Magnesium in PDB 1p4d: F Factor Trai Relaxase Domain

The structure of F Factor Trai Relaxase Domain, PDB code: 1p4d was solved by S.Datta, C.Larkin, J.F.Schildbach, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.60
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	128.219, 128.219, 121.184, 90.00, 90.00, 120.00
R / Rfree (%)	23.3 / 27.8

The binding sites of Magnesium atom in the F Factor Trai Relaxase Domain (pdb code 1p4d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the F Factor Trai Relaxase Domain, PDB code: 1p4d:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the F Factor Trai Relaxase Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of F Factor Trai Relaxase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg900 b:36.8 occ:1.00 O A:HOH942 2.0 34.8 1.0 O A:HOH981 2.1 67.3 1.0 NE2 A:HIS159 2.2 36.1 1.0 O A:HOH956 2.2 45.4 1.0 NE2 A:HIS157 2.3 36.6 1.0 ND1 A:HIS146 2.5 28.6 1.0 CD2 A:HIS159 3.2 32.2 1.0 CE1 A:HIS157 3.2 35.0 1.0 CE1 A:HIS159 3.2 35.5 1.0 CD2 A:HIS157 3.3 35.2 1.0 CG A:HIS146 3.4 31.0 1.0 CE1 A:HIS146 3.5 28.0 1.0 CB A:HIS146 3.6 30.0 1.0 CG A:HIS159 4.3 32.4 1.0 ND1 A:HIS159 4.3 32.2 1.0 ND1 A:HIS157 4.4 36.2 1.0 CG A:HIS157 4.4 32.1 1.0 O A:HOH932 4.5 43.1 1.0 CD2 A:HIS146 4.6 28.6 1.0 NE2 A:HIS146 4.6 26.9 1.0 O A:THR148 4.8 43.3 1.0 OH A:TYR16 4.8 59.0 1.0

Magnesium binding site 2 out of 3 in the F Factor Trai Relaxase Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of F Factor Trai Relaxase Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:52.3 occ:1.00 ND1 B:HIS146 2.3 38.6 1.0 O B:HOH934 2.4 27.5 1.0 NE2 B:HIS157 2.5 42.6 1.0 NE2 B:HIS159 2.7 42.5 1.0 CG B:HIS146 3.2 38.6 1.0 CE1 B:HIS157 3.3 39.8 1.0 CE1 B:HIS146 3.3 39.3 1.0 CB B:HIS146 3.4 34.8 1.0 CD2 B:HIS159 3.4 39.9 1.0 CD2 B:HIS157 3.7 41.7 1.0 CE1 B:HIS159 3.8 41.1 1.0 CD2 B:HIS146 4.4 39.6 1.0 NE2 B:HIS146 4.4 41.3 1.0 O B:THR148 4.4 36.2 1.0 ND1 B:HIS157 4.5 40.0 1.0 OD1 B:ASN22 4.5 50.2 1.0 CG B:HIS159 4.7 38.8 1.0 CG B:HIS157 4.7 38.3 1.0 ND1 B:HIS159 4.8 39.9 1.0 CA B:HIS146 4.9 35.4 1.0 O B:HOH944 4.9 58.9 1.0

Magnesium binding site 3 out of 3 in the F Factor Trai Relaxase Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of F Factor Trai Relaxase Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg902 b:78.3 occ:1.00 NE2 C:HIS159 2.1 72.0 1.0 O C:HOH905 2.6 55.2 1.0 CE1 C:HIS159 2.7 72.1 1.0 ND1 C:HIS146 2.8 0.9 1.0 NE2 C:HIS157 2.8 71.9 1.0 CD2 C:HIS157 3.3 72.2 1.0 CD2 C:HIS159 3.4 72.3 1.0 CE1 C:HIS146 3.5 0.5 1.0 CG C:HIS146 3.7 0.5 1.0 ND1 C:HIS159 4.0 72.4 1.0 CE1 C:HIS157 4.0 71.4 1.0 CB C:HIS146 4.0 0.6 1.0 CG C:HIS159 4.3 72.3 1.0 OH C:TYR16 4.3 0.8 1.0 NE2 C:HIS146 4.5 0.6 1.0 CG C:HIS157 4.6 72.4 1.0 CD2 C:HIS146 4.6 0.8 1.0 O C:THR148 4.8 0.8 1.0 ND1 C:HIS157 4.9 71.5 1.0

S.Datta, C.Larkin, J.F.Schildbach. Structural Insights Into Single-Stranded Dna Binding and Cleavage By F Factor Trai. Structure V. 11 1369 2003.
ISSN: ISSN 0969-2126
PubMed: 14604527
DOI: 10.1016/J.STR.2003.10.001