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Magnesium in PDB 3qvq: The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate

Enzymatic activity of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate

All present enzymatic activity of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate:
3.1.4.2;

Protein crystallography data

The structure of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate, PDB code: 3qvq was solved by A.U.Singer, O.Kagan, E.Evdokimova, M.E.Cuff, A.M.Edwards, A.Joachimiak, A.F.Yakunin, A.Savchenko, Midwest Center For Structural Genomics(Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.26 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.861, 92.717, 125.240, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.1

Other elements in 3qvq:

The structure of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Chlorine (Cl) 18 atoms
Sodium (Na) 7 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate (pdb code 3qvq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate, PDB code: 3qvq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 3qvq

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Magnesium binding site 1 out of 13 in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg310

b:8.4
occ:1.00
 HO2 A:G3P301 1.6 12.5 1.0
OE2 A:GLU41 2.0 7.2 1.0
OE1 A:GLU116 2.1 7.3 1.0
OD1 A:ASP43 2.1 7.8 1.0
O A:HOH287 2.1 9.2 1.0
O2 A:G3P301 2.2 10.4 1.0
O4P A:G3P301 2.2 11.3 1.0
HO1 A:G3P301 2.7 13.5 1.0
H32 A:G3P301 3.0 28.3 1.0
CD A:GLU41 3.1 7.8 1.0
CG A:ASP43 3.1 8.5 1.0
CD A:GLU116 3.2 10.2 1.0
C2 A:G3P301 3.4 13.5 1.0
P A:G3P301 3.4 23.7 1.0
OD2 A:ASP43 3.4 6.7 1.0
OE1 A:GLU41 3.4 9.0 1.0
O1 A:G3P301 3.5 11.2 1.0
C3 A:G3P301 3.6 23.6 1.0
O2P A:G3P301 3.7 16.8 1.0
O1P A:G3P301 3.9 17.6 1.0
CB A:GLU116 3.9 8.7 1.0
OE2 A:GLU116 4.0 11.5 1.0
C1 A:G3P301 4.0 14.3 1.0
O A:HOH289 4.1 22.1 1.0
CG A:GLU116 4.1 8.9 1.0
H2 A:G3P301 4.2 16.2 1.0
CG A:GLU41 4.4 6.9 1.0
CB A:ASP43 4.4 6.8 1.0
H11 A:G3P301 4.5 17.2 1.0
NE2 A:HIS14 4.5 9.3 1.0
CD2 A:HIS56 4.6 10.1 1.0
H31 A:G3P301 4.6 28.3 1.0
O3P A:G3P301 4.6 20.6 1.0
CD2 A:HIS14 4.7 11.0 1.0
NE A:ARG15 4.8 8.4 1.0
CD A:LYS118 4.8 17.3 1.0
CA A:ASP43 4.9 6.9 1.0
H12 A:G3P301 4.9 17.2 1.0
N A:ASP43 5.0 5.5 1.0

Magnesium binding site 2 out of 13 in 3qvq

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Magnesium binding site 2 out of 13 in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg311

b:17.7
occ:1.00
 O A:HOH333 2.1 20.0 1.0
O A:HOH371 2.1 21.0 1.0
O A:HOH361 2.1 19.7 1.0
O A:HOH579 2.1 22.5 1.0
O A:HOH296 2.1 16.2 1.0
O A:HOH454 4.1 24.1 1.0
O A:LEU81 4.1 14.5 1.0
O A:GLN93 4.3 15.2 1.0
O A:GLN92 4.3 16.6 1.0
O A:HOH831 4.3 33.7 1.0
OE1 A:GLN93 4.3 18.8 1.0
O A:GLN80 4.4 19.5 1.0
CG2 A:THR95 4.4 21.1 1.0
C A:GLN93 4.6 13.6 1.0
C A:LEU81 4.6 12.7 1.0
CA A:GLN93 4.6 13.9 1.0
O A:GLU94 4.7 13.2 1.0
O A:LYS79 4.7 17.6 1.0
CA A:ASP82 4.8 14.4 1.0
C A:GLN80 4.9 17.4 1.0
N A:ASP82 4.9 14.3 1.0

Magnesium binding site 3 out of 13 in 3qvq

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Magnesium binding site 3 out of 13 in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg252

b:25.1
occ:1.00
 O A:HOH605 2.0 28.9 1.0
O A:HOH504 2.1 32.4 1.0
O A:HOH374 2.1 29.8 1.0
OE2 A:GLU90 3.8 32.8 1.0
OE1 A:GLU90 4.2 25.9 1.0
O A:HOH360 4.2 22.4 1.0
CL A:CL261 4.3 50.2 1.0
CD A:GLU90 4.4 22.6 1.0
O A:LYS87 4.6 21.7 1.0
CA A:GLY88 4.7 16.8 1.0

Magnesium binding site 4 out of 13 in 3qvq

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Magnesium binding site 4 out of 13 in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg310

b:9.3
occ:1.00
 HO2 B:G3P301 1.6 16.2 1.0
OE1 B:GLU116 2.0 10.0 1.0
O B:HOH268 2.0 9.5 1.0
OE2 B:GLU41 2.1 10.5 1.0
OD1 B:ASP43 2.1 10.1 1.0
O2P B:G3P301 2.1 14.2 1.0
O2 B:G3P301 2.2 13.5 1.0
HO1 B:G3P301 2.6 18.0 1.0
CD B:GLU41 3.1 12.2 1.0
H32 B:G3P301 3.1 23.4 1.0
CG B:ASP43 3.1 7.8 1.0
CD B:GLU116 3.1 12.2 1.0
P B:G3P301 3.3 22.2 1.0
C2 B:G3P301 3.4 16.7 1.0
OE1 B:GLU41 3.4 11.8 1.0
OD2 B:ASP43 3.5 8.8 1.0
O1 B:G3P301 3.5 15.0 1.0
C3 B:G3P301 3.6 19.5 1.0
O3P B:G3P301 3.7 20.5 1.0
OE2 B:GLU116 3.9 12.1 1.0
O1P B:G3P301 3.9 15.1 1.0
CB B:GLU116 3.9 9.5 1.0
C1 B:G3P301 4.0 23.6 1.0
CG B:GLU116 4.1 9.4 1.0
H2 B:G3P301 4.2 20.1 1.0
NZ B:LYS118 4.2 20.4 1.0
CG B:GLU41 4.4 8.6 1.0
CB B:ASP43 4.5 9.6 1.0
NE2 B:HIS14 4.5 11.3 1.0
O4P B:G3P301 4.5 21.1 1.0
H12 B:G3P301 4.5 28.3 1.0
CD2 B:HIS56 4.5 13.2 1.0
H31 B:G3P301 4.6 23.4 1.0
NE B:ARG15 4.8 12.7 1.0
CD2 B:HIS14 4.8 11.9 1.0
H11 B:G3P301 4.9 28.3 1.0
CA B:ASP43 5.0 8.8 1.0

Magnesium binding site 5 out of 13 in 3qvq

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Magnesium binding site 5 out of 13 in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg311

b:21.8
occ:1.00
 O B:HOH308 2.0 22.0 1.0
O B:HOH386 2.1 23.2 1.0
O B:HOH319 2.1 19.0 1.0
OD1 B:ASP204 3.6 20.7 1.0
OD2 B:ASP204 3.7 20.9 1.0
CG B:ASP204 4.0 21.8 1.0
O B:HOH322 4.3 25.1 1.0
O B:GLN200 4.4 13.6 1.0
O B:HOH758 4.6 33.5 1.0
CB B:GLN200 5.0 11.8 1.0

Magnesium binding site 6 out of 13 in 3qvq

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Magnesium binding site 6 out of 13 in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg252

b:31.9
occ:1.00
 O B:HOH340 2.1 28.9 1.0
O B:HOH341 2.1 35.9 1.0
O B:HOH671 2.1 32.1 1.0
O B:HOH600 2.1 21.6 1.0
OE2 B:GLU90 4.0 23.6 1.0
O B:HOH327 4.1 20.9 1.0
OE1 B:GLU90 4.1 17.5 1.0
O B:LYS87 4.5 16.7 1.0
CD B:GLU90 4.5 19.1 1.0
CA B:GLY88 4.6 14.0 1.0

Magnesium binding site 7 out of 13 in 3qvq

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Magnesium binding site 7 out of 13 in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg253

b:26.5
occ:1.00
 OE1 B:GLU121 2.0 28.1 1.0
OD2 B:ASP58 2.0 24.2 1.0
O B:HOH343 2.1 28.1 1.0
CG B:ASP58 3.0 33.6 1.0
CD B:GLU121 3.1 27.2 1.0
OD1 B:ASP58 3.4 29.6 1.0
OE2 B:GLU121 3.6 27.5 1.0
O B:HOH479 3.9 32.0 1.0
N B:GLU121 4.0 8.6 1.0
OH B:TYR71 4.1 30.4 1.0
CB B:ASP58 4.4 22.2 1.0
CG B:GLU121 4.4 14.6 1.0
CA B:CYS120 4.5 9.3 1.0
CB B:GLU121 4.6 10.9 1.0
O B:PRO119 4.7 10.9 1.0
C B:CYS120 4.8 11.3 1.0
CA B:GLU121 4.9 11.9 1.0
CE1 B:TYR71 5.0 36.5 1.0
CZ B:TYR71 5.0 27.0 1.0

Magnesium binding site 8 out of 13 in 3qvq

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Magnesium binding site 8 out of 13 in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg310

b:8.3
occ:1.00
 OD1 C:ASP43 2.0 8.4 1.0
OE1 C:GLU116 2.0 8.6 1.0
OE2 C:GLU41 2.1 8.1 1.0
O C:HOH270 2.1 8.8 1.0
O2 C:G3P301 2.2 10.1 1.0
HO2 C:G3P301 2.2 12.2 1.0
O3P C:G3P301 2.3 12.9 1.0
CG C:ASP43 3.1 7.6 1.0
CD C:GLU41 3.1 8.4 1.0
CD C:GLU116 3.2 8.6 1.0
HO1 C:G3P301 3.2 16.7 1.0
C2 C:G3P301 3.4 14.7 1.0
P C:G3P301 3.4 22.9 1.0
OE1 C:GLU41 3.4 8.7 1.0
OD2 C:ASP43 3.4 6.8 1.0
H12 C:G3P301 3.5 30.5 1.0
O1 C:G3P301 3.6 13.9 1.0
C1 C:G3P301 3.7 25.4 1.0
O4P C:G3P301 3.9 18.0 1.0
O1P C:G3P301 3.9 15.4 1.0
CB C:GLU116 3.9 7.5 1.0
OE2 C:GLU116 4.0 10.7 1.0
O C:HOH900 4.1 18.7 1.0
CG C:GLU116 4.1 8.7 1.0
H2 C:G3P301 4.1 17.6 1.0
C3 C:G3P301 4.2 22.0 1.0
CB C:ASP43 4.4 9.0 1.0
CG C:GLU41 4.4 7.8 1.0
NE2 C:HIS14 4.4 8.6 1.0
CD2 C:HIS56 4.6 10.7 1.0
O2P C:G3P301 4.7 20.9 1.0
H32 C:G3P301 4.7 26.4 1.0
CD2 C:HIS14 4.7 9.7 1.0
H11 C:G3P301 4.8 30.5 1.0
NE C:ARG15 4.9 8.7 1.0
CA C:ASP43 4.9 6.4 1.0
N C:ASP43 5.0 6.6 1.0

Magnesium binding site 9 out of 13 in 3qvq

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Magnesium binding site 9 out of 13 in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg311

b:16.3
occ:1.00
 O C:THR64 2.0 12.0 1.0
O C:HOH556 2.1 17.4 1.0
O C:HOH545 2.1 16.0 1.0
O C:SER61 2.1 13.6 1.0
O C:HOH314 2.1 16.1 1.0
O C:HOH332 2.1 14.2 1.0
C C:SER61 3.2 13.9 1.0
C C:THR64 3.2 10.0 1.0
CA C:SER61 3.8 14.3 1.0
CA C:ASP65 3.9 15.6 1.0
N C:ASP65 4.0 14.4 1.0
N C:THR64 4.2 11.8 1.0
O C:ARG62 4.3 13.9 1.0
N C:ARG62 4.3 10.8 1.0
CA C:THR64 4.3 11.4 1.0
C C:ARG62 4.4 12.9 1.0
O C:GLY66 4.4 14.9 1.0
CB C:SER61 4.4 18.8 1.0
C C:ASP65 4.5 18.1 1.0
CA C:ARG62 4.6 11.8 1.0
N C:GLY66 4.7 14.8 1.0
O C:LEU60 4.7 11.0 1.0
N C:THR63 4.9 10.4 1.0

Magnesium binding site 10 out of 13 in 3qvq

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Magnesium binding site 10 out of 13 in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg310

b:8.9
occ:1.00
 OE1 D:GLU116 1.9 9.2 1.0
OE2 D:GLU41 2.0 8.0 1.0
OD1 D:ASP43 2.1 9.0 1.0
O D:HOH263 2.1 9.4 1.0
HO2 D:G3P301 2.2 15.7 1.0
O2 D:G3P301 2.2 13.1 1.0
O3P D:G3P301 2.2 14.2 1.0
CG D:ASP43 3.1 9.7 1.0
CD D:GLU41 3.1 11.4 1.0
HO1 D:G3P301 3.1 17.2 1.0
CD D:GLU116 3.1 9.9 1.0
P D:G3P301 3.4 27.3 1.0
OD2 D:ASP43 3.4 9.3 1.0
C2 D:G3P301 3.4 19.5 1.0
OE1 D:GLU41 3.4 10.0 1.0
O1 D:G3P301 3.5 14.3 1.0
H12 D:G3P301 3.7 30.2 1.0
O1P D:G3P301 3.7 18.4 1.0
O2P D:G3P301 3.8 21.2 1.0
C1 D:G3P301 3.8 25.2 1.0
CB D:GLU116 3.9 7.4 1.0
OE2 D:GLU116 3.9 10.7 1.0
O D:HOH319 4.1 21.0 1.0
CG D:GLU116 4.1 7.3 1.0
C3 D:G3P301 4.2 18.7 1.0
H2 D:G3P301 4.2 23.4 1.0
CG D:GLU41 4.4 8.8 1.0
CB D:ASP43 4.4 8.8 1.0
NE2 D:HIS14 4.4 10.6 1.0
O4P D:G3P301 4.6 19.9 1.0
CD2 D:HIS56 4.6 10.2 1.0
H31 D:G3P301 4.6 22.4 1.0
CD2 D:HIS14 4.8 12.3 1.0
H11 D:G3P301 4.9 30.2 1.0
NE D:ARG15 4.9 9.7 1.0
CA D:ASP43 4.9 6.6 1.0

Reference:

A.U.Singer, O.Kagan, E.Evdokimova, M.E.Cuff, A.M.Edwards, A.Joachimiak, A.F.Yakunin, A.Savchenko. The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate To Be Published.
Page generated: Thu Aug 15 10:12:11 2024

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