Magnesium in PDB 4bg4: Crystal Structure of Litopenaeus Vannamei Arginine Kinase in Ternary Complex with Arginine, Adp-Mg and NO3

All present enzymatic activity of Crystal Structure of Litopenaeus Vannamei Arginine Kinase in Ternary Complex with Arginine, Adp-Mg and NO3:
2.7.3.3;

The structure of Crystal Structure of Litopenaeus Vannamei Arginine Kinase in Ternary Complex with Arginine, Adp-Mg and NO3, PDB code: 4bg4 was solved by A.A.Lopez-Zavala, K.D.Garcia-Orozco, J.S.Carrasco-Miranda, R.Sugich-Miranda, E.F.Velazquez-Contreras, M.F.Criscitiello, L.Gbrieba, 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)	14.847 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.320, 67.150, 78.770, 90.00, 92.12, 90.00
R / Rfree (%)	19.14 / 22.48

The binding sites of Magnesium atom in the Crystal Structure of Litopenaeus Vannamei Arginine Kinase in Ternary Complex with Arginine, Adp-Mg and NO3 (pdb code 4bg4). 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 Litopenaeus Vannamei Arginine Kinase in Ternary Complex with Arginine, Adp-Mg and NO3, PDB code: 4bg4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Litopenaeus Vannamei Arginine Kinase in Ternary Complex with Arginine, Adp-Mg and NO3


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 Litopenaeus Vannamei Arginine Kinase in Ternary Complex with Arginine, Adp-Mg and NO3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:6.1 occ:1.00 O1B A:ADP400 2.2 4.3 1.0 O1A A:ADP400 2.3 5.1 1.0 O1 A:NO3405 2.3 5.2 1.0 O A:HOH2314 2.3 9.3 1.0 O A:HOH2272 2.3 8.1 1.0 O A:HOH2273 2.4 8.8 1.0 N A:NO3405 3.2 7.3 1.0 PB A:ADP400 3.4 4.7 1.0 PA A:ADP400 3.4 5.0 1.0 O3 A:NO3405 3.4 7.3 1.0 O3A A:ADP400 3.6 5.1 1.0 O A:HOH2330 3.9 7.6 1.0 OE2 A:GLU224 4.1 5.6 1.0 NH1 A:ARG229 4.1 4.7 1.0 OE2 A:GLU314 4.2 8.3 1.0 NH2 A:ARG403 4.2 5.3 1.0 O3B A:ADP400 4.2 6.0 1.0 O A:HOH2250 4.2 5.4 1.0 OE1 A:GLU225 4.3 6.2 1.0 CZ3 A:TRP221 4.4 6.5 1.0 OE1 A:GLU224 4.4 6.3 1.0 O2A A:ADP400 4.4 6.3 1.0 O2B A:ADP400 4.4 5.8 1.0 O5' A:ADP400 4.5 5.8 1.0 O2 A:NO3405 4.5 7.1 1.0 C5' A:ADP400 4.5 3.5 1.0 O A:HOH2243 4.6 6.3 1.0 CD A:GLU224 4.7 3.5 1.0 CH2 A:TRP221 4.7 4.4 1.0 CD A:GLU314 4.8 6.3 1.0 NH2 A:ARG229 4.8 4.5 1.0 NH1 A:ARG309 4.8 6.4 1.0 CZ A:ARG229 4.9 5.8 1.0 CG A:GLU314 5.0 6.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Litopenaeus Vannamei Arginine Kinase in Ternary Complex with Arginine, Adp-Mg and NO3


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 Litopenaeus Vannamei Arginine Kinase in Ternary Complex with Arginine, Adp-Mg and NO3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg407 b:5.8 occ:1.00 O1B B:ADP400 2.2 6.1 1.0 O1A B:ADP400 2.3 4.5 1.0 O1 B:NO3405 2.4 7.5 1.0 O B:HOH2245 2.4 9.3 1.0 O B:HOH2211 2.4 9.1 1.0 O B:HOH2210 2.4 8.9 1.0 N B:NO3405 3.3 8.0 1.0 PB B:ADP400 3.4 6.4 1.0 O3 B:NO3405 3.4 9.9 1.0 PA B:ADP400 3.4 6.6 1.0 O3A B:ADP400 3.5 5.2 1.0 O B:HOH2254 3.9 9.1 1.0 NH1 B:ARG229 4.1 7.7 1.0 OE2 B:GLU314 4.1 9.5 1.0 OE2 B:GLU224 4.2 6.8 1.0 O3B B:ADP400 4.2 7.3 1.0 NH2 B:ARG403 4.3 3.9 1.0 OE1 B:GLU225 4.3 6.8 1.0 O B:HOH2196 4.3 10.4 1.0 O2A B:ADP400 4.4 6.8 1.0 CZ3 B:TRP221 4.4 5.1 1.0 O2B B:ADP400 4.4 7.0 1.0 OE1 B:GLU224 4.5 6.7 1.0 O5' B:ADP400 4.5 7.6 1.0 C5' B:ADP400 4.5 7.1 1.0 O2 B:NO3405 4.6 12.3 1.0 O B:HOH2186 4.6 5.1 1.0 CH2 B:TRP221 4.7 5.7 1.0 CD B:GLU314 4.8 5.1 1.0 CD B:GLU224 4.8 4.4 1.0 NH1 B:ARG309 4.8 6.7 1.0 NH2 B:ARG229 4.9 8.5 1.0 CG B:GLU314 4.9 5.7 1.0 CZ B:ARG229 5.0 6.0 1.0

A.A.Lopez-Zavala, K.D.Garcia-Orozco, J.S.Carrasco-Miranda, R.Sugich-Miranda, E.F.Velazquez-Contreras, M.F.Criscitiello, L.G.Brieba, E.Rudino-Pinera, R.R.Sotelo-Mundo. Crystal Structure of Shrimp Arginine Kinase in Binary Complex with Arginine-A Molecular View of the Phosphagen Precursor Binding to the Enzyme. J.Bioenerg.Biomembr. V. 45 511 2013.
ISSN: ISSN 0145-479X
PubMed: 23873077
DOI: 10.1007/S10863-013-9521-0