Magnesium in PDB 1f9a: Crystal Structure Analysis of Nmn Adenylyltransferase From Methanococcus Jannaschii

The structure of Crystal Structure Analysis of Nmn Adenylyltransferase From Methanococcus Jannaschii, PDB code: 1f9a was solved by I.D'angelo, N.Raffaelli, V.Dabusti, T.Lorenzi, G.Magni, M.Rizzi, 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 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.768, 112.642, 79.869, 90.00, 116.94, 90.00
R / Rfree (%)	21.5 / 26.4

The binding sites of Magnesium atom in the Crystal Structure Analysis of Nmn Adenylyltransferase From Methanococcus Jannaschii (pdb code 1f9a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure Analysis of Nmn Adenylyltransferase From Methanococcus Jannaschii, PDB code: 1f9a:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure Analysis of Nmn Adenylyltransferase From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure Analysis of Nmn Adenylyltransferase From Methanococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg706 b:72.9 occ:1.00 O2B A:ATP700 2.2 37.9 1.0 O3A A:ATP700 2.5 44.8 1.0 O2G A:ATP700 2.6 37.0 1.0 PB A:ATP700 2.6 37.0 1.0 O3B A:ATP700 2.8 39.0 1.0 O1A A:ATP700 3.1 42.1 1.0 PG A:ATP700 3.3 38.6 1.0 PA A:ATP700 3.3 38.0 1.0 O1G A:ATP700 4.0 33.2 1.0 C5' A:ATP700 4.1 40.3 1.0 O1B A:ATP700 4.1 34.8 1.0 NH2 A:ARG121 4.2 77.2 1.0 O5' A:ATP700 4.2 41.1 1.0 NH1 A:ARG121 4.2 73.9 1.0 O2A A:ATP700 4.4 42.8 1.0 NH1 A:ARG8 4.4 31.7 1.0 O3G A:ATP700 4.6 36.1 1.0 CZ A:ARG121 4.6 72.1 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure Analysis of Nmn Adenylyltransferase From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure Analysis of Nmn Adenylyltransferase From Methanococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg709 b:50.9 occ:1.00 O2B B:ATP701 3.5 33.1 1.0 O2G B:ATP701 3.6 36.1 1.0 NH1 B:ARG121 3.8 72.4 1.0 O1G B:ATP701 4.4 34.3 1.0 NH2 B:ARG121 4.5 74.8 1.0 PG B:ATP701 4.5 36.6 1.0 CZ B:ARG121 4.6 71.6 1.0 PB B:ATP701 4.7 38.7 1.0 O3B B:ATP701 4.9 37.8 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure Analysis of Nmn Adenylyltransferase From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure Analysis of Nmn Adenylyltransferase From Methanococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg708 b:63.1 occ:1.00 O2G C:ATP702 2.4 41.3 1.0 O2B C:ATP702 2.5 36.5 1.0 O1A C:ATP702 2.8 41.5 1.0 O3B C:ATP702 3.1 38.7 1.0 PG C:ATP702 3.2 39.4 1.0 PB C:ATP702 3.2 41.5 1.0 O3A C:ATP702 3.5 43.5 1.0 PA C:ATP702 3.8 43.4 1.0 O1G C:ATP702 4.0 34.3 1.0 NH1 C:ARG8 4.1 44.0 1.0 O3G C:ATP702 4.5 37.1 1.0 NH2 C:ARG121 4.6 75.2 1.0 O1B C:ATP702 4.6 34.6 1.0 C5' C:ATP702 4.6 46.8 1.0 O5' C:ATP702 4.8 48.0 1.0 O2A C:ATP702 4.9 42.0 1.0 NH1 C:ARG121 4.9 75.8 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure Analysis of Nmn Adenylyltransferase From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure Analysis of Nmn Adenylyltransferase From Methanococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg707 b:58.7 occ:1.00 O2B D:ATP703 2.3 43.2 1.0 O2G D:ATP703 2.5 34.7 1.0 O1A D:ATP703 2.8 51.0 1.0 O3A D:ATP703 2.8 52.9 1.0 PB D:ATP703 2.9 49.6 1.0 O3B D:ATP703 3.0 46.0 1.0 PG D:ATP703 3.2 44.3 1.0 PA D:ATP703 3.3 44.1 1.0 O1G D:ATP703 3.9 46.1 1.0 NH1 D:ARG8 4.1 35.4 1.0 O1B D:ATP703 4.3 48.2 1.0 O D:HOH745 4.3 55.7 1.0 O2A D:ATP703 4.4 49.2 1.0 O5' D:ATP703 4.4 49.3 1.0 O D:HOH790 4.4 43.2 1.0 C5' D:ATP703 4.4 53.8 1.0 O3G D:ATP703 4.4 43.2 1.0 NH2 D:ARG121 4.8 76.8 1.0 O D:HOH786 4.8 54.8 1.0 NH1 D:ARG121 4.8 74.5 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure Analysis of Nmn Adenylyltransferase From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure Analysis of Nmn Adenylyltransferase From Methanococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg801 b:64.8 occ:1.00 O2G E:ATP704 2.9 33.2 1.0 O1A E:ATP704 3.6 44.4 1.0 O E:HOH917 3.7 46.1 1.0 O E:HOH860 3.9 58.1 1.0 O2B E:ATP704 3.9 34.9 1.0 PG E:ATP704 4.1 30.2 1.0 NH1 E:ARG8 4.1 37.9 1.0 O3B E:ATP704 4.2 34.9 1.0 O3A E:ATP704 4.3 41.8 1.0 PA E:ATP704 4.4 37.0 1.0 PB E:ATP704 4.5 40.4 1.0 O E:HOH919 4.6 74.7 1.0 C5' E:ATP704 4.9 41.6 1.0 O1G E:ATP704 4.9 24.0 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure Analysis of Nmn Adenylyltransferase From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure Analysis of Nmn Adenylyltransferase From Methanococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg800 b:36.7 occ:1.00 O F:HOH941 2.0 33.4 1.0 O F:HOH869 2.1 37.5 1.0 O2G F:ATP705 2.2 27.8 1.0 O F:HOH879 2.3 39.4 1.0 O2B F:ATP705 2.3 24.9 1.0 O1A F:ATP705 2.5 33.0 1.0 PG F:ATP705 3.3 27.8 1.0 PB F:ATP705 3.3 26.6 1.0 O3B F:ATP705 3.6 26.0 1.0 O3A F:ATP705 3.6 29.0 1.0 PA F:ATP705 3.7 27.8 1.0 O1G F:ATP705 4.1 21.9 1.0 NH1 F:ARG8 4.2 28.0 1.0 O F:HOH881 4.3 39.6 1.0 NH1 F:ARG121 4.4 65.9 1.0 O F:HOH938 4.4 56.1 1.0 NH2 F:ARG121 4.4 73.1 1.0 C5' F:ATP705 4.5 26.8 1.0 O3G F:ATP705 4.6 25.6 1.0 O2A F:ATP705 4.6 35.1 1.0 O1B F:ATP705 4.6 26.1 1.0 O5' F:ATP705 4.7 28.4 1.0 CZ F:ARG121 5.0 66.9 1.0

I.D'angelo, N.Raffaelli, V.Dabusti, T.Lorenzi, G.Magni, M.Rizzi. Structure of Nicotinamide Mononucleotide Adenylyltransferase: A Key Enzyme in Nad(+) Biosynthesis. Structure Fold.Des. V. 8 993 2000.
ISSN: ISSN 0969-2126
PubMed: 10986466
DOI: 10.1016/S0969-2126(00)00190-8