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

Protein crystallography data

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

Other elements in 6yhn:

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

Magnesium Binding Sites:

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 6yhn

Go back to Magnesium Binding Sites List in 6yhn
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 6yhn

Go back to Magnesium Binding Sites List in 6yhn
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 6yhn

Go back to Magnesium Binding Sites List in 6yhn
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 6yhn

Go back to Magnesium Binding Sites List in 6yhn
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

Reference:

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
Page generated: Mon Jan 25 15:19:17 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy