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Magnesium in PDB 2pui: 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: 2pui 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) 65.82 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 213.780, 83.530, 51.240, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 24.9

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 2pui). 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: 2pui:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2pui

Go back to Magnesium Binding Sites List in 2pui
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:44.0
occ:1.00
 O2A A:ADP999 1.9 36.9 1.0
OD2 A:ASP250 2.3 25.0 1.0
O3B A:ADP999 2.5 37.0 1.0
PA A:ADP999 3.3 36.1 1.0
CG A:ASP250 3.3 26.1 1.0
O A:HOH1136 3.5 40.1 1.0
PB A:ADP999 3.6 36.3 1.0
CB A:ASP250 3.7 27.0 1.0
O3A A:ADP999 3.8 35.0 1.0
MG A:MG401 4.0 28.3 1.0
O2B A:ADP999 4.0 37.8 1.0
OG A:SER238 4.2 30.4 1.0
O A:GLY237 4.2 29.2 1.0
O1A A:ADP999 4.2 37.5 1.0
OD1 A:ASP250 4.4 27.4 1.0
O5' A:ADP999 4.4 36.1 1.0
O A:HOH1059 4.5 37.6 1.0
C A:GLY237 4.9 29.0 1.0
C5' A:ADP999 4.9 36.8 1.0
CA A:SER238 4.9 29.7 1.0
NE2 A:HIS235 4.9 29.6 1.0
O1B A:ADP999 4.9 35.6 1.0
CE1 A:HIS235 4.9 29.9 1.0

Magnesium binding site 2 out of 4 in 2pui

Go back to Magnesium Binding Sites List in 2pui
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:28.3
occ:1.00
 O2B A:ADP999 1.9 37.8 1.0
OE2 A:GLU252 2.1 34.7 1.0
OD2 A:ASP250 2.2 25.0 1.0
OD1 A:ASP250 2.3 27.4 1.0
CG A:ASP250 2.6 26.1 1.0
O A:HOH1059 2.6 37.6 1.0
PB A:ADP999 3.2 36.3 1.0
CD A:GLU252 3.3 32.3 1.0
O3B A:ADP999 3.4 37.0 1.0
O A:HOH1136 3.9 40.1 1.0
CB A:GLU252 3.9 29.0 1.0
MG A:MG400 4.0 44.0 1.0
OE1 A:GLU252 4.0 35.2 1.0
ND2 A:ASN44 4.1 47.5 1.0
CB A:ASP250 4.1 27.0 1.0
NZ A:LYS61 4.2 31.9 1.0
CG A:GLU252 4.2 31.5 1.0
O3A A:ADP999 4.2 35.0 1.0
O1B A:ADP999 4.3 35.6 1.0
O2A A:ADP999 4.5 36.9 1.0
O A:ASP250 4.6 27.6 1.0
CE1 A:PHE253 4.8 26.3 1.0
PA A:ADP999 4.8 36.1 1.0
OD1 A:ASP233 4.8 29.2 1.0
CA A:ASP250 4.9 26.9 1.0
O1A A:ADP999 4.9 37.5 1.0

Magnesium binding site 3 out of 4 in 2pui

Go back to Magnesium Binding Sites List in 2pui
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:50.4
occ:1.00
 O3B B:ADP999 2.3 41.2 1.0
O2A B:ADP999 2.4 42.9 1.0
OD2 B:ASP250 2.5 27.9 1.0
O B:HOH1110 3.0 37.1 1.0
CG B:ASP250 3.5 27.3 1.0
PB B:ADP999 3.6 40.3 1.0
PA B:ADP999 3.7 41.8 1.0
MG B:MG401 3.9 37.3 1.0
O2B B:ADP999 4.0 40.2 1.0
CB B:ASP250 4.1 27.6 1.0
O3A B:ADP999 4.1 41.5 1.0
O B:GLY237 4.3 28.9 1.0
O B:HOH1049 4.4 34.5 1.0
OG B:SER238 4.4 32.4 1.0
NE2 B:HIS235 4.4 24.3 1.0
OD1 B:ASP250 4.5 30.4 1.0
O B:HOH1212 4.6 41.7 1.0
CE1 B:HIS235 4.6 24.9 1.0
O B:HOH1146 4.6 42.0 1.0
O1A B:ADP999 4.7 41.5 1.0
O1B B:ADP999 4.8 41.4 1.0
O5' B:ADP999 4.8 41.3 1.0
OD2 B:ASP233 4.9 26.2 1.0
C B:GLY237 5.0 29.0 1.0

Magnesium binding site 4 out of 4 in 2pui

Go back to Magnesium Binding Sites List in 2pui
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:37.3
occ:1.00
 OE1 B:GLU252 2.1 32.0 1.0
OD2 B:ASP250 2.2 27.9 1.0
O2B B:ADP999 2.2 40.2 1.0
O B:HOH1212 2.3 41.7 1.0
OD1 B:ASP250 2.4 30.4 1.0
O B:HOH1049 2.6 34.5 1.0
CG B:ASP250 2.6 27.3 1.0
CD B:GLU252 3.2 33.2 1.0
PB B:ADP999 3.3 40.3 1.0
O3B B:ADP999 3.4 41.2 1.0
MG B:MG400 3.9 50.4 1.0
O B:HOH1110 3.9 37.1 1.0
CG B:GLU252 4.0 31.6 1.0
O B:HOH1216 4.1 35.2 1.0
CB B:GLU252 4.1 28.6 1.0
CB B:ASP250 4.2 27.6 1.0
OE2 B:GLU252 4.2 33.6 1.0
O1B B:ADP999 4.3 41.4 1.0
ND2 B:ASN44 4.3 48.6 1.0
CE1 B:PHE253 4.3 26.5 1.0
O3A B:ADP999 4.4 41.5 1.0
NZ B:LYS61 4.4 37.8 1.0
OD2 B:ASP233 4.6 26.2 1.0
O B:ASP250 4.6 27.9 1.0
O2A B:ADP999 4.7 42.9 1.0
CD1 B:PHE253 4.8 29.3 1.0
PA B:ADP999 5.0 41.8 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 02:17:42 2024

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