Magnesium in PDB 1nf2: X-Ray Crystal Structure of TM0651 From Thermotoga Maritima

The structure of X-Ray Crystal Structure of TM0651 From Thermotoga Maritima, PDB code: 1nf2 was solved by D.H.Shin, Berkeley Structural Genomics Center (Bsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	158.410, 93.880, 98.420, 90.00, 127.91, 90.00
R / Rfree (%)	21.7 / 26.3

The binding sites of Magnesium atom in the X-Ray Crystal Structure of TM0651 From Thermotoga Maritima (pdb code 1nf2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the X-Ray Crystal Structure of TM0651 From Thermotoga Maritima, PDB code: 1nf2:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the X-Ray Crystal Structure of TM0651 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 X-Ray Crystal Structure of TM0651 From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg282 b:44.0 occ:1.00 OD1 A:ASP8 2.5 20.7 1.0 O A:ASP10 2.6 16.6 1.0 O A:HOH1126 2.7 27.2 1.0 O4 A:SO4280 2.7 23.7 0.9 OD2 A:ASP214 2.7 23.1 1.0 OD1 A:ASN215 3.0 34.3 1.0 CG A:ASP8 3.3 22.9 1.0 CG A:ASN215 3.4 32.8 1.0 C A:ASP10 3.5 18.6 1.0 CG A:ASP214 3.5 23.6 1.0 S A:SO4280 3.6 23.4 0.8 OD2 A:ASP8 3.6 21.1 1.0 O3 A:SO4280 3.6 26.0 1.0 OD1 A:ASP214 3.7 23.2 1.0 ND2 A:ASN215 3.8 37.3 1.0 O1 A:SO4280 3.9 24.2 0.9 CB A:ASP10 3.9 27.0 1.0 OD1 A:ASP218 4.0 21.7 1.0 CA A:ASP10 4.2 18.2 1.0 CB A:ASN215 4.2 28.3 1.0 O A:HOH1140 4.3 50.6 1.0 N A:GLY11 4.4 23.7 1.0 N A:ASP10 4.4 19.1 1.0 O A:HOH1492 4.5 61.7 1.0 OG1 A:THR12 4.5 26.2 1.0 CB A:ASP8 4.5 21.4 1.0 O A:HOH1002 4.7 23.4 1.0 CA A:GLY11 4.7 22.4 1.0 N A:ASN215 4.8 27.6 1.0 CG A:ASP218 4.9 22.0 1.0 O2 A:SO4280 4.9 26.4 1.0 NZ A:LYS191 4.9 17.7 1.0 CB A:ASP214 5.0 21.6 1.0

Magnesium binding site 2 out of 3 in the X-Ray Crystal Structure of TM0651 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 X-Ray Crystal Structure of TM0651 From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg582 b:39.1 occ:1.00 O B:ASP310 2.5 25.9 1.0 O4 B:SO4580 2.7 33.0 0.9 OD1 B:ASP308 2.7 29.7 1.0 OD2 B:ASP514 2.8 38.6 1.0 O B:HOH1206 2.8 38.1 1.0 OD1 B:ASN515 3.1 40.3 1.0 C B:ASP310 3.4 25.5 1.0 CG B:ASP308 3.4 28.6 1.0 CG B:ASN515 3.6 39.6 1.0 CB B:ASP310 3.7 32.8 1.0 S B:SO4580 3.7 31.1 0.8 CG B:ASP514 3.7 40.4 1.0 OD2 B:ASP308 3.7 28.2 1.0 O3 B:SO4580 3.9 29.9 1.0 OD1 B:ASP514 3.9 37.6 1.0 O1 B:SO4580 3.9 31.2 0.9 CA B:ASP310 3.9 25.0 1.0 ND2 B:ASN515 4.0 41.7 1.0 N B:ASP310 4.2 23.9 1.0 OD1 B:ASP518 4.3 19.4 1.0 N B:GLY311 4.4 26.6 1.0 CB B:ASN515 4.4 38.7 1.0 OG1 B:THR312 4.5 32.5 1.0 CB B:ASP308 4.6 25.9 1.0 O B:HOH1015 4.6 31.0 1.0 CA B:GLY311 4.7 26.0 1.0 C B:LEU309 4.9 27.0 1.0 O B:HOH1180 4.9 59.0 1.0 O2 B:SO4580 5.0 33.5 1.0 CG B:ASP310 5.0 35.9 1.0

Magnesium binding site 3 out of 3 in the X-Ray Crystal Structure of TM0651 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 X-Ray Crystal Structure of TM0651 From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg882 b:34.2 occ:1.00 O C:ASP610 2.5 26.9 1.0 OD1 C:ASP608 2.5 24.5 1.0 O4 C:SO4880 2.6 25.5 0.9 OD2 C:ASP814 2.8 29.5 1.0 O C:HOH1124 2.9 35.4 1.0 OD1 C:ASN815 3.1 36.9 1.0 CG C:ASP608 3.3 24.2 1.0 C C:ASP610 3.3 26.3 1.0 OD2 C:ASP608 3.5 21.5 1.0 S C:SO4880 3.6 24.7 0.8 CG C:ASN815 3.6 35.9 1.0 CG C:ASP814 3.7 30.2 1.0 CB C:ASP610 3.8 26.1 1.0 O3 C:SO4880 3.8 25.6 1.0 OD1 C:ASP814 3.9 31.4 1.0 O1 C:SO4880 4.0 25.7 0.9 CA C:ASP610 4.0 26.2 1.0 OD1 C:ASP818 4.1 20.8 1.0 N C:GLY611 4.2 23.4 1.0 ND2 C:ASN815 4.3 39.3 1.0 CB C:ASN815 4.3 34.4 1.0 N C:ASP610 4.4 26.0 1.0 OG1 C:THR612 4.4 28.0 1.0 CA C:GLY611 4.5 20.6 1.0 CB C:ASP608 4.5 23.2 1.0 O C:HOH1007 4.6 22.8 1.0 NZ C:LYS791 4.9 19.9 1.0 O2 C:SO4880 4.9 28.4 1.0 N C:ASN815 4.9 31.3 1.0 C C:GLY611 4.9 20.6 1.0 CG C:ASP818 5.0 19.0 1.0 O C:HOH1133 5.0 35.1 1.0

D.H.Shin, A.Roberts, J.Jancarik, H.Yokota, R.Kim, D.E.Wemmer, S.H.Kim. Crystal Structure of A Phosphatase with A Unique Substrate Binding Domain From Thermotoga Maritima Protein Sci. V. 12 1464 2003.
ISSN: ISSN 0961-8368
PubMed: 12824492
DOI: 10.1110/PS.0302703