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Magnesium in PDB 2pup: Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding

Enzymatic activity of Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding

All present enzymatic activity of Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding:
2.7.1.100;

Protein crystallography data

The structure of Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding, PDB code: 2pup was solved by S.-Y.Ku, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.34 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 213.930, 83.290, 51.420, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 27.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding (pdb code 2pup). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding, PDB code: 2pup:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2pup

Go back to Magnesium Binding Sites List in 2pup
Magnesium binding site 1 out of 4 in the Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg400

b:53.8
occ:1.00
 OE1 A:GLU252 2.0 35.4 1.0
O2B A:ADP999 2.1 58.5 1.0
OD2 A:ASP250 2.2 43.8 1.0
OD1 A:ASP250 2.9 42.1 1.0
CG A:ASP250 2.9 38.5 1.0
CD A:GLU252 3.1 34.4 1.0
PB A:ADP999 3.2 60.7 1.0
O3B A:ADP999 3.4 57.9 1.0
O A:HOH1000 3.5 32.9 1.0
CG A:GLU252 3.6 33.2 1.0
MG A:MG401 3.7 49.6 1.0
O1B A:ADP999 4.1 59.8 1.0
OE2 A:GLU252 4.2 37.0 1.0
CB A:ASP250 4.4 35.3 1.0
O3A A:ADP999 4.5 57.4 1.0
CE1 A:PHE253 4.6 30.1 1.0
O A:ASP250 4.6 34.2 1.0
ND2 A:ASN44 4.7 53.3 1.0
NZ A:LYS61 4.7 37.3 1.0
OD1 A:ASP233 4.8 33.0 1.0
CB A:GLU252 4.9 32.9 1.0
O1A A:ADP999 4.9 57.8 1.0
CD1 A:PHE253 5.0 31.4 1.0

Magnesium binding site 2 out of 4 in 2pup

Go back to Magnesium Binding Sites List in 2pup
Magnesium binding site 2 out of 4 in the Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:49.6
occ:1.00
 OD2 A:ASP250 2.3 43.8 1.0
O2A A:ADP999 2.3 56.6 1.0
O3B A:ADP999 2.7 57.9 1.0
CG A:ASP250 3.2 38.5 1.0
PA A:ADP999 3.3 57.6 1.0
PB A:ADP999 3.5 60.7 1.0
CB A:ASP250 3.6 35.3 1.0
O2B A:ADP999 3.6 58.5 1.0
O1A A:ADP999 3.7 57.8 1.0
MG A:MG400 3.7 53.8 1.0
O3A A:ADP999 3.8 57.4 1.0
O A:GLY237 4.0 33.7 1.0
O A:HOH1000 4.0 32.9 1.0
OG A:SER238 4.0 37.1 1.0
OD1 A:ASP250 4.2 42.1 1.0
CD1 A:ILE249 4.6 29.5 1.0
O5' A:ADP999 4.7 56.0 1.0
C A:GLY237 4.8 33.1 1.0
CA A:SER238 4.8 33.8 1.0
CE1 A:HIS235 4.9 32.0 1.0
O1B A:ADP999 5.0 59.8 1.0
CB A:SER238 5.0 34.1 1.0

Magnesium binding site 3 out of 4 in 2pup

Go back to Magnesium Binding Sites List in 2pup
Magnesium binding site 3 out of 4 in the Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg400

b:48.2
occ:1.00
 OD2 B:ASP250 2.1 43.6 1.0
OE1 B:GLU252 2.2 34.9 1.0
O2B B:ADP999 2.4 64.9 1.0
O1 B:PO4998 2.8 87.3 1.0
CG B:ASP250 2.9 38.7 1.0
OD1 B:ASP250 2.9 42.5 1.0
O2 B:PO4998 3.0 86.7 1.0
CD B:GLU252 3.2 33.8 1.0
PB B:ADP999 3.4 64.5 1.0
O3B B:ADP999 3.5 65.0 1.0
P B:PO4998 3.5 86.9 1.0
CG B:GLU252 3.6 33.0 1.0
MG B:MG401 3.7 55.3 1.0
CB B:ASP250 4.3 35.4 1.0
CE1 B:PHE253 4.3 29.6 1.0
OE2 B:GLU252 4.3 37.1 1.0
O B:ASP250 4.4 34.1 1.0
O3 B:PO4998 4.4 86.8 1.0
O1B B:ADP999 4.4 64.8 1.0
OD2 B:ASP233 4.5 27.9 1.0
O3A B:ADP999 4.6 65.9 1.0
O4 B:PO4998 4.6 86.9 1.0
CD1 B:PHE253 4.7 31.7 1.0
CB B:GLU252 4.8 32.3 1.0
NZ B:LYS61 4.8 37.0 1.0
O2A B:ADP999 4.9 67.1 1.0
ND2 B:ASN44 4.9 53.4 1.0

Magnesium binding site 4 out of 4 in 2pup

Go back to Magnesium Binding Sites List in 2pup
Magnesium binding site 4 out of 4 in the Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:55.3
occ:1.00
 O2 B:PO4998 1.8 86.7 1.0
O2A B:ADP999 2.4 67.1 1.0
OD2 B:ASP250 2.5 43.6 1.0
O3B B:ADP999 2.7 65.0 1.0
P B:PO4998 3.3 86.9 1.0
CG B:ASP250 3.5 38.7 1.0
PA B:ADP999 3.7 66.0 1.0
MG B:MG400 3.7 48.2 1.0
PB B:ADP999 3.8 64.5 1.0
O4 B:PO4998 3.9 86.9 1.0
O3 B:PO4998 4.0 86.8 1.0
O B:GLY237 4.0 33.2 1.0
CB B:ASP250 4.0 35.4 1.0
OG B:SER238 4.0 37.4 1.0
O2B B:ADP999 4.1 64.9 1.0
O3A B:ADP999 4.2 65.9 1.0
O1 B:PO4998 4.2 87.3 1.0
O1A B:ADP999 4.3 64.9 1.0
CE1 B:HIS235 4.6 31.9 1.0
OD1 B:ASP250 4.6 42.5 1.0
NE2 B:HIS235 4.6 33.4 1.0
C B:GLY237 4.8 32.9 1.0
O5' B:ADP999 4.9 64.8 1.0
CA B:SER238 4.9 34.0 1.0
CB B:SER238 4.9 34.4 1.0
OD2 B:ASP233 4.9 27.9 1.0

Reference:

S.-Y.Ku, P.Yip, K.A.Cornell, M.K.Riscoe, J.-B.Behr, G.Guillerm, P.L.Howell. Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding J.Biol.Chem. V. 282 22195 2007.
ISSN: ISSN 0021-9258
PubMed: 17522047
DOI: 10.1074/JBC.M611045200
Page generated: Wed Aug 14 02:18:17 2024

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