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Magnesium in PDB 2pyw: Structure of A. Thaliana 5-Methylthioribose Kinase in Complex with Adp and Mtr

Enzymatic activity of Structure of A. Thaliana 5-Methylthioribose Kinase in Complex with Adp and Mtr

All present enzymatic activity of Structure of A. Thaliana 5-Methylthioribose Kinase in Complex with Adp and Mtr:
2.7.1.100;

Protein crystallography data

The structure of Structure of A. Thaliana 5-Methylthioribose Kinase in Complex with Adp and Mtr, PDB code: 2pyw 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) 80.58 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.460, 82.240, 91.080, 90.00, 117.83, 90.00
R / Rfree (%) 16.3 / 19.7

Other elements in 2pyw:

The structure of Structure of A. Thaliana 5-Methylthioribose Kinase in Complex with Adp and Mtr also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of A. Thaliana 5-Methylthioribose Kinase in Complex with Adp and Mtr (pdb code 2pyw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of A. Thaliana 5-Methylthioribose Kinase in Complex with Adp and Mtr, PDB code: 2pyw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 2pyw

Go back to Magnesium Binding Sites List in 2pyw
Magnesium binding site 1 out of 5 in the Structure of A. Thaliana 5-Methylthioribose Kinase in Complex with Adp and Mtr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A. Thaliana 5-Methylthioribose Kinase in Complex with Adp and Mtr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg500

b:13.2
occ:1.00
 OE2 A:GLU257 2.0 13.0 1.0
O A:HOH1003 2.0 15.8 1.0
O2B A:ADP999 2.1 11.5 1.0
OD2 A:ASP255 2.1 9.2 1.0
OD1 A:ASP255 2.2 10.5 1.0
O A:HOH1004 2.3 12.5 1.0
CG A:ASP255 2.5 10.6 1.0
CD A:GLU257 3.0 11.3 1.0
PB A:ADP999 3.2 12.6 1.0
O3B A:ADP999 3.3 11.0 1.0
CG A:GLU257 3.6 7.4 1.0
MG A:MG501 3.6 16.6 1.0
O A:HOH1002 3.8 15.2 1.0
ND2 A:ASN48 4.0 10.9 1.0
CB A:ASP255 4.0 8.5 1.0
NZ A:LYS63 4.0 10.4 1.0
OE1 A:GLU257 4.0 14.5 1.0
O3A A:ADP999 4.2 12.2 1.0
O1B A:ADP999 4.2 12.4 1.0
O1' A:SR1998 4.3 19.1 1.0
OD2 A:ASP238 4.3 11.3 1.0
O A:ASP255 4.4 8.0 1.0
CE2 A:PHE258 4.5 11.0 1.0
CB A:LEU47 4.6 15.4 1.0
O2A A:ADP999 4.7 10.9 1.0
PA A:ADP999 4.8 11.4 1.0
CB A:GLU257 4.8 9.1 1.0
CD2 A:PHE258 4.8 11.6 1.0
CA A:ASP255 4.8 8.8 1.0
O1A A:ADP999 4.9 13.6 1.0
O A:HOH1000 5.0 11.3 1.0
C A:ASP255 5.0 8.4 1.0
CE A:LYS63 5.0 12.2 1.0

Magnesium binding site 2 out of 5 in 2pyw

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Magnesium binding site 2 out of 5 in the Structure of A. Thaliana 5-Methylthioribose Kinase in Complex with Adp and Mtr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A. Thaliana 5-Methylthioribose Kinase in Complex with Adp and Mtr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:16.6
occ:1.00
 O2A A:ADP999 2.0 10.9 1.0
O3B A:ADP999 2.1 11.0 1.0
O A:HOH1001 2.1 13.2 1.0
OD2 A:ASP255 2.1 9.2 1.0
O A:HOH1000 2.1 11.3 1.0
O A:HOH1002 2.2 15.2 1.0
PB A:ADP999 3.1 12.6 1.0
PA A:ADP999 3.2 11.4 1.0
CG A:ASP255 3.2 10.6 1.0
O3A A:ADP999 3.5 12.2 1.0
MG A:MG500 3.6 13.2 1.0
O2B A:ADP999 3.7 11.5 1.0
O A:HOH1003 3.7 15.8 1.0
CB A:ASP255 3.8 8.5 1.0
O1A A:ADP999 4.1 13.6 1.0
O A:HOH1367 4.2 13.9 1.0
OD1 A:ASP255 4.2 10.5 1.0
O A:GLY242 4.3 9.7 1.0
O5' A:ADP999 4.3 11.6 1.0
O A:HOH1369 4.4 29.7 1.0
O A:HOH1004 4.4 12.5 1.0
CA A:GLY45 4.5 19.9 1.0
O1B A:ADP999 4.5 12.4 1.0
OG A:SER243 4.5 10.6 1.0
C5' A:ADP999 4.6 9.8 1.0
CE1 A:HIS240 4.9 10.5 1.0
OD2 A:ASP238 4.9 11.3 1.0
O1' A:SR1998 4.9 19.1 1.0
NE2 A:HIS240 5.0 10.9 1.0

Magnesium binding site 3 out of 5 in 2pyw

Go back to Magnesium Binding Sites List in 2pyw
Magnesium binding site 3 out of 5 in the Structure of A. Thaliana 5-Methylthioribose Kinase in Complex with Adp and Mtr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A. Thaliana 5-Methylthioribose Kinase in Complex with Adp and Mtr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:23.8
occ:1.00
 O A:HOH1312 2.1 21.4 1.0
O A:HOH1359 2.2 24.1 1.0
O A:HOH1142 2.2 16.4 1.0
OD2 A:ASP205 2.2 16.1 1.0
CG A:ASP205 3.2 14.4 1.0
OD1 A:ASP205 3.5 17.2 1.0
O A:HOH1246 4.0 21.3 1.0
CB A:ASP205 4.6 12.3 1.0

Magnesium binding site 4 out of 5 in 2pyw

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Magnesium binding site 4 out of 5 in the Structure of A. Thaliana 5-Methylthioribose Kinase in Complex with Adp and Mtr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A. Thaliana 5-Methylthioribose Kinase in Complex with Adp and Mtr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg500

b:21.1
occ:1.00
 OE2 B:GLU257 1.9 18.8 1.0
O2B B:ADP999 2.1 21.2 1.0
O B:HOH1003 2.1 17.3 1.0
OD2 B:ASP255 2.2 13.2 1.0
O B:HOH1004 2.3 18.1 1.0
OD1 B:ASP255 2.4 13.8 1.0
CG B:ASP255 2.6 13.7 1.0
CD B:GLU257 3.0 16.9 1.0
PB B:ADP999 3.1 19.6 1.0
O3B B:ADP999 3.2 17.7 1.0
CG B:GLU257 3.5 13.0 1.0
MG B:MG501 3.6 21.0 1.0
O B:HOH1001 3.8 20.3 1.0
ND2 B:ASN48 3.9 20.5 1.0
OE1 B:GLU257 4.0 17.6 1.0
CB B:ASP255 4.1 13.1 1.0
O1B B:ADP999 4.1 20.4 1.0
O1' B:SR1998 4.2 25.4 1.0
NZ B:LYS63 4.2 15.5 1.0
O3A B:ADP999 4.2 19.5 1.0
OD2 B:ASP238 4.4 14.4 1.0
CE2 B:PHE258 4.4 13.5 1.0
CB B:LEU47 4.5 24.4 1.0
O B:ASP255 4.5 12.6 1.0
O2A B:ADP999 4.7 20.6 1.0
CB B:GLU257 4.8 12.2 1.0
CD2 B:PHE258 4.8 12.0 1.0
PA B:ADP999 4.8 17.9 1.0
CD2 B:LEU47 4.9 23.8 1.0
CA B:ASP255 5.0 12.8 1.0
O1A B:ADP999 5.0 18.2 1.0

Magnesium binding site 5 out of 5 in 2pyw

Go back to Magnesium Binding Sites List in 2pyw
Magnesium binding site 5 out of 5 in the Structure of A. Thaliana 5-Methylthioribose Kinase in Complex with Adp and Mtr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of A. Thaliana 5-Methylthioribose Kinase in Complex with Adp and Mtr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:21.0
occ:1.00
 O3B B:ADP999 2.0 17.7 1.0
O B:HOH1002 2.0 18.4 1.0
O B:HOH1000 2.1 19.4 1.0
O2A B:ADP999 2.1 20.6 1.0
O B:HOH1001 2.1 20.3 1.0
OD2 B:ASP255 2.1 13.2 1.0
PB B:ADP999 3.2 19.6 1.0
CG B:ASP255 3.2 13.7 1.0
PA B:ADP999 3.3 17.9 1.0
O3A B:ADP999 3.6 19.5 1.0
MG B:MG500 3.6 21.1 1.0
O B:HOH1003 3.7 17.3 1.0
O2B B:ADP999 3.8 21.2 1.0
CB B:ASP255 3.8 13.1 1.0
O1A B:ADP999 4.2 18.2 1.0
O B:HOH1154 4.2 31.2 1.0
OD1 B:ASP255 4.3 13.8 1.0
O B:GLY242 4.3 14.3 1.0
O B:HOH1124 4.3 23.0 1.0
OG B:SER243 4.4 14.3 1.0
O5' B:ADP999 4.5 19.2 1.0
O B:HOH1004 4.5 18.1 1.0
O1B B:ADP999 4.5 20.4 1.0
CA B:GLY45 4.6 29.4 1.0
C5' B:ADP999 4.7 17.2 1.0
O1' B:SR1998 4.7 25.4 1.0
CE1 B:HIS240 4.8 15.7 1.0
OD2 B:ASP238 4.8 14.4 1.0
NE2 B:HIS240 4.9 13.9 1.0

Reference:

S.Y.Ku, K.A.Cornell, P.L.Howell. Structure of A. Thaliana 5-Methylthioribose Kinase in Complex with Adp and Mtr Reveals A More Occluded Active Site Than Its Bacterial Homolog Bmc Struct.Biol. V. 7 70 2007.
ISSN: ESSN 1472-6807
PubMed: 17961230
DOI: 10.1186/1472-6807-7-70
Page generated: Mon Dec 14 07:35:22 2020

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