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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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