 B:ASP217 4.0 43.7 1.0
OG1 B:THR111 4.1 30.9 1.0
OD1 B:ASP107 4.2 37.5 1.0
O B:HOH281 4.3 36.6 1.0
CB B:GLU110 4.4 31.0 1.0
CA B:ASP109 4.5 31.0 1.0
OE1 B:GLU110 4.5 33.5 1.0
N B:ASP109 4.6 30.0 1.0
CB B:ASP107 4.6 32.6 1.0
CB B:ASN218 4.6 28.2 1.0
CB B:ASP109 4.7 32.4 1.0
N B:GLU110 4.7 30.0 1.0
N B:ASN218 4.7 27.1 1.0
N B:SER219 4.7 28.6 1.0
CB B:SER219 4.9 29.6 1.0
CA B:GLU110 4.9 30.3 1.0
N B:THR111 4.9 30.4 1.0
CG B:ASP217 5.0 36.3 1.0
C B:GLU110 5.0 30.7 1.0

Magnesium binding site 3 out of 8 in 2q5e

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Magnesium binding site 3 out of 8 in the Crystal Structure of Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2


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 Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1

b:60.9
occ:1.00
 O C:ASP109 2.2 36.5 1.0
OD2 C:ASP107 2.5 48.2 1.0
OD1 C:ASN218 2.7 36.9 1.0
C C:ASP109 3.2 36.5 1.0
CG C:ASN218 3.6 39.8 1.0
CG C:ASP107 3.7 38.5 1.0
ND2 C:ASN218 3.8 44.4 1.0
OE1 C:GLU110 3.8 44.8 1.0
CB C:ASP109 3.8 38.5 1.0
CA C:ASP109 3.9 37.5 1.0
CB C:GLU110 4.1 38.4 1.0
N C:GLU110 4.1 37.5 1.0
OD1 C:ASP217 4.2 43.2 1.0
OD1 C:ASP107 4.2 47.8 1.0
N C:ASP109 4.3 36.9 1.0
OG C:SER219 4.4 44.8 1.0
OG1 C:THR111 4.5 39.7 1.0
CA C:GLU110 4.5 38.1 1.0
CD C:GLU110 4.6 41.6 1.0
CB C:ASP107 4.7 33.2 1.0
CG C:GLU110 4.7 37.5 1.0
C C:GLU110 4.8 38.6 1.0
N C:THR111 4.9 38.9 1.0
C C:LEU108 5.0 36.0 1.0

Magnesium binding site 4 out of 8 in 2q5e

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Magnesium binding site 4 out of 8 in the Crystal Structure of Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2


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 Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1

b:58.8
occ:1.00
 OD2 D:ASP107 2.0 42.1 1.0
O D:ASP109 2.3 38.3 1.0
OD1 D:ASN218 2.3 39.5 1.0
CG D:ASP107 3.1 37.9 1.0
CG D:ASN218 3.4 40.5 1.0
C D:ASP109 3.4 38.2 1.0
OG1 D:THR111 3.5 36.0 1.0
OD1 D:ASP217 3.8 41.8 1.0
ND2 D:ASN218 3.8 42.0 1.0
OD1 D:ASP107 3.8 43.8 1.0
CB D:ASP107 4.0 34.6 1.0
CA D:ASP109 4.1 38.8 1.0
N D:ASP109 4.2 38.3 1.0
CB D:ASP109 4.2 39.9 1.0
CB D:GLU110 4.4 37.4 1.0
OE1 D:GLU110 4.4 49.1 1.0
N D:GLU110 4.5 37.3 1.0
OG D:SER219 4.5 45.2 1.0
N D:THR111 4.5 35.1 1.0
CB D:THR111 4.6 35.0 1.0
CB D:ASN218 4.7 37.3 1.0
N D:ASN218 4.7 34.8 1.0
CA D:GLU110 4.7 36.9 1.0
C D:GLU110 4.7 35.6 1.0
C D:LEU108 4.8 36.8 1.0
CG D:ASP217 4.8 37.3 1.0
N D:LEU108 5.0 35.6 1.0

Magnesium binding site 5 out of 8 in 2q5e

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Magnesium binding site 5 out of 8 in the Crystal Structure of Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2


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 Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1

b:47.1
occ:1.00
 OD1 E:ASN218 2.2 29.8 1.0
OD2 E:ASP107 2.2 46.3 1.0
O E:ASP109 2.4 36.0 1.0
CG E:ASN218 3.3 30.3 1.0
CG E:ASP107 3.3 43.2 1.0
C E:ASP109 3.5 36.5 1.0
OG1 E:THR111 3.6 38.3 1.0
ND2 E:ASN218 3.7 29.1 1.0
OD1 E:ASP217 3.9 44.4 1.0
OD1 E:ASP107 3.9 43.7 1.0
OG E:SER219 4.0 41.7 1.0
CA E:ASP109 4.3 37.6 1.0
CB E:GLU110 4.3 36.8 1.0
CB E:ASP109 4.4 38.6 1.0
O E:HOH273 4.5 44.7 1.0
CB E:ASP107 4.5 41.8 1.0
N E:THR111 4.5 37.7 1.0
N E:GLU110 4.5 36.6 1.0
N E:ASP109 4.6 36.4 1.0
CB E:ASN218 4.6 31.9 1.0
N E:ASN218 4.6 34.5 1.0
C E:GLU110 4.7 37.5 1.0
OE1 E:GLU110 4.7 38.4 1.0
CA E:GLU110 4.7 36.9 1.0
CG E:ASP217 4.8 40.4 1.0
CB E:THR111 4.8 38.8 1.0
N E:SER219 4.9 32.7 1.0

Magnesium binding site 6 out of 8 in 2q5e

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Magnesium binding site 6 out of 8 in the Crystal Structure of Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2


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 Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1

b:59.1
occ:1.00
 OD2 F:ASP107 2.0 44.8 1.0
O F:ASP109 2.3 43.5 1.0
OD1 F:ASN218 2.6 48.6 1.0
CG F:ASP107 3.0 42.0 1.0
CG F:ASN218 3.4 47.2 1.0
OD1 F:ASP107 3.4 44.2 1.0
C F:ASP109 3.5 42.9 1.0
ND2 F:ASN218 3.5 48.0 1.0
OD1 F:ASP217 3.6 42.9 1.0
OG1 F:THR111 3.9 36.0 1.0
CB F:ASP107 4.1 39.0 1.0
CA F:ASP109 4.3 43.0 1.0
CB F:GLU110 4.3 42.6 1.0
OG F:SER219 4.3 52.8 1.0
N F:ASP109 4.4 42.0 1.0
CB F:ASP109 4.4 43.3 1.0
N F:GLU110 4.5 42.8 1.0
N F:ASN218 4.7 44.2 1.0
CG F:ASP217 4.7 44.6 1.0
CA F:GLU110 4.7 42.5 1.0
CB F:ASN218 4.8 46.0 1.0
N F:THR111 4.8 38.9 1.0
C F:GLU110 4.8 41.1 1.0
OE1 F:GLU110 4.9 54.5 1.0
C F:LEU108 4.9 39.9 1.0
N F:LEU108 5.0 39.6 1.0

Magnesium binding site 7 out of 8 in 2q5e

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Magnesium binding site 7 out of 8 in the Crystal Structure of Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2


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 Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1

b:50.5
occ:1.00
 OD1 G:ASN218 2.1 39.3 1.0
OD2 G:ASP107 2.4 49.1 1.0
O G:ASP109 2.8 41.7 1.0
CG G:ASN218 3.0 38.9 1.0
CG G:ASP107 3.3 44.1 1.0
OD1 G:ASP217 3.3 50.7 1.0
ND2 G:ASN218 3.4 35.8 1.0
OG G:SER219 3.5 36.2 1.0
OG1 G:THR111 3.6 45.1 1.0
OD1 G:ASP107 3.7 43.7 1.0
C G:ASP109 3.9 41.3 1.0
N G:SER219 4.3 39.0 1.0
CG G:ASP217 4.4 46.9 1.0
N G:ASN218 4.4 40.0 1.0
CB G:ASN218 4.4 38.7 1.0
CB G:ASP107 4.5 44.4 1.0
CB G:SER219 4.5 35.9 1.0
CA G:ASP109 4.8 42.2 1.0
CB G:GLU110 4.8 40.6 1.0
CA G:ASN218 4.8 39.6 1.0
OD2 G:ASP217 4.8 50.0 1.0
N G:GLU110 4.8 41.1 1.0
CB G:ASP109 4.8 42.3 1.0
OE1 G:GLU110 4.9 45.5 1.0
N G:THR111 4.9 41.5 1.0
C G:ASN218 4.9 39.8 1.0

Magnesium binding site 8 out of 8 in 2q5e

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Magnesium binding site 8 out of 8 in the Crystal Structure of Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2


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 Human Carboxy-Terminal Domain Rna Polymerase II Polypeptide A Small Phosphatase 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1

b:47.7
occ:1.00
 OD2 H:ASP107 2.2 42.2 1.0
O H:ASP109 2.3 34.4 1.0
OD1 H:ASN218 2.6 32.6 1.0
C H:ASP109 3.4 33.9 1.0
CG H:ASP107 3.4 34.8 1.0
CG H:ASN218 3.7 35.2 1.0
CB H:ASP109 3.9 36.4 1.0
OD1 H:ASP107 4.0 40.2 1.0
ND2 H:ASN218 4.0 39.8 1.0
CA H:ASP109 4.0 35.0 1.0
N H:ASP109 4.2 35.2 1.0
OE1 H:GLU110 4.3 44.5 1.0
N H:GLU110 4.4 33.9 1.0
OG1 H:THR111 4.4 35.1 1.0
CB H:GLU110 4.5 33.8 1.0
OD1 H:ASP217 4.5 33.0 1.0
OG H:SER219 4.6 39.5 1.0
CB H:ASP107 4.6 28.4 1.0
CA H:GLU110 4.8 32.6 1.0
C H:GLU110 4.9 31.9 1.0

Reference:

S.C.Almo, J.B.Bonanno, J.M.Sauder, S.Emtage, T.P.Dilorenzo, V.Malashkevich, S.R.Wasserman, S.Swaminathan, S.Eswaramoorthy, R.Agarwal, D.Kumaran, M.Madegowda, S.Ragumani, Y.Patskovsky, J.Alvarado, U.A.Ramagopal, J.Faber-Barata, M.R.Chance, A.Sali, A.Fiser, Z.Y.Zhang, D.S.Lawrence, S.K.Burley. Structural Genomics of Protein Phosphatases. J.Struct.Funct.Genom. V. 8 121 2007.
ISSN: ISSN 1345-711X
PubMed: 18058037
DOI: 10.1007/S10969-007-9036-1
Page generated: Wed Aug 14 02:35:56 2024

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