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Magnesium in PDB 2jg1: Structure of Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase with Cofactor and Substrate

Enzymatic activity of Structure of Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase with Cofactor and Substrate

All present enzymatic activity of Structure of Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase with Cofactor and Substrate:
2.7.1.144;

Protein crystallography data

The structure of Structure of Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase with Cofactor and Substrate, PDB code: 2jg1 was solved by L.Miallau, W.N.Hunter, S.M.Mcsweeney, G.A.Leonard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.85 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.200, 97.090, 154.470, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase with Cofactor and Substrate (pdb code 2jg1). 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 Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase with Cofactor and Substrate, PDB code: 2jg1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 2jg1

Go back to Magnesium Binding Sites List in 2jg1
Magnesium binding site 1 out of 5 in the Structure of Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase with Cofactor and Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase with Cofactor and Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1311

b:27.8
occ:1.00
 O A:HOH2172 1.8 36.8 1.0
O1G A:ANP1312 1.9 30.4 1.0
O A:HOH2219 2.0 34.5 1.0
O A:HOH2155 2.0 26.8 1.0
O A:HOH2154 2.0 25.2 1.0
O2B A:ANP1312 2.2 30.8 1.0
PG A:ANP1312 3.2 31.8 1.0
PB A:ANP1312 3.3 31.1 1.0
N3B A:ANP1312 3.7 30.6 1.0
O2G A:ANP1312 3.8 30.8 1.0
NZ A:LYS183 3.8 32.3 1.0
NZ A:LYS38 4.0 35.3 1.0
O A:HOH2153 4.0 33.7 1.0
OE2 A:GLU188 4.0 44.9 1.0
OD2 A:ASP163 4.1 27.9 1.0
OD1 A:ASP163 4.1 23.8 1.0
O1B A:ANP1312 4.1 31.8 1.0
OE1 A:GLU188 4.3 44.0 1.0
O3G A:ANP1312 4.5 28.6 1.0
CG A:ASP163 4.6 26.1 1.0
O3A A:ANP1312 4.6 30.8 1.0
CD A:GLU188 4.6 44.9 1.0
ND2 A:ASN185 4.6 36.2 1.0
CA A:GLY253 4.6 24.2 1.0
CE A:LYS38 4.7 32.9 1.0
OD1 A:ASP254 4.9 24.9 1.0

Magnesium binding site 2 out of 5 in 2jg1

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Magnesium binding site 2 out of 5 in the Structure of Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase with Cofactor and Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase with Cofactor and Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1311

b:35.0
occ:1.00
 O B:HOH2173 1.9 28.0 1.0
O B:HOH2213 2.0 45.6 1.0
O1G B:ANP1312 2.0 34.8 1.0
O B:HOH2156 2.1 29.5 1.0
O2B B:ANP1312 2.1 37.5 1.0
O B:HOH2175 2.1 28.6 1.0
PB B:ANP1312 3.3 35.6 1.0
PG B:ANP1312 3.3 36.8 1.0
N3B B:ANP1312 3.8 35.6 1.0
NZ B:LYS38 3.9 36.2 1.0
O2G B:ANP1312 3.9 36.4 1.0
OD1 B:ASP163 3.9 25.2 1.0
OE2 B:GLU188 3.9 45.6 1.0
O B:HOH2158 3.9 41.9 1.0
NZ B:LYS183 3.9 32.2 1.0
O1B B:ANP1312 4.0 36.5 1.0
OD2 B:ASP163 4.1 25.8 1.0
OE1 B:GLU188 4.2 45.3 1.0
CG B:ASP163 4.4 25.5 1.0
CD B:GLU188 4.5 46.2 1.0
O3A B:ANP1312 4.5 37.5 1.0
CA B:GLY253 4.6 29.8 1.0
CE B:LYS38 4.6 34.0 1.0
O3G B:ANP1312 4.6 36.6 1.0
ND2 B:ASN185 4.6 38.3 1.0
CE B:LYS183 4.9 32.4 1.0

Magnesium binding site 3 out of 5 in 2jg1

Go back to Magnesium Binding Sites List in 2jg1
Magnesium binding site 3 out of 5 in the Structure of Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase with Cofactor and Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase with Cofactor and Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1310

b:37.6
occ:1.00
 O C:HOH2194 2.0 34.1 1.0
O C:HOH2195 2.0 30.0 1.0
O2A C:ANP1313 2.1 28.2 1.0
O1B C:ANP1313 2.1 32.5 1.0
O C:HOH2097 2.3 33.3 1.0
O C:HOH2163 2.4 33.0 1.0
PB C:ANP1313 3.2 30.8 1.0
PA C:ANP1313 3.3 29.7 1.0
O3A C:ANP1313 3.6 29.4 1.0
N3B C:ANP1313 3.7 29.4 1.0
O C:HOH2198 4.0 35.1 1.0
NE2 C:GLN99 4.1 23.7 1.0
O1A C:ANP1313 4.1 30.6 1.0
O C:HOH2199 4.2 31.1 1.0
ND2 C:ASN185 4.5 32.7 1.0
OE1 C:GLN99 4.5 27.5 1.0
O5' C:ANP1313 4.5 28.5 1.0
O2B C:ANP1313 4.6 30.7 1.0
CD C:GLN99 4.7 23.0 1.0
O1G C:ANP1313 4.9 29.0 0.5
PG C:ANP1313 4.9 31.1 0.5
O C:PRO249 4.9 25.7 1.0

Magnesium binding site 4 out of 5 in 2jg1

Go back to Magnesium Binding Sites List in 2jg1
Magnesium binding site 4 out of 5 in the Structure of Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase with Cofactor and Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase with Cofactor and Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1311

b:42.8
occ:1.00
 O2B C:ANP1313 2.0 30.7 1.0
O C:HOH2197 2.0 38.0 1.0
O C:HOH2129 2.1 37.1 1.0
O C:HOH2143 2.2 32.8 1.0
O2G C:ANP1313 2.4 30.5 0.5
PB C:ANP1313 3.2 30.8 1.0
PG C:ANP1313 3.4 31.1 0.5
O3G C:ANP1313 3.7 27.6 0.5
N3B C:ANP1313 3.8 29.4 1.0
NZ C:LYS38 3.8 25.0 1.0
O1B C:ANP1313 3.9 32.5 1.0
NZ C:LYS183 3.9 30.5 1.0
OD2 C:ASP163 3.9 26.5 1.0
OE2 C:GLU188 4.0 35.6 1.0
OD1 C:ASP163 4.2 23.7 1.0
CE C:LYS38 4.2 24.8 1.0
OE1 C:GLU188 4.2 34.8 1.0
ND2 C:ASN185 4.2 32.7 1.0
CA C:GLY253 4.4 24.2 1.0
O3A C:ANP1313 4.4 29.4 1.0
O C:HOH2130 4.5 32.0 1.0
CD C:GLU188 4.5 37.2 1.0
CG C:ASP163 4.5 27.2 1.0
CD C:LYS38 4.6 21.9 1.0
O1 C:TA61312 4.7 29.4 1.0
OD1 C:ASP254 4.8 26.5 1.0
O1G C:ANP1313 4.8 29.0 0.5
CE C:LYS183 4.8 31.3 1.0
C C:GLY253 4.9 24.5 1.0
CG C:ASN185 4.9 32.6 1.0
CB C:ASN185 5.0 32.6 1.0

Magnesium binding site 5 out of 5 in 2jg1

Go back to Magnesium Binding Sites List in 2jg1
Magnesium binding site 5 out of 5 in the Structure of Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase with Cofactor and Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase with Cofactor and Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1311

b:26.9
occ:1.00
 O D:HOH2154 1.9 24.7 1.0
O D:HOH2233 2.0 22.7 1.0
O1G D:ANP1312 2.0 22.2 1.0
O2B D:ANP1312 2.1 23.9 1.0
O D:HOH2155 2.1 26.3 1.0
O D:HOH2232 2.3 29.6 1.0
PG D:ANP1312 3.2 24.5 1.0
PB D:ANP1312 3.2 23.3 1.0
N3B D:ANP1312 3.6 22.3 1.0
O2G D:ANP1312 3.6 24.1 1.0
NZ D:LYS183 3.8 26.2 1.0
O1B D:ANP1312 3.9 23.7 1.0
OD2 D:ASP163 3.9 28.0 1.0
O D:HOH2239 4.1 53.8 1.0
OD1 D:ASP163 4.3 24.6 1.0
OE2 D:GLU188 4.3 33.7 1.0
NZ D:LYS38 4.4 22.0 0.3
CA D:GLY253 4.4 21.1 1.0
O D:HOH2174 4.4 31.6 1.0
O3A D:ANP1312 4.4 23.1 1.0
OE1 D:GLU188 4.4 31.0 1.0
CE D:LYS38 4.4 21.6 0.3
O3G D:ANP1312 4.5 21.0 1.0
OD1 D:ASP254 4.5 25.7 1.0
CG D:ASP163 4.5 24.9 1.0
ND2 D:ASN185 4.6 24.8 1.0
CD D:GLU188 4.7 33.4 1.0
O D:HOH2156 4.8 36.3 1.0
C D:GLY253 4.8 21.2 1.0

Reference:

L.Miallau, W.N.Hunter, S.M.Mcsweeney, G.A.Leonard. Structures of Staphylococcus Aureus D-Tagatose-6- Phosphate Kinase Implicate Domain Motions in Specificity and Mechanism. J.Biol.Chem. V. 282 19948 2007.
ISSN: ISSN 0021-9258
PubMed: 17459874
DOI: 10.1074/JBC.M701480200
Page generated: Wed Aug 14 00:44:30 2024

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