Magnesium in PDB 6kbz: Crystal Structure of Yedk with Ssdna Containing A Tetrahydrofuran Abasic Site

The structure of Crystal Structure of Yedk with Ssdna Containing A Tetrahydrofuran Abasic Site, PDB code: 6kbz was solved by N.Wang, H.Bao, H.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.27 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.530, 111.391, 104.102, 90.00, 96.14, 90.00
R / Rfree (%)	16 / 19.6

The binding sites of Magnesium atom in the Crystal Structure of Yedk with Ssdna Containing A Tetrahydrofuran Abasic Site (pdb code 6kbz). 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 Yedk with Ssdna Containing A Tetrahydrofuran Abasic Site, PDB code: 6kbz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Yedk with Ssdna Containing A Tetrahydrofuran Abasic Site


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 Yedk with Ssdna Containing A Tetrahydrofuran Abasic Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:34.8 occ:1.00 O B:HOH518 2.1 33.3 1.0 OD2 B:ASP140 2.2 32.8 1.0 O B:HOH432 2.2 26.5 1.0 O B:HOH581 2.3 37.1 1.0 O B:HOH514 2.4 33.6 1.0 O B:HOH436 2.4 24.5 1.0 CG B:ASP140 3.2 25.3 1.0 OD1 B:ASP140 3.6 18.6 1.0 O B:HOH493 4.2 21.2 1.0 OE2 B:GLU143 4.3 28.7 1.0 NE B:ARG138 4.5 22.8 1.0 CB B:ASP140 4.5 21.9 1.0 NH2 B:ARG138 4.6 19.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Yedk with Ssdna Containing A Tetrahydrofuran Abasic Site


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 Yedk with Ssdna Containing A Tetrahydrofuran Abasic Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:40.7 occ:1.00 OD2 B:ASP111 2.1 54.1 1.0 O F:HOH415 2.2 33.1 1.0 O B:HOH475 2.2 46.2 1.0 O B:HOH462 2.3 39.0 1.0 CG B:ASP111 2.9 49.0 1.0 MG F:MG301 3.0 33.1 1.0 OD1 B:ASP111 3.1 48.2 1.0 O F:HOH443 3.9 30.6 1.0 OE2 F:GLU143 4.0 21.6 1.0 CB B:ASP111 4.4 41.1 1.0 O F:HOH571 4.5 38.3 1.0 OD1 F:ASP140 4.6 24.9 1.0 O F:HOH460 4.7 30.6 1.0 OD2 F:ASP140 4.7 15.7 1.0 O F:HOH496 5.0 29.7 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Yedk with Ssdna Containing A Tetrahydrofuran Abasic Site


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 Yedk with Ssdna Containing A Tetrahydrofuran Abasic Site within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg301 b:33.1 occ:1.00 OD1 F:ASP140 2.1 24.9 1.0 O B:HOH462 2.1 39.0 1.0 O F:HOH496 2.2 29.7 1.0 O F:HOH443 2.2 30.6 1.0 O F:HOH415 2.3 33.1 1.0 O F:HOH571 2.8 38.3 1.0 MG B:MG302 3.0 40.7 1.0 CG F:ASP140 3.1 20.1 1.0 OD2 F:ASP140 3.4 15.7 1.0 O F:HOH588 3.9 44.0 1.0 OE2 F:GLU143 4.1 21.6 1.0 OD2 B:ASP111 4.3 54.1 1.0 O F:HOH518 4.3 24.1 1.0 NH2 F:ARG138 4.3 13.3 1.0 NE F:ARG138 4.4 13.5 1.0 O B:HOH475 4.4 46.2 1.0 CB F:ASP140 4.4 19.1 1.0 CZ F:ARG138 4.9 12.3 1.0 CD F:GLU143 5.0 19.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Yedk with Ssdna Containing A Tetrahydrofuran Abasic Site


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 Yedk with Ssdna Containing A Tetrahydrofuran Abasic Site within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg301 b:32.1 occ:1.00 OD2 H:ASP140 2.1 19.5 1.0 O H:HOH517 2.2 36.8 1.0 O D:HOH390 2.2 39.6 1.0 O H:HOH557 2.3 31.9 1.0 O D:HOH303 2.3 35.0 1.0 O H:HOH491 2.3 32.7 1.0 CG H:ASP140 3.1 16.7 1.0 OD1 H:ASP140 3.5 13.2 1.0 OD2 D:ASP111 3.7 57.0 1.0 O H:HOH552 4.2 22.0 1.0 NE H:ARG138 4.3 15.0 1.0 OE2 H:GLU143 4.4 30.5 1.0 CB H:ASP140 4.4 11.8 1.0 NH2 H:ARG138 4.4 15.3 1.0 CG D:ASP111 4.8 54.6 1.0 CZ H:ARG138 4.9 14.2 1.0

N.Wang, H.Bao, H.Huang. Crystal Structure of Yedk To Be Published.