Magnesium in PDB 3vb9: Crystal Structure of VPA0735 From Vibrio Parahaemolyticus in Monoclinic Form, Northeast Structural Genomics Target VPR109

The structure of Crystal Structure of VPA0735 From Vibrio Parahaemolyticus in Monoclinic Form, Northeast Structural Genomics Target VPR109, PDB code: 3vb9 was solved by J.Seetharaman, H.Neely, K.Cunningham, C.Ciccosanti, S.Bjelic, T.B.Acton, R.Xiao, J.K.Everett, G.T.Montelione, L.Tong, J.F.Hunt, Northeaststructural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.99 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.267, 106.929, 157.178, 90.00, 94.80, 90.00
R / Rfree (%)	22.4 / 27.4

The binding sites of Magnesium atom in the Crystal Structure of VPA0735 From Vibrio Parahaemolyticus in Monoclinic Form, Northeast Structural Genomics Target VPR109 (pdb code 3vb9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of VPA0735 From Vibrio Parahaemolyticus in Monoclinic Form, Northeast Structural Genomics Target VPR109, PDB code: 3vb9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Crystal Structure of VPA0735 From Vibrio Parahaemolyticus in Monoclinic Form, Northeast Structural Genomics Target VPR109


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 VPA0735 From Vibrio Parahaemolyticus in Monoclinic Form, Northeast Structural Genomics Target VPR109 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:17.0 occ:1.00 O A:HOH736 2.9 20.1 1.0 OG A:SER349 3.0 21.3 1.0 NH1 A:ARG191 3.1 19.0 1.0 OE1 A:GLN361 3.6 30.4 1.0 CG A:MSE352 3.7 27.5 1.0 N A:GLY133 3.9 24.4 1.0 CB A:ALA132 3.9 21.6 1.0 CB A:SER349 3.9 21.9 1.0 C A:ALA132 4.0 15.8 1.0 CZ A:ARG191 4.0 29.7 1.0 NH2 A:ARG191 4.0 24.6 1.0 CE A:MSE134 4.1 18.0 1.0 O A:GLY133 4.2 20.1 1.0 CA A:GLY133 4.2 24.4 1.0 SE A:MSE352 4.3 37.8 1.0 NE2 A:GLN361 4.3 19.0 1.0 O A:ALA132 4.3 27.0 1.0 CA A:ALA132 4.4 26.5 1.0 CD A:GLN361 4.4 26.6 1.0 C A:GLY133 4.4 13.7 1.0 C A:GLY351 4.5 27.8 1.0 CA A:GLY351 4.6 29.7 1.0 O A:GLY351 4.8 44.0 1.0 N A:MSE352 4.8 30.7 1.0 CB A:MSE352 4.9 12.7 1.0 OD2 A:ASP145 5.0 23.2 1.0 N A:GLY351 5.0 24.0 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of VPA0735 From Vibrio Parahaemolyticus in Monoclinic Form, Northeast Structural Genomics Target VPR109


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 VPA0735 From Vibrio Parahaemolyticus in Monoclinic Form, Northeast Structural Genomics Target VPR109 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:16.7 occ:1.00 O A:HOH669 3.3 39.0 1.0 OH A:TYR109 3.5 28.9 1.0 NE A:ARG191 3.6 20.2 1.0 OH A:TYR463 3.6 23.0 1.0 NE A:ARG461 3.8 13.5 1.0 OH A:TYR363 3.8 16.6 1.0 O A:HOH742 3.8 31.0 1.0 CE2 A:TYR363 3.9 18.0 1.0 OD1 A:ASN104 3.9 22.4 1.0 NH2 A:ARG461 3.9 11.6 1.0 NH2 A:ARG191 4.1 24.6 1.0 CZ A:ARG191 4.3 29.7 1.0 CZ A:TYR363 4.3 18.8 1.0 CZ A:ARG461 4.3 18.7 1.0 CD A:ARG191 4.4 34.7 1.0 CZ A:TYR109 4.6 25.7 1.0 CG A:ASN104 4.6 25.5 1.0 CB A:ASN104 4.6 19.5 1.0 CZ A:TYR463 4.7 30.6 1.0 N A:ASN104 4.8 21.1 1.0 CD A:ARG461 4.8 17.0 1.0 O A:THR102 4.9 22.0 1.0 CE1 A:TYR109 4.9 26.1 1.0 CE1 A:TYR463 5.0 24.4 1.0 CE A:MSE352 5.0 32.5 1.0 CD2 A:TYR363 5.0 24.1 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of VPA0735 From Vibrio Parahaemolyticus in Monoclinic Form, Northeast Structural Genomics Target VPR109


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 VPA0735 From Vibrio Parahaemolyticus in Monoclinic Form, Northeast Structural Genomics Target VPR109 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:18.6 occ:1.00 CE B:MSE352 2.7 49.3 1.0 OG B:SER349 3.0 13.6 1.0 O B:HOH632 3.1 19.6 1.0 O B:HOH703 3.2 33.7 1.0 NH1 B:ARG191 3.4 28.0 1.0 N B:GLY133 3.7 22.3 1.0 OE1 B:GLN361 3.7 27.6 1.0 CE B:MSE134 3.8 27.6 1.0 CB B:ALA132 3.9 18.0 1.0 O B:GLY133 3.9 16.0 1.0 C B:ALA132 3.9 25.4 1.0 CB B:SER349 3.9 26.4 1.0 CA B:GLY133 4.1 14.3 1.0 C B:GLY133 4.2 17.2 1.0 SE B:MSE352 4.3 38.2 1.0 CA B:ALA132 4.3 19.1 1.0 NE2 B:GLN361 4.4 19.0 1.0 CZ B:ARG191 4.4 40.0 1.0 O B:ALA132 4.4 28.8 1.0 N B:MSE352 4.5 15.2 1.0 CG B:MSE352 4.5 35.4 1.0 CD B:GLN361 4.5 18.9 1.0 NH2 B:ARG191 4.6 35.0 1.0 CA B:GLY351 4.7 10.7 1.0 OD2 B:ASP145 4.8 20.9 1.0 C B:GLY351 4.8 17.2 1.0 O B:HOH686 4.9 14.4 1.0 N B:GLY351 5.0 15.6 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of VPA0735 From Vibrio Parahaemolyticus in Monoclinic Form, Northeast Structural Genomics Target VPR109


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 VPA0735 From Vibrio Parahaemolyticus in Monoclinic Form, Northeast Structural Genomics Target VPR109 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:21.5 occ:1.00 O B:HOH712 3.4 28.9 1.0 CE2 B:PHE460 3.5 17.6 1.0 NE B:ARG191 3.5 28.3 1.0 OH B:TYR363 3.6 24.2 1.0 OH B:TYR109 3.6 26.0 1.0 OD1 B:ASN104 3.7 28.3 1.0 NH2 B:ARG191 3.8 35.0 1.0 CE2 B:TYR363 3.9 20.7 1.0 CZ B:ARG191 4.1 40.0 1.0 CZ B:TYR363 4.2 10.2 1.0 CD2 B:PHE460 4.3 7.2 1.0 CZ B:PHE462 4.4 23.9 1.0 CG B:ASN104 4.4 26.1 1.0 CZ B:PHE460 4.5 21.7 1.0 CD B:ARG191 4.5 25.3 1.0 CB B:ASN104 4.6 26.1 1.0 CZ B:TYR109 4.6 22.9 1.0 CE1 B:PHE462 4.7 13.7 1.0 N B:ASN104 4.7 12.8 1.0 CE1 B:TYR109 4.8 22.1 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of VPA0735 From Vibrio Parahaemolyticus in Monoclinic Form, Northeast Structural Genomics Target VPR109


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 VPA0735 From Vibrio Parahaemolyticus in Monoclinic Form, Northeast Structural Genomics Target VPR109 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:13.0 occ:1.00 OG C:SER349 3.0 22.9 1.0 O C:HOH762 3.2 29.1 1.0 CE C:MSE352 3.2 42.1 1.0 NH1 C:ARG191 3.3 36.2 1.0 OE1 C:GLN361 3.5 24.2 1.0 NH2 C:ARG191 3.9 23.8 1.0 N C:GLY133 3.9 22.9 1.0 C C:ALA132 3.9 21.0 1.0 CG C:MSE352 3.9 28.0 1.0 CB C:ALA132 4.0 19.3 1.0 CZ C:ARG191 4.0 24.8 1.0 CB C:SER349 4.1 23.0 1.0 O C:GLY133 4.1 23.0 1.0 NE2 C:GLN361 4.2 17.6 1.0 CD C:GLN361 4.3 22.5 1.0 O C:ALA132 4.3 21.2 1.0 CA C:GLY133 4.3 20.0 1.0 CA C:ALA132 4.3 28.0 1.0 C C:GLY133 4.4 20.4 1.0 N C:MSE352 4.4 19.7 1.0 SE C:MSE352 4.4 37.9 1.0 CA C:GLY351 4.6 24.3 1.0 C C:GLY351 4.8 27.9 1.0 OD2 C:ASP145 4.9 23.4 1.0 N C:GLY351 5.0 27.4 1.0 CB C:MSE352 5.0 18.0 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of VPA0735 From Vibrio Parahaemolyticus in Monoclinic Form, Northeast Structural Genomics Target VPR109


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 VPA0735 From Vibrio Parahaemolyticus in Monoclinic Form, Northeast Structural Genomics Target VPR109 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:14.2 occ:1.00 OG D:SER349 2.9 27.4 1.0 O D:HOH653 3.1 26.0 1.0 NH1 D:ARG191 3.1 23.8 1.0 O D:HOH717 3.6 24.3 1.0 N D:GLY133 3.7 19.6 1.0 CE D:MSE134 3.7 27.5 1.0 OE1 D:GLN361 3.7 31.1 1.0 CB D:SER349 3.8 16.5 1.0 CG D:MSE352 3.9 13.8 1.0 O D:GLY133 3.9 16.8 1.0 CZ D:ARG191 4.0 34.0 1.0 CB D:ALA132 4.0 17.9 1.0 C D:ALA132 4.0 20.2 1.0 NH2 D:ARG191 4.0 32.3 1.0 CA D:GLY133 4.0 19.9 1.0 C D:GLY133 4.1 24.2 1.0 NE2 D:GLN361 4.3 13.1 1.0 SE D:MSE352 4.3 29.7 1.0 CA D:ALA132 4.4 15.7 1.0 CD D:GLN361 4.4 18.6 1.0 N D:MSE352 4.5 16.0 1.0 O D:ALA132 4.5 22.1 1.0 CA D:GLY351 4.6 12.9 1.0 C D:GLY351 4.7 17.9 1.0 OD2 D:ASP145 4.8 26.0 1.0 N D:GLY351 4.8 13.3 1.0 CB D:MSE352 5.0 14.6 1.0 N D:MSE134 5.0 20.8 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of VPA0735 From Vibrio Parahaemolyticus in Monoclinic Form, Northeast Structural Genomics Target VPR109


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 VPA0735 From Vibrio Parahaemolyticus in Monoclinic Form, Northeast Structural Genomics Target VPR109 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:20.4 occ:1.00 ND2 D:ASN104 3.5 23.8 1.0 OH D:TYR463 3.5 11.7 1.0 OH D:TYR363 3.6 13.6 1.0 OH D:TYR109 3.7 23.0 1.0 NE D:ARG461 3.7 15.0 1.0 NE D:ARG191 3.7 30.2 1.0 NH2 D:ARG461 3.7 12.3 1.0 CE1 D:TYR363 3.8 16.1 1.0 CZ D:TYR363 4.2 9.8 1.0 CZ D:ARG461 4.2 11.0 1.0 NH2 D:ARG191 4.3 32.3 1.0 CG D:ASN104 4.5 18.9 1.0 CZ D:ARG191 4.5 34.0 1.0 CD D:ARG191 4.5 26.8 1.0 CB D:ASN104 4.5 17.9 1.0 CZ D:TYR109 4.6 17.0 1.0 CZ D:TYR463 4.7 10.9 1.0 CE1 D:TYR109 4.8 25.2 1.0 CD D:ARG461 4.8 13.1 1.0 N D:ASN104 4.9 19.1 1.0 CD1 D:TYR363 5.0 12.7 1.0 CE2 D:TYR463 5.0 15.0 1.0

J.Seetharaman, H.Neely, K.Cunningham, C.Ciccosanti, S.Bjelic, T.B.Acton, R.Xiao, J.K.Everett, G.T.Montelione, L.Tong, J.F.Hunt. Crystal Structure of VPA0735 From Vibrio Parahaemolyticus in Monoclinic Form, Northeast Structural Genomics Target VPR109 To Be Published.