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Magnesium in PDB 2fv7: Crystal Structure of Human Ribokinase

Enzymatic activity of Crystal Structure of Human Ribokinase

All present enzymatic activity of Crystal Structure of Human Ribokinase:
2.7.1.15;

Protein crystallography data

The structure of Crystal Structure of Human Ribokinase, PDB code: 2fv7 was solved by W.M.Rabeh, W.Tempel, L.Nedyalkova, C.Arrowsmith, A.Edwards, M.Sundstrom, J.Weigelt, A.Bochkarev, H.Park, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.530, 72.978, 90.958, 90.00, 91.08, 90.00
R / Rfree (%) 19.8 / 24.8

Other elements in 2fv7:

The structure of Crystal Structure of Human Ribokinase also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Ribokinase (pdb code 2fv7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Ribokinase, PDB code: 2fv7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2fv7

Go back to Magnesium Binding Sites List in 2fv7
Magnesium binding site 1 out of 2 in the Crystal Structure of Human Ribokinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Ribokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:61.8
occ:1.00
O A:HOH825 2.3 27.6 1.0
O A:HOH817 2.3 17.7 1.0
O2B A:ADP401 2.3 41.4 1.0
O A:HOH819 2.4 20.9 1.0
O A:HOH856 3.2 29.1 1.0
O A:HOH838 3.3 29.3 1.0
PB A:ADP401 3.6 43.2 1.0
CA A:GLY268 3.8 27.5 1.0
O3B A:ADP401 4.0 43.3 1.0
NZ A:LYS54 4.0 31.5 1.0
C A:GLY268 4.1 26.7 1.0
OE2 A:GLU202 4.2 34.6 1.0
OD1 A:ASP269 4.2 31.3 1.0
OD1 A:ASN177 4.2 30.7 1.0
OE1 A:GLU202 4.3 32.4 1.0
ND2 A:ASN177 4.4 24.9 1.0
ND2 A:ASN199 4.4 30.5 1.0
N A:ASP269 4.4 26.7 1.0
O3A A:ADP401 4.5 39.6 1.0
CB A:ALA179 4.6 29.4 1.0
N A:GLY268 4.6 28.3 1.0
CD A:GLU202 4.7 32.1 1.0
UNK A:UNX510 4.7 2.0 0.0
O1B A:ADP401 4.7 45.2 1.0
O A:GLY268 4.7 26.1 1.0
CG A:ASN177 4.7 26.9 1.0
CG A:ASP269 5.0 28.9 1.0

Magnesium binding site 2 out of 2 in 2fv7

Go back to Magnesium Binding Sites List in 2fv7
Magnesium binding site 2 out of 2 in the Crystal Structure of Human Ribokinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Ribokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg406

b:52.1
occ:1.00
O B:HOH859 2.3 23.6 1.0
O2B B:ADP402 2.3 45.9 1.0
O B:HOH842 2.5 23.5 1.0
O B:HOH864 2.7 31.5 1.0
O B:HOH871 2.7 30.3 1.0
PB B:ADP402 3.7 47.4 1.0
CA B:GLY268 3.8 26.3 1.0
C B:GLY268 4.1 25.9 1.0
O3B B:ADP402 4.2 47.5 1.0
OD1 B:ASP269 4.2 30.6 1.0
N B:ASP269 4.3 25.7 1.0
NZ B:LYS54 4.3 30.7 1.0
OE2 B:GLU202 4.4 39.6 1.0
OD1 B:ASN177 4.4 27.0 1.0
O3A B:ADP402 4.5 44.7 1.0
ND2 B:ASN177 4.5 27.3 1.0
ND2 B:ASN199 4.6 28.1 1.0
N B:GLY268 4.6 26.9 1.0
OE1 B:GLU202 4.7 39.6 1.0
O B:GLY268 4.7 25.4 1.0
O1B B:ADP402 4.7 47.6 1.0
CB B:ALA179 4.8 29.3 1.0
CG B:ASN177 4.9 27.9 1.0
CG B:ASP269 4.9 28.3 1.0

Reference:

W.M.Rabeh, W.Tempel, L.Nedyalkova, C.Arrowsmith, A.Edwards, M.Sundstrom, J.Weigelt, A.Bochkarev, H.Park, Structural Genomics Consortium (Sgc). Crystal Structure of Human Ribokinase To Be Published.
Page generated: Mon Dec 14 07:23:38 2020

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