Magnesium in PDB 6eac: Pseudomonas Syringae Selo

The structure of Pseudomonas Syringae Selo, PDB code: 6eac was solved by D.R.Tomchick, V.S.Tagliabracci, A.Sreelatha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.14 / 2.27
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	136.174, 158.056, 227.248, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.2

The structure of Pseudomonas Syringae Selo also contains other interesting chemical elements:

Calcium	(Ca)	14 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Magnesium atom in the Pseudomonas Syringae Selo (pdb code 6eac). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Pseudomonas Syringae Selo, PDB code: 6eac:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Pseudomonas Syringae Selo


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pseudomonas Syringae Selo within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:10.8 occ:1.00 O1G A:ANP506 2.1 17.9 1.0 OD1 A:ASN253 2.1 27.4 1.0 O A:HOH656 2.2 30.5 1.0 OD2 A:ASP262 2.2 21.8 1.0 O1A A:ANP506 2.2 25.6 1.0 O3A A:ANP506 2.3 31.6 1.0 PA A:ANP506 2.8 33.7 1.0 CG A:ASN253 3.1 27.8 1.0 HD21 A:ASN253 3.1 37.1 1.0 CG A:ASP262 3.3 23.1 1.0 HH12 A:ARG183 3.3 37.8 1.0 PG A:ANP506 3.5 25.9 1.0 HB2 A:ASP262 3.5 28.5 1.0 ND2 A:ASN253 3.5 30.9 1.0 PB A:ANP506 3.5 29.1 1.0 O2A A:ANP506 3.8 31.5 1.0 CB A:ASP262 3.9 23.8 1.0 OD2 A:ASP252 3.9 23.0 1.0 N3B A:ANP506 4.0 29.4 1.0 H3' A:ANP506 4.0 30.2 1.0 O2G A:ANP506 4.0 29.7 1.0 O5' A:ANP506 4.0 33.6 1.0 O2B A:ANP506 4.1 26.9 1.0 HB3 A:ASP262 4.1 28.5 1.0 H5'2 A:ANP506 4.1 35.7 1.0 NH1 A:ARG183 4.1 31.5 1.0 HNB1 A:ANP506 4.2 35.3 1.0 HH11 A:ARG183 4.2 37.8 1.0 O A:HOH652 4.3 25.8 1.0 CA A:CA502 4.3 25.1 1.0 HA A:ASN253 4.3 26.5 1.0 OD1 A:ASP262 4.4 27.5 1.0 HD22 A:ASN253 4.4 37.1 1.0 CB A:ASN253 4.5 21.4 1.0 OH A:TYR77 4.6 27.7 1.0 C5' A:ANP506 4.6 29.8 1.0 O3G A:ANP506 4.7 29.7 1.0 O A:ASP252 4.7 21.4 1.0 O1B A:ANP506 4.8 30.9 1.0 HH A:TYR77 4.8 33.3 1.0 CA A:ASN253 4.8 22.1 1.0 HB3 A:ASN253 4.8 25.7 1.0 H2' A:ANP506 4.8 34.3 1.0 C3' A:ANP506 4.9 25.1 1.0 HH22 A:ARG183 4.9 25.7 1.0 CG A:ASP252 4.9 25.2 1.0

Magnesium binding site 2 out of 4 in the Pseudomonas Syringae Selo


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pseudomonas Syringae Selo within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:13.1 occ:1.00 OD1 B:ASN253 2.1 29.8 1.0 O2A B:ANP507 2.1 24.5 1.0 O2G B:ANP507 2.1 16.5 1.0 O B:HOH618 2.2 18.9 1.0 OD2 B:ASP262 2.3 24.9 1.0 O3A B:ANP507 2.3 29.3 1.0 PA B:ANP507 2.8 33.4 1.0 CG B:ASN253 3.1 28.3 1.0 HD21 B:ASN253 3.2 33.4 1.0 CG B:ASP262 3.3 29.8 1.0 HH12 B:ARG183 3.4 35.4 1.0 HB2 B:ASP262 3.5 34.2 1.0 PG B:ANP507 3.6 26.8 1.0 ND2 B:ASN253 3.6 27.8 1.0 PB B:ANP507 3.6 29.1 1.0 O1A B:ANP507 3.8 30.8 1.0 CB B:ASP262 3.9 28.5 1.0 OD2 B:ASP252 3.9 28.9 1.0 H5'2 B:ANP507 4.0 39.3 1.0 H3' B:ANP507 4.0 33.7 1.0 O5' B:ANP507 4.0 35.0 1.0 HB3 B:ASP262 4.0 34.2 1.0 N3B B:ANP507 4.1 30.5 1.0 NH1 B:ARG183 4.1 29.4 1.0 O1B B:ANP507 4.1 22.3 1.0 O B:HOH683 4.1 31.0 1.0 O1G B:ANP507 4.2 28.1 1.0 HH11 B:ARG183 4.3 35.4 1.0 HA B:ASN253 4.3 30.6 1.0 HNB1 B:ANP507 4.3 36.6 1.0 CA B:CA502 4.3 28.8 1.0 OD1 B:ASP262 4.4 30.4 1.0 HD22 B:ASN253 4.4 33.4 1.0 CB B:ASN253 4.5 24.3 1.0 C5' B:ANP507 4.5 32.7 1.0 OH B:TYR77 4.6 27.7 1.0 O B:ASP252 4.7 20.4 1.0 O3G B:ANP507 4.7 29.4 1.0 CA B:ASN253 4.8 25.5 1.0 HB3 B:ASN253 4.8 29.1 1.0 H2' B:ANP507 4.8 33.8 1.0 HH B:TYR77 4.9 33.3 1.0 O2B B:ANP507 4.9 33.1 1.0 C3' B:ANP507 4.9 28.0 1.0 CG B:ASP252 4.9 29.0 1.0 HH22 B:ARG183 5.0 28.6 1.0

Magnesium binding site 3 out of 4 in the Pseudomonas Syringae Selo


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pseudomonas Syringae Selo within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:20.2 occ:1.00 OD1 C:ASN253 2.0 34.2 1.0 O2G C:ANP506 2.1 22.9 1.0 OD2 C:ASP262 2.1 26.7 1.0 O C:HOH642 2.1 26.1 1.0 O1A C:ANP506 2.2 30.9 1.0 O3A C:ANP506 2.2 31.8 1.0 PA C:ANP506 2.7 36.5 1.0 CG C:ASN253 3.1 30.6 1.0 HD21 C:ASN253 3.1 41.3 1.0 CG C:ASP262 3.2 29.1 1.0 HB2 C:ASP262 3.4 33.7 1.0 HH12 C:ARG183 3.4 40.5 1.0 ND2 C:ASN253 3.5 34.4 1.0 PG C:ANP506 3.5 29.0 1.0 PB C:ANP506 3.5 29.4 1.0 O2A C:ANP506 3.7 26.2 1.0 CB C:ASP262 3.8 28.1 1.0 H5'2 C:ANP506 3.9 45.4 1.0 O5' C:ANP506 3.9 37.2 1.0 OD2 C:ASP252 4.0 32.0 1.0 N3B C:ANP506 4.0 33.7 1.0 HB3 C:ASP262 4.0 33.7 1.0 O1B C:ANP506 4.0 24.5 1.0 H3' C:ANP506 4.1 47.5 1.0 NH1 C:ARG183 4.1 33.7 1.0 O3G C:ANP506 4.1 26.1 1.0 O C:HOH616 4.2 31.3 1.0 HH11 C:ARG183 4.2 40.5 1.0 OD1 C:ASP262 4.3 26.3 1.0 HNB1 C:ANP506 4.3 40.5 1.0 CA C:CA502 4.3 30.9 1.0 HA C:ASN253 4.3 33.3 1.0 HD22 C:ASN253 4.3 41.3 1.0 CB C:ASN253 4.4 25.6 1.0 C5' C:ANP506 4.4 37.8 1.0 OH C:TYR77 4.6 37.1 1.0 O1G C:ANP506 4.6 33.4 1.0 O C:ASP252 4.7 31.8 1.0 O2B C:ANP506 4.7 29.1 1.0 H2' C:ANP506 4.7 46.8 1.0 HB3 C:ASN253 4.8 30.8 1.0 CA C:ASN253 4.8 27.7 1.0 HH C:TYR77 4.9 44.6 1.0 CG C:ASP252 4.9 31.5 1.0 C3' C:ANP506 5.0 39.6 1.0

Magnesium binding site 4 out of 4 in the Pseudomonas Syringae Selo


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pseudomonas Syringae Selo within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:17.1 occ:1.00 O1G D:ANP506 2.0 19.6 1.0 O D:HOH617 2.0 25.1 1.0 OD2 D:ASP262 2.0 29.9 1.0 OD1 D:ASN253 2.1 33.4 1.0 O3A D:ANP506 2.2 32.1 1.0 O2A D:ANP506 2.2 34.2 1.0 PA D:ANP506 2.8 37.5 1.0 CG D:ASN253 3.0 31.6 1.0 HD21 D:ASN253 3.1 40.6 1.0 CG D:ASP262 3.2 29.7 1.0 HH12 D:ARG183 3.4 36.7 1.0 HB2 D:ASP262 3.4 31.1 1.0 PG D:ANP506 3.4 28.4 1.0 ND2 D:ASN253 3.4 33.8 1.0 PB D:ANP506 3.5 32.3 1.0 O1A D:ANP506 3.7 29.6 1.0 CB D:ASP262 3.8 26.0 1.0 O2B D:ANP506 3.9 25.2 1.0 H5'2 D:ANP506 3.9 39.9 1.0 N3B D:ANP506 3.9 31.6 1.0 OD2 D:ASP252 3.9 29.2 1.0 O5' D:ANP506 4.0 35.6 1.0 HB3 D:ASP262 4.0 31.1 1.0 O2G D:ANP506 4.0 27.3 1.0 H3' D:ANP506 4.1 42.6 1.0 NH1 D:ARG183 4.1 30.6 1.0 OD1 D:ASP262 4.2 26.2 1.0 HH11 D:ARG183 4.2 36.7 1.0 CA D:CA502 4.3 31.2 1.0 HD22 D:ASN253 4.3 40.6 1.0 HA D:ASN253 4.3 31.6 1.0 CB D:ASN253 4.4 26.2 1.0 O D:HOH641 4.5 24.8 1.0 C5' D:ANP506 4.5 33.2 1.0 OH D:TYR77 4.5 35.0 1.0 O3G D:ANP506 4.6 33.6 1.0 HB3 D:ASN253 4.7 31.5 1.0 O D:ASP252 4.7 31.8 1.0 HNB1 D:ANP506 4.7 37.9 1.0 O1B D:ANP506 4.8 33.9 1.0 HH D:TYR77 4.8 42.0 1.0 H2' D:ANP506 4.8 44.6 1.0 CA D:ASN253 4.8 26.3 1.0 CG D:ASP252 5.0 31.7 1.0 C3' D:ANP506 5.0 35.5 1.0

A.Sreelatha, S.S.Yee, V.A.Lopez, B.C.Park, L.N.Kinch, S.Pilch, K.A.Servage, J.Zhang, J.Jiou, M.Karasiewicz-Urbanska, M.Lobocka, N.V.Grishin, K.Orth, R.Kucharczyk, K.Pawlowski, D.R.Tomchick, V.S.Tagliabracci. Protein Ampylation By An Evolutionarily Conserved Pseudokinase. Cell V. 175 809 2018.
ISSN: ISSN 1097-4172
PubMed: 30270044
DOI: 10.1016/J.CELL.2018.08.046