Magnesium in PDB 4uog: Crystallographic Structure of Nucleoside Diphosphate Kinase From Litopenaeus Vannamei Complexed with Dcdp

All present enzymatic activity of Crystallographic Structure of Nucleoside Diphosphate Kinase From Litopenaeus Vannamei Complexed with Dcdp:
2.7.4.6;

The structure of Crystallographic Structure of Nucleoside Diphosphate Kinase From Litopenaeus Vannamei Complexed with Dcdp, PDB code: 4uog was solved by A.A.Lopez-Zavala, V.Stojanoff, E.Rudino-Pinera, R.R.Sotelo-Mundo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.304 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	70.160, 135.370, 104.820, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 25.69

The binding sites of Magnesium atom in the Crystallographic Structure of Nucleoside Diphosphate Kinase From Litopenaeus Vannamei Complexed with Dcdp (pdb code 4uog). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystallographic Structure of Nucleoside Diphosphate Kinase From Litopenaeus Vannamei Complexed with Dcdp, PDB code: 4uog:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystallographic Structure of Nucleoside Diphosphate Kinase From Litopenaeus Vannamei Complexed with Dcdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystallographic Structure of Nucleoside Diphosphate Kinase From Litopenaeus Vannamei Complexed with Dcdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1153 b:32.3 occ:1.00 O1A A:YYY1152 2.4 33.2 1.0 O2B A:YYY1152 2.9 34.7 1.0 OD2 A:ASP120 3.0 34.7 1.0 O A:HOH2079 3.4 23.2 1.0 PA A:YYY1152 3.7 32.9 1.0 CG A:ASP120 3.8 27.7 1.0 PB A:YYY1152 4.1 40.0 1.0 O3A A:YYY1152 4.1 32.0 1.0 O2A A:YYY1152 4.3 37.6 1.0 CB A:ASP120 4.3 29.2 1.0 O A:HOH2047 4.4 25.8 1.0 O A:HOH2080 4.6 31.1 1.0 NH1 A:ARG87 4.7 34.0 1.0 OD1 A:ASP120 4.7 26.0 1.0 O3B A:YYY1152 4.8 26.0 1.0 NH2 A:ARG87 4.9 39.1 1.0 O5' A:YYY1152 4.9 32.1 1.0

Magnesium binding site 2 out of 3 in the Crystallographic Structure of Nucleoside Diphosphate Kinase From Litopenaeus Vannamei Complexed with Dcdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystallographic Structure of Nucleoside Diphosphate Kinase From Litopenaeus Vannamei Complexed with Dcdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1153 b:31.4 occ:1.00 O2A B:YYY1152 2.5 29.1 1.0 O3B B:YYY1152 2.5 32.0 1.0 PB B:YYY1152 3.6 31.9 1.0 PA B:YYY1152 3.8 30.4 1.0 O B:HOH2101 3.8 18.6 1.0 CE1 B:HIS117 3.9 16.1 1.0 O1B B:YYY1152 4.0 19.5 1.0 O3A B:YYY1152 4.0 27.7 1.0 OD2 B:ASP120 4.1 30.6 1.0 NH1 B:ARG87 4.2 24.7 1.0 ND1 B:HIS117 4.3 17.4 1.0 O B:GLY118 4.3 17.6 1.0 C5' B:YYY1152 4.5 26.9 1.0 CG B:ASP120 4.7 26.3 1.0 O5' B:YYY1152 4.7 22.4 1.0 O1A B:YYY1152 4.8 32.9 1.0 CE1 B:TYR51 4.8 22.8 1.0 CB B:ASP120 4.8 18.4 1.0 CD1 B:LEU54 4.9 26.0 1.0 O2B B:YYY1152 4.9 20.3 1.0

Magnesium binding site 3 out of 3 in the Crystallographic Structure of Nucleoside Diphosphate Kinase From Litopenaeus Vannamei Complexed with Dcdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystallographic Structure of Nucleoside Diphosphate Kinase From Litopenaeus Vannamei Complexed with Dcdp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1153 b:27.5 occ:1.00 O C:HOH2060 2.0 28.2 1.0 O2A C:YYY1152 2.2 24.1 1.0 O C:HOH2093 2.5 20.1 1.0 O C:HOH2059 2.7 28.8 1.0 OD2 C:ASP120 3.3 35.2 1.0 PA C:YYY1152 3.6 23.0 1.0 O2B C:YYY1152 3.8 21.4 1.0 O C:HOH2080 3.8 24.8 1.0 O C:HOH2092 3.9 32.3 1.0 O1A C:YYY1152 4.0 26.6 1.0 O C:HOH2054 4.1 13.0 1.0 OD1 C:ASP53 4.4 33.4 1.0 O3A C:YYY1152 4.4 31.6 1.0 CG C:ASP120 4.4 28.1 1.0 OD2 C:ASP53 4.5 34.8 1.0 O5' C:YYY1152 4.6 17.6 1.0 PB C:YYY1152 4.7 26.1 1.0 CG C:ASP53 4.9 36.2 1.0 CD1 C:LEU54 4.9 19.1 1.0 C5' C:YYY1152 4.9 21.4 1.0

A.A.Lopez-Zavala, I.E.Quintero-Reyes, J.S.Carrasco-Miranda, V.Stojanoff, A.Weichsel, E.Rudino-Pinera, R.R.Sotelo-Mundo. Structure of Nucleoside Diphosphate Kinase From Pacific Shrimp (Litopenaeus Vannamei) in Binary Complexes with Purine and Pyrimidine Nucleoside Diphosphates Acta Crystallogr.,Sect.F V. 79 1150 2014.
ISSN: ISSN 1744-3091
PubMed: 25195883
DOI: 10.1107/S2053230X1401557X