Magnesium in PDB 3wjq: Crystal Structure of the Hype Cn Form

The structure of Crystal Structure of the Hype Cn Form, PDB code: 3wjq was solved by T.Tominaga, S.Watanabe, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.38 / 1.65
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	102.846, 102.846, 104.315, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 19.6

The binding sites of Magnesium atom in the Crystal Structure of the Hype Cn Form (pdb code 3wjq). 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 the Hype Cn Form, PDB code: 3wjq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Hype Cn Form


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 the Hype Cn Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:14.0 occ:0.81 O1G A:ATP411 2.0 13.0 0.6 OD1 A:ASP59 2.0 19.1 1.0 O1A A:ATP411 2.1 18.9 0.9 O1B A:ATP411 2.3 17.7 0.8 O3 A:PO4419 2.3 18.5 0.3 CG A:ASP59 3.1 19.5 1.0 PG A:ATP411 3.1 20.4 0.6 PB A:ATP411 3.2 15.9 0.8 PA A:ATP411 3.3 19.0 0.9 O3A A:ATP411 3.4 16.9 0.9 O3B A:ATP411 3.4 23.3 0.8 OD2 A:ASP59 3.5 21.2 1.0 NH2 A:ARG224 3.7 16.3 1.0 O3G A:ATP411 3.7 16.4 0.6 MG A:MG402 3.7 12.7 0.7 P A:PO4419 3.8 20.3 0.3 O A:HOH544 4.0 22.4 1.0 O1 A:PO4419 4.1 24.0 0.3 O A:HOH502 4.2 17.1 1.0 O A:ILE58 4.3 11.4 1.0 O5' A:ATP411 4.3 16.6 0.9 O2A A:ATP411 4.4 22.6 0.9 O2G A:ATP411 4.4 18.2 0.6 CB A:ASP59 4.4 13.5 1.0 O2 A:PO4419 4.6 19.4 0.3 O2B A:ATP411 4.6 18.8 0.8 CA A:ASP59 4.6 10.9 1.0 O4 A:PO4419 4.8 27.4 0.3 O A:HOH832 4.8 27.2 1.0 CZ A:ARG224 4.9 18.0 1.0 OD2 A:ASP84 4.9 16.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Hype Cn Form


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 the Hype Cn Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:12.7 occ:0.71 O3G A:ATP411 2.1 16.4 0.6 OD2 A:ASP59 2.1 21.2 1.0 O A:HOH660 2.1 22.6 1.0 OD2 A:ASP84 2.2 16.4 1.0 O A:HOH662 2.2 17.5 1.0 O1B A:ATP411 2.2 17.7 0.8 O1 A:PO4419 2.5 24.0 0.3 CG A:ASP59 3.1 19.5 1.0 PG A:ATP411 3.1 20.4 0.6 PB A:ATP411 3.1 15.9 0.8 CG A:ASP84 3.2 17.2 1.0 O3B A:ATP411 3.4 23.3 0.8 OD1 A:ASP59 3.5 19.1 1.0 OD1 A:ASP84 3.5 17.5 1.0 O2B A:ATP411 3.6 18.8 0.8 O1G A:ATP411 3.6 13.0 0.6 P A:PO4419 3.7 20.3 0.3 MG A:MG401 3.7 14.0 0.8 O3 A:PO4419 3.8 18.5 0.3 MG A:MG403 3.8 15.5 0.8 O A:HOH544 4.0 22.4 1.0 O A:HOH734 4.1 29.3 1.0 OG1 A:THR223 4.1 19.9 1.0 OD2 A:ASP221 4.2 15.8 1.0 O A:HOH539 4.3 17.6 1.0 O A:GLY80 4.3 14.1 1.0 CB A:ASP59 4.4 13.5 1.0 O2G A:ATP411 4.4 18.2 0.6 CG2 A:THR223 4.5 15.1 1.0 CB A:ASP84 4.5 13.2 1.0 O2 A:PO4419 4.6 19.4 0.3 O3A A:ATP411 4.6 16.9 0.9 NC A:XCN338 4.7 27.4 0.5 CB A:THR223 4.8 15.4 1.0 O4 A:PO4419 4.8 27.4 0.3 OD1 A:ASP221 4.8 17.8 1.0 CG A:ASP221 4.9 19.1 1.0 O A:HOH659 5.0 21.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Hype Cn Form


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 the Hype Cn Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:15.5 occ:0.84 O2B A:ATP411 1.9 18.8 0.8 OD1 A:ASP43 2.0 16.5 1.0 OD1 A:ASP84 2.1 17.5 1.0 O A:HOH659 2.1 21.8 1.0 OD1 A:ASP221 2.2 17.8 1.0 O A:HOH662 2.2 17.5 1.0 CG A:ASP43 3.1 21.1 1.0 CG A:ASP221 3.2 19.1 1.0 CG A:ASP84 3.2 17.2 1.0 PB A:ATP411 3.2 15.9 0.8 OD2 A:ASP221 3.6 15.8 1.0 CB A:ASP43 3.6 12.7 1.0 OD2 A:ASP84 3.7 16.4 1.0 MG A:MG402 3.8 12.7 0.7 O1B A:ATP411 3.9 17.7 0.8 O A:ASP221 4.0 16.7 1.0 O3B A:ATP411 4.0 23.3 0.8 O A:HOH525 4.1 24.1 1.0 CA A:ASP43 4.2 10.2 1.0 OD2 A:ASP43 4.2 15.0 1.0 OG1 A:THR223 4.3 19.9 1.0 N A:ASP221 4.3 17.8 1.0 O3A A:ATP411 4.4 16.9 0.9 CB A:ASP84 4.4 13.2 1.0 CB A:ASP221 4.5 19.1 1.0 CG2 A:VAL87 4.6 11.8 1.0 O3G A:ATP411 4.6 16.4 0.6 CA A:ASP84 4.7 13.1 1.0 NZ A:LYS220 4.7 21.5 0.4 CA A:ASP221 4.7 16.6 1.0 O A:HOH660 4.7 22.6 1.0 C A:ASP221 4.8 16.9 1.0 CE A:LYS220 4.9 28.5 0.6 CE A:LYS220 4.9 27.7 0.4 O A:HOH544 4.9 22.4 1.0 O A:HOH833 5.0 34.9 1.0 O A:ASP43 5.0 13.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Hype Cn Form


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 the Hype Cn Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:18.6 occ:0.43 O A:HOH832 1.8 27.2 1.0 O A:HOH514 2.1 39.5 1.0 O A:HOH833 2.1 34.9 1.0 O A:HOH629 2.2 35.0 1.0 O2A A:ATP411 2.3 22.6 0.9 O3B A:ATP411 2.4 23.3 0.8 O A:HOH784 3.2 41.4 1.0 PA A:ATP411 3.3 19.0 0.9 O3A A:ATP411 3.4 16.9 0.9 O2G A:ATP411 3.4 18.2 0.6 PB A:ATP411 3.4 15.9 0.8 PG A:ATP411 3.6 20.4 0.6 O2B A:ATP411 3.9 18.8 0.8 O A:HOH659 4.1 21.8 1.0 OG1 A:THR223 4.1 19.9 1.0 O A:HOH788 4.1 35.8 1.0 O1A A:ATP411 4.2 18.9 0.9 NZ A:LYS220 4.3 21.5 0.4 O1G A:ATP411 4.3 13.0 0.6 CE A:MET16 4.5 21.8 1.0 O A:ARG224 4.5 17.9 1.0 O A:HOH525 4.5 24.1 1.0 O A:GLY12 4.5 29.2 1.0 O5' A:ATP411 4.6 16.6 0.9 O1B A:ATP411 4.7 17.7 0.8 ND2 A:ASN229 4.7 18.9 1.0 O3G A:ATP411 4.7 16.4 0.6 C5' A:ATP411 4.8 17.9 0.9 O A:HOH542 4.9 24.9 1.0 N A:ARG224 4.9 15.8 1.0 CB A:ARG224 4.9 17.8 1.0

T.Tominaga, S.Watanabe, R.Matsumi, H.Atomi, T.Imanaka, K.Miki. Crystal Structures of the Carbamoylated and Cyanated Forms of Hype For [Nife] Hydrogenase Maturation Proc.Natl.Acad.Sci.Usa V. 110 20485 2013.
ISSN: ISSN 0027-8424
PubMed: 24297906
DOI: 10.1073/PNAS.1313620110