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Magnesium in PDB 4bkm: Crystal Structure of the Murine Aum (Phosphoglycolate Phosphatase) Capping Domain As A Fusion Protein with the Catalytic Core Domain of Murine Chronophin (Pyridoxal Phosphate Phosphatase)

Enzymatic activity of Crystal Structure of the Murine Aum (Phosphoglycolate Phosphatase) Capping Domain As A Fusion Protein with the Catalytic Core Domain of Murine Chronophin (Pyridoxal Phosphate Phosphatase)

All present enzymatic activity of Crystal Structure of the Murine Aum (Phosphoglycolate Phosphatase) Capping Domain As A Fusion Protein with the Catalytic Core Domain of Murine Chronophin (Pyridoxal Phosphate Phosphatase):
3.1.3.18; 3.1.3.3; 3.1.3.74;

Protein crystallography data

The structure of Crystal Structure of the Murine Aum (Phosphoglycolate Phosphatase) Capping Domain As A Fusion Protein with the Catalytic Core Domain of Murine Chronophin (Pyridoxal Phosphate Phosphatase), PDB code: 4bkm was solved by G.Knobloch, A.Seifried, A.Gohla, H.Schindelin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.737 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.500, 91.960, 105.920, 90.00, 90.20, 90.00
R / Rfree (%) 19.76 / 25.64

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Murine Aum (Phosphoglycolate Phosphatase) Capping Domain As A Fusion Protein with the Catalytic Core Domain of Murine Chronophin (Pyridoxal Phosphate Phosphatase) (pdb code 4bkm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Murine Aum (Phosphoglycolate Phosphatase) Capping Domain As A Fusion Protein with the Catalytic Core Domain of Murine Chronophin (Pyridoxal Phosphate Phosphatase), PDB code: 4bkm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4bkm

Go back to Magnesium Binding Sites List in 4bkm
Magnesium binding site 1 out of 4 in the Crystal Structure of the Murine Aum (Phosphoglycolate Phosphatase) Capping Domain As A Fusion Protein with the Catalytic Core Domain of Murine Chronophin (Pyridoxal Phosphate Phosphatase)


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 Murine Aum (Phosphoglycolate Phosphatase) Capping Domain As A Fusion Protein with the Catalytic Core Domain of Murine Chronophin (Pyridoxal Phosphate Phosphatase) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1304

b:88.9
occ:1.00
 OD1 A:ASP247 1.9 67.4 1.0
OD2 A:ASP25 2.1 92.0 1.0
O A:ASP27 2.4 67.2 1.0
O A:HOH2004 2.5 47.5 1.0
CG A:ASP247 2.6 71.4 1.0
OD2 A:ASP247 2.8 78.3 1.0
CG A:ASP25 3.3 77.1 1.0
H A:ASP247 3.5 74.4 1.0
C A:ASP27 3.6 80.9 1.0
OD2 A:ASP252 3.7 65.3 1.0
HB2 A:ASP27 3.8 99.0 1.0
H A:ARG248 3.8 0.2 1.0
OD1 A:ASP25 3.9 60.4 1.0
HG21 A:VAL29 4.0 85.5 1.0
HA3 A:GLY28 4.0 89.8 1.0
HB2 A:ARG248 4.0 86.9 1.0
CB A:ASP247 4.1 61.0 1.0
N A:ASP247 4.3 62.0 1.0
HB3 A:ASP25 4.3 71.7 1.0
N A:ARG248 4.4 83.5 1.0
HB3 A:ARG248 4.4 86.9 1.0
CA A:ASP27 4.4 81.3 1.0
HB3 A:ASP247 4.4 73.1 1.0
CB A:ASP27 4.5 82.5 1.0
CB A:ASP25 4.5 59.8 1.0
H A:ASP27 4.5 98.1 1.0
N A:GLY28 4.6 84.0 1.0
N A:ASP27 4.6 81.8 1.0
HB3 A:ASP27 4.6 99.0 1.0
CG A:ASP252 4.6 70.5 1.0
CB A:ARG248 4.6 72.4 1.0
CA A:ASP247 4.7 67.1 1.0
HB2 A:ASP247 4.7 73.1 1.0
CA A:GLY28 4.7 74.8 1.0
OD1 A:ASP252 4.8 81.8 1.0
CG2 A:VAL29 4.8 71.2 1.0
HG22 A:VAL29 4.8 85.5 1.0
HB2 A:ASP25 4.8 71.7 1.0
HG1 A:THR251 4.8 0.1 1.0
C A:ASP247 4.9 76.1 1.0
O A:HOH2006 4.9 50.5 1.0

Magnesium binding site 2 out of 4 in 4bkm

Go back to Magnesium Binding Sites List in 4bkm
Magnesium binding site 2 out of 4 in the Crystal Structure of the Murine Aum (Phosphoglycolate Phosphatase) Capping Domain As A Fusion Protein with the Catalytic Core Domain of Murine Chronophin (Pyridoxal Phosphate Phosphatase)


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 Murine Aum (Phosphoglycolate Phosphatase) Capping Domain As A Fusion Protein with the Catalytic Core Domain of Murine Chronophin (Pyridoxal Phosphate Phosphatase) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1304

b:59.9
occ:1.00
 OD2 B:ASP25 2.4 92.7 1.0
O B:HOH2003 2.5 52.1 1.0
HB2 B:ASP27 2.6 93.7 1.0
O B:ASP27 2.6 69.1 1.0
OD1 B:ASP25 3.1 57.0 1.0
CG B:ASP25 3.1 73.0 1.0
H B:ASP27 3.4 87.6 1.0
OD1 B:ASP247 3.4 83.9 1.0
CB B:ASP27 3.4 78.1 1.0
C B:ASP27 3.5 77.0 1.0
CA B:ASP27 3.7 68.4 1.0
N B:ASP27 3.8 73.0 1.0
HB3 B:ASP27 3.8 93.7 1.0
O B:HOH2002 3.8 67.3 1.0
OD2 B:ASP247 4.0 97.5 1.0
CG B:ASP247 4.1 90.1 1.0
HZ2 B:LYS222 4.6 0.5 1.0
H B:CYS26 4.6 78.5 1.0
CG B:ASP27 4.6 83.8 1.0
CB B:ASP25 4.6 63.2 1.0
HA B:ASP27 4.7 82.0 1.0
N B:GLY28 4.7 92.4 1.0
HG22 B:VAL29 4.8 94.9 1.0
OD2 B:ASP27 4.8 87.9 1.0
C B:CYS26 4.8 79.5 1.0
HA3 B:GLY28 4.8 0.1 1.0
HZ3 B:LYS222 4.8 0.5 1.0
HB3 B:ASP25 4.9 75.9 1.0
N B:CYS26 4.9 65.4 1.0
OD2 B:ASP252 5.0 76.8 1.0
HB2 B:ARG248 5.0 92.8 1.0

Magnesium binding site 3 out of 4 in 4bkm

Go back to Magnesium Binding Sites List in 4bkm
Magnesium binding site 3 out of 4 in the Crystal Structure of the Murine Aum (Phosphoglycolate Phosphatase) Capping Domain As A Fusion Protein with the Catalytic Core Domain of Murine Chronophin (Pyridoxal Phosphate Phosphatase)


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 Murine Aum (Phosphoglycolate Phosphatase) Capping Domain As A Fusion Protein with the Catalytic Core Domain of Murine Chronophin (Pyridoxal Phosphate Phosphatase) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1304

b:61.7
occ:1.00
 O C:HOH2004 2.1 52.3 1.0
OD2 C:ASP25 2.2 88.3 1.0
O C:ASP27 2.4 70.9 1.0
HB2 C:ASP27 2.7 0.6 1.0
OD1 C:ASP247 3.0 58.8 1.0
CG C:ASP25 3.1 80.7 1.0
OD1 C:ASP25 3.2 81.5 1.0
C C:ASP27 3.4 81.1 1.0
CB C:ASP27 3.5 96.4 1.0
H C:ASP27 3.5 0.1 1.0
OD2 C:ASP247 3.6 75.6 1.0
CG C:ASP247 3.7 63.0 1.0
CA C:ASP27 3.8 86.8 1.0
O C:HOH2040 3.8 66.6 1.0
HB3 C:ASP27 3.8 0.6 1.0
N C:ASP27 3.9 90.1 1.0
O C:HOH2003 4.1 56.1 1.0
OD2 C:ASP252 4.4 83.1 1.0
CB C:ASP25 4.5 71.4 1.0
HA3 C:GLY28 4.5 80.5 1.0
N C:GLY28 4.6 75.3 1.0
HB3 C:ASP25 4.6 85.6 1.0
HG21 C:VAL29 4.7 96.4 1.0
H C:ASP247 4.7 76.1 1.0
HZ3 C:LYS222 4.7 93.6 1.0
HZ2 C:LYS222 4.7 93.6 1.0
HA C:ASP27 4.7 0.1 1.0
H C:CYS26 4.7 94.4 1.0
CG C:ASP27 4.8 0.2 1.0
C C:CYS26 4.8 83.2 1.0
HB2 C:ASP25 4.9 85.6 1.0

Magnesium binding site 4 out of 4 in 4bkm

Go back to Magnesium Binding Sites List in 4bkm
Magnesium binding site 4 out of 4 in the Crystal Structure of the Murine Aum (Phosphoglycolate Phosphatase) Capping Domain As A Fusion Protein with the Catalytic Core Domain of Murine Chronophin (Pyridoxal Phosphate Phosphatase)


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 Murine Aum (Phosphoglycolate Phosphatase) Capping Domain As A Fusion Protein with the Catalytic Core Domain of Murine Chronophin (Pyridoxal Phosphate Phosphatase) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1304

b:67.6
occ:1.00
 OD2 D:ASP25 2.1 92.0 1.0
O D:HOH2004 2.2 57.9 1.0
O D:ASP27 2.4 91.8 1.0
HB2 D:ASP27 2.6 0.8 1.0
CG D:ASP25 2.9 86.2 1.0
OD1 D:ASP247 3.0 67.9 1.0
OD1 D:ASP25 3.0 84.2 1.0
C D:ASP27 3.4 97.0 1.0
CB D:ASP27 3.5 95.7 1.0
H D:ASP27 3.5 0.7 1.0
O D:HOH2003 3.7 70.2 1.0
CA D:ASP27 3.7 94.7 1.0
HB3 D:ASP27 3.8 0.8 1.0
N D:ASP27 3.8 95.5 1.0
CG D:ASP247 3.9 80.0 1.0
OD2 D:ASP247 3.9 91.4 1.0
CB D:ASP25 4.4 76.1 1.0
OD2 D:ASP252 4.5 86.3 1.0
HA3 D:GLY28 4.5 92.5 1.0
HB3 D:ASP25 4.5 91.3 1.0
N D:GLY28 4.6 85.0 1.0
HG21 D:VAL29 4.6 79.2 1.0
CG D:ASP27 4.6 0.0 1.0
H D:CYS26 4.6 0.2 1.0
H D:ASP247 4.7 0.3 1.0
HA D:ASP27 4.7 0.7 1.0
HZ2 D:LYS222 4.7 0.4 1.0
HB2 D:ASP25 4.7 91.3 1.0
HZ3 D:LYS222 4.8 0.4 1.0
HB2 D:ARG248 4.8 0.5 1.0
OD2 D:ASP27 4.8 0.8 1.0
C D:CYS26 4.9 0.1 1.0
OD1 D:ASP252 4.9 89.3 1.0
N D:CYS26 5.0 87.7 1.0
HB3 D:ARG248 5.0 0.5 1.0

Reference:

A.Seifried, G.Knobloch, P.S.Duraphe, G.Segerer, J.Manhard, H.Schindelin, J.Schultz, A.Gohla. Evolutionary and Structural Analyses of the Mammalian Haloacid Dehalogenase-Type Phosphatases Aum and Chronophin Provide Insight Into the Basis of Their Different Substrate Specificities. J.Biol.Chem. V. 289 3416 2014.
ISSN: ISSN 0021-9258
PubMed: 24338473
DOI: 10.1074/JBC.M113.503359
Page generated: Mon Dec 14 09:12:10 2020

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