Magnesium in PDB 6ci7: The Structure of Ycao From Methanopyrus Kandleri Bound with Amppcp and MG2+

The structure of The Structure of Ycao From Methanopyrus Kandleri Bound with Amppcp and MG2+, PDB code: 6ci7 was solved by S.-H.Dong, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	123.193, 106.755, 141.446, 90.00, 103.66, 90.00
R / Rfree (%)	18.5 / 22.6

The binding sites of Magnesium atom in the The Structure of Ycao From Methanopyrus Kandleri Bound with Amppcp and MG2+ (pdb code 6ci7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the The Structure of Ycao From Methanopyrus Kandleri Bound with Amppcp and MG2+, PDB code: 6ci7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the The Structure of Ycao From Methanopyrus Kandleri Bound with Amppcp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Ycao From Methanopyrus Kandleri Bound with Amppcp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:53.3 occ:1.00 O1G A:ACP500 1.9 82.0 1.0 O A:HOH624 2.1 56.7 1.0 O A:HOH691 2.1 45.9 1.0 O A:HOH634 2.2 39.5 1.0 O1B A:ACP500 2.3 74.6 1.0 OE2 A:GLU165 2.3 53.2 1.0 PG A:ACP500 3.3 82.8 1.0 CD A:GLU165 3.3 52.4 1.0 PB A:ACP500 3.4 71.5 1.0 OE1 A:GLU165 3.5 49.6 1.0 O2B A:ACP500 3.6 84.6 1.0 O A:LEU149 3.8 47.4 1.0 OE2 A:GLU82 3.8 52.8 1.0 O2G A:ACP500 3.9 81.3 1.0 C3B A:ACP500 3.9 82.7 1.0 OE1 A:GLU82 4.1 49.8 1.0 CD A:GLU82 4.4 51.4 1.0 O3G A:ACP500 4.4 94.0 1.0 OE1 A:GLN161 4.4 58.4 1.0 O A:HOH765 4.4 53.9 1.0 NE2 A:GLN161 4.6 60.5 1.0 CG A:GLU165 4.6 49.7 1.0 OE1 A:GLU79 4.7 59.9 1.0 O3A A:ACP500 4.8 67.2 1.0 C3' A:ACP500 4.8 47.8 1.0 CD A:GLN161 5.0 57.6 1.0 C A:LEU149 5.0 45.7 1.0

Magnesium binding site 2 out of 6 in the The Structure of Ycao From Methanopyrus Kandleri Bound with Amppcp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Ycao From Methanopyrus Kandleri Bound with Amppcp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:63.6 occ:1.00 O1G B:ACP500 2.0 70.9 1.0 O B:HOH617 2.1 53.6 1.0 O B:HOH653 2.1 39.6 1.0 O B:HOH642 2.2 39.7 1.0 O1B B:ACP500 2.2 62.4 1.0 OE2 B:GLU165 2.4 51.0 1.0 CD B:GLU165 3.3 47.3 1.0 PB B:ACP500 3.3 69.9 1.0 PG B:ACP500 3.3 78.7 1.0 OE1 B:GLU165 3.5 47.6 1.0 O B:HOH720 3.5 47.5 1.0 O2B B:ACP500 3.6 80.2 1.0 OE2 B:GLU82 3.7 46.3 1.0 O B:LEU149 3.8 42.2 1.0 C3B B:ACP500 3.9 75.3 1.0 OE1 B:GLU82 4.0 43.0 1.0 O2G B:ACP500 4.2 78.5 1.0 NE2 B:GLN161 4.3 56.6 1.0 CD B:GLU82 4.3 46.9 1.0 O3G B:ACP500 4.3 84.6 1.0 NH1 B:ARG83 4.4 56.4 1.0 OE1 B:GLU79 4.5 48.2 1.0 O B:HOH798 4.5 58.1 1.0 CG B:GLU165 4.7 42.5 1.0 O3A B:ACP500 4.7 61.4 1.0 C3' B:ACP500 4.9 41.3 1.0

Magnesium binding site 3 out of 6 in the The Structure of Ycao From Methanopyrus Kandleri Bound with Amppcp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of Ycao From Methanopyrus Kandleri Bound with Amppcp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:73.6 occ:1.00 O C:HOH605 2.1 54.0 1.0 O C:HOH621 2.1 48.1 1.0 O2B C:ACP500 2.1 91.0 1.0 OE2 C:GLU165 2.2 65.9 1.0 O C:HOH634 2.2 59.6 1.0 O3G C:ACP500 2.9 98.7 1.0 CD C:GLU165 3.2 63.9 1.0 PB C:ACP500 3.4 86.6 1.0 OE1 C:GLU165 3.4 62.4 1.0 O1B C:ACP500 3.4 95.0 1.0 O C:LEU149 3.9 53.8 1.0 PG C:ACP500 3.9 0.9 1.0 OE2 C:GLU82 3.9 62.7 1.0 OE1 C:GLU82 4.1 57.1 1.0 O2G C:ACP500 4.2 0.1 1.0 C3B C:ACP500 4.3 96.8 1.0 OE2 C:GLU79 4.3 68.7 1.0 CD C:GLU82 4.5 61.8 1.0 NH1 C:ARG83 4.5 84.7 1.0 CG C:GLU165 4.5 57.7 1.0 O3A C:ACP500 4.6 76.7 1.0 O C:HOH732 4.6 68.9 1.0 OE1 C:GLN161 4.7 62.1 1.0 NE2 C:GLN161 5.0 63.4 1.0

Magnesium binding site 4 out of 6 in the The Structure of Ycao From Methanopyrus Kandleri Bound with Amppcp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of Ycao From Methanopyrus Kandleri Bound with Amppcp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:74.4 occ:1.00 O D:HOH700 2.0 74.3 1.0 O D:HOH640 2.2 44.0 1.0 O3G D:ACP500 2.2 83.9 1.0 O D:HOH603 2.3 56.5 1.0 O1B D:ACP500 2.4 94.4 1.0 OE2 D:GLU165 2.4 60.2 1.0 O2B D:ACP500 3.2 86.3 1.0 PB D:ACP500 3.3 85.1 1.0 CD D:GLU165 3.3 54.2 1.0 OE1 D:GLU165 3.4 53.5 1.0 O D:LEU149 3.5 44.5 1.0 PG D:ACP500 3.6 93.8 1.0 OE2 D:GLU82 3.8 51.8 1.0 O D:HOH674 3.8 67.7 1.0 NE2 D:GLN161 3.9 61.6 1.0 OE1 D:GLU82 3.9 52.8 1.0 C3B D:ACP500 4.0 90.4 1.0 CD D:GLU82 4.3 53.7 1.0 O2G D:ACP500 4.5 0.3 1.0 O D:HOH608 4.5 51.3 1.0 C3' D:ACP500 4.6 43.6 1.0 CG D:GLU165 4.6 51.9 1.0 O1G D:ACP500 4.7 91.8 1.0 O3A D:ACP500 4.7 67.3 1.0 C D:LEU149 4.7 42.6 1.0 O D:HOH649 4.8 69.6 1.0 O3' D:ACP500 4.8 44.5 1.0 OE1 D:GLU79 5.0 59.9 1.0

Magnesium binding site 5 out of 6 in the The Structure of Ycao From Methanopyrus Kandleri Bound with Amppcp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structure of Ycao From Methanopyrus Kandleri Bound with Amppcp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg501 b:59.7 occ:1.00 O E:HOH619 2.0 47.2 1.0 O E:HOH632 2.1 37.6 1.0 O E:HOH685 2.2 41.3 1.0 OE2 E:GLU165 2.3 46.7 1.0 O3G E:ACP500 2.3 90.7 1.0 O2B E:ACP500 2.3 72.6 1.0 CD E:GLU165 3.2 42.8 1.0 OE1 E:GLU165 3.4 43.5 1.0 PB E:ACP500 3.4 75.2 1.0 O1B E:ACP500 3.6 86.0 1.0 PG E:ACP500 3.6 0.0 1.0 O E:LEU149 3.7 38.5 1.0 OE2 E:GLU82 3.7 44.8 1.0 O E:HOH750 3.8 50.6 1.0 C3B E:ACP500 4.0 88.9 1.0 OE1 E:GLU82 4.2 42.6 1.0 NH1 E:ARG83 4.2 67.1 1.0 O2G E:ACP500 4.4 95.9 1.0 CD E:GLU82 4.4 44.7 1.0 OE1 E:GLN161 4.4 53.4 1.0 OE1 E:GLU79 4.6 51.7 1.0 CG E:GLU165 4.6 38.6 1.0 NE2 E:GLN161 4.6 46.4 1.0 O1G E:ACP500 4.7 0.6 1.0 NH2 E:ARG83 4.7 63.7 1.0 O3A E:ACP500 4.8 61.5 1.0 C E:LEU149 4.9 39.0 1.0 C3' E:ACP500 4.9 40.1 1.0 CZ E:ARG83 5.0 59.8 1.0 O E:THR146 5.0 44.4 1.0

Magnesium binding site 6 out of 6 in the The Structure of Ycao From Methanopyrus Kandleri Bound with Amppcp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Structure of Ycao From Methanopyrus Kandleri Bound with Amppcp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg501 b:68.4 occ:1.00 O F:HOH634 1.6 71.6 1.0 O1G F:ACP500 2.0 76.5 1.0 O1B F:ACP500 2.1 76.1 1.0 OE2 F:GLU165 2.2 52.7 1.0 O F:HOH751 2.3 40.0 1.0 O F:HOH605 2.6 45.1 1.0 O F:HOH655 2.6 63.8 1.0 CD F:GLU165 3.3 51.6 1.0 PB F:ACP500 3.3 71.8 1.0 PG F:ACP500 3.3 86.0 1.0 O2B F:ACP500 3.6 83.5 1.0 OE1 F:GLU165 3.7 52.0 1.0 O F:LEU149 3.7 47.4 1.0 C3B F:ACP500 3.8 83.8 1.0 OE2 F:GLU82 3.9 49.1 1.0 O F:HOH682 3.9 51.7 1.0 OE1 F:GLU82 4.0 42.3 1.0 O2G F:ACP500 4.1 83.3 1.0 NE2 F:GLN161 4.1 52.0 1.0 CD F:GLU82 4.4 46.0 1.0 O3G F:ACP500 4.4 94.6 1.0 CG F:GLU165 4.6 49.3 1.0 O3A F:ACP500 4.6 62.7 1.0 OE1 F:GLU79 4.8 54.8 1.0 C F:LEU149 4.9 45.4 1.0 C3' F:ACP500 4.9 44.9 1.0

N.Mahanta, A.Liu, S.Dong, S.K.Nair, D.A.Mitchell. Enzymatic Reconstitution of Ribosomal Peptide Backbone Thioamidation. Proc. Natl. Acad. Sci. V. 115 3030 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29507203
DOI: 10.1073/PNAS.1722324115