Manganese in PDB 5ert: Gephe in Complex with Mn(2+) - Adp

All present enzymatic activity of Gephe in Complex with Mn(2+) - Adp:
2.10.1.1; 2.7.7.75;

The structure of Gephe in Complex with Mn(2+) - Adp, PDB code: 5ert was solved by V.B.Kasaragod, H.Schindelin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.56 / 2.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	87.440, 99.090, 111.895, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.5

The binding sites of Manganese atom in the Gephe in Complex with Mn(2+) - Adp (pdb code 5ert). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Gephe in Complex with Mn(2+) - Adp, PDB code: 5ert:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Gephe in Complex with Mn(2+) - Adp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Gephe in Complex with Mn(2+) - Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn802 b:23.5 occ:1.00 O A:HOH964 2.1 16.7 1.0 O2A A:ADP801 2.2 21.7 1.0 O A:HOH1026 2.2 25.1 1.0 O A:HOH930 2.3 23.1 1.0 O A:HOH1157 2.3 23.8 1.0 O A:HOH945 2.3 23.3 1.0 PA A:ADP801 3.3 21.5 1.0 H A:GLY573 3.6 25.9 1.0 HA2 A:GLY507 3.8 27.7 1.0 O1A A:ADP801 3.8 22.2 1.0 O5' A:ADP801 3.9 21.4 1.0 H8 A:ADP801 3.9 23.0 1.0 H2' A:ADP801 3.9 24.7 1.0 OE2 A:GLU509 3.9 22.4 1.0 HA3 A:GLY507 4.0 27.7 1.0 OD1 A:ASP549 4.0 27.4 1.0 O A:THR506 4.1 20.6 1.0 N A:GLY573 4.1 21.6 1.0 OE1 A:GLU509 4.2 23.3 1.0 HA3 A:GLY572 4.2 24.4 1.0 HA2 A:GLY573 4.3 26.7 1.0 CA A:GLY507 4.3 23.1 1.0 OD2 A:ASP549 4.4 26.4 1.0 OD1 A:ASP580 4.5 26.7 1.0 CD A:GLU509 4.5 22.8 1.0 CG A:ASP549 4.6 27.3 1.0 HA2 A:GLY572 4.6 24.4 1.0 CA A:GLY573 4.7 22.2 1.0 O3A A:ADP801 4.7 27.0 1.0 C A:THR506 4.7 21.2 1.0 HA3 A:GLY573 4.8 26.7 1.0 CA A:GLY572 4.8 20.3 1.0 C8 A:ADP801 4.8 19.2 1.0 OG1 A:THR506 4.8 21.5 1.0 C A:GLY572 4.8 21.2 1.0 N A:GLY507 4.9 23.2 1.0 H3' A:ADP801 5.0 24.4 1.0 MN A:MN803 5.0 23.1 1.0

Manganese binding site 2 out of 2 in the Gephe in Complex with Mn(2+) - Adp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Gephe in Complex with Mn(2+) - Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn803 b:23.1 occ:1.00 O1B A:ADP801 2.1 26.0 1.0 O1A A:ADP801 2.1 22.2 1.0 OD2 A:ASP580 2.2 26.2 1.0 OD1 A:ASP580 2.4 26.7 1.0 CG A:ASP580 2.7 26.9 1.0 HB2 A:SER575 2.8 31.5 1.0 PA A:ADP801 3.2 21.5 1.0 PB A:ADP801 3.3 24.7 1.0 O3A A:ADP801 3.6 27.0 1.0 H A:SER575 3.7 28.1 1.0 CB A:SER575 3.8 26.3 1.0 O2B A:ADP801 3.9 26.4 1.0 H A:GLY577 3.9 38.7 1.0 O2A A:ADP801 3.9 21.7 1.0 HA2 A:GLY573 3.9 26.7 1.0 O A:HOH994 4.0 30.9 1.0 HA3 A:GLY577 4.0 39.7 1.0 H A:GLY573 4.1 25.9 1.0 O A:HOH1026 4.1 25.1 1.0 CB A:ASP580 4.2 27.5 1.0 HG A:SER575 4.2 31.7 1.0 HB3 A:SER575 4.3 31.5 1.0 OG A:SER575 4.4 26.4 1.0 N A:SER575 4.4 23.4 1.0 HB3 A:ASP580 4.5 33.0 1.0 H5'2 A:ADP801 4.5 25.0 1.0 O A:HOH1058 4.5 26.2 1.0 O5' A:ADP801 4.5 21.4 1.0 O3B A:ADP801 4.5 24.7 1.0 CA A:SER575 4.6 24.6 1.0 HB2 A:ASP580 4.6 33.0 1.0 N A:GLY577 4.6 32.2 1.0 CA A:GLY573 4.7 22.2 1.0 H A:VAL574 4.7 29.6 1.0 N A:GLY573 4.7 21.6 1.0 CA A:GLY577 4.8 33.1 1.0 C A:SER575 4.9 25.2 1.0 HA A:ASP580 4.9 34.5 1.0 O A:HOH1157 4.9 23.8 1.0 MN A:MN802 5.0 23.5 1.0

V.B.Kasaragod, H.Schindelin. Structural Framework For Metal Incorporation During Molybdenum Cofactor Biosynthesis. Structure V. 24 782 2016.
ISSN: ISSN 0969-2126
PubMed: 27112598
DOI: 10.1016/J.STR.2016.02.023