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Magnesium in PDB 3i6b: Crystal Structure of Yrbi Lacking the Last 8 Residues, in Complex with Kdo and Inorganic Phosphate

Enzymatic activity of Crystal Structure of Yrbi Lacking the Last 8 Residues, in Complex with Kdo and Inorganic Phosphate

All present enzymatic activity of Crystal Structure of Yrbi Lacking the Last 8 Residues, in Complex with Kdo and Inorganic Phosphate:
3.1.3.45;

Protein crystallography data

The structure of Crystal Structure of Yrbi Lacking the Last 8 Residues, in Complex with Kdo and Inorganic Phosphate, PDB code: 3i6b was solved by T.Biswas, O.V.Tsodikov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.49
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 64.964, 144.104, 145.854, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 23.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Yrbi Lacking the Last 8 Residues, in Complex with Kdo and Inorganic Phosphate (pdb code 3i6b). 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 Yrbi Lacking the Last 8 Residues, in Complex with Kdo and Inorganic Phosphate, PDB code: 3i6b:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3i6b

Go back to Magnesium Binding Sites List in 3i6b
Magnesium binding site 1 out of 4 in the Crystal Structure of Yrbi Lacking the Last 8 Residues, in Complex with Kdo and Inorganic Phosphate


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 Yrbi Lacking the Last 8 Residues, in Complex with Kdo and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:49.5
occ:1.00
O1 A:PO4800 2.3 75.7 1.0
O A:ASP34 2.4 25.4 1.0
O A:HOH699 2.6 34.1 1.0
OD2 A:ASP125 2.9 26.9 1.0
C A:ASP34 3.6 25.4 1.0
OD2 A:ASP32 3.8 30.4 1.0
P A:PO4800 3.8 75.3 1.0
CG A:ASP125 3.9 26.1 1.0
CG1 B:VAL56 4.1 23.8 1.0
CB A:ASP34 4.1 25.9 1.0
CB A:ASP125 4.2 23.6 1.0
CA A:ASP34 4.3 25.6 1.0
O2 A:PO4800 4.4 75.3 1.0
CB A:ASP126 4.6 22.4 1.0
N A:ASP34 4.6 25.3 1.0
CG A:ASP32 4.6 27.9 1.0
O4 A:PO4800 4.6 75.8 1.0
N A:GLY35 4.6 25.2 1.0
O3 A:PO4800 4.6 75.3 1.0
OD2 A:ASP129 4.8 23.2 1.0
CB A:ASP32 4.8 25.8 1.0
N A:ASP126 4.8 22.4 1.0
CA A:GLY35 4.8 25.1 1.0
O8 B:KDO900 4.9 77.3 1.0
CA A:ASP125 5.0 23.1 1.0

Magnesium binding site 2 out of 4 in 3i6b

Go back to Magnesium Binding Sites List in 3i6b
Magnesium binding site 2 out of 4 in the Crystal Structure of Yrbi Lacking the Last 8 Residues, in Complex with Kdo and Inorganic Phosphate


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 Yrbi Lacking the Last 8 Residues, in Complex with Kdo and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:55.6
occ:1.00
O1 B:PO4800 2.6 33.1 1.0
OD2 B:ASP32 2.7 28.6 1.0
O B:ASP34 2.7 23.1 1.0
OD2 B:ASP125 2.8 29.0 1.0
CG B:ASP32 3.3 25.9 1.0
O4 B:PO4800 3.4 31.3 1.0
P B:PO4800 3.5 33.4 1.0
CB B:ASP32 3.6 24.3 1.0
C B:ASP34 3.7 23.2 1.0
CG B:ASP125 3.9 26.2 1.0
O2 B:PO4800 3.9 30.4 1.0
N B:ASP34 4.0 23.5 1.0
CB B:ASP34 4.0 23.4 1.0
CA B:ASP34 4.1 23.3 1.0
OD1 B:ASP32 4.1 27.6 1.0
OD2 B:ASP129 4.1 26.0 1.0
O B:HOH701 4.2 34.9 1.0
OD1 B:ASP129 4.6 25.8 1.0
OD1 B:ASP125 4.6 28.8 1.0
CA B:ASP32 4.7 23.8 1.0
N B:VAL33 4.8 23.5 1.0
CG B:ASP129 4.8 25.0 1.0
O3 B:PO4800 4.8 31.1 1.0
C B:VAL33 4.9 23.6 1.0
CB B:ASP125 4.9 24.0 1.0
N B:ASP125 4.9 22.8 1.0
N B:GLY35 4.9 23.0 1.0

Magnesium binding site 3 out of 4 in 3i6b

Go back to Magnesium Binding Sites List in 3i6b
Magnesium binding site 3 out of 4 in the Crystal Structure of Yrbi Lacking the Last 8 Residues, in Complex with Kdo and Inorganic Phosphate


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 Yrbi Lacking the Last 8 Residues, in Complex with Kdo and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg204

b:32.5
occ:1.00
O3 C:PO4800 2.2 60.3 1.0
OD1 C:ASP125 2.2 32.3 1.0
O C:ASP34 2.5 24.9 1.0
CG C:ASP125 3.2 29.0 1.0
OD2 C:ASP32 3.2 27.5 1.0
OD2 C:ASP125 3.5 31.9 1.0
P C:PO4800 3.6 60.1 1.0
C C:ASP34 3.7 25.1 1.0
O2 C:PO4800 4.0 59.7 1.0
CG C:ASP32 4.0 25.8 1.0
O C:HOH549 4.0 28.2 1.0
CB C:ASP32 4.3 23.7 1.0
O4 C:PO4800 4.3 60.7 1.0
CG1 D:VAL56 4.4 24.8 1.0
CB C:ASP34 4.4 25.5 1.0
CA C:ASP34 4.4 25.2 1.0
CB C:ASP126 4.5 25.8 1.0
OD2 C:ASP129 4.5 27.5 1.0
CB C:ASP125 4.5 26.3 1.0
O1 C:PO4800 4.6 60.7 1.0
N C:GLY35 4.7 24.9 1.0
N C:ASP34 4.7 24.8 1.0
N C:ASP126 4.7 25.6 1.0
CA C:GLY35 4.8 24.7 1.0
N C:ASP125 4.9 25.0 1.0

Magnesium binding site 4 out of 4 in 3i6b

Go back to Magnesium Binding Sites List in 3i6b
Magnesium binding site 4 out of 4 in the Crystal Structure of Yrbi Lacking the Last 8 Residues, in Complex with Kdo and Inorganic Phosphate


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 Yrbi Lacking the Last 8 Residues, in Complex with Kdo and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg203

b:49.2
occ:1.00
O2 D:PO4800 2.2 33.1 1.0
OD2 D:ASP125 2.9 28.8 1.0
O D:ASP34 3.4 24.4 1.0
P D:PO4800 3.5 33.7 1.0
OD2 D:ASP32 3.5 28.6 1.0
OD2 D:ASP129 3.6 27.9 1.0
O1 D:PO4800 3.8 33.0 1.0
CD1 D:ILE128 3.8 30.6 1.0
CG D:ASP32 3.9 26.8 1.0
O D:HOH677 3.9 31.5 1.0
OD1 D:ASP129 4.0 28.5 1.0
CB D:ASP32 4.1 24.8 1.0
CG D:ASP125 4.2 27.1 1.0
CG D:ASP129 4.2 26.9 1.0
O4 D:PO4800 4.3 32.3 1.0
C D:ASP34 4.5 24.1 1.0
O3 D:PO4800 4.5 32.1 1.0
OD1 D:ASP32 4.6 29.8 1.0
CG1 D:ILE128 4.7 28.1 1.0
CB D:ASP34 4.7 24.1 1.0
CB D:ASP126 4.8 24.9 1.0
N D:ASP126 4.8 25.1 1.0
N D:ASP125 4.9 24.8 1.0
OD1 D:ASP125 4.9 29.1 1.0
CA D:ASP34 5.0 24.1 1.0

Reference:

T.Biswas, L.Yi, P.Aggarwal, J.Wu, J.R.Rubin, J.A.Stuckey, R.W.Woodard, O.V.Tsodikov. The Tail of Kdsc: Conformational Changes Control the Activity of A Haloacid Dehalogenase Superfamily Phosphatase. J.Biol.Chem. V. 284 30594 2009.
ISSN: ISSN 0021-9258
PubMed: 19726684
DOI: 10.1074/JBC.M109.012278
Page generated: Mon Dec 14 08:16:16 2020

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