Magnesium in PDB 6yhn: Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis

The structure of Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis, PDB code: 6yhn was solved by P.Lukat, E.M.Gazdag, T.V.Heidler, W.Blankenfeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.27 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.271, 90.531, 120.717, 90, 90, 90
R / Rfree (%)	15.8 / 19.1

The structure of Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis (pdb code 6yhn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis, PDB code: 6yhn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1202 b:19.5 occ:1.00 H A:GLU603 2.5 22.6 1.0 HA A:THR602 2.9 23.1 1.0 O A:HOH1634 3.0 39.5 1.0 HD3 A:ARG694 3.0 27.2 1.0 HA A:HIS654 3.1 23.5 1.0 O A:HOH1642 3.2 42.1 1.0 ND1 A:HIS654 3.3 25.4 1.0 N A:GLU603 3.3 18.9 1.0 HD1 A:PHE655 3.3 23.3 1.0 HB2 A:GLU603 3.4 21.7 1.0 HB3 A:HIS654 3.5 24.2 1.0 CA A:THR602 3.7 19.2 1.0 HB A:THR602 3.7 29.3 1.0 HG2 A:ARG694 3.8 24.6 1.0 HE1 A:PHE655 3.8 25.4 1.0 CD A:ARG694 3.9 22.6 1.0 C A:THR602 3.9 22.5 1.0 CA A:HIS654 3.9 19.6 1.0 CB A:HIS654 4.0 20.2 1.0 CG A:HIS654 4.0 25.7 1.0 CD1 A:PHE655 4.1 19.4 1.0 CB A:GLU603 4.1 18.1 1.0 HG22 A:THR602 4.1 27.1 1.0 HG3 A:ARG694 4.2 24.6 1.0 HB3 A:GLU603 4.2 21.7 1.0 CG A:ARG694 4.2 20.5 1.0 CB A:THR602 4.2 24.4 1.0 CA A:GLU603 4.2 15.2 1.0 CE1 A:HIS654 4.3 28.0 1.0 HD2 A:ARG694 4.3 27.2 1.0 CE1 A:PHE655 4.3 21.1 1.0 HE1 A:HIS654 4.4 33.6 1.0 O A:LYS653 4.5 19.2 1.0 HA A:GLU603 4.5 18.2 1.0 O A:THR601 4.5 19.5 1.0 O A:HOH1416 4.6 44.4 1.0 C A:HIS654 4.6 18.7 1.0 CG2 A:THR602 4.7 22.6 1.0 H A:PHE655 4.7 23.4 1.0 O A:HOH1559 4.8 21.0 1.0 N A:PHE655 4.9 19.5 1.0 N A:THR602 4.9 17.8 1.0 HB2 A:HIS654 4.9 24.2 1.0 O A:HOH1470 4.9 41.2 1.0 NE A:ARG694 4.9 26.1 1.0 HH11 A:ARG694 4.9 32.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1203 b:31.6 occ:1.00 HE A:ARG743 2.3 28.0 1.0 HH21 A:ARG743 2.6 29.1 1.0 NE A:ARG743 3.1 23.3 1.0 NH2 A:ARG743 3.3 24.2 1.0 HE2 A:TYR818 3.6 36.4 1.0 HG2 A:ARG743 3.7 29.8 1.0 CZ A:ARG743 3.7 22.8 1.0 O A:HOH1617 3.9 68.5 1.0 CE2 A:TYR818 4.0 30.3 1.0 HG3 A:ARG743 4.0 29.8 1.0 HH22 A:ARG743 4.1 29.1 1.0 CG A:ARG743 4.2 24.8 1.0 CD A:ARG743 4.2 21.8 1.0 HD2 A:TYR818 4.3 27.7 1.0 CD2 A:TYR818 4.4 23.1 1.0 HH A:TYR818 4.6 32.4 1.0 CZ A:TYR818 4.7 24.0 1.0 HD2 A:ARG743 4.7 26.2 1.0 O A:HOH1651 4.8 60.9 1.0 HD3 A:ARG743 4.9 26.2 1.0 OH A:TYR818 4.9 27.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1204 b:25.4 occ:1.00 H A:GLY600 2.3 21.3 1.0 HA A:ARG599 2.7 22.8 1.0 O A:HOH1585 2.8 69.0 1.0 O A:HOH1313 3.0 22.6 1.0 HB3 A:ALA650 3.1 24.3 1.0 N A:GLY600 3.1 17.7 1.0 HB2 A:ALA650 3.3 24.3 1.0 HB1 A:ALA650 3.3 24.3 1.0 HG3 A:ARG599 3.3 27.8 1.0 CB A:ALA650 3.4 20.3 1.0 HG22 A:THR641 3.6 26.0 1.0 HG21 A:THR641 3.6 26.0 1.0 CA A:ARG599 3.6 19.0 1.0 HA A:ALA647 3.8 24.9 1.0 C A:ARG599 3.8 23.1 1.0 HA3 A:GLY600 4.0 21.9 1.0 CG A:ARG599 4.0 23.2 1.0 CG2 A:THR641 4.0 21.7 1.0 HG2 A:ARG599 4.1 27.8 1.0 CA A:GLY600 4.1 18.3 1.0 HB A:THR641 4.3 23.3 1.0 O A:GLY600 4.3 21.0 1.0 CB A:ARG599 4.3 19.0 1.0 HG A:SER646 4.4 27.8 0.5 HE1 A:HIS676 4.5 32.4 1.0 O A:HOH1522 4.5 59.1 1.0 O A:MET598 4.6 18.8 1.0 HB2 A:ARG599 4.6 22.8 1.0 O A:SER646 4.6 20.1 0.5 O A:SER646 4.6 20.1 0.5 N A:ARG599 4.7 17.6 1.0 HA A:TYR640 4.7 24.0 1.0 NE2 A:HIS676 4.7 27.9 1.0 C A:GLY600 4.7 18.3 1.0 CA A:ALA647 4.7 20.8 1.0 O A:HOH1420 4.7 31.3 1.0 CB A:THR641 4.8 19.4 1.0 O A:GLU639 4.8 22.5 1.0 CE1 A:HIS676 4.8 27.0 1.0 HG23 A:THR641 4.8 26.0 1.0 HA2 A:GLY600 4.9 21.9 1.0 CA A:ALA650 4.9 19.0 1.0 O A:MET781 5.0 30.8 1.0 C A:MET598 5.0 18.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1205 b:32.9 occ:1.00 H A:THR862 2.4 23.2 1.0 HA3 A:GLY861 2.7 22.2 1.0 O A:HOH1561 2.9 29.7 1.0 O A:HOH1336 2.9 24.3 1.0 HZ3 A:LYS832 2.9 59.2 1.0 HZ1 A:LYS832 3.2 59.2 1.0 N A:THR862 3.2 19.4 1.0 O A:HOH1354 3.4 39.6 1.0 NZ A:LYS832 3.5 49.3 1.0 CA A:GLY861 3.5 18.5 1.0 HE3 A:LYS832 3.6 50.1 1.0 HA2 A:GLY861 3.6 22.2 1.0 HB3 A:SER747 3.7 29.7 1.0 HB2 A:SER747 3.7 29.7 1.0 HB A:THR862 3.8 21.3 1.0 C A:GLY861 3.9 18.7 1.0 CB A:SER747 4.0 24.8 1.0 OG1 A:THR862 4.0 20.6 1.0 CE A:LYS832 4.1 41.8 1.0 OG A:SER747 4.1 28.8 1.0 HA A:SER813 4.1 26.2 1.0 CB A:THR862 4.2 17.7 1.0 HZ2 A:LYS832 4.2 59.2 1.0 CA A:THR862 4.3 17.0 1.0 H A:GLN814 4.3 26.1 1.0 HG1 A:THR862 4.3 24.7 1.0 HG A:SER813 4.5 28.1 1.0 HG A:SER747 4.5 34.5 1.0 O A:HOH1356 4.6 29.9 1.0 HE2 A:LYS832 4.6 50.1 1.0 O A:SER860 4.6 13.8 0.4 O A:THR862 4.7 20.7 1.0 N A:GLY861 4.7 13.8 1.0 O A:SER860 4.7 18.3 0.6 O A:HOH1575 4.8 56.5 1.0 C A:THR862 5.0 23.2 1.0 HG21 A:VAL745 5.0 27.5 1.0

P.Chaoprasid, P.Lukat, S.Muhlen, T.Heidler, E.M.Gazdag, S.Dong, W.Bi, C.Ruter, M.Kirchenwitz, A.Steffen, L.Jansch, T.E.B.Stradal, P.Dersch, W.Blankenfeldt. Crystal Structure of Bacterial Cytotoxic Necrotizing Factor Cnf Y Reveals Molecular Building Blocks For Intoxication. Embo J. 05202 2021.
ISSN: ESSN 1460-2075
PubMed: 33410511
DOI: 10.15252/EMBJ.2020105202