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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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