Calcium 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:

Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Calcium atom in the Pseudomonas Syringae Selo (pdb code 6eac). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the Pseudomonas Syringae Selo, PDB code: 6eac:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in the Pseudomonas Syringae Selo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pseudomonas Syringae Selo within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:25.1 occ:1.00 O2B A:ANP506 2.3 26.9 1.0 O2A A:ANP506 2.3 31.5 1.0 OD1 A:ASP262 2.3 27.5 1.0 O A:HOH774 2.4 28.9 1.0 O A:HOH737 2.5 25.2 1.0 O A:HOH744 2.5 22.8 1.0 OD2 A:ASP262 2.6 21.8 1.0 CG A:ASP262 2.8 23.1 1.0 HZ1 A:LYS113 3.2 38.5 1.0 HH21 A:ARG93 3.3 35.3 1.0 PA A:ANP506 3.3 33.7 1.0 PB A:ANP506 3.4 29.1 1.0 O3A A:ANP506 3.5 31.6 1.0 NH2 A:ARG93 4.0 29.4 1.0 HH22 A:ARG93 4.0 35.3 1.0 HA3 A:GLY264 4.0 28.3 1.0 O1A A:ANP506 4.1 25.6 1.0 NZ A:LYS113 4.1 32.1 1.0 O1B A:ANP506 4.2 30.9 1.0 MG A:MG501 4.3 10.8 1.0 CB A:ASP262 4.3 23.8 1.0 HZ2 A:LYS113 4.4 38.5 1.0 HZ3 A:LYS113 4.5 38.5 1.0 O2G A:ANP506 4.5 29.7 1.0 O A:HOH787 4.6 36.2 1.0 O5' A:ANP506 4.6 33.6 1.0 HA2 A:GLY264 4.6 28.3 1.0 CA A:GLY264 4.7 23.5 1.0 HD21 A:ASN253 4.7 37.1 1.0 HB3 A:ASP262 4.7 28.5 1.0 N3B A:ANP506 4.7 29.4 1.0 HB2 A:ASP262 4.8 28.5 1.0 O A:HOH753 4.8 32.7 1.0 O A:PHE263 4.8 27.5 1.0 HE3 A:LYS113 4.8 36.1 1.0 N A:GLY264 4.8 24.9 1.0 HA A:ASP262 4.9 30.7 1.0 C A:PHE263 4.9 28.1 1.0 O1G A:ANP506 5.0 17.9 1.0 CE A:LYS113 5.0 30.1 1.0 PG A:ANP506 5.0 25.9 1.0 C A:ASP262 5.0 25.5 1.0

Calcium binding site 2 out of 14 in the Pseudomonas Syringae Selo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pseudomonas Syringae Selo within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:55.9 occ:1.00 O A:SER362 2.4 38.7 1.0 O A:ASP388 2.5 32.6 1.0 O A:GLY363 2.6 31.2 1.0 HA A:ASP388 3.3 61.4 1.0 HB3 A:ASP388 3.3 75.4 1.0 C A:GLY363 3.4 34.2 1.0 C A:ASP388 3.5 39.2 1.0 HA3 A:GLY363 3.6 40.9 1.0 C A:SER362 3.6 39.4 1.0 CA A:ASP388 3.7 51.2 1.0 HG22 A:VAL364 3.8 45.8 1.0 CA A:GLY363 3.9 34.1 1.0 HH22 A:ARG473 3.9 52.0 1.0 CB A:ASP388 4.0 62.8 1.0 HH12 A:ARG473 4.1 56.0 1.0 HA A:VAL364 4.1 40.2 1.0 N A:GLY363 4.2 39.4 1.0 HB3 A:SER362 4.2 73.7 1.0 N A:VAL364 4.3 34.3 1.0 HG23 A:VAL364 4.5 45.8 1.0 CG2 A:VAL364 4.5 38.1 1.0 HB2 A:ASP388 4.6 75.4 1.0 N A:PHE389 4.7 40.3 1.0 CA A:VAL364 4.7 33.5 1.0 HA A:PHE389 4.7 48.4 1.0 CA A:SER362 4.7 52.3 1.0 NH2 A:ARG473 4.8 43.3 1.0 HA2 A:GLY363 4.8 40.9 1.0 HA A:SER362 4.9 62.8 1.0 CB A:SER362 4.9 61.4 1.0 CG A:ASP388 4.9 69.9 1.0 NH1 A:ARG473 4.9 46.6 1.0 OD1 A:ASP388 4.9 72.9 1.0 H A:VAL364 5.0 41.2 1.0

Calcium binding site 3 out of 14 in the Pseudomonas Syringae Selo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pseudomonas Syringae Selo within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:82.9 occ:1.00 O A:HOH759 2.4 52.9 1.0 O A:GLN357 2.5 32.0 1.0 O A:HOH771 2.5 63.6 1.0 H A:ASN361 2.8 71.5 1.0 HA A:LEU358 3.1 36.3 1.0 O A:LEU358 3.2 28.6 1.0 HG A:SER362 3.4 77.9 1.0 HB3 A:GLN360 3.4 47.9 1.0 HB2 A:ASN361 3.5 81.4 1.0 C A:LEU358 3.6 29.7 1.0 C A:GLN357 3.6 28.4 1.0 HD22 A:ASN361 3.6 84.2 1.0 N A:ASN361 3.7 59.6 1.0 CA A:LEU358 3.7 30.2 1.0 H A:GLN360 3.8 43.3 1.0 OD2 A:ASP391 4.0 61.5 1.0 N A:GLN360 4.1 36.1 1.0 OG A:SER362 4.1 64.9 1.0 N A:LEU358 4.1 29.3 1.0 CB A:GLN360 4.3 39.9 1.0 CB A:ASN361 4.3 67.8 1.0 ND2 A:ASN361 4.4 70.2 1.0 CA A:ASN361 4.4 61.6 1.0 HD23 A:LEU358 4.4 54.0 1.0 CA A:GLN360 4.5 47.6 1.0 N A:MET359 4.5 28.4 1.0 C A:MET359 4.6 32.5 1.0 C A:GLN360 4.6 64.3 1.0 H A:SER362 4.6 61.4 1.0 C A:ASN361 4.7 50.9 1.0 HB2 A:GLN360 4.7 47.9 1.0 N A:SER362 4.7 51.2 1.0 CG A:ASN361 4.8 67.0 1.0 HA A:GLN357 4.9 34.7 1.0 CA A:GLN357 4.9 28.9 1.0 HB3 A:GLN357 4.9 38.8 1.0 HD21 A:ASN361 5.0 84.2 1.0 H A:LEU358 5.0 35.2 1.0

Calcium binding site 4 out of 14 in the Pseudomonas Syringae Selo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Pseudomonas Syringae Selo within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:60.4 occ:1.00 O A:HOH766 2.5 37.5 1.0 OE2 A:GLU410 2.5 30.8 1.0 O A:HOH757 2.5 43.1 1.0 O A:HOH763 2.5 41.0 1.0 O A:HOH788 2.6 33.8 1.0 OE1 A:GLU410 2.6 26.7 1.0 CD A:GLU410 2.9 26.7 1.0 H A:ASN411 3.7 40.6 1.0 HA A:GLU410 3.9 33.5 1.0 H A:GLY412 3.9 43.7 1.0 CG A:GLU410 4.4 26.9 1.0 O A:HOH655 4.4 32.7 1.0 O A:GLY412 4.5 30.6 1.0 N A:ASN411 4.5 33.8 1.0 N A:GLY412 4.5 36.4 1.0 CA A:GLU410 4.7 27.9 1.0 HG3 A:GLU410 4.7 32.3 1.0 HA2 A:GLY412 4.8 43.1 1.0 O A:HOH613 4.9 32.8 1.0 HG2 A:GLU410 4.9 32.3 1.0 O A:HOH778 4.9 39.6 1.0 C A:GLY412 4.9 31.2 1.0 CB A:GLU410 5.0 25.1 1.0 CA A:GLY412 5.0 35.9 1.0

Calcium binding site 5 out of 14 in the Pseudomonas Syringae Selo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Pseudomonas Syringae Selo within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:28.8 occ:1.00 O1A B:ANP507 2.2 30.8 1.0 O1B B:ANP507 2.3 22.3 1.0 OD1 B:ASP262 2.4 30.4 1.0 O B:HOH713 2.4 27.5 1.0 O B:HOH731 2.4 24.1 1.0 O B:HOH762 2.4 29.6 1.0 OD2 B:ASP262 2.6 24.9 1.0 CG B:ASP262 2.8 29.8 1.0 HH21 B:ARG93 3.2 26.9 1.0 HZ1 B:LYS113 3.2 41.9 1.0 PA B:ANP507 3.3 33.4 1.0 PB B:ANP507 3.4 29.1 1.0 O3A B:ANP507 3.5 29.3 1.0 NH2 B:ARG93 3.9 22.4 1.0 HH22 B:ARG93 3.9 26.9 1.0 O2A B:ANP507 4.0 24.5 1.0 HA3 B:GLY264 4.0 29.0 1.0 NZ B:LYS113 4.1 34.9 1.0 O2B B:ANP507 4.2 33.1 1.0 MG B:MG501 4.3 13.1 1.0 O B:HOH766 4.3 36.7 1.0 HZ2 B:LYS113 4.3 41.9 1.0 CB B:ASP262 4.4 28.5 1.0 HZ3 B:LYS113 4.4 41.9 1.0 O1G B:ANP507 4.6 28.1 1.0 HA2 B:GLY264 4.6 29.0 1.0 O5' B:ANP507 4.6 35.0 1.0 CA B:GLY264 4.6 24.1 1.0 N3B B:ANP507 4.7 30.5 1.0 HB3 B:ASP262 4.8 34.2 1.0 HD21 B:ASN253 4.8 33.4 1.0 O B:PHE263 4.8 28.2 1.0 HB2 B:ASP262 4.8 34.2 1.0 O2G B:ANP507 4.8 16.5 1.0 N B:GLY264 4.8 27.8 1.0 HE3 B:LYS113 4.8 38.6 1.0 HA B:ASP262 4.9 33.7 1.0 PG B:ANP507 5.0 26.8 1.0 C B:PHE263 5.0 28.4 1.0 CE B:LYS113 5.0 32.2 1.0 HE B:ARG93 5.0 35.4 1.0

Calcium binding site 6 out of 14 in the Pseudomonas Syringae Selo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Pseudomonas Syringae Selo within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:58.8 occ:1.00 O B:SER362 2.4 38.2 1.0 O B:HOH692 2.4 41.6 1.0 O B:HOH740 2.5 49.3 1.0 O B:ASP388 2.5 38.4 1.0 O B:HOH763 2.6 44.3 1.0 O B:GLY363 2.6 42.6 1.0 C B:GLY363 3.4 42.9 1.0 HA B:ASP388 3.5 65.0 1.0 HB3 B:ASP388 3.5 81.9 1.0 HA3 B:GLY363 3.5 51.5 1.0 C B:ASP388 3.5 44.5 1.0 C B:SER362 3.6 44.0 1.0 HG22 B:VAL364 3.8 52.1 1.0 HH22 B:ARG473 3.8 54.7 1.0 CA B:GLY363 3.8 42.9 1.0 CA B:ASP388 3.9 54.2 1.0 HH12 B:ARG473 4.1 61.9 1.0 HG23 B:VAL364 4.1 52.1 1.0 CB B:ASP388 4.1 68.2 1.0 N B:GLY363 4.2 44.0 1.0 HA B:VAL364 4.2 49.2 1.0 HB3 B:SER362 4.3 75.5 1.0 N B:VAL364 4.3 40.4 1.0 CG2 B:VAL364 4.4 43.4 1.0 HA B:PHE389 4.6 53.8 1.0 NH2 B:ARG473 4.7 45.6 1.0 N B:PHE389 4.7 43.8 1.0 CA B:SER362 4.7 53.2 1.0 HA2 B:GLY363 4.8 51.5 1.0 CA B:VAL364 4.8 41.0 1.0 HA B:SER362 4.8 63.9 1.0 OD1 B:ASP388 4.9 88.5 1.0 NH1 B:ARG473 4.9 51.6 1.0 HB2 B:ASP388 4.9 81.9 1.0 CG B:ASP388 4.9 82.2 1.0 H B:VAL364 5.0 48.5 1.0

Calcium binding site 7 out of 14 in the Pseudomonas Syringae Selo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Pseudomonas Syringae Selo within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:67.2 occ:1.00 O B:HOH761 2.4 38.9 1.0 O B:HOH682 2.5 36.2 1.0 OE2 B:GLU410 2.5 36.5 1.0 OE1 B:GLU410 3.1 35.6 1.0 CD B:GLU410 3.2 32.4 1.0 H B:GLY412 3.4 41.2 1.0 H B:ASN411 3.6 37.8 1.0 N B:GLY412 4.0 34.3 1.0 O B:GLY412 4.1 33.8 1.0 HA B:GLU410 4.2 37.0 1.0 HA2 B:GLY412 4.2 42.4 1.0 N B:ASN411 4.4 31.5 1.0 C B:GLY412 4.4 34.6 1.0 CA B:GLY412 4.4 35.3 1.0 CG B:GLU410 4.6 31.5 1.0 HG3 B:GLU410 4.9 37.9 1.0 C B:ASN411 4.9 32.0 1.0 CA B:GLU410 5.0 30.9 1.0

Calcium binding site 8 out of 14 in the Pseudomonas Syringae Selo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Pseudomonas Syringae Selo within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:71.5 occ:1.00 O B:ALA70 2.4 41.4 1.0 O B:ALA68 2.5 32.4 1.0 O B:HOH764 2.5 44.0 1.0 C B:ALA70 3.6 33.4 1.0 C B:ALA68 3.6 30.8 1.0 HA B:GLU71 3.7 47.9 1.0 HA B:ALA68 3.8 40.2 1.0 O B:HOH769 4.1 35.6 1.0 HB2 B:GLU71 4.1 50.2 1.0 N B:ALA70 4.3 33.2 1.0 CA B:ALA68 4.3 33.5 1.0 H B:ALA70 4.3 39.9 1.0 CA B:GLU71 4.4 39.9 1.0 N B:GLU71 4.4 35.8 1.0 O B:TRP67 4.5 33.7 1.0 C B:GLU69 4.5 34.3 1.0 CA B:ALA70 4.5 35.0 1.0 N B:GLU69 4.6 31.3 1.0 HA B:GLU69 4.6 42.3 1.0 HD2 B:PRO72 4.6 47.7 1.0 HG3 B:GLU71 4.7 49.2 1.0 CB B:GLU71 4.7 41.8 1.0 HB1 B:ALA68 4.8 37.4 1.0 CA B:GLU69 4.8 35.2 1.0 HB3 B:ALA70 4.9 40.9 1.0 HD3 B:PRO72 5.0 47.7 1.0

Calcium binding site 9 out of 14 in the Pseudomonas Syringae Selo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Pseudomonas Syringae Selo within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:30.9 occ:1.00 O C:HOH715 2.2 29.4 1.0 O1B C:ANP506 2.3 24.5 1.0 OD1 C:ASP262 2.3 26.3 1.0 O C:HOH703 2.3 29.7 1.0 O2A C:ANP506 2.4 26.2 1.0 O C:HOH717 2.6 29.2 1.0 OD2 C:ASP262 2.7 26.7 1.0 CG C:ASP262 2.9 29.1 1.0 HZ1 C:LYS113 3.2 40.7 1.0 PA C:ANP506 3.4 36.5 1.0 PB C:ANP506 3.4 29.4 1.0 O3A C:ANP506 3.5 31.8 1.0 HA3 C:GLY264 4.0 35.6 1.0 O C:HOH684 4.0 32.2 1.0 O1A C:ANP506 4.1 30.9 1.0 HH12 C:ARG93 4.1 35.8 1.0 HH11 C:ARG93 4.1 35.8 1.0 NZ C:LYS113 4.1 33.9 1.0 O2B C:ANP506 4.2 29.1 1.0 MG C:MG501 4.3 20.2 1.0 CB C:ASP262 4.4 28.1 1.0 HZ3 C:LYS113 4.4 40.7 1.0 NH1 C:ARG93 4.4 29.8 1.0 HZ2 C:LYS113 4.5 40.7 1.0 O C:HOH720 4.5 36.8 1.0 HA2 C:GLY264 4.6 35.6 1.0 CA C:GLY264 4.6 29.7 1.0 O3G C:ANP506 4.7 26.1 1.0 O5' C:ANP506 4.7 37.2 1.0 N3B C:ANP506 4.7 33.7 1.0 O C:PHE263 4.7 34.5 1.0 HD21 C:ASN253 4.7 41.3 1.0 HB3 C:ASP262 4.8 33.7 1.0 N C:GLY264 4.8 35.2 1.0 HB2 C:ASP262 4.9 33.7 1.0 O2G C:ANP506 4.9 22.9 1.0 HA C:ASP262 4.9 30.5 1.0 C C:PHE263 4.9 34.0 1.0 HE2 C:LYS113 4.9 41.9 1.0 HE3 C:LYS113 5.0 41.9 1.0 CE C:LYS113 5.0 34.9 1.0

Calcium binding site 10 out of 14 in the Pseudomonas Syringae Selo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Pseudomonas Syringae Selo within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:66.2 occ:1.00 OD1 C:ASP388 2.2 0.1 1.0 O C:SER362 2.3 53.4 1.0 O C:HOH714 2.4 44.0 1.0 O C:ASP388 2.6 44.8 1.0 O C:GLY363 2.6 47.5 1.0 CG C:ASP388 3.3 99.9 1.0 C C:GLY363 3.4 47.0 1.0 C C:SER362 3.5 50.4 1.0 C C:ASP388 3.6 55.8 1.0 HA C:ASP388 3.7 87.3 1.0 HA3 C:GLY363 3.7 53.8 1.0 HG22 C:VAL364 3.8 51.8 1.0 HB3 C:SER362 4.0 70.6 1.0 CA C:GLY363 4.0 44.9 1.0 HH22 C:ARG473 4.0 75.3 1.0 CA C:ASP388 4.0 72.7 1.0 OD2 C:ASP388 4.1 0.6 1.0 HH12 C:ARG473 4.1 82.3 1.0 HA C:VAL364 4.2 46.0 1.0 N C:GLY363 4.2 48.2 1.0 CB C:ASP388 4.2 89.9 1.0 HG23 C:VAL364 4.3 51.8 1.0 N C:VAL364 4.4 42.7 1.0 CG2 C:VAL364 4.5 43.2 1.0 CA C:SER362 4.6 54.5 1.0 CB C:SER362 4.7 58.9 1.0 HA C:PHE389 4.7 63.7 1.0 HB3 C:ASP388 4.7 0.9 1.0 HA C:SER362 4.7 65.5 1.0 CA C:VAL364 4.8 38.3 1.0 N C:PHE389 4.8 53.5 1.0 NH2 C:ARG473 4.8 62.8 1.0 HB2 C:SER362 4.9 70.6 1.0 HA2 C:GLY363 4.9 53.8 1.0 HG23 C:VAL390 4.9 77.3 1.0 NH1 C:ARG473 5.0 68.6 1.0 HB2 C:ASP388 5.0 0.9 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