Magnesium in PDB 2yxh: Crystal Structure of Mazg-Related Protein From Thermotoga Maritima

The structure of Crystal Structure of Mazg-Related Protein From Thermotoga Maritima, PDB code: 2yxh was solved by B.Padmanabhan, Y.Bessho, S.Yokoyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	74.829, 56.788, 61.615, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 26.3

The binding sites of Magnesium atom in the Crystal Structure of Mazg-Related Protein From Thermotoga Maritima (pdb code 2yxh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Mazg-Related Protein From Thermotoga Maritima, PDB code: 2yxh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Mazg-Related Protein From Thermotoga Maritima


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 Mazg-Related Protein From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:33.2 occ:1.00 O A:HOH607 2.0 27.5 1.0 OE2 A:GLU34 2.0 30.6 1.0 O A:HOH608 2.1 38.0 1.0 O A:HOH569 2.1 37.1 1.0 O A:HOH609 2.2 31.8 1.0 OD2 A:ASP60 2.2 27.5 1.0 CD A:GLU34 3.1 29.9 1.0 CG A:ASP60 3.1 30.9 1.0 OD1 A:ASP60 3.2 32.4 1.0 CG A:GLU34 3.5 30.5 1.0 O A:HOH605 3.9 24.6 1.0 O A:HOH542 4.1 50.7 1.0 O A:HOH573 4.1 37.8 1.0 OE1 A:GLU34 4.2 31.0 1.0 O A:HOH602 4.3 47.7 1.0 O A:ALA30 4.5 32.6 1.0 CB A:ASP60 4.5 25.8 1.0 CB A:ALA30 4.7 31.6 1.0 O A:ASP56 4.9 24.1 1.0 CB A:GLU34 4.9 28.3 1.0 C A:ALA30 5.0 32.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Mazg-Related Protein From Thermotoga Maritima


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 Mazg-Related Protein From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:29.2 occ:1.00 OD2 A:ASP56 1.9 31.2 1.0 OE2 A:GLU37 2.0 41.6 1.0 OE1 A:GLU53 2.1 27.1 1.0 OE1 A:GLU34 2.2 31.0 1.0 O A:HOH605 2.3 24.6 1.0 O A:HOH606 2.3 27.7 1.0 CG A:ASP56 2.9 22.5 1.0 CD A:GLU53 3.1 26.1 1.0 CD A:GLU34 3.2 29.9 1.0 CD A:GLU37 3.3 44.4 1.0 CB A:ASP56 3.3 23.4 1.0 OE2 A:GLU53 3.4 27.1 1.0 OE2 A:GLU34 3.4 30.6 1.0 O A:HOH570 3.9 57.3 1.0 OE1 A:GLU37 3.9 48.5 1.0 O B:HOH614 3.9 39.0 1.0 OD1 A:ASP56 4.0 31.2 1.0 OE2 A:GLU52 4.1 44.9 1.0 NZ B:LYS86 4.2 29.4 1.0 O A:HOH573 4.3 37.8 1.0 CB A:GLU37 4.4 32.9 1.0 CG A:GLU37 4.4 34.4 1.0 O A:HOH555 4.4 49.2 1.0 CG A:GLU53 4.4 21.3 1.0 CA A:GLU53 4.5 24.4 1.0 CG A:GLU34 4.6 30.5 1.0 CB A:GLU53 4.7 26.3 1.0 CD A:GLU52 4.8 35.0 1.0 CA A:ASP56 4.8 22.6 1.0 CB A:GLU34 4.9 28.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Mazg-Related Protein From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Mazg-Related Protein From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:31.6 occ:1.00 O B:HOH626 1.9 40.6 1.0 OE2 B:GLU34 2.0 31.1 1.0 O B:HOH523 2.1 28.9 1.0 O B:HOH620 2.1 35.3 1.0 O B:HOH507 2.1 23.3 1.0 OD2 B:ASP60 2.3 30.3 1.0 CD B:GLU34 3.0 35.2 1.0 CG B:ASP60 3.3 31.2 1.0 CG B:GLU34 3.3 33.2 1.0 O B:HOH590 3.4 44.7 1.0 OD1 B:ASP60 3.5 24.7 1.0 O B:HOH570 3.7 46.8 1.0 O B:ALA30 3.8 30.9 1.0 O B:HOH544 4.0 30.6 1.0 CB B:ALA30 4.2 28.8 1.0 OE1 B:GLU34 4.2 33.1 1.0 O B:HOH526 4.2 42.1 1.0 C B:ALA30 4.4 30.9 1.0 O B:HOH549 4.5 47.4 1.0 CB B:ASP60 4.7 24.9 1.0 CA B:ALA30 4.7 31.6 1.0 CB B:GLU34 4.7 32.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Mazg-Related Protein From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Mazg-Related Protein From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:35.6 occ:1.00 OE1 B:GLU37 1.7 50.6 1.0 OD2 B:ASP56 1.9 24.6 1.0 OE1 B:GLU53 2.2 34.7 1.0 OE1 B:GLU34 2.3 33.1 1.0 O B:HOH544 2.3 30.6 1.0 O B:HOH532 2.5 37.7 1.0 CD B:GLU37 2.7 41.5 1.0 OE2 B:GLU37 3.1 52.3 1.0 CG B:ASP56 3.1 33.5 1.0 CD B:GLU53 3.1 40.9 1.0 CD B:GLU34 3.2 35.2 1.0 OE2 B:GLU53 3.3 38.8 1.0 OE2 B:GLU34 3.4 31.1 1.0 CB B:ASP56 3.6 29.7 1.0 O B:HOH604 4.0 52.3 1.0 O A:HOH528 4.0 39.8 1.0 O B:HOH590 4.0 44.7 1.0 CG B:GLU37 4.0 40.8 1.0 CB B:GLU37 4.1 38.5 1.0 OD1 B:ASP56 4.2 18.7 1.0 CG B:GLU53 4.5 30.9 1.0 O B:HOH588 4.5 45.5 1.0 CG B:GLU34 4.6 33.2 1.0 NZ A:LYS86 4.7 34.3 1.0 CA B:GLU53 4.7 29.6 1.0 OE2 B:GLU52 4.8 41.5 1.0 CB B:GLU34 4.8 32.8 1.0 CB B:GLU53 4.8 30.2 1.0 CA B:GLU34 4.9 34.7 1.0

B.Padmanabhan, Y.Bessho, S.Yokoyama. Crystal Structure of Mazg-Related Protein From Thermotoga Maritima To Be Published.