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Manganese in PDB 8br0: Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin (Residue Q3455 to L3863) in Complex with 3'Deoxyctp and Two Manganese Cations Bound to Latrunculin-B-Adp-Mn-Actin

Enzymatic activity of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin (Residue Q3455 to L3863) in Complex with 3'Deoxyctp and Two Manganese Cations Bound to Latrunculin-B-Adp-Mn-Actin

All present enzymatic activity of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin (Residue Q3455 to L3863) in Complex with 3'Deoxyctp and Two Manganese Cations Bound to Latrunculin-B-Adp-Mn-Actin:
4.6.1.1;

Protein crystallography data

The structure of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin (Residue Q3455 to L3863) in Complex with 3'Deoxyctp and Two Manganese Cations Bound to Latrunculin-B-Adp-Mn-Actin, PDB code: 8br0 was solved by M.Texeira-Nuns, P.Retailleau, L.Renault, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.05 / 2.22
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.469, 132.503, 96.217, 90, 110.4, 90
R / Rfree (%) 20.9 / 24.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin (Residue Q3455 to L3863) in Complex with 3'Deoxyctp and Two Manganese Cations Bound to Latrunculin-B-Adp-Mn-Actin (pdb code 8br0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin (Residue Q3455 to L3863) in Complex with 3'Deoxyctp and Two Manganese Cations Bound to Latrunculin-B-Adp-Mn-Actin, PDB code: 8br0:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 8br0

Go back to Manganese Binding Sites List in 8br0
Manganese binding site 1 out of 6 in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin (Residue Q3455 to L3863) in Complex with 3'Deoxyctp and Two Manganese Cations Bound to Latrunculin-B-Adp-Mn-Actin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin (Residue Q3455 to L3863) in Complex with 3'Deoxyctp and Two Manganese Cations Bound to Latrunculin-B-Adp-Mn-Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:69.2
occ:1.00
 O A:HOH541 2.1 41.8 1.0
O A:HOH562 2.1 55.9 1.0
O1B A:ADP402 2.2 46.7 1.0
O A:HOH504 2.5 50.5 1.0
O A:HOH520 2.6 43.7 1.0
O A:HOH510 3.0 64.2 1.0
PB A:ADP402 3.3 46.0 1.0
O3B A:ADP402 3.5 46.2 1.0
O A:HOH555 4.0 43.4 1.0
O3A A:ADP402 4.0 45.6 1.0
O2A A:ADP402 4.2 44.3 1.0
OD1 A:ASP154 4.2 45.4 1.0
OE1 A:GLN137 4.2 39.9 1.0
O A:HOH512 4.3 50.8 1.0
NZ A:LYS18 4.4 42.3 1.0
CA A:GLY13 4.4 44.3 1.0
OD2 A:ASP154 4.5 44.6 1.0
OD2 A:ASP11 4.5 49.5 1.0
O2B A:ADP402 4.6 45.7 1.0
PA A:ADP402 4.6 44.8 1.0
CD A:GLN137 4.6 42.0 1.0
CA A:GLY156 4.7 38.6 1.0
OD1 A:ASP11 4.7 47.1 1.0
CG A:ASP154 4.8 44.4 1.0

Manganese binding site 2 out of 6 in 8br0

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Manganese binding site 2 out of 6 in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin (Residue Q3455 to L3863) in Complex with 3'Deoxyctp and Two Manganese Cations Bound to Latrunculin-B-Adp-Mn-Actin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin (Residue Q3455 to L3863) in Complex with 3'Deoxyctp and Two Manganese Cations Bound to Latrunculin-B-Adp-Mn-Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1101

b:55.0
occ:1.00
 OD2 B:ASP667 2.0 41.9 1.0
O2B B:CH11103 2.2 55.9 1.0
OD1 B:ASP665 2.2 45.8 1.0
O2G B:CH11103 2.3 56.2 1.0
O B:HOH1281 2.3 52.5 1.0
O2A B:CH11103 2.3 54.5 1.0
CG B:ASP667 3.1 42.2 1.0
PB B:CH11103 3.2 55.9 1.0
CG B:ASP665 3.3 46.3 1.0
PA B:CH11103 3.4 54.5 1.0
O3B B:CH11103 3.4 55.9 1.0
PG B:CH11103 3.4 55.5 1.0
O3A B:CH11103 3.5 55.1 1.0
OD1 B:ASP667 3.6 43.8 1.0
MN B:MN1102 3.7 54.6 1.0
OD2 B:ASP665 3.8 47.9 1.0
O B:HOH1249 3.9 49.9 1.0
O B:ASP665 4.1 44.6 1.0
N B:ASP665 4.1 45.0 1.0
O3G B:CH11103 4.2 55.2 1.0
O5' B:CH11103 4.3 54.4 1.0
CB B:ASP667 4.4 41.5 1.0
NH1 B:ARG510 4.4 36.3 1.0
O1G B:CH11103 4.5 55.1 1.0
CB B:ASP665 4.5 43.8 1.0
C B:ASP665 4.5 43.9 1.0
O1B B:CH11103 4.6 56.8 1.0
CA B:ASP665 4.6 44.1 1.0
O1A B:CH11103 4.6 53.9 1.0
CE B:LYS528 4.6 39.8 1.0
O B:HOH1245 4.7 42.4 1.0
NZ B:LYS528 4.8 38.0 1.0
CB B:ALA664 4.9 47.6 1.0
N B:ASP667 4.9 41.6 1.0
CD B:LYS528 4.9 39.7 1.0
O B:HOH1257 5.0 55.5 1.0
C5' B:CH11103 5.0 55.9 1.0

Manganese binding site 3 out of 6 in 8br0

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Manganese binding site 3 out of 6 in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin (Residue Q3455 to L3863) in Complex with 3'Deoxyctp and Two Manganese Cations Bound to Latrunculin-B-Adp-Mn-Actin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin (Residue Q3455 to L3863) in Complex with 3'Deoxyctp and Two Manganese Cations Bound to Latrunculin-B-Adp-Mn-Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1102

b:54.6
occ:1.00
 OD1 B:ASP667 2.1 43.8 1.0
OD2 B:ASP665 2.3 47.9 1.0
O B:HOH1257 2.3 55.5 1.0
NE2 B:HIS753 2.3 43.1 1.0
O2A B:CH11103 2.4 54.5 1.0
C5' B:CH11103 3.0 55.9 1.0
CG B:ASP667 3.0 42.2 1.0
CE1 B:HIS753 3.1 43.1 1.0
CG B:ASP665 3.1 46.3 1.0
OD1 B:ASP665 3.2 45.8 1.0
OD2 B:ASP667 3.3 41.9 1.0
PA B:CH11103 3.4 54.5 1.0
CD2 B:HIS753 3.5 43.0 1.0
O5' B:CH11103 3.5 54.4 1.0
MN B:MN1101 3.7 55.0 1.0
O B:HOH1248 4.0 39.3 1.0
O1A B:CH11103 4.1 53.9 1.0
O B:HOH1232 4.2 33.8 1.0
ND1 B:HIS753 4.3 43.7 1.0
CB B:ASP667 4.3 41.5 1.0
C4' B:CH11103 4.4 60.1 1.0
CG B:HIS753 4.5 42.8 1.0
CB B:ASP665 4.5 43.8 1.0
O B:LYS528 4.5 41.7 1.0
O4' B:CH11103 4.6 62.9 1.0
O2B B:CH11103 4.6 55.9 1.0
O3A B:CH11103 4.8 55.1 1.0
CD1 B:LEU530 4.8 48.4 1.0
CA B:ASP667 4.9 40.8 1.0

Manganese binding site 4 out of 6 in 8br0

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Manganese binding site 4 out of 6 in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin (Residue Q3455 to L3863) in Complex with 3'Deoxyctp and Two Manganese Cations Bound to Latrunculin-B-Adp-Mn-Actin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin (Residue Q3455 to L3863) in Complex with 3'Deoxyctp and Two Manganese Cations Bound to Latrunculin-B-Adp-Mn-Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn403

b:90.5
occ:1.00
 O C:HOH535 2.1 43.5 1.0
O3B C:ADP402 2.2 63.9 1.0
O C:HOH506 2.4 68.2 1.0
O C:HOH502 2.4 61.1 1.0
O C:HOH517 2.6 64.5 1.0
O C:HOH510 3.3 76.7 1.0
PB C:ADP402 3.3 64.4 1.0
O1B C:ADP402 3.5 64.4 1.0
O C:HOH516 3.7 62.3 1.0
O3A C:ADP402 4.0 63.9 1.0
OD1 C:ASP154 4.2 58.5 1.0
O1A C:ADP402 4.2 62.9 1.0
OE1 C:GLN137 4.2 58.1 1.0
O C:HOH503 4.3 53.8 1.0
NZ C:LYS18 4.4 59.7 1.0
CA C:GLY13 4.4 62.3 1.0
OD2 C:ASP154 4.5 56.5 1.0
OD2 C:ASP11 4.6 69.1 1.0
O2B C:ADP402 4.6 64.4 1.0
PA C:ADP402 4.6 63.4 1.0
CD C:GLN137 4.6 58.9 1.0
CA C:GLY156 4.7 51.6 1.0
CG C:ASP154 4.7 56.9 1.0
OD1 C:ASP11 4.7 67.8 1.0

Manganese binding site 5 out of 6 in 8br0

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Manganese binding site 5 out of 6 in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin (Residue Q3455 to L3863) in Complex with 3'Deoxyctp and Two Manganese Cations Bound to Latrunculin-B-Adp-Mn-Actin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin (Residue Q3455 to L3863) in Complex with 3'Deoxyctp and Two Manganese Cations Bound to Latrunculin-B-Adp-Mn-Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1101

b:45.2
occ:1.00
 O D:HOH1268 2.0 39.3 1.0
OD1 D:ASP667 2.1 38.6 1.0
OD2 D:ASP665 2.3 43.5 1.0
NE2 D:HIS753 2.3 42.5 1.0
O1A D:CH11103 2.4 49.0 1.0
C5' D:CH11103 3.0 54.6 1.0
CG D:ASP667 3.0 35.5 1.0
CG D:ASP665 3.1 41.1 1.0
CE1 D:HIS753 3.1 42.1 1.0
OD1 D:ASP665 3.2 44.0 1.0
OD2 D:ASP667 3.3 35.6 1.0
PA D:CH11103 3.4 49.3 1.0
O5' D:CH11103 3.5 51.4 1.0
CD2 D:HIS753 3.5 41.5 1.0
MN D:MN1102 3.6 45.3 1.0
O2A D:CH11103 4.1 47.6 1.0
O D:HOH1218 4.1 30.3 1.0
O D:HOH1265 4.2 36.8 1.0
CB D:ASP667 4.3 34.5 1.0
C4' D:CH11103 4.3 59.6 1.0
ND1 D:HIS753 4.4 42.5 1.0
O D:LYS528 4.5 40.1 1.0
CB D:ASP665 4.5 34.3 1.0
CG D:HIS753 4.5 40.2 1.0
O4' D:CH11103 4.6 63.3 1.0
O1B D:CH11103 4.7 49.3 1.0
O3A D:CH11103 4.8 49.5 1.0
CA D:ASP667 4.9 36.0 1.0
CD1 D:LEU530 4.9 55.6 1.0

Manganese binding site 6 out of 6 in 8br0

Go back to Manganese Binding Sites List in 8br0
Manganese binding site 6 out of 6 in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin (Residue Q3455 to L3863) in Complex with 3'Deoxyctp and Two Manganese Cations Bound to Latrunculin-B-Adp-Mn-Actin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin (Residue Q3455 to L3863) in Complex with 3'Deoxyctp and Two Manganese Cations Bound to Latrunculin-B-Adp-Mn-Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1102

b:45.3
occ:1.00
 OD2 D:ASP667 2.1 35.6 1.0
OD1 D:ASP665 2.2 44.0 1.0
O1B D:CH11103 2.2 49.3 1.0
O1A D:CH11103 2.3 49.0 1.0
O1G D:CH11103 2.3 45.5 1.0
O D:HOH1279 2.4 38.8 1.0
CG D:ASP667 3.2 35.5 1.0
PB D:CH11103 3.2 49.6 1.0
CG D:ASP665 3.3 41.1 1.0
PA D:CH11103 3.4 49.3 1.0
PG D:CH11103 3.4 45.7 1.0
O3B D:CH11103 3.5 48.0 1.0
O3A D:CH11103 3.5 49.5 1.0
OD1 D:ASP667 3.6 38.6 1.0
MN D:MN1101 3.6 45.2 1.0
OD2 D:ASP665 3.8 43.5 1.0
O D:ASP665 4.0 32.7 1.0
N D:ASP665 4.1 36.2 1.0
O5' D:CH11103 4.3 51.4 1.0
O D:HOH1223 4.3 48.4 1.0
O2G D:CH11103 4.3 44.9 1.0
CB D:ASP667 4.4 34.5 1.0
CB D:ASP665 4.4 34.3 1.0
C D:ASP665 4.5 33.7 1.0
NH1 D:ARG510 4.5 42.1 1.0
O3G D:CH11103 4.5 45.8 1.0
O D:HOH1292 4.6 28.9 1.0
O2B D:CH11103 4.6 51.4 1.0
CA D:ASP665 4.6 33.8 1.0
CE D:LYS528 4.6 28.8 1.0
O2A D:CH11103 4.6 47.6 1.0
O D:HOH1276 4.7 41.8 1.0
NZ D:LYS528 4.8 28.5 1.0
O D:HOH1268 4.8 39.3 1.0
CB D:ALA664 4.9 36.8 1.0
CD D:LYS528 4.9 32.2 1.0
N D:ASP667 4.9 36.0 1.0
C5' D:CH11103 5.0 54.6 1.0

Reference:

M.Teixeira-Nunes, P.Retailleau, D.Raoux-Barbot, M.Comisso, A.A.Missinou, C.Velours, S.Plancqueel, D.Ladant, U.Mechold, L.Renault. Functional and Structural Insights Into the Multi-Step Activation and Catalytic Mechanism of Bacterial Exoy Nucleotidyl Cyclase Toxins Bound to Actin-Profilin Plos Pathog. 2023.
ISSN: ESSN 1553-7374
DOI: 10.1371/JOURNAL.PPAT.1011654
Page generated: Sun Oct 6 11:27:08 2024

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