Atomistry » Magnesium » PDB 7t21-7tgn » 7tdp
Atomistry »
  Magnesium »
    PDB 7t21-7tgn »
      7tdp »

Magnesium in PDB 7tdp: Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom

Enzymatic activity of Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom

All present enzymatic activity of Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom:
6.3.1.2;

Protein crystallography data

The structure of Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom, PDB code: 7tdp was solved by M.A.Schumacher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.70 / 1.98
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 164.009, 164.009, 141.528, 90, 90, 90
R / Rfree (%) 17.1 / 20.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom (pdb code 7tdp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom, PDB code: 7tdp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 7tdp

Go back to Magnesium Binding Sites List in 7tdp
Magnesium binding site 1 out of 9 in the Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:27.8
occ:1.00
 O A:HOH628 1.9 32.5 1.0
OE1 A:GLU194 2.0 29.4 1.0
O2A A:P3S502 2.0 33.6 1.0
OE2 A:GLU187 2.1 33.3 1.0
OE1 A:GLU132 2.2 26.7 1.0
NE A:P3S502 2.7 29.7 1.0
PA A:P3S502 2.8 30.4 1.0
CD A:GLU194 3.0 30.4 1.0
CD A:GLU187 3.2 32.9 1.0
CD A:GLU132 3.2 26.4 1.0
OE2 A:GLU194 3.3 30.4 1.0
MG A:MG505 3.6 28.9 1.0
SD A:P3S502 3.6 31.1 1.0
CG A:GLU132 3.8 25.9 1.0
O1A A:P3S502 3.8 30.4 1.0
CG A:GLU187 3.9 29.3 1.0
O3A A:P3S502 3.9 31.1 1.0
OE1 A:GLU130 3.9 33.6 1.0
CG A:P3S502 4.0 27.7 1.0
OE1 A:GLU187 4.1 27.9 1.0
CE1 A:HIS243 4.3 30.1 1.0
OE2 A:GLU132 4.3 34.9 1.0
O A:HOH706 4.3 29.9 1.0
CG A:GLU194 4.4 26.0 1.0
CE A:P3S502 4.4 28.3 1.0
O A:HOH722 4.5 32.1 1.0
OE A:P3S502 4.6 29.4 1.0
CB A:P3S502 4.6 27.9 1.0
ND1 A:HIS243 4.7 31.5 1.0
CB A:GLU194 4.7 25.6 1.0
CE1 A:HIS185 4.7 26.5 1.0
O A:HOH633 4.8 28.7 1.0
MG A:MG504 4.9 29.2 1.0
O2B A:ADP501 4.9 29.6 1.0
NE2 A:HIS185 5.0 31.3 1.0

Magnesium binding site 2 out of 9 in 7tdp

Go back to Magnesium Binding Sites List in 7tdp
Magnesium binding site 2 out of 9 in the Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:29.2
occ:1.00
 O1A A:P3S502 1.9 30.4 1.0
OE1 A:GLU331 2.1 35.3 1.0
O1B A:ADP501 2.1 29.8 1.0
OE2 A:GLU130 2.3 34.0 1.0
ND1 A:HIS243 2.3 31.5 1.0
OE1 A:GLU130 2.3 33.6 1.0
CD A:GLU130 2.6 31.5 1.0
CE1 A:HIS243 3.1 30.1 1.0
PA A:P3S502 3.2 30.4 1.0
PB A:ADP501 3.3 29.6 1.0
CD A:GLU331 3.3 31.2 1.0
CG A:HIS243 3.4 31.7 1.0
O2B A:ADP501 3.5 29.6 1.0
O2A A:P3S502 3.6 33.6 1.0
CB A:HIS243 3.8 29.1 1.0
O A:HOH628 3.8 32.5 1.0
NH2 A:ARG333 3.8 30.2 1.0
MG A:MG505 3.8 28.9 1.0
NH2 A:ARG319 3.8 32.6 1.0
OE2 A:GLU331 4.0 34.0 1.0
O A:HOH652 4.0 28.4 1.0
O3A A:ADP501 4.1 29.9 1.0
CG A:GLU130 4.1 28.0 1.0
NE A:P3S502 4.2 29.7 1.0
O3A A:P3S502 4.2 31.1 1.0
NE2 A:HIS243 4.3 32.1 1.0
CG A:GLU331 4.3 32.0 1.0
CD2 A:HIS243 4.4 33.5 1.0
O3B A:ADP501 4.5 30.2 1.0
O1A A:ADP501 4.6 29.6 1.0
CB A:GLU130 4.7 30.3 1.0
MG A:MG503 4.9 27.8 1.0
PA A:ADP501 4.9 28.9 1.0
CZ A:ARG333 4.9 30.1 1.0
ND2 A:ASN245 4.9 29.9 1.0

Magnesium binding site 3 out of 9 in 7tdp

Go back to Magnesium Binding Sites List in 7tdp
Magnesium binding site 3 out of 9 in the Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:28.9
occ:1.00
 O2B A:ADP501 2.1 29.6 1.0
O2A A:P3S502 2.1 33.6 1.0
O1A A:ADP501 2.1 29.6 1.0
O A:HOH706 2.1 29.9 1.0
OE2 A:GLU194 2.1 30.4 1.0
OE1 A:GLU130 2.2 33.6 1.0
CD A:GLU194 3.1 30.4 1.0
PB A:ADP501 3.2 29.6 1.0
CD A:GLU130 3.3 31.5 1.0
PA A:ADP501 3.3 28.9 1.0
PA A:P3S502 3.3 30.4 1.0
OE1 A:GLU194 3.5 29.4 1.0
O A:HOH628 3.5 32.5 1.0
MG A:MG503 3.6 27.8 1.0
O3A A:ADP501 3.6 29.9 1.0
O1A A:P3S502 3.7 30.4 1.0
O1B A:ADP501 3.8 29.8 1.0
O A:HOH670 3.8 48.0 1.0
MG A:MG504 3.8 29.2 1.0
O A:HOH633 3.8 28.7 1.0
OD2 A:ASP196 3.9 33.6 1.0
OD1 A:ASP196 3.9 37.2 1.0
O3A A:P3S502 4.0 31.1 1.0
CG A:GLU130 4.0 28.0 1.0
OE2 A:GLU130 4.2 34.0 1.0
CG A:ASP196 4.2 33.9 1.0
O5' A:ADP501 4.3 32.6 1.0
O2A A:ADP501 4.4 37.8 1.0
CG A:GLU194 4.5 26.0 1.0
NE2 A:HIS185 4.5 31.3 1.0
O3B A:ADP501 4.5 30.2 1.0
CB A:GLU130 4.6 30.3 1.0
NE A:P3S502 4.7 29.7 1.0
O A:HOH687 4.7 41.7 1.0
OE2 A:GLU187 4.9 33.3 1.0

Magnesium binding site 4 out of 9 in 7tdp

Go back to Magnesium Binding Sites List in 7tdp
Magnesium binding site 4 out of 9 in the Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:31.0
occ:1.00
 O C:HOH688 2.0 29.7 1.0
OE2 C:GLU130 2.1 35.2 1.0
O2A C:ADP501 2.1 32.8 1.0
O3B C:ADP501 2.1 28.7 1.0
O3A C:P3S502 2.1 37.5 1.0
OE2 C:GLU194 2.1 27.7 1.0
CD C:GLU194 3.1 28.1 1.0
CD C:GLU130 3.1 31.6 1.0
PB C:ADP501 3.2 33.4 1.0
PA C:ADP501 3.3 33.0 1.0
PA C:P3S502 3.3 34.1 1.0
OE1 C:GLU194 3.5 31.7 1.0
O3A C:ADP501 3.6 32.5 1.0
MG C:MG505 3.6 52.2 1.0
O1A C:P3S502 3.7 32.6 1.0
O1B C:ADP501 3.7 30.4 1.0
MG C:MG504 3.7 29.4 1.0
CG C:GLU130 3.8 28.3 1.0
O C:HOH614 3.8 35.1 1.0
OD2 C:ASP196 3.8 37.6 1.0
O2A C:P3S502 3.9 32.1 1.0
OD1 C:ASP196 4.0 38.8 1.0
O C:HOH667 4.1 46.6 1.0
OE1 C:GLU130 4.1 34.9 1.0
CG C:ASP196 4.2 38.3 1.0
O5' C:ADP501 4.2 30.3 1.0
O1A C:ADP501 4.4 34.4 1.0
CG C:GLU194 4.5 25.6 1.0
NE2 C:HIS185 4.5 30.7 1.0
O2B C:ADP501 4.5 34.0 1.0
CB C:GLU130 4.6 33.2 1.0
NE C:P3S502 4.7 33.3 1.0
O C:HOH647 4.9 33.4 1.0
OE1 C:GLU187 4.9 33.3 1.0

Magnesium binding site 5 out of 9 in 7tdp

Go back to Magnesium Binding Sites List in 7tdp
Magnesium binding site 5 out of 9 in the Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg504

b:29.4
occ:1.00
 O1B C:ADP501 2.0 30.4 1.0
OE2 C:GLU331 2.0 31.9 1.0
O1A C:P3S502 2.0 32.6 1.0
OE2 C:GLU130 2.2 35.2 1.0
OE1 C:GLU130 2.3 34.9 1.0
ND1 C:HIS243 2.5 30.3 1.0
CD C:GLU130 2.6 31.6 1.0
PB C:ADP501 3.2 33.4 1.0
CD C:GLU331 3.3 36.9 1.0
PA C:P3S502 3.3 34.1 1.0
CE1 C:HIS243 3.3 29.8 1.0
O3B C:ADP501 3.5 28.7 1.0
CG C:HIS243 3.5 30.9 1.0
O3A C:P3S502 3.6 37.5 1.0
MG C:MG503 3.7 31.0 1.0
NH2 C:ARG319 3.8 39.9 1.0
CB C:HIS243 3.9 29.8 1.0
NH2 C:ARG333 3.9 30.5 1.0
O C:HOH620 4.0 30.8 1.0
OE1 C:GLU331 4.0 31.8 1.0
O3A C:ADP501 4.1 32.5 1.0
CG C:GLU130 4.1 28.3 1.0
NE C:P3S502 4.2 33.3 1.0
O2A C:P3S502 4.3 32.1 1.0
CG C:GLU331 4.3 31.8 1.0
O2B C:ADP501 4.4 34.0 1.0
NE2 C:HIS243 4.5 29.6 1.0
O2A C:ADP501 4.5 32.8 1.0
CD2 C:HIS243 4.6 29.2 1.0
CB C:GLU130 4.6 33.2 1.0
ND2 C:ASN245 4.8 30.7 1.0
PA C:ADP501 4.8 33.0 1.0
O5' C:ADP501 4.9 30.3 1.0

Magnesium binding site 6 out of 9 in 7tdp

Go back to Magnesium Binding Sites List in 7tdp
Magnesium binding site 6 out of 9 in the Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg505

b:52.2
occ:1.00
 OE1 C:GLU194 2.0 31.7 1.0
OE1 C:GLU187 2.0 33.3 1.0
OE2 C:GLU132 2.0 33.2 1.0
O3A C:P3S502 2.1 37.5 1.0
NE C:P3S502 2.7 33.3 1.0
PA C:P3S502 2.9 34.1 1.0
CD C:GLU187 2.9 26.6 1.0
CD C:GLU194 3.0 28.1 1.0
CD C:GLU132 3.2 34.8 1.0
OE2 C:GLU194 3.4 27.7 1.0
SD C:P3S502 3.5 28.2 1.0
CG C:GLU187 3.6 25.0 1.0
MG C:MG503 3.6 31.0 1.0
CG C:GLU132 3.8 33.0 1.0
OE2 C:GLU187 3.8 33.1 1.0
CG C:P3S502 3.8 34.9 1.0
O2A C:P3S502 3.8 32.1 1.0
O1A C:P3S502 4.0 32.6 1.0
O C:HOH688 4.2 29.7 1.0
OE2 C:GLU130 4.2 35.2 1.0
OE1 C:GLU132 4.2 35.2 1.0
CG C:GLU194 4.4 25.6 1.0
CE C:P3S502 4.4 32.7 1.0
CE1 C:HIS185 4.5 28.9 1.0
O C:HOH614 4.6 35.1 1.0
CE1 C:HIS243 4.6 29.8 1.0
OE C:P3S502 4.6 31.9 1.0
CB C:GLU194 4.6 24.9 1.0
CB C:P3S502 4.6 29.7 1.0
O C:HOH656 4.7 25.9 1.0
NE2 C:HIS185 4.8 30.7 1.0
O3B C:ADP501 5.0 28.7 1.0

Magnesium binding site 7 out of 9 in 7tdp

Go back to Magnesium Binding Sites List in 7tdp
Magnesium binding site 7 out of 9 in the Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:28.9
occ:1.00
 O2A B:P3S502 2.0 31.9 1.0
O3B B:ADP501 2.0 30.9 1.0
OE2 B:GLU331 2.1 35.4 1.0
OE1 B:GLU130 2.3 28.7 1.0
ND1 B:HIS243 2.4 29.7 1.0
OE2 B:GLU130 2.4 32.5 1.0
CD B:GLU130 2.7 32.5 1.0
CE1 B:HIS243 3.2 28.3 1.0
PA B:P3S502 3.2 29.4 1.0
PB B:ADP501 3.3 31.9 1.0
CD B:GLU331 3.3 33.6 1.0
CG B:HIS243 3.5 28.7 1.0
O3A B:P3S502 3.5 33.3 1.0
O2B B:ADP501 3.6 28.3 1.0
NH2 B:ARG333 3.8 30.0 1.0
MG B:MG504 3.8 30.3 1.0
O B:HOH764 3.9 25.6 1.0
CB B:HIS243 3.9 29.0 1.0
NH2 B:ARG319 3.9 33.3 1.0
OE1 B:GLU331 4.0 34.7 1.0
O B:HOH622 4.0 31.4 1.0
O3A B:ADP501 4.1 29.0 1.0
NE B:P3S502 4.2 27.7 1.0
CG B:GLU130 4.2 27.6 1.0
O1A B:P3S502 4.2 32.1 1.0
NE2 B:HIS243 4.4 30.6 1.0
CG B:GLU331 4.4 34.2 1.0
O1B B:ADP501 4.4 32.4 1.0
CD2 B:HIS243 4.5 30.0 1.0
O2A B:ADP501 4.6 32.2 1.0
CB B:GLU130 4.7 27.1 1.0
ND2 B:ASN245 4.9 29.7 1.0
CZ B:ARG333 4.9 31.2 1.0
PA B:ADP501 4.9 33.6 1.0
MG B:MG505 5.0 29.2 1.0

Magnesium binding site 8 out of 9 in 7tdp

Go back to Magnesium Binding Sites List in 7tdp
Magnesium binding site 8 out of 9 in the Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:30.3
occ:1.00
 O2B B:ADP501 2.1 28.3 1.0
O3A B:P3S502 2.1 33.3 1.0
O2A B:ADP501 2.1 32.2 1.0
O B:HOH713 2.1 32.5 1.0
OE2 B:GLU194 2.2 27.4 1.0
OE1 B:GLU130 2.3 28.7 1.0
CD B:GLU194 3.1 30.0 1.0
PB B:ADP501 3.2 31.9 1.0
PA B:P3S502 3.3 29.4 1.0
PA B:ADP501 3.3 33.6 1.0
CD B:GLU130 3.3 32.5 1.0
OE1 B:GLU194 3.5 27.7 1.0
O3A B:ADP501 3.6 29.0 1.0
O3B B:ADP501 3.7 30.9 1.0
O2A B:P3S502 3.7 31.9 1.0
MG B:MG505 3.7 29.2 1.0
O B:HOH630 3.7 30.2 1.0
MG B:MG503 3.8 28.9 1.0
OD2 B:ASP196 3.8 32.3 1.0
O B:HOH677 3.8 40.4 1.0
O B:HOH764 3.9 25.6 1.0
OD1 B:ASP196 3.9 37.7 1.0
O1A B:P3S502 3.9 32.1 1.0
CG B:GLU130 4.0 27.6 1.0
CG B:ASP196 4.2 35.2 1.0
OE2 B:GLU130 4.2 32.5 1.0
O5' B:ADP501 4.3 29.3 1.0
O1A B:ADP501 4.4 33.7 1.0
NE2 B:HIS185 4.5 25.6 1.0
CG B:GLU194 4.5 29.5 1.0
O1B B:ADP501 4.5 32.4 1.0
CB B:GLU130 4.5 27.1 1.0
NE B:P3S502 4.7 27.7 1.0
O B:HOH661 4.9 37.7 1.0
OE2 B:GLU187 5.0 30.2 1.0

Magnesium binding site 9 out of 9 in 7tdp

Go back to Magnesium Binding Sites List in 7tdp
Magnesium binding site 9 out of 9 in the Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Paenibacillus Polymyxa Gs Bound to Met-Sox-P-Adp (Transition State Complex) to 1.98 Angstom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg505

b:29.2
occ:1.00
 OE2 B:GLU187 2.0 30.2 1.0
OE1 B:GLU194 2.1 27.7 1.0
OE2 B:GLU132 2.1 29.6 1.0
O3A B:P3S502 2.1 33.3 1.0
O B:HOH764 2.4 25.6 1.0
NE B:P3S502 2.6 27.7 1.0
PA B:P3S502 2.9 29.4 1.0
CD B:GLU187 3.0 32.0 1.0
CD B:GLU194 3.1 30.0 1.0
CD B:GLU132 3.2 32.9 1.0
SD B:P3S502 3.5 29.9 1.0
OE2 B:GLU194 3.5 27.4 1.0
MG B:MG504 3.7 30.3 1.0
CG B:GLU187 3.7 25.0 1.0
CG B:GLU132 3.8 31.2 1.0
CG B:P3S502 3.8 27.1 1.0
O1A B:P3S502 3.9 32.1 1.0
O2A B:P3S502 4.0 31.9 1.0
OE1 B:GLU187 4.0 28.4 1.0
OE1 B:GLU130 4.2 28.7 1.0
OE1 B:GLU132 4.2 32.9 1.0
CE1 B:HIS243 4.3 28.3 1.0
CE B:P3S502 4.4 33.0 1.0
CB B:P3S502 4.5 30.1 1.0
CG B:GLU194 4.5 29.5 1.0
O B:HOH713 4.5 32.5 1.0
O B:HOH665 4.5 28.3 1.0
OE B:P3S502 4.5 28.4 1.0
CB B:GLU194 4.7 24.7 1.0
CE1 B:HIS185 4.7 32.2 1.0
O B:HOH630 4.8 30.2 1.0
ND1 B:HIS243 4.8 29.7 1.0
MG B:MG503 5.0 28.9 1.0

Reference:

B.A.Travis, J.V.Peck, R.Salinas, B.Dopkins, N.Lent, V.D.Nguyen, M.J.Borgnia, R.G.Brennan, M.A.Schumacher. Molecular Dissection of the Glutamine Synthetase-Glnr Nitrogen Regulatory Circuitry in Gram-Positive Bacteria. Nat Commun V. 13 3793 2022.
ISSN: ESSN 2041-1723
PubMed: 35778410
DOI: 10.1038/S41467-022-31573-0
Page generated: Thu Oct 3 09:06:26 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy