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Magnesium in PDB 2dya: Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase

Enzymatic activity of Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase

All present enzymatic activity of Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase, PDB code: 2dya was solved by M.Kato-Murayama, K.Murayama, T.Terada, M.Shirouzu, S.Yokoyama, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.06 / 1.77
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 69.707, 69.707, 107.117, 90.00, 90.00, 120.00
R / Rfree (%) 11.4 / 16.9

Other elements in 2dya:

The structure of Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase (pdb code 2dya). 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 Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase, PDB code: 2dya:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2dya

Go back to Magnesium Binding Sites List in 2dya
Magnesium binding site 1 out of 2 in the Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase


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 Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:16.0
occ:1.00
O1A A:ADP501 2.1 14.0 1.0
O1B A:ADP501 2.3 13.5 1.0
O A:HOH720 2.4 15.0 1.0
O A:HOH721 2.5 11.8 1.0
O A:HOH718 2.6 14.3 1.0
PB A:ADP501 3.4 14.8 1.0
O A:HOH749 3.5 20.6 1.0
PA A:ADP501 3.5 14.7 1.0
O3B A:ADP501 3.8 16.0 1.0
O3A A:ADP501 3.9 15.4 1.0
NH1 A:ARG91 4.1 14.5 1.0
OE2 A:GLU57 4.1 22.6 1.0
NE2 A:HIS58 4.3 13.8 1.0
O A:HOH725 4.3 13.0 1.0
O A:HOH724 4.3 10.1 1.0
C5' A:ADP501 4.4 13.2 1.0
O5' A:ADP501 4.4 12.8 1.0
CE1 A:HIS124 4.4 13.2 1.0
O2A A:ADP501 4.5 14.1 1.0
OD2 A:ASP127 4.6 15.7 1.0
OE1 A:GLU57 4.6 19.7 1.0
CD A:GLU57 4.6 22.5 1.0
O A:HOH719 4.6 8.7 1.0
ND1 A:HIS124 4.7 12.4 1.0
O A:HOH747 4.8 10.1 1.0
O2B A:ADP501 4.8 12.6 1.0
O A:ALA125 4.9 12.5 1.0
CZ A:ARG91 4.9 15.8 1.0
CB A:ASP127 4.9 15.8 1.0
NH2 A:ARG91 5.0 14.6 1.0
O A:HOH803 5.0 19.7 1.0
CE1 A:HIS58 5.0 13.8 1.0

Magnesium binding site 2 out of 2 in 2dya

Go back to Magnesium Binding Sites List in 2dya
Magnesium binding site 2 out of 2 in the Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase


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 Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:36.3
occ:1.00
O1A B:ADP502 2.2 24.7 1.0
O1B B:ADP502 2.2 24.9 1.0
O B:HOH752 2.3 21.7 1.0
O B:HOH743 2.5 16.0 1.0
O B:HOH738 2.6 16.3 1.0
PB B:ADP502 3.5 25.1 1.0
PA B:ADP502 3.6 25.0 1.0
OE2 B:GLU57 3.8 32.0 1.0
O B:HOH779 4.0 40.9 1.0
O3A B:ADP502 4.0 26.5 1.0
O3B B:ADP502 4.1 26.5 1.0
O B:HOH725 4.1 11.6 1.0
NH1 B:ARG91 4.2 18.9 1.0
OD2 B:ASP127 4.2 24.0 1.0
NE2 B:HIS58 4.2 30.5 1.0
C5' B:ADP502 4.4 23.2 1.0
CE1 B:HIS124 4.5 9.8 1.0
O5' B:ADP502 4.5 24.2 1.0
O B:HOH729 4.5 10.2 1.0
O2A B:ADP502 4.6 25.9 1.0
O B:HOH720 4.7 18.2 1.0
O B:HOH781 4.7 23.2 1.0
CD B:GLU57 4.8 30.4 1.0
O2B B:ADP502 4.8 25.3 1.0
ND1 B:HIS124 4.8 7.7 1.0
CB B:ASP127 4.8 18.8 1.0
CG B:ASP127 4.9 21.1 1.0
O B:HOH721 4.9 6.4 1.0
CE1 B:HIS58 5.0 30.1 1.0

Reference:

M.Kato-Murayama, K.Murayama, T.Terada, M.Shirouzu, S.Yokoyama. Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase To Be Published.
Page generated: Mon Dec 14 07:20:47 2020

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