Magnesium in PDB 3dls: Crystal Structure of Human Pas Kinase Bound to Adp

All present enzymatic activity of Crystal Structure of Human Pas Kinase Bound to Adp:
2.7.11.1;

The structure of Crystal Structure of Human Pas Kinase Bound to Adp, PDB code: 3dls was solved by S.Antonysamy, J.B.Bonanno, R.Romero, M.Russell, M.Iizuka, T.Gheyi, S.R.Wasserman, J.Rutter, J.M.Sauder, S.K.Burley, New York Sgx Researchcenter For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	85.778, 85.840, 94.154, 77.28, 77.50, 60.09
R / Rfree (%)	24.1 / 29.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Pas Kinase Bound to Adp (pdb code 3dls). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 19 binding sites of Magnesium where determined in the Crystal Structure of Human Pas Kinase Bound to Adp, PDB code: 3dls:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 19 in the Crystal Structure of Human Pas Kinase Bound to Adp


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 Pas Kinase Bound to Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg7 b:10.2 occ:1.00 O2B A:ADP1 2.0 33.9 1.0 OD2 A:ASP1146 2.1 13.6 1.0 O1A A:ADP1 2.2 16.8 1.0 OD1 A:ASN1133 2.4 28.3 1.0 O A:HOH271 2.8 27.0 1.0 CG A:ASP1146 3.2 19.3 1.0 PB A:ADP1 3.4 25.1 1.0 PA A:ADP1 3.5 20.6 1.0 CG A:ASN1133 3.5 21.1 1.0 CB A:ASP1146 3.7 16.0 1.0 O3A A:ADP1 3.8 30.5 1.0 ND2 A:ASN1133 4.1 20.2 1.0 MG A:MG8 4.1 28.4 1.0 OD1 A:ASP1146 4.2 16.8 1.0 O1B A:ADP1 4.2 24.9 1.0 O3B A:ADP1 4.5 36.3 1.0 O2A A:ADP1 4.5 22.2 1.0 O A:GLU1132 4.6 17.3 1.0 O5' A:ADP1 4.6 31.3 1.0 C5' A:ADP1 4.8 16.9 1.0 CB A:ASN1133 4.8 20.9 1.0 CE A:LYS1130 4.9 45.0 1.0 CA A:ASN1133 4.9 25.4 1.0 O3' A:ADP1 5.0 18.9 1.0 OD2 A:ASP1128 5.0 27.4 1.0

Magnesium binding site 2 out of 19 in the Crystal Structure of Human Pas Kinase Bound to Adp


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 Pas Kinase Bound to Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8 b:28.4 occ:1.00 OD1 A:ASP1146 2.4 16.8 1.0 OD2 A:ASP1146 2.7 13.6 1.0 O1B A:ADP1 2.8 24.9 1.0 CG A:ASP1146 2.9 19.3 1.0 O2B A:ADP1 3.4 33.9 1.0 PB A:ADP1 3.6 25.1 1.0 O A:HOH222 3.8 29.6 1.0 MG A:MG7 4.1 10.2 1.0 NZ A:LYS1028 4.1 24.7 1.0 CB A:ASP1146 4.4 16.0 1.0 O A:HOH271 4.5 27.0 1.0 CA A:GLY1148 4.5 17.7 1.0 N A:GLY1148 4.7 18.6 1.0 O3A A:ADP1 4.7 30.5 1.0 O3B A:ADP1 4.8 36.3 1.0 O1A A:ADP1 4.9 16.8 1.0

Magnesium binding site 3 out of 19 in the Crystal Structure of Human Pas Kinase Bound to Adp


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 Pas Kinase Bound to Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg20 b:24.4 occ:1.00 O A:PRO1098 2.1 36.7 1.0 OE2 A:GLU1199 2.3 42.2 1.0 OE1 A:GLU1199 2.8 53.3 1.0 CD A:GLU1199 2.9 42.3 1.0 C A:PRO1098 3.4 29.7 1.0 N A:PRO1098 4.1 35.7 1.0 CA A:ARG1099 4.2 28.9 1.0 C A:HIS1097 4.2 40.2 1.0 N A:ARG1099 4.2 29.0 1.0 O A:HIS1097 4.3 34.7 1.0 CA A:PRO1098 4.3 32.4 1.0 CG A:GLU1199 4.4 38.9 1.0 OH A:TYR1218 4.5 24.1 1.0 CD A:PRO1098 4.6 32.0 1.0 N A:LEU1100 4.7 23.6 1.0 CA A:HIS1097 4.8 42.8 1.0 CG A:PRO1098 5.0 30.5 1.0 CG A:ARG1099 5.0 31.8 1.0

Magnesium binding site 4 out of 19 in the Crystal Structure of Human Pas Kinase Bound to Adp


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 Pas Kinase Bound to Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg25 b:22.2 occ:1.00 O C:GLY1008 2.2 38.3 1.0 OE2 A:GLU1207 2.3 36.2 1.0 O C:GLY1006 2.6 39.6 1.0 OE1 A:GLU1207 2.8 35.5 1.0 CD A:GLU1207 2.9 35.5 1.0 C C:GLY1008 3.4 43.8 1.0 C C:GLY1006 3.7 44.9 1.0 O C:LEU1005 4.1 29.8 1.0 N C:GLY1008 4.1 51.0 1.0 N C:PHE1010 4.1 35.0 1.0 C C:SER1007 4.2 49.7 1.0 N C:ALA1009 4.3 42.6 1.0 C C:LEU1005 4.3 33.5 1.0 CA C:ALA1009 4.3 38.6 1.0 CG A:GLU1207 4.3 35.1 1.0 CA C:GLY1008 4.4 47.4 1.0 N C:GLY1006 4.4 39.6 1.0 O C:SER1007 4.5 52.2 1.0 N C:SER1007 4.6 46.4 1.0 CA C:SER1007 4.6 49.0 1.0 C C:ALA1009 4.6 35.7 1.0 CA C:GLY1006 4.6 40.8 1.0 CB C:PRO1004 4.7 24.9 1.0 O C:PRO1004 4.9 25.7 1.0 O C:PHE1010 4.9 27.1 1.0 C C:PRO1004 4.9 27.7 1.0 CG C:PRO1004 5.0 29.3 1.0

Magnesium binding site 5 out of 19 in the Crystal Structure of Human Pas Kinase Bound to Adp


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 Pas Kinase Bound to Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg9 b:15.6 occ:1.00 OD2 B:ASP1146 2.1 16.8 1.0 O1A B:ADP2 2.3 28.8 1.0 OD1 B:ASN1133 2.5 29.0 1.0 O B:HOH171 2.7 25.4 1.0 CG B:ASP1146 3.1 28.4 1.0 O2B B:ADP2 3.1 29.0 1.0 O1B B:ADP2 3.5 34.9 1.0 CG B:ASN1133 3.6 22.9 1.0 PA B:ADP2 3.6 22.5 1.0 CB B:ASP1146 3.6 24.0 1.0 PB B:ADP2 3.7 24.8 1.0 O3A B:ADP2 4.0 36.0 1.0 ND2 B:ASN1133 4.0 24.3 1.0 OD1 B:ASP1146 4.1 18.4 1.0 MG B:MG10 4.2 23.4 1.0 O2A B:ADP2 4.5 28.3 1.0 NZ B:LYS1130 4.7 42.3 1.0 CE B:LYS1130 4.7 39.1 1.0 O B:GLU1132 4.7 23.1 1.0 O5' B:ADP2 4.7 34.7 1.0 CB B:ASN1133 4.9 20.9 1.0 C5' B:ADP2 4.9 28.1 1.0

Magnesium binding site 6 out of 19 in the Crystal Structure of Human Pas Kinase Bound to Adp


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 Pas Kinase Bound to Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg10 b:23.4 occ:1.00 OD1 B:ASP1146 2.3 18.4 1.0 O1B B:ADP2 2.4 34.9 1.0 OD2 B:ASP1146 2.7 16.8 1.0 CG B:ASP1146 2.8 28.4 1.0 PB B:ADP2 3.8 24.8 1.0 NZ B:LYS1028 4.0 45.2 1.0 MG B:MG9 4.2 15.6 1.0 CB B:ASP1146 4.4 24.0 1.0 CA B:GLY1148 4.4 21.7 1.0 O B:HOH171 4.4 25.4 1.0 N B:GLY1148 4.5 20.5 1.0 O2B B:ADP2 4.6 29.0 1.0 O3A B:ADP2 4.6 36.0 1.0 O3B B:ADP2 4.7 41.4 1.0 C B:GLY1148 4.9 24.8 1.0

Magnesium binding site 7 out of 19 in the Crystal Structure of Human Pas Kinase Bound to Adp


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 Pas Kinase Bound to Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg19 b:33.1 occ:1.00 OE2 B:GLU1199 2.4 33.0 1.0 O B:PRO1098 2.5 34.7 1.0 CD B:GLU1199 3.2 43.2 1.0 OE1 B:GLU1199 3.5 45.6 1.0 C B:PRO1098 3.7 34.9 1.0 OH B:TYR1218 4.2 23.9 1.0 C B:HIS1097 4.3 38.4 1.0 O B:HIS1097 4.3 36.6 1.0 N B:PRO1098 4.4 32.7 1.0 CA B:ARG1099 4.4 30.7 1.0 N B:ARG1099 4.5 32.2 1.0 CG B:GLU1199 4.5 39.1 1.0 CA B:PRO1098 4.6 35.8 1.0 CA B:HIS1097 4.8 43.0 1.0 N B:LEU1100 4.9 28.7 1.0 CD B:PRO1098 4.9 29.6 1.0

Magnesium binding site 8 out of 19 in the Crystal Structure of Human Pas Kinase Bound to Adp


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 Pas Kinase Bound to Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg24 b:26.6 occ:1.00 O A:GLY1006 2.5 47.3 1.0 OE2 B:GLU1207 2.7 49.2 1.0 OE1 B:GLU1207 2.9 54.7 1.0 CD B:GLU1207 3.1 45.6 1.0 C A:GLY1006 3.7 51.6 1.0 N A:ALA1009 3.9 50.9 1.0 N A:GLY1008 3.9 58.3 1.0 CA A:GLY1008 3.9 57.5 1.0 O A:LEU1005 4.0 28.2 1.0 C A:SER1007 4.1 57.8 1.0 C A:GLY1008 4.2 53.8 1.0 C A:LEU1005 4.2 30.2 1.0 O A:SER1007 4.2 56.5 1.0 N A:PHE1010 4.3 39.6 1.0 N A:GLY1006 4.3 37.6 1.0 CG B:GLU1207 4.5 45.2 1.0 CA A:GLY1006 4.6 44.3 1.0 N A:SER1007 4.7 58.4 1.0 CA A:ALA1009 4.8 43.7 1.0 CA A:SER1007 4.8 59.9 1.0 O A:PHE1010 4.8 39.3 1.0 C A:ALA1009 4.9 41.3 1.0 N A:LEU1005 4.9 26.2 1.0 CA A:LEU1005 4.9 27.6 1.0 O A:PRO1004 5.0 32.2 1.0 CB A:PRO1004 5.0 30.2 1.0

Magnesium binding site 9 out of 19 in the Crystal Structure of Human Pas Kinase Bound to Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Human Pas Kinase Bound to Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg11 b:13.6 occ:1.00 O2B C:ADP3 1.9 26.2 1.0 O1A C:ADP3 2.3 23.6 1.0 OD2 C:ASP1146 2.3 17.9 1.0 OD1 C:ASN1133 2.6 34.0 1.0 PB C:ADP3 3.3 21.4 1.0 CG C:ASP1146 3.3 25.6 1.0 PA C:ADP3 3.5 19.1 1.0 CG C:ASN1133 3.7 24.2 1.0 O3A C:ADP3 3.8 30.2 1.0 CB C:ASP1146 3.9 20.2 1.0 ND2 C:ASN1133 4.1 26.4 1.0 O3B C:ADP3 4.2 36.1 1.0 O1B C:ADP3 4.3 23.4 1.0 MG C:MG12 4.3 35.6 1.0 OD1 C:ASP1146 4.4 11.8 1.0 O5' C:ADP3 4.5 31.9 1.0 O2A C:ADP3 4.5 23.1 1.0 C5' C:ADP3 4.6 21.7 1.0 O C:GLU1132 4.7 27.3 1.0 O3' C:ADP3 4.8 25.6 1.0 CE C:LYS1130 4.9 38.2 1.0 OE2 C:GLU1132 5.0 41.7 1.0 CB C:ASN1133 5.0 22.6 1.0

Magnesium binding site 10 out of 19 in the Crystal Structure of Human Pas Kinase Bound to Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Human Pas Kinase Bound to Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg12 b:35.6 occ:1.00 OD1 C:ASP1146 2.6 11.8 1.0 O1B C:ADP3 2.8 23.4 1.0 OD2 C:ASP1146 2.9 17.9 1.0 CG C:ASP1146 3.1 25.6 1.0 O2B C:ADP3 3.4 26.2 1.0 PB C:ADP3 3.6 21.4 1.0 NZ C:LYS1028 4.1 30.2 1.0 MG C:MG11 4.3 13.6 1.0 CA C:GLY1148 4.5 27.6 1.0 CB C:ASP1146 4.6 20.2 1.0 O3A C:ADP3 4.7 30.2 1.0 N C:GLY1148 4.7 28.1 1.0 O3B C:ADP3 4.8 36.1 1.0 CE C:LYS1028 4.9 33.8 1.0

C.K.Kikani, S.A.Antonysamy, J.B.Bonanno, R.Romero, F.F.Zhang, M.Russell, T.Gheyi, M.Iizuka, S.Emtage, J.M.Sauder, B.E.Turk, S.K.Burley, J.Rutter. Structural Bases of Pas Domain-Regulated Kinase (Pask) Activation in the Absence of Activation Loop Phosphorylation. J.Biol.Chem. V. 285 41034 2010.
ISSN: ISSN 0021-9258
PubMed: 20943661
DOI: 10.1074/JBC.M110.157594