Magnesium in PDB 2dcn: Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)

All present enzymatic activity of Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form):
2.7.1.45;

The structure of Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form), PDB code: 2dcn was solved by S.Okazaki, H.Onda, A.Suzuki, S.Kuramitsu, R.Masui, T.Yamane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.37 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.638, 150.229, 154.757, 90.00, 93.73, 90.00
R / Rfree (%)	17.5 / 22.8

The structure of Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) also contains other interesting chemical elements:

Potassium

(K)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 45;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) (pdb code 2dcn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 45 binding sites of Magnesium where determined in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form), PDB code: 2dcn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 45 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)


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 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4001 b:11.8 occ:1.00 O3P A:CKP2001 2.1 36.6 1.0 O2B A:ADP3001 2.2 38.6 1.0 OD1 A:ASN164 2.3 23.5 1.0 O A:HOH5134 2.3 25.6 1.0 O A:HOH5133 2.3 23.8 1.0 O A:HOH5135 2.5 22.7 1.0 CG A:ASN164 3.4 24.5 1.0 PB A:ADP3001 3.5 39.7 1.0 P A:CKP2001 3.5 34.7 1.0 O A:HOH5136 3.9 27.1 1.0 O3B A:ADP3001 3.9 40.6 1.0 NZ A:LYS224 4.0 34.7 1.0 ND2 A:ASN164 4.0 23.5 1.0 O1P A:CKP2001 4.0 34.9 1.0 NH2 A:ARG166 4.1 26.8 1.0 O1B A:ADP3001 4.1 37.6 1.0 NH1 A:ARG166 4.2 25.0 1.0 O1 A:CKP2001 4.3 32.8 1.0 OD2 A:ASP162 4.4 22.9 1.0 CA A:GLY255 4.4 22.9 1.0 OD1 A:ASP162 4.4 22.0 1.0 OD1 A:ASP256 4.5 25.0 1.0 O2P A:CKP2001 4.6 32.0 1.0 CB A:ASN164 4.6 25.2 1.0 CZ A:ARG166 4.6 25.6 1.0 CA A:ASN164 4.7 25.2 1.0 O3A A:ADP3001 4.7 34.9 1.0 CG A:ASP162 4.8 23.2 1.0 C A:GLY255 4.8 23.2 1.0 N A:ASP256 5.0 23.0 1.0 CE A:LYS224 5.0 32.5 1.0

Magnesium binding site 2 out of 45 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)


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 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4002 b:33.4 occ:1.00 O2A A:ADP3001 2.3 31.6 1.0 O A:HOH5061 2.6 33.3 1.0 O3B A:ADP3001 2.8 40.6 1.0 PA A:ADP3001 3.3 31.2 1.0 PB A:ADP3001 3.6 39.7 1.0 O1B A:ADP3001 3.6 37.6 1.0 O1A A:ADP3001 3.8 33.8 1.0 O3A A:ADP3001 3.8 34.9 1.0 O A:HOH5073 3.9 30.6 1.0 OD2 A:ASP196 4.2 39.9 1.0 OD1 A:ASP194 4.4 30.0 1.0 O A:HOH5117 4.4 39.0 1.0 CA A:GLY226 4.5 34.2 1.0 O A:HOH5072 4.7 35.9 1.0 O5' A:ADP3001 4.7 29.4 1.0 N A:GLY226 4.9 34.3 1.0 O A:HOH5137 5.0 36.7 1.0

Magnesium binding site 3 out of 45 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)


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 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4003 b:37.4 occ:0.60 CE1 A:TYR63 3.9 34.0 1.0 O A:ASP58 4.0 23.1 1.0 O D:HOH5169 4.0 38.3 1.0 CD1 A:TYR63 4.3 31.9 1.0 OE1 A:GLU60 4.3 20.5 1.0 OD2 A:ASP58 4.3 26.7 1.0 CA A:ASP59 4.4 21.5 1.0 C A:ASP59 4.5 21.1 1.0 C A:ASP58 4.5 22.1 1.0 N A:ASP59 4.7 22.3 1.0 N A:GLU60 4.7 20.2 1.0 NH2 B:ARG23 4.7 20.5 1.0 CZ A:TYR63 4.8 35.4 1.0 O A:ASP59 4.9 21.8 1.0

Magnesium binding site 4 out of 45 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)


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 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4004 b:40.6 occ:0.60 CE1 A:HIS78 3.6 27.0 1.0 CA A:TYR125 4.0 29.1 1.0 NE2 A:HIS78 4.0 28.4 1.0 CB A:TYR125 4.0 29.0 1.0 N A:TYR125 4.2 29.1 1.0 CD2 A:TYR125 4.2 28.3 1.0 CG A:GLU124 4.3 28.6 1.0 CD A:GLU124 4.3 29.4 1.0 OE1 A:GLU124 4.3 30.2 1.0 O A:GLU124 4.3 28.6 1.0 C A:GLU124 4.3 29.1 1.0 CG A:TYR125 4.6 29.4 1.0 CB A:GLU124 4.7 29.1 1.0 ND1 A:HIS78 4.8 26.6 1.0 OE2 A:GLU124 4.8 29.8 1.0 OD2 A:ASP122 4.9 36.3 1.0

Magnesium binding site 5 out of 45 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)


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 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4005 b:29.3 occ:0.60 O A:VAL76 4.2 19.3 1.0 CD1 A:ILE81 4.5 26.8 1.0 O A:MET79 4.5 24.0 1.0 CD1 A:ILE66 4.7 16.2 1.0 CG2 A:ILE66 5.0 18.3 1.0 CB A:MET79 5.0 24.2 1.0

Magnesium binding site 6 out of 45 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)


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 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4006 b:13.1 occ:1.00 O3P B:CKP2002 2.1 36.1 1.0 O2B B:ADP3002 2.1 30.6 1.0 O B:HOH5153 2.4 19.7 1.0 O B:HOH5154 2.4 15.4 1.0 OD1 B:ASN164 2.4 17.2 1.0 PB B:ADP3002 3.4 33.7 1.0 NH2 B:ARG166 3.5 33.7 1.0 P B:CKP2002 3.6 36.6 1.0 CG B:ASN164 3.6 20.6 1.0 O B:HOH5155 3.9 24.1 1.0 O B:HOH5156 4.0 25.1 1.0 O3B B:ADP3002 4.0 35.6 1.0 OD2 B:ASP162 4.0 20.4 1.0 O1B B:ADP3002 4.1 29.4 1.0 NZ B:LYS224 4.2 21.4 1.0 OD1 B:ASP162 4.3 19.6 1.0 ND2 B:ASN164 4.3 20.6 1.0 O1P B:CKP2002 4.3 38.2 1.0 O2P B:CKP2002 4.3 36.0 1.0 CA B:GLY255 4.4 16.7 1.0 O1 B:CKP2002 4.4 32.0 1.0 CZ B:ARG166 4.5 29.8 1.0 CG B:ASP162 4.5 20.3 1.0 NH1 B:ARG166 4.6 26.1 1.0 O3A B:ADP3002 4.6 29.7 1.0 OD1 B:ASP256 4.6 12.4 1.0 CA B:ASN164 4.6 20.9 1.0 CB B:ASN164 4.7 20.3 1.0 C B:GLY255 4.9 16.5 1.0 OD1 B:ASP194 5.0 24.3 1.0

Magnesium binding site 7 out of 45 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)


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 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4007 b:33.2 occ:1.00 O2A B:ADP3002 2.6 26.8 1.0 O3B B:ADP3002 2.6 35.6 1.0 O B:HOH5097 3.4 38.5 1.0 PA B:ADP3002 3.4 25.5 1.0 PB B:ADP3002 3.8 33.7 1.0 O1A B:ADP3002 3.8 28.7 1.0 O3A B:ADP3002 4.0 29.7 1.0 O1B B:ADP3002 4.1 29.4 1.0 OD2 B:ASP196 4.3 32.5 1.0 O B:HOH5066 4.4 29.8 1.0 OD1 B:ASP194 4.5 24.3 1.0 CA B:GLY226 4.6 27.4 1.0 O B:HOH5094 4.6 31.8 1.0 O5' B:ADP3002 4.8 24.1 1.0 O B:HOH5156 4.9 25.1 1.0

Magnesium binding site 8 out of 45 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)


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 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4008 b:31.9 occ:0.50 O B:VAL76 3.9 21.2 1.0 CG1 B:VAL76 4.4 20.6 1.0 O B:MET79 4.6 23.5 1.0 CA B:SER77 4.7 21.3 1.0 C B:VAL76 4.7 20.7 1.0 O B:SER77 5.0 21.9 1.0 CD1 B:ILE66 5.0 17.9 1.0

Magnesium binding site 9 out of 45 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)


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 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4009 b:30.5 occ:0.50 MG B:MG4009 0.0 30.5 0.5 MG B:MG4009 2.9 18.0 0.5 O B:TYR266 4.2 19.5 1.0 CE1 B:TYR266 4.5 21.1 1.0 O B:HOH5035 4.6 14.9 1.0 CZ B:TYR266 4.8 21.8 1.0 OH B:TYR266 4.9 22.8 1.0 O B:TYR267 5.0 20.5 1.0 CA B:TYR267 5.0 21.0 1.0 CD1 B:TYR266 5.0 19.7 1.0

Magnesium binding site 10 out of 45 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)


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 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4009 b:18.0 occ:0.50 MG B:MG4009 0.0 18.0 0.5 MG B:MG4009 2.9 30.5 0.5 O B:HOH5035 3.1 14.9 1.0 O B:TYR266 4.5 19.5 1.0 CZ B:TYR266 4.6 21.8 1.0 CE2 B:TYR266 4.6 21.4 1.0 OH B:TYR266 4.6 22.8 1.0 CA B:GLY269 4.9 19.6 1.0

S.Okazaki, H.Onda, A.Suzuki, S.Kuramitsu, R.Masui, T.Yamane. Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate To Be Published.