Atomistry » Zinc » PDB 4mi5-4mth » 4mko
Atomistry »
  Zinc »
    PDB 4mi5-4mth »
      4mko »

Zinc in PDB 4mko: Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin

Protein crystallography data

The structure of Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin, PDB code: 4mko was solved by P.Leone, A.Roussel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.78 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.844, 117.649, 150.584, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 20.5

Other elements in 4mko:

The structure of Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin also contains other interesting chemical elements:

Mercury (Hg) 12 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin (pdb code 4mko). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin, PDB code: 4mko:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 4mko

Go back to Zinc Binding Sites List in 4mko
Zinc binding site 1 out of 10 in the Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:25.2
occ:0.34
 ZN A:ZN1003 0.0 25.2 0.3
OD2 A:ASP266 2.2 18.0 1.0
O A:HOH1312 2.6 37.7 1.0
ZN A:ZN1003 2.7 30.8 0.3
CG A:ASP266 3.0 19.1 1.0
OD1 A:ASP266 3.2 19.9 1.0
CB A:HIS268 4.1 16.9 0.4
O A:HOH1273 4.1 29.9 1.0
NE A:ARG269 4.2 12.9 1.0
CD2 A:HIS268 4.3 23.5 0.4
CB A:HIS268 4.3 18.0 0.6
CB A:ASP266 4.4 11.5 1.0
CD2 A:HIS268 4.6 25.3 0.6
CG A:HIS268 4.6 21.1 0.4
CG A:ARG269 4.8 10.2 1.0
CD A:ARG269 4.8 10.3 1.0
CG A:HIS268 4.8 22.6 0.6

Zinc binding site 2 out of 10 in 4mko

Go back to Zinc Binding Sites List in 4mko
Zinc binding site 2 out of 10 in the Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:30.8
occ:0.30
 ZN A:ZN1003 0.0 30.8 0.3
OD1 A:ASP266 2.0 19.9 1.0
CD2 A:HIS268 2.5 25.3 0.6
ZN A:ZN1003 2.7 25.2 0.3
CG A:ASP266 3.0 19.1 1.0
CG A:HIS268 3.2 22.6 0.6
CB A:HIS268 3.3 16.9 0.4
OD2 A:ASP266 3.3 18.0 1.0
CB A:HIS268 3.4 18.0 0.6
NE2 A:HIS268 3.7 25.4 0.6
N A:HIS268 3.9 14.6 1.0
CA A:HIS268 4.2 15.3 0.4
CA A:HIS268 4.3 15.9 0.6
CB A:ASP266 4.3 11.5 1.0
CG A:HIS268 4.4 21.1 0.4
ND1 A:HIS268 4.5 25.0 0.6
N A:PRO267 4.7 12.1 1.0
CD A:PRO267 4.7 15.2 1.0
CE1 A:HIS268 4.7 24.9 0.6
CA A:ASP266 4.7 9.9 1.0
C A:ASP266 4.7 12.9 1.0
CD2 A:HIS268 4.8 23.5 0.4
CG A:PRO267 4.9 20.1 1.0

Zinc binding site 3 out of 10 in 4mko

Go back to Zinc Binding Sites List in 4mko
Zinc binding site 3 out of 10 in the Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1004

b:11.7
occ:0.23
 OD1 A:ASP68 1.9 16.3 1.0
O A:HOH1146 2.2 20.9 1.0
O A:HOH1408 2.3 29.5 1.0
O A:HOH1225 2.6 46.4 1.0
CG A:ASP68 2.9 16.6 1.0
O A:HOH1422 3.0 52.5 1.0
OD2 A:ASP68 3.3 20.3 1.0
O A:HOH1267 3.3 24.9 1.0
O A:HOH1358 3.8 52.9 1.0
O A:GLY69 4.2 7.8 1.0
CB A:ASP68 4.3 9.8 1.0
O A:HOH1147 4.4 22.6 1.0
C A:ASP68 4.5 10.5 1.0
N A:GLY69 4.6 8.1 1.0
CA A:ASP68 4.6 7.7 1.0
C A:GLY69 4.7 8.7 1.0
O A:HOH1148 4.8 22.6 1.0
O A:ASP68 4.9 10.4 1.0

Zinc binding site 4 out of 10 in 4mko

Go back to Zinc Binding Sites List in 4mko
Zinc binding site 4 out of 10 in the Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1003

b:9.6
occ:0.93
 O B:ACT1005 1.9 12.7 1.0
OD1 B:ASP266 1.9 11.0 1.0
ND1 B:HIS268 2.1 10.5 1.0
OXT B:ACT1006 2.1 13.2 1.0
O B:ACT1006 2.6 16.9 1.0
C B:ACT1005 2.6 15.2 1.0
C B:ACT1006 2.7 12.4 1.0
OXT B:ACT1005 2.8 14.8 1.0
CG B:ASP266 2.8 12.5 1.0
CE1 B:HIS268 2.9 9.9 1.0
OD2 B:ASP266 3.1 11.6 1.0
CG B:HIS268 3.2 9.5 1.0
CB B:HIS268 3.7 7.5 1.0
N B:HIS268 3.8 7.4 1.0
OH A:TYR86 3.9 11.4 1.0
NH1 A:ARG208 4.0 12.8 1.0
NE2 B:HIS268 4.1 9.4 1.0
CH3 B:ACT1005 4.1 15.3 1.0
CH3 B:ACT1006 4.2 9.4 1.0
CB B:ASP266 4.2 10.1 1.0
NH2 A:ARG208 4.2 17.7 1.0
CD2 B:HIS268 4.3 9.5 1.0
CA B:HIS268 4.3 7.2 1.0
O B:HOH1150 4.4 25.7 1.0
N B:PRO267 4.5 9.3 1.0
C B:ASP266 4.6 11.2 1.0
CZ A:ARG208 4.6 19.9 1.0
CD B:PRO267 4.7 10.2 1.0
CA B:ASP266 4.7 9.4 1.0
CZ A:TYR86 4.9 12.5 1.0
C B:PRO267 4.9 10.0 1.0

Zinc binding site 5 out of 10 in 4mko

Go back to Zinc Binding Sites List in 4mko
Zinc binding site 5 out of 10 in the Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1004

b:11.5
occ:0.32
 OD1 B:ASP68 2.0 16.9 1.0
O B:HOH1244 2.1 20.2 1.0
O B:HOH1253 2.1 30.4 1.0
O B:HOH1192 2.3 22.7 1.0
O B:HOH1347 2.6 37.5 1.0
CG B:ASP68 3.0 18.6 1.0
O B:HOH1245 3.3 18.2 1.0
OD2 B:ASP68 3.4 21.7 1.0
O B:HOH1275 4.1 39.5 1.0
O B:GLY69 4.2 7.9 1.0
CB B:ASP68 4.3 8.5 1.0
O B:HOH1180 4.4 18.5 1.0
C B:ASP68 4.5 9.7 1.0
N B:GLY69 4.5 6.6 1.0
C B:GLY69 4.6 8.1 1.0
CA B:ASP68 4.7 6.2 1.0
O B:HOH1392 4.9 21.4 1.0
O B:ASP68 4.9 9.4 1.0
CA B:GLY69 5.0 6.3 1.0

Zinc binding site 6 out of 10 in 4mko

Go back to Zinc Binding Sites List in 4mko
Zinc binding site 6 out of 10 in the Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1003

b:9.3
occ:0.91
 O C:ACT1006 1.8 9.2 1.0
OD1 C:ASP266 2.0 8.7 1.0
ND1 C:HIS268 2.1 10.7 1.0
OXT C:ACT1005 2.2 10.9 1.0
O C:ACT1005 2.5 16.4 1.0
C C:ACT1006 2.6 15.4 1.0
C C:ACT1005 2.6 10.7 1.0
OXT C:ACT1006 2.7 13.3 1.0
CG C:ASP266 2.9 8.8 1.0
CE1 C:HIS268 2.9 10.3 1.0
OD2 C:ASP266 3.1 10.4 1.0
CG C:HIS268 3.2 9.8 1.0
CB C:HIS268 3.7 7.5 1.0
OH D:TYR86 3.8 10.7 1.0
N C:HIS268 3.9 6.7 1.0
NH1 D:ARG208 4.0 15.9 1.0
CH3 C:ACT1006 4.1 15.4 1.0
CH3 C:ACT1005 4.1 10.9 1.0
NE2 C:HIS268 4.1 10.0 1.0
NH2 D:ARG208 4.2 17.9 1.0
CB C:ASP266 4.3 7.2 1.0
CD2 C:HIS268 4.3 10.2 1.0
CA C:HIS268 4.3 7.3 1.0
O C:HOH1140 4.4 26.1 1.0
N C:PRO267 4.6 7.0 1.0
C C:ASP266 4.6 9.0 1.0
CZ D:ARG208 4.6 23.9 1.0
CD C:PRO267 4.6 9.9 1.0
CA C:ASP266 4.7 6.3 1.0
CZ D:TYR86 4.9 13.9 1.0

Zinc binding site 7 out of 10 in 4mko

Go back to Zinc Binding Sites List in 4mko
Zinc binding site 7 out of 10 in the Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1004

b:10.8
occ:0.30
 OD1 C:ASP68 2.0 17.1 1.0
O C:HOH1222 2.0 20.4 1.0
O C:HOH1198 2.1 30.2 1.0
O C:HOH1158 2.3 24.2 1.0
O C:HOH1368 2.8 39.6 1.0
CG C:ASP68 3.0 18.9 1.0
O C:HOH1227 3.2 20.2 1.0
OD2 C:ASP68 3.3 24.8 1.0
O C:HOH1365 3.9 36.1 1.0
O C:GLY69 4.2 7.8 1.0
CB C:ASP68 4.3 8.9 1.0
O C:HOH1201 4.4 23.0 1.0
C C:ASP68 4.5 9.4 1.0
N C:GLY69 4.5 6.5 1.0
C C:GLY69 4.7 7.5 1.0
CA C:ASP68 4.7 7.2 1.0
O C:ASP68 4.8 9.0 1.0
CA C:GLY69 5.0 5.5 1.0

Zinc binding site 8 out of 10 in 4mko

Go back to Zinc Binding Sites List in 4mko
Zinc binding site 8 out of 10 in the Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1003

b:23.3
occ:0.34
 ZN D:ZN1003 0.0 23.3 0.3
OD2 D:ASP266 2.2 17.0 1.0
O D:HOH1274 2.2 38.7 1.0
ZN D:ZN1003 2.7 26.7 0.3
CG D:ASP266 3.0 19.5 1.0
OD1 D:ASP266 3.2 20.6 1.0
ND1 D:HIS268 3.9 24.9 0.4
O D:HOH1212 4.1 26.6 1.0
CB D:HIS268 4.1 18.3 0.4
NE D:ARG269 4.2 10.9 1.0
CB D:HIS268 4.2 19.5 0.6
ND1 D:HIS268 4.3 26.8 0.6
CB D:ASP266 4.4 14.0 1.0
CG D:HIS268 4.5 22.6 0.4
O D:HOH1290 4.6 39.7 1.0
O D:HOH1384 4.6 48.7 1.0
CG D:HIS268 4.7 24.2 0.6
CG D:ARG269 4.8 10.5 1.0
CD D:ARG269 4.8 11.9 1.0
O D:HOH1413 5.0 50.7 1.0

Zinc binding site 9 out of 10 in 4mko

Go back to Zinc Binding Sites List in 4mko
Zinc binding site 9 out of 10 in the Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1003

b:26.7
occ:0.27
 ZN D:ZN1003 0.0 26.7 0.3
OD1 D:ASP266 2.1 20.6 1.0
ND1 D:HIS268 2.2 26.8 0.6
ZN D:ZN1003 2.7 23.3 0.3
O D:HOH1384 2.8 48.7 1.0
CG D:ASP266 2.9 19.5 1.0
CE1 D:HIS268 3.2 26.6 0.6
OD2 D:ASP266 3.2 17.0 1.0
CG D:HIS268 3.2 24.2 0.6
CB D:HIS268 3.4 18.3 0.4
CB D:HIS268 3.5 19.5 0.6
N D:HIS268 4.1 16.0 1.0
CB D:ASP266 4.3 14.0 1.0
NE2 D:HIS268 4.4 27.0 0.6
CD2 D:HIS268 4.4 26.9 0.6
CA D:HIS268 4.4 16.6 0.4
CA D:HIS268 4.4 17.1 0.6
CG D:HIS268 4.5 22.6 0.4
ND1 D:HIS268 4.7 24.9 0.4
CD D:PRO267 4.7 17.4 1.0
CA D:ASP266 4.7 12.3 1.0
N D:PRO267 4.8 14.1 1.0
O D:HOH1274 4.8 38.7 1.0
C D:ASP266 4.9 14.9 1.0
CG D:PRO267 4.9 21.4 1.0

Zinc binding site 10 out of 10 in 4mko

Go back to Zinc Binding Sites List in 4mko
Zinc binding site 10 out of 10 in the Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Monomeric, Cleaved Form of the Pore-Forming Toxin Monalysin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1004

b:8.1
occ:0.21
 OD1 D:ASP68 2.0 18.2 1.0
O D:HOH1248 2.0 22.8 1.0
O D:HOH1352 2.1 31.6 1.0
O D:HOH1353 2.8 38.0 1.0
CG D:ASP68 3.0 18.6 1.0
O D:HOH1285 3.2 25.6 1.0
OD2 D:ASP68 3.3 22.0 1.0
O D:GLY69 4.2 9.1 1.0
CB D:ASP68 4.3 8.6 1.0
O D:HOH1199 4.4 26.4 1.0
O D:HOH1449 4.5 38.9 1.0
C D:ASP68 4.5 10.9 1.0
N D:GLY69 4.6 8.4 1.0
C D:GLY69 4.7 10.3 1.0
CA D:ASP68 4.7 7.0 1.0
O D:ASP68 4.9 10.3 1.0

Reference:

P.Leone, A.Roussel. A Monalysin Toxin Hypothetical Pore Formation Mechanism Deduced From X-Ray and Cryoem Studies To Be Published.
Page generated: Sun Oct 27 02:32:48 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy