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Magnesium in PDB 4dkw: Structure of P22 Large Terminase Nuclease Domain

Protein crystallography data

The structure of Structure of P22 Large Terminase Nuclease Domain, PDB code: 4dkw was solved by A.Roy, G.Cingolani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.97 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.921, 139.795, 61.005, 90.00, 95.10, 90.00
R / Rfree (%) 16.6 / 19.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of P22 Large Terminase Nuclease Domain (pdb code 4dkw). 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 P22 Large Terminase Nuclease Domain, PDB code: 4dkw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4dkw

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Magnesium binding site 1 out of 8 in the Structure of P22 Large Terminase Nuclease Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of P22 Large Terminase Nuclease Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:36.8
occ:1.00
 O A:HOH887 2.0 30.0 1.0
OD2 A:ASP321 2.1 33.7 1.0
O A:HOH760 2.2 40.3 1.0
OD1 A:ASP459 2.3 32.1 1.0
O A:HOH653 2.6 25.1 1.0
O A:HOH601 2.7 39.5 1.0
CG A:ASP321 3.1 30.1 1.0
OD1 A:ASP321 3.4 36.9 1.0
CG A:ASP459 3.5 31.4 1.0
O A:HOH710 3.7 34.8 1.0
O A:PHE322 3.9 36.1 1.0
O A:HOH762 4.0 41.3 1.0
CB A:ASP459 4.0 27.5 1.0
O A:HOH613 4.1 48.0 1.0
CA A:ASP459 4.2 23.9 1.0
O A:PRO327 4.3 34.6 1.0
O A:HOH786 4.4 45.7 1.0
OD2 A:ASP462 4.4 26.4 1.0
CB A:ASP321 4.4 28.4 1.0
O A:HOH801 4.5 52.7 1.0
OD2 A:ASP459 4.5 33.0 1.0
O A:HOH669 4.6 32.3 1.0
OD1 A:ASP458 4.6 22.3 1.0
N A:ASP459 4.7 27.7 1.0
O A:HOH680 4.9 41.1 1.0
O A:HOH614 5.0 24.1 1.0
CB A:HIS326 5.0 51.1 1.0

Magnesium binding site 2 out of 8 in 4dkw

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Magnesium binding site 2 out of 8 in the Structure of P22 Large Terminase Nuclease Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of P22 Large Terminase Nuclease Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:33.3
occ:1.00
 O A:HOH731 2.9 56.3 1.0
O A:HOH744 4.1 37.4 1.0
N A:TRP324 4.1 50.8 1.0
ND1 A:HIS326 4.2 79.0 1.0
N A:ASN325 4.3 61.4 1.0
O A:HOH762 4.6 41.3 1.0
NE2 A:GLN379 4.7 0.9 1.0
CB A:ASN325 4.7 58.9 1.0
ND2 A:ASN325 4.7 66.8 1.0
CB A:TRP324 4.7 57.1 1.0
N A:HIS326 4.8 56.4 1.0
CA A:TRP324 4.8 57.4 1.0
CA A:GLY323 4.9 37.5 1.0
CE1 A:HIS326 4.9 82.0 1.0

Magnesium binding site 3 out of 8 in 4dkw

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Magnesium binding site 3 out of 8 in the Structure of P22 Large Terminase Nuclease Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of P22 Large Terminase Nuclease Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:28.5
occ:1.00
 OD1 B:ASP459 1.9 32.2 1.0
O B:HOH867 1.9 30.0 1.0
O B:HOH755 2.0 21.4 1.0
O B:HOH708 2.0 29.2 1.0
O B:HOH709 2.3 24.5 1.0
OD2 B:ASP321 2.3 35.1 1.0
CG B:ASP459 3.0 31.6 1.0
CG B:ASP321 3.5 31.8 1.0
CB B:ASP459 3.7 26.3 1.0
O B:HOH646 3.9 28.0 1.0
CA B:ASP459 3.9 26.3 1.0
OD1 B:ASP321 4.0 37.8 1.0
O B:PRO327 4.0 33.2 1.0
OD2 B:ASP459 4.1 30.4 1.0
O B:HOH798 4.1 34.6 1.0
O B:HOH710 4.2 34.0 1.0
OD1 B:ASP458 4.3 25.7 1.0
N B:ASP459 4.3 27.3 1.0
O B:PHE322 4.3 37.2 1.0
O B:HOH612 4.6 27.4 1.0
OD2 B:ASP462 4.6 26.0 1.0
CB B:HIS326 4.7 50.8 1.0
CB B:ASP321 4.7 26.4 1.0
C B:ASP458 4.9 27.4 1.0

Magnesium binding site 4 out of 8 in 4dkw

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Magnesium binding site 4 out of 8 in the Structure of P22 Large Terminase Nuclease Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of P22 Large Terminase Nuclease Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:32.0
occ:1.00
 O B:HOH760 2.6 59.4 1.0
O B:HOH797 2.6 28.1 1.0
O B:HOH716 3.6 47.9 1.0
O B:HOH707 3.8 29.6 1.0
ND1 B:HIS326 4.0 79.6 1.0
N B:TRP324 4.1 50.9 1.0
NE2 B:GLN379 4.4 0.5 1.0
N B:ASN325 4.5 61.8 1.0
CA B:GLY323 4.6 34.3 1.0
N B:HIS326 4.7 54.7 1.0
CE1 B:HIS326 4.8 81.6 1.0
C B:GLY323 4.9 44.7 1.0
CG B:HIS326 4.9 62.0 1.0
CA B:TRP324 4.9 56.9 1.0
CB B:ASN325 5.0 59.5 1.0
CB B:TRP324 5.0 56.8 1.0

Magnesium binding site 5 out of 8 in 4dkw

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Magnesium binding site 5 out of 8 in the Structure of P22 Large Terminase Nuclease Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of P22 Large Terminase Nuclease Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:22.8
occ:1.00
 O C:HOH895 1.8 30.0 1.0
O C:HOH894 2.0 30.0 1.0
OD2 C:ASP321 2.1 34.1 1.0
OD1 C:ASP459 2.2 34.3 1.0
O C:HOH770 2.6 32.6 1.0
O C:HOH601 2.7 26.9 1.0
CG C:ASP321 3.1 30.4 1.0
CG C:ASP459 3.3 30.6 1.0
O C:HOH717 3.4 53.6 1.0
OD1 C:ASP321 3.6 33.9 1.0
CB C:ASP459 3.9 27.0 1.0
CA C:ASP459 4.0 23.8 1.0
O C:HOH724 4.1 42.7 1.0
O C:PHE322 4.1 37.9 1.0
O C:HOH896 4.2 30.0 1.0
OD2 C:ASP462 4.3 24.3 1.0
O C:PRO327 4.3 31.9 1.0
OD2 C:ASP459 4.4 31.2 1.0
OD1 C:ASP458 4.4 25.9 1.0
CB C:ASP321 4.4 25.4 1.0
N C:ASP459 4.5 25.7 1.0
O C:HOH810 4.6 39.0 1.0
O C:HOH725 4.6 31.5 1.0
O C:HOH625 4.7 32.7 1.0
C C:ASP458 5.0 28.7 1.0

Magnesium binding site 6 out of 8 in 4dkw

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Magnesium binding site 6 out of 8 in the Structure of P22 Large Terminase Nuclease Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of P22 Large Terminase Nuclease Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:24.6
occ:1.00
 N C:ASN325 3.4 61.8 1.0
ND1 C:HIS326 3.5 79.2 1.0
N C:TRP324 3.7 52.1 1.0
N C:HIS326 3.8 55.4 1.0
CB C:ASN325 3.8 59.7 1.0
CA C:ASN325 4.1 58.4 1.0
ND2 C:ASN325 4.2 66.0 1.0
C C:TRP324 4.3 57.6 1.0
CG C:ASN325 4.3 62.0 1.0
CA C:TRP324 4.3 57.8 1.0
CE1 C:HIS326 4.4 81.7 1.0
CB C:TRP324 4.5 57.2 1.0
C C:ASN325 4.5 55.8 1.0
CG C:HIS326 4.5 62.6 1.0
CB C:HIS326 4.6 50.4 1.0
O C:HOH724 4.6 42.7 1.0
C C:GLY323 4.7 46.5 1.0
CA C:GLY323 4.7 36.4 1.0
CA C:HIS326 4.8 48.3 1.0
O C:HOH725 4.9 31.5 1.0

Magnesium binding site 7 out of 8 in 4dkw

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Magnesium binding site 7 out of 8 in the Structure of P22 Large Terminase Nuclease Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of P22 Large Terminase Nuclease Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:42.8
occ:1.00
 OD1 D:ASP459 2.0 30.7 1.0
O D:HOH862 2.0 30.0 1.0
OD2 D:ASP321 2.1 36.2 1.0
O D:HOH711 2.2 37.0 1.0
O D:HOH769 2.3 17.7 1.0
O D:HOH726 2.4 18.3 1.0
CG D:ASP459 3.1 31.3 1.0
CG D:ASP321 3.2 32.4 1.0
OD1 D:ASP321 3.6 37.4 1.0
CB D:ASP459 3.7 28.4 1.0
O D:PHE322 3.9 38.5 1.0
O D:PRO327 3.9 33.2 1.0
CA D:ASP459 4.0 24.6 1.0
OD2 D:ASP459 4.2 34.1 1.0
O D:HOH846 4.4 36.1 1.0
O D:HOH723 4.4 27.1 1.0
O D:HOH692 4.4 31.7 1.0
CB D:ASP321 4.4 26.6 1.0
N D:ASP459 4.6 25.1 1.0
OD2 D:ASP462 4.7 25.9 1.0
OD1 D:ASP458 4.7 25.0 1.0
CB D:HIS326 4.7 51.0 1.0
O D:HOH609 4.9 20.4 1.0

Magnesium binding site 8 out of 8 in 4dkw

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Magnesium binding site 8 out of 8 in the Structure of P22 Large Terminase Nuclease Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of P22 Large Terminase Nuclease Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:29.8
occ:1.00
 N D:ASN325 3.4 60.2 1.0
ND1 D:HIS326 3.6 79.6 1.0
O D:HOH842 3.6 48.3 1.0
N D:TRP324 3.7 51.7 1.0
CB D:ASN325 3.8 59.5 1.0
N D:HIS326 3.8 56.1 1.0
CA D:ASN325 4.0 57.5 1.0
O D:HOH859 4.1 55.9 1.0
ND2 D:ASN325 4.1 65.3 1.0
C D:TRP324 4.3 58.3 1.0
CG D:ASN325 4.3 63.9 1.0
CA D:TRP324 4.3 57.3 1.0
CB D:TRP324 4.4 56.9 1.0
C D:ASN325 4.5 56.5 1.0
CE1 D:HIS326 4.5 82.3 1.0
CG D:HIS326 4.6 61.9 1.0
CB D:HIS326 4.6 51.0 1.0
C D:GLY323 4.7 45.9 1.0
CA D:GLY323 4.7 39.0 1.0
CA D:HIS326 4.8 50.1 1.0

Reference:

A.Roy, G.Cingolani. Structure of P22 Headful Packaging Nuclease. J.Biol.Chem. V. 287 28196 2012.
ISSN: ISSN 0021-9258
PubMed: 22715098
DOI: 10.1074/JBC.M112.349894
Page generated: Mon Dec 14 12:30:53 2020

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