Magnesium in PDB 7drp: Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp

Protein crystallography data

The structure of Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp, PDB code: 7drp was solved by I.Song, J.Yu, W.Song, S.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.19 / 2.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.587, 91.656, 98.198, 90, 101.31, 90
R / Rfree (%) 20.7 / 21

Other elements in 7drp:

The structure of Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp (pdb code 7drp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp, PDB code: 7drp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7drp

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Magnesium binding site 1 out of 8 in the Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:48.3
occ:1.00
OD2 A:ASP269 2.1 57.4 1.0
O2B A:ADP401 2.1 61.3 1.0
O1A A:ADP401 2.3 57.9 1.0
OE2 A:GLU282 2.5 59.8 1.0
CG A:ASP269 3.1 58.4 1.0
PB A:ADP401 3.4 64.0 1.0
PA A:ADP401 3.5 56.6 1.0
O3A A:ADP401 3.6 59.0 1.0
CD A:GLU282 3.7 60.6 1.0
C5' A:ADP401 3.9 59.0 1.0
OD1 A:ASP269 3.9 57.7 1.0
CB A:ASP269 4.0 54.8 1.0
O1B A:ADP401 4.1 62.5 1.0
O5' A:ADP401 4.2 57.5 1.0
CG A:GLU282 4.2 59.5 1.0
ND2 A:ASN284 4.4 60.2 1.0
NH1 A:ARG213 4.5 60.5 1.0
O3B A:ADP401 4.6 61.5 1.0
OD1 A:ASN284 4.6 61.4 1.0
OE1 A:GLU282 4.7 60.7 1.0
MG A:MG403 4.7 67.3 1.0
O2A A:ADP401 4.8 57.8 1.0
CG A:ASN284 4.9 59.9 1.0

Magnesium binding site 2 out of 8 in 7drp

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Magnesium binding site 2 out of 8 in the Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:67.3
occ:1.00
OD1 A:ASN284 2.6 61.4 1.0
OE1 A:GLU282 2.6 60.7 1.0
OE2 A:GLU282 2.8 59.8 1.0
O1B A:ADP401 2.9 62.5 1.0
CD A:GLU282 3.0 60.6 1.0
CG A:ASN284 3.8 59.9 1.0
PB A:ADP401 4.1 64.0 1.0
O2B A:ADP401 4.2 61.3 1.0
NZ A:LYS133 4.3 64.8 1.0
OXT E:GLU25 4.4 75.5 1.0
CG A:GLU282 4.4 59.5 1.0
CB E:GLU25 4.5 71.2 1.0
C E:GLU25 4.5 76.0 1.0
ND2 A:ASN284 4.5 60.2 1.0
O E:GLU25 4.6 75.9 1.0
CE A:LYS133 4.6 61.4 1.0
MG A:MG402 4.7 48.3 1.0
O3A A:ADP401 4.8 59.0 1.0
CB A:ASN284 4.8 58.3 1.0

Magnesium binding site 3 out of 8 in 7drp

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Magnesium binding site 3 out of 8 in the Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:68.9
occ:1.00
O3B B:ADP401 1.9 78.6 1.0
OD2 B:ASP269 2.0 70.5 1.0
O2A B:ADP401 2.4 74.3 1.0
OE2 B:GLU282 2.6 83.3 1.0
PB B:ADP401 3.2 77.3 1.0
CG B:ASP269 3.2 73.3 1.0
PA B:ADP401 3.5 73.8 1.0
O3A B:ADP401 3.6 75.5 1.0
CD B:GLU282 3.7 79.8 1.0
O2B B:ADP401 3.9 79.5 1.0
C5' B:ADP401 4.0 72.3 1.0
OD1 B:ASP269 4.1 72.0 1.0
CB B:ASP269 4.1 74.8 1.0
CG B:GLU282 4.2 76.7 1.0
MG B:MG403 4.3 69.1 1.0
O5' B:ADP401 4.3 73.9 1.0
O1B B:ADP401 4.4 77.0 1.0
ND2 B:ASN284 4.6 74.9 1.0
OE1 B:GLU282 4.7 80.5 1.0
O1A B:ADP401 4.7 74.7 1.0
NH2 B:ARG213 4.8 89.3 1.0
OD1 B:ASN284 5.0 74.1 1.0

Magnesium binding site 4 out of 8 in 7drp

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Magnesium binding site 4 out of 8 in the Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:69.1
occ:1.00
OE1 B:GLU282 2.3 80.5 1.0
OE2 B:GLU282 2.4 83.3 1.0
O2B B:ADP401 2.5 79.5 1.0
OD1 B:ASN284 2.6 74.1 1.0
CD B:GLU282 2.7 79.8 1.0
PB B:ADP401 3.7 77.3 1.0
CG B:ASN284 3.8 73.1 1.0
O3B B:ADP401 3.8 78.6 1.0
NZ B:LYS133 4.0 68.8 1.0
CG B:GLU282 4.2 76.7 1.0
MG B:MG402 4.3 68.9 1.0
ND2 B:ASN284 4.4 74.9 1.0
O3A B:ADP401 4.4 75.5 1.0
CE B:LYS133 4.4 66.8 1.0
O1B B:ADP401 4.9 77.0 1.0
CB B:GLU282 5.0 72.0 1.0

Magnesium binding site 5 out of 8 in 7drp

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Magnesium binding site 5 out of 8 in the Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:50.7
occ:1.00
O3B C:ADP401 2.1 56.4 1.0
OD2 C:ASP269 2.1 54.4 1.0
O2A C:ADP401 2.5 59.5 1.0
OE1 C:GLU282 2.6 58.6 1.0
CG C:ASP269 3.2 53.5 1.0
PB C:ADP401 3.5 58.7 1.0
PA C:ADP401 3.7 56.6 1.0
CD C:GLU282 3.8 59.5 1.0
O3A C:ADP401 3.8 58.1 1.0
C5' C:ADP401 4.0 55.1 1.0
CB C:ASP269 4.1 52.4 1.0
OD1 C:ASP269 4.1 54.4 1.0
MG C:MG403 4.2 62.1 1.0
ND2 C:ASN284 4.3 52.8 1.0
OE2 C:GLU282 4.3 58.8 1.0
O1B C:ADP401 4.3 56.6 1.0
OD1 C:ASN284 4.3 57.2 1.0
OE1 F:GLU25 4.4 56.5 1.0
O5' C:ADP401 4.4 55.2 1.0
O2B C:ADP401 4.5 65.0 1.0
NH2 C:ARG213 4.5 56.0 1.0
CG C:ASN284 4.8 54.2 1.0
CG C:GLU282 4.9 60.1 1.0
O1A C:ADP401 4.9 57.5 1.0
O3' C:ADP401 5.0 60.5 1.0

Magnesium binding site 6 out of 8 in 7drp

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Magnesium binding site 6 out of 8 in the Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:62.1
occ:1.00
OE2 C:GLU282 2.0 58.8 1.0
O1B C:ADP401 2.4 56.6 1.0
OD1 C:ASN284 2.8 57.2 1.0
CD C:GLU282 3.0 59.5 1.0
O3B C:ADP401 3.2 56.4 1.0
OE1 C:GLU282 3.2 58.6 1.0
PB C:ADP401 3.3 58.7 1.0
CG C:ASN284 4.0 54.2 1.0
NZ C:LYS133 4.2 48.3 1.0
MG C:MG402 4.2 50.7 1.0
CG C:GLU282 4.3 60.1 1.0
O3A C:ADP401 4.3 58.1 1.0
O2B C:ADP401 4.5 65.0 1.0
CB F:GLU25 4.5 59.2 1.0
ND2 C:ASN284 4.7 52.8 1.0
CE C:LYS133 4.7 47.1 1.0
OXT F:GLU25 4.8 71.4 1.0
OE1 F:GLU25 4.9 56.5 1.0
C F:GLU25 4.9 66.9 1.0

Magnesium binding site 7 out of 8 in 7drp

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Magnesium binding site 7 out of 8 in the Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:72.3
occ:1.00
OD2 D:ASP269 2.0 74.4 1.0
O1B D:ADP401 2.1 78.2 1.0
O1A D:ADP401 2.3 78.2 1.0
OE2 D:GLU282 2.3 76.3 1.0
CG D:ASP269 2.9 74.6 1.0
PB D:ADP401 3.3 77.3 1.0
CD D:GLU282 3.4 74.8 1.0
PA D:ADP401 3.4 77.5 1.0
O3A D:ADP401 3.5 76.8 1.0
OD1 D:ASP269 3.7 74.9 1.0
CB D:ASP269 3.8 75.0 1.0
CG D:GLU282 3.8 73.5 1.0
MG D:MG403 3.8 66.1 1.0
OD1 D:ASN284 3.9 70.2 1.0
O3B D:ADP401 3.9 76.2 1.0
C5' D:ADP401 3.9 75.7 1.0
O5' D:ADP401 4.2 76.8 1.0
OE1 D:GLU282 4.4 75.2 1.0
O2B D:ADP401 4.5 77.7 1.0
O2A D:ADP401 4.7 80.1 1.0
CG D:ASN284 4.7 68.3 1.0
ND2 D:ASN284 4.7 68.6 1.0
NH1 D:ARG213 4.7 76.2 1.0

Magnesium binding site 8 out of 8 in 7drp

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Magnesium binding site 8 out of 8 in the Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Atp-Grasp Ligase Psnb Complexed with Phosphomimetic Variant of Minimal Precursor, Mg, and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:66.1
occ:1.00
OE2 D:GLU282 2.0 76.3 1.0
ND2 D:ASN284 2.1 68.6 1.0
OE1 D:GLU282 2.4 75.2 1.0
CD D:GLU282 2.5 74.8 1.0
O3B D:ADP401 2.7 76.2 1.0
CG D:ASN284 3.1 68.3 1.0
OD1 D:ASN284 3.4 70.2 1.0
PB D:ADP401 3.8 77.3 1.0
O1B D:ADP401 3.8 78.2 1.0
MG D:MG402 3.8 72.3 1.0
CG D:GLU282 3.9 73.5 1.0
NZ D:LYS133 4.1 73.2 1.0
O3A D:ADP401 4.3 76.8 1.0
CB D:ASN284 4.5 66.8 1.0
CE D:LYS133 4.5 71.7 1.0
OD2 D:ASP269 4.7 74.4 1.0
CB D:GLU282 4.8 70.6 1.0
CA D:ASN284 4.9 65.2 1.0

Reference:

I.Song, Y.Kim, J.Yu, S.Go, H.Lee, W.Song, S.Kim. Molecular Mechanism Underlying Substrate Recognition of the Peptide Macrocyclase Psnb To Be Published.
Page generated: Fri Sep 24 15:13:31 2021

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