Atomistry » Magnesium » PDB 2ppq-2q0e » 2pui
Atomistry »
  Magnesium »
    PDB 2ppq-2q0e »
      2pui »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy