Atomistry » Magnesium » PDB 8beg-8bsh » 8br1
Atomistry »
  Magnesium »
    PDB 8beg-8bsh »
      8br1 »

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

Go back to Magnesium Binding Sites List in 8br1
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

Go back to Magnesium Binding Sites List in 8br1
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

Go back to Magnesium Binding Sites List in 8br1
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

Go back to Magnesium Binding Sites List in 8br1
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

Go back to Magnesium Binding Sites List in 8br1
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy