Magnesium in PDB 6cib: 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: 6cib 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 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	123.232, 105.627, 139.298, 90.00, 103.64, 90.00
R / Rfree (%)	19.5 / 23.4

The binding sites of Magnesium atom in the The Structure of Ycao From Methanopyrus Kandleri Bound with Amppcp and MG2+ (pdb code 6cib). 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: 6cib:
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:Mg402 b:40.2 occ:1.00 O A:HOH575 2.2 25.8 1.0 O A:HOH513 2.2 32.9 1.0 O A:HOH654 2.3 34.5 1.0 O A:LEU148 2.3 29.7 1.0 OE2 A:GLU81 2.6 31.6 1.0 OE1 A:GLU81 2.8 30.1 1.0 CD A:GLU81 3.0 31.5 1.0 C A:LEU148 3.5 27.0 1.0 OE2 A:GLU164 3.7 36.1 1.0 O1B A:ADP401 4.0 47.8 1.0 OG A:SER149 4.0 36.4 1.0 OE1 A:GLU164 4.1 30.4 1.0 O A:HOH516 4.1 42.0 1.0 O3' A:ADP401 4.1 30.8 1.0 CA A:SER149 4.2 28.3 1.0 N A:SER149 4.3 26.9 1.0 CD A:GLU164 4.3 31.9 1.0 C3' A:ADP401 4.3 31.6 1.0 CA A:LEU148 4.5 26.9 1.0 CG A:GLU81 4.6 30.5 1.0 O3B A:ADP401 4.6 48.0 1.0 CB A:LEU148 4.6 26.7 1.0 CB A:SER149 4.7 29.5 1.0 O A:THR145 4.8 30.1 1.0 N A:LEU148 4.8 26.4 1.0 PB A:ADP401 4.8 48.3 1.0 OE1 A:GLU78 5.0 45.0 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:Mg402 b:47.4 occ:1.00 O B:HOH587 1.9 27.1 1.0 O B:HOH534 2.1 34.2 1.0 O B:LEU148 2.4 27.2 1.0 O B:HOH544 2.5 37.0 1.0 OE2 B:GLU81 2.5 28.2 1.0 OE1 B:GLU81 2.8 28.0 1.0 CD B:GLU81 3.0 29.7 1.0 C B:LEU148 3.6 26.8 1.0 OE2 B:GLU164 3.6 38.3 1.0 O1B B:ADP401 3.9 44.8 1.0 OE1 B:GLU164 3.9 31.8 1.0 CD B:GLU164 4.2 33.5 1.0 NH1 B:ARG82 4.2 45.3 1.0 CA B:SER149 4.3 29.4 1.0 O3' B:ADP401 4.3 27.6 1.0 N B:SER149 4.4 28.3 1.0 C3' B:ADP401 4.5 27.6 1.0 O B:THR145 4.5 27.6 1.0 CG B:GLU81 4.5 29.4 1.0 CA B:LEU148 4.5 27.9 1.0 CB B:LEU148 4.6 27.2 1.0 CB B:SER149 4.6 31.0 1.0 O2B B:ADP401 4.7 43.7 1.0 N B:LEU148 4.8 26.6 1.0 PB B:ADP401 4.8 45.2 1.0 OE1 B:GLU78 5.0 31.2 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:Mg402 b:47.5 occ:1.00 O C:HOH551 2.2 33.0 1.0 O C:LEU148 2.3 30.7 1.0 O C:HOH579 2.3 46.4 1.0 O C:HOH648 2.4 41.9 1.0 OE1 C:GLU81 2.6 35.0 1.0 OE2 C:GLU81 2.7 37.5 1.0 CD C:GLU81 3.0 36.9 1.0 C C:LEU148 3.4 31.3 1.0 OE2 C:GLU164 3.7 44.6 1.0 OE1 C:GLU164 4.0 38.4 1.0 O2B C:ADP401 4.1 53.0 1.0 CA C:SER149 4.2 33.4 1.0 CD C:GLU164 4.2 38.7 1.0 O3' C:ADP401 4.2 37.7 1.0 N C:SER149 4.3 31.0 1.0 CA C:LEU148 4.4 31.4 1.0 C3' C:ADP401 4.4 36.2 1.0 O C:THR145 4.5 34.8 1.0 CB C:LEU148 4.5 32.5 1.0 CG C:GLU81 4.5 35.0 1.0 CB C:SER149 4.6 34.6 1.0 N C:LEU148 4.7 30.2 1.0 O3B C:ADP401 4.9 51.6 1.0 CG C:LEU148 4.9 33.0 1.0 OE1 C:GLU78 4.9 47.1 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:Mg402 b:42.8 occ:1.00 O D:HOH541 2.0 28.5 1.0 O D:HOH557 2.1 38.0 1.0 O D:HOH501 2.3 31.3 1.0 O D:LEU148 2.5 27.9 1.0 OE2 D:GLU81 2.5 38.9 1.0 OE1 D:GLU81 2.9 34.5 1.0 CD D:GLU81 3.1 36.8 1.0 C D:LEU148 3.6 28.6 1.0 OE2 D:GLU164 3.7 37.6 1.0 O2B D:ADP401 4.0 50.9 1.0 OE1 D:GLU164 4.1 32.7 1.0 CD D:GLU164 4.3 33.1 1.0 O D:HOH546 4.4 53.7 1.0 CG2 D:THR145 4.4 41.4 1.0 O3' D:ADP401 4.4 32.0 1.0 CA D:SER149 4.4 29.9 1.0 N D:SER149 4.4 28.8 1.0 OE1 D:GLU78 4.5 44.8 1.0 O D:THR145 4.5 34.2 1.0 C3' D:ADP401 4.5 32.6 1.0 O1B D:ADP401 4.6 46.5 1.0 CA D:LEU148 4.6 29.4 1.0 CG D:GLU81 4.6 35.8 1.0 CB D:LEU148 4.7 30.5 1.0 O D:HOH661 4.7 51.1 1.0 CB D:SER149 4.8 31.5 1.0 PB D:ADP401 4.8 50.3 1.0 N D:LEU148 4.8 30.3 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:Mg402 b:43.3 occ:1.00 O E:HOH531 2.2 34.7 1.0 O E:HOH606 2.2 23.9 1.0 O E:HOH545 2.3 33.3 1.0 O E:LEU148 2.4 23.9 1.0 OE2 E:GLU81 2.4 29.9 1.0 OE1 E:GLU81 2.6 30.2 1.0 CD E:GLU81 2.9 30.9 1.0 C E:LEU148 3.5 26.0 1.0 OE2 E:GLU164 3.8 33.5 1.0 NH1 E:ARG82 3.8 45.6 1.0 O2B E:ADP401 4.0 51.1 1.0 OE1 E:GLU164 4.1 29.9 1.0 O3' E:ADP401 4.2 25.3 1.0 CA E:SER149 4.2 28.6 1.0 N E:SER149 4.3 26.3 1.0 C3' E:ADP401 4.4 27.7 1.0 CD E:GLU164 4.4 30.6 1.0 CG E:GLU81 4.4 29.1 1.0 CA E:LEU148 4.6 26.8 1.0 O E:THR145 4.6 30.6 1.0 O3B E:ADP401 4.7 48.2 1.0 CB E:SER149 4.7 31.8 1.0 CB E:LEU148 4.7 27.7 1.0 PB E:ADP401 4.8 48.4 1.0 N E:LEU148 4.9 26.6 1.0 OE1 E:GLU78 4.9 34.5 1.0 CG E:LEU148 5.0 28.3 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:Mg402 b:41.3 occ:1.00 O F:HOH573 2.1 24.8 1.0 O F:HOH504 2.2 27.8 1.0 O F:LEU148 2.3 24.7 1.0 O F:HOH530 2.4 31.5 1.0 OE2 F:GLU81 2.6 31.6 1.0 OE1 F:GLU81 2.7 30.8 1.0 CD F:GLU81 3.0 30.9 1.0 O F:HOH760 3.3 40.4 1.0 C F:LEU148 3.4 25.4 1.0 OE2 F:GLU164 3.6 36.1 1.0 O1B F:ADP401 3.9 46.4 1.0 OE1 F:GLU164 4.1 28.7 1.0 O F:HOH532 4.1 41.5 1.0 CA F:SER149 4.2 27.3 1.0 N F:SER149 4.2 26.1 1.0 CD F:GLU164 4.2 29.9 1.0 O3' F:ADP401 4.3 32.4 1.0 C3' F:ADP401 4.4 31.9 1.0 CA F:LEU148 4.4 25.3 1.0 CG F:GLU81 4.5 30.2 1.0 CB F:LEU148 4.5 24.8 1.0 CB F:SER149 4.6 30.9 1.0 OE1 F:GLU78 4.6 39.6 1.0 N F:LEU148 4.7 24.3 1.0 O2B F:ADP401 4.7 45.2 1.0 O F:THR145 4.7 25.5 1.0 PB F:ADP401 4.8 44.7 1.0 CG F:LEU148 4.9 25.7 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