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Magnesium in PDB 8br1: Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions

Enzymatic activity of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions

All present enzymatic activity of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions:
4.6.1.1;

Protein crystallography data

The structure of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions, PDB code: 8br1 was solved by M.Teixeira-Nunes, L.Renault, P.Retailleau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.76 / 2.04
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.116, 132.443, 96.396, 90, 110.57, 90
R / Rfree (%) 19 / 22.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions (pdb code 8br1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions, PDB code: 8br1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8br1

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Magnesium binding site 1 out of 6 in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:44.4
occ:1.00
 O3G A:ATP402 1.9 44.0 1.0
O A:HOH541 1.9 43.9 1.0
O A:HOH584 2.1 43.6 1.0
O1B A:ATP402 2.1 42.4 1.0
O A:HOH510 2.2 41.3 1.0
O A:HOH532 2.3 37.6 1.0
PG A:ATP402 3.3 45.8 1.0
PB A:ATP402 3.3 42.5 1.0
O3B A:ATP402 3.5 44.4 1.0
O A:HOH519 4.0 46.2 1.0
O3A A:ATP402 4.1 43.6 1.0
O2A A:ATP402 4.1 42.4 1.0
O A:HOH504 4.1 59.8 1.0
O1G A:ATP402 4.1 47.4 1.0
OE1 A:GLN137 4.2 40.2 1.0
O2G A:ATP402 4.3 47.2 1.0
OD2 A:ASP11 4.4 45.3 1.0
OD2 A:ASP154 4.4 50.5 1.0
OD1 A:ASP11 4.5 44.5 1.0
NZ A:LYS18 4.6 45.0 1.0
CD A:GLN137 4.6 41.4 1.0
O2B A:ATP402 4.6 41.5 1.0
PA A:ATP402 4.6 43.9 1.0
CA A:GLY13 4.6 45.1 1.0
CA A:GLY156 4.8 41.8 1.0
OD1 A:ASP154 4.8 54.7 1.0
CG A:ASP11 4.9 45.0 1.0
CG2 A:VAL339 5.0 39.8 1.0
O1A A:ATP402 5.0 44.3 1.0

Magnesium binding site 2 out of 6 in 8br1

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Magnesium binding site 2 out of 6 in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:50.1
occ:1.00
 O C:HOH517 2.0 45.5 1.0
O C:HOH547 2.0 44.0 1.0
O1B C:ATP401 2.1 47.8 1.0
O C:HOH514 2.1 46.5 1.0
O3G C:ATP401 2.2 49.4 1.0
O C:HOH545 2.3 60.1 1.0
PB C:ATP401 3.3 48.4 1.0
PG C:ATP401 3.5 49.7 1.0
O3B C:ATP401 3.7 49.5 1.0
O C:HOH501 4.0 58.6 1.0
O2A C:ATP401 4.0 50.2 1.0
O C:HOH502 4.0 57.0 1.0
O C:HOH535 4.0 50.4 1.0
O1G C:ATP401 4.1 50.1 1.0
O3A C:ATP401 4.2 49.4 1.0
OD2 C:ASP11 4.2 54.1 1.0
OE1 C:GLN137 4.2 49.3 1.0
OD1 C:ASP11 4.4 52.8 1.0
OD2 C:ASP154 4.4 56.5 1.0
NZ C:LYS18 4.4 56.2 1.0
O2B C:ATP401 4.5 48.9 1.0
O2G C:ATP401 4.6 50.4 1.0
CA C:GLY13 4.6 54.1 1.0
CD C:GLN137 4.6 49.6 1.0
PA C:ATP401 4.6 50.4 1.0
CG C:ASP11 4.7 53.7 1.0
OD1 C:ASP154 4.8 61.2 1.0
CG2 C:VAL339 4.9 49.0 1.0
O1A C:ATP401 4.9 51.0 1.0
CA C:GLY156 5.0 46.6 1.0

Magnesium binding site 3 out of 6 in 8br1

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Magnesium binding site 3 out of 6 in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1102

b:54.4
occ:1.00
 OD2 B:ASP665 2.0 50.7 1.0
OD1 B:ASP667 2.0 48.9 1.0
O B:HOH1350 2.1 50.2 1.0
NE2 B:HIS753 2.2 46.0 1.0
O1A B:3AT1101 2.4 46.4 1.0
CG B:ASP665 2.9 47.7 1.0
CE1 B:HIS753 3.0 45.6 1.0
CG B:ASP667 3.0 46.9 1.0
OD1 B:ASP665 3.2 48.1 1.0
CD2 B:HIS753 3.4 44.8 1.0
PA B:3AT1101 3.4 46.8 1.0
OD2 B:ASP667 3.4 46.8 1.0
C5' B:3AT1101 3.4 51.4 1.0
O5' B:3AT1101 3.7 48.9 1.0
MG B:MG1103 3.8 51.3 1.0
O2A B:3AT1101 4.0 45.0 1.0
O B:HOH1340 4.0 45.5 1.0
O B:HOH1333 4.1 45.2 1.0
ND1 B:HIS753 4.3 45.5 1.0
O B:LYS528 4.3 46.3 1.0
CB B:ASP665 4.3 44.1 1.0
CB B:ASP667 4.3 42.1 1.0
CG B:HIS753 4.4 44.7 1.0
C4' B:3AT1101 4.6 56.0 1.0
C3' B:3AT1101 4.7 58.0 1.0
O3A B:3AT1101 4.8 47.5 1.0
CA B:ASP667 4.8 42.0 1.0
O2B B:3AT1101 4.8 47.0 1.0
CE B:LYS528 4.9 41.2 1.0

Magnesium binding site 4 out of 6 in 8br1

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Magnesium binding site 4 out of 6 in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1103

b:51.3
occ:1.00
 O1G B:3AT1101 1.9 46.5 1.0
OD2 B:ASP667 2.0 46.8 1.0
OD1 B:ASP665 2.1 48.1 1.0
O2B B:3AT1101 2.2 47.0 1.0
O B:HOH1402 2.3 47.4 1.0
O1A B:3AT1101 2.4 46.4 1.0
CG B:ASP667 3.1 46.9 1.0
PG B:3AT1101 3.2 46.5 1.0
CG B:ASP665 3.2 47.7 1.0
PB B:3AT1101 3.3 47.6 1.0
PA B:3AT1101 3.5 46.8 1.0
O3A B:3AT1101 3.5 47.5 1.0
O3B B:3AT1101 3.5 46.9 1.0
OD1 B:ASP667 3.6 48.9 1.0
OD2 B:ASP665 3.7 50.7 1.0
MG B:MG1102 3.8 54.4 1.0
O B:ASP665 4.0 44.7 1.0
O B:HOH1355 4.0 44.0 1.0
N B:ASP665 4.1 44.1 1.0
O3G B:3AT1101 4.1 46.5 1.0
O B:HOH1329 4.3 50.5 1.0
O2G B:3AT1101 4.3 45.8 1.0
CB B:ASP667 4.4 42.1 1.0
O5' B:3AT1101 4.4 48.9 1.0
CB B:ASP665 4.4 44.1 1.0
C B:ASP665 4.4 44.2 1.0
CE B:LYS528 4.5 41.2 1.0
NH1 B:ARG510 4.5 45.5 1.0
CA B:ASP665 4.6 43.7 1.0
O2A B:3AT1101 4.6 45.0 1.0
O1B B:3AT1101 4.6 49.1 1.0
CB B:ALA664 4.7 45.2 1.0
O B:HOH1373 4.8 45.5 1.0
NZ B:LYS528 4.9 40.2 1.0
O B:HOH1350 4.9 50.2 1.0
N B:ASP667 4.9 42.0 1.0
CD B:LYS528 4.9 41.1 1.0
C B:ALA664 5.0 44.5 1.0

Magnesium binding site 5 out of 6 in 8br1

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Magnesium binding site 5 out of 6 in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1102

b:51.4
occ:1.00
 OD1 D:ASP667 1.9 44.2 1.0
OD2 D:ASP665 2.0 49.1 1.0
O D:HOH1429 2.2 44.8 1.0
NE2 D:HIS753 2.4 40.7 1.0
O1A D:3AT1101 2.5 42.8 1.0
CG D:ASP665 2.9 44.9 1.0
CG D:ASP667 2.9 42.4 1.0
OD1 D:ASP665 3.0 44.0 1.0
CE1 D:HIS753 3.2 40.5 1.0
OD2 D:ASP667 3.3 42.6 1.0
C5' D:3AT1101 3.4 49.1 1.0
CD2 D:HIS753 3.5 39.4 1.0
MG D:MG1103 3.5 41.1 1.0
PA D:3AT1101 3.6 43.4 1.0
O5' D:3AT1101 3.8 45.6 1.0
O D:HOH1363 4.0 37.4 1.0
O D:HOH1396 4.1 41.5 1.0
O2A D:3AT1101 4.2 40.3 1.0
CB D:ASP667 4.2 40.8 1.0
CB D:ASP665 4.3 40.4 1.0
O D:LYS528 4.3 41.8 1.0
ND1 D:HIS753 4.4 40.3 1.0
CG D:HIS753 4.6 39.3 1.0
C4' D:3AT1101 4.7 55.7 1.0
CA D:ASP667 4.7 40.2 1.0
C3' D:3AT1101 4.8 58.5 1.0
O2B D:3AT1101 4.8 42.0 1.0
O3A D:3AT1101 4.9 42.3 1.0
CE D:LYS528 5.0 39.3 1.0

Magnesium binding site 6 out of 6 in 8br1

Go back to Magnesium Binding Sites List in 8br1
Magnesium binding site 6 out of 6 in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1103

b:41.1
occ:1.00
 OD2 D:ASP667 2.0 42.6 1.0
O1G D:3AT1101 2.1 40.7 1.0
OD1 D:ASP665 2.1 44.0 1.0
O2B D:3AT1101 2.2 42.0 1.0
O D:HOH1394 2.2 38.2 1.0
O1A D:3AT1101 2.2 42.8 1.0
CG D:ASP667 3.0 42.4 1.0
CG D:ASP665 3.2 44.9 1.0
PB D:3AT1101 3.3 41.9 1.0
PG D:3AT1101 3.4 41.3 1.0
PA D:3AT1101 3.4 43.4 1.0
OD1 D:ASP667 3.4 44.2 1.0
O3A D:3AT1101 3.5 42.3 1.0
MG D:MG1102 3.5 51.4 1.0
O3B D:3AT1101 3.6 41.9 1.0
OD2 D:ASP665 3.7 49.1 1.0
O D:ASP665 4.0 40.4 1.0
O D:HOH1366 4.1 55.7 1.0
N D:ASP665 4.2 38.7 1.0
O2G D:3AT1101 4.3 40.7 1.0
CB D:ASP667 4.3 40.8 1.0
O D:HOH1389 4.4 40.4 1.0
O5' D:3AT1101 4.4 45.6 1.0
NH1 D:ARG510 4.4 38.6 1.0
CB D:ASP665 4.4 40.4 1.0
O3G D:3AT1101 4.5 41.5 1.0
C D:ASP665 4.5 40.0 1.0
O2A D:3AT1101 4.5 40.3 1.0
CE D:LYS528 4.5 39.3 1.0
O1B D:3AT1101 4.6 42.4 1.0
CA D:ASP665 4.6 38.9 1.0
NZ D:LYS528 4.7 40.0 1.0
CB D:ALA664 4.8 39.6 1.0
O D:HOH1392 4.8 40.3 1.0
O D:HOH1429 4.8 44.8 1.0
N D:ASP667 4.9 40.3 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: Thu Oct 3 19:51:22 2024

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