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Potassium in PDB 1n7b: Rip-Radiation-Damage Induced Phasing

Protein crystallography data

The structure of Rip-Radiation-Damage Induced Phasing, PDB code: 1n7b was solved by R.B.G.Ravelli, H.-K.S.Leiros, B.Pan, M.Caffrey, S.Mcsweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 31.247, 51.154, 70.834, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 19.9

Other elements in 1n7b:

The structure of Rip-Radiation-Damage Induced Phasing also contains other interesting chemical elements:

Bromine (Br) 8 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Rip-Radiation-Damage Induced Phasing (pdb code 1n7b). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 9 binding sites of Potassium where determined in the Rip-Radiation-Damage Induced Phasing, PDB code: 1n7b:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Potassium binding site 1 out of 9 in 1n7b

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Potassium binding site 1 out of 9 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Rip-Radiation-Damage Induced Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K103

b:4.0
occ:0.80
 O4 H:U6 2.7 8.1 1.0
O4 D:U6 2.7 8.6 1.0
O4 C:U6 2.8 6.3 1.0
O4 A:U6 2.8 5.2 1.0
O6 H:G5 2.8 4.8 1.0
O6 A:G5 2.8 4.1 1.0
O6 D:G5 2.9 4.4 1.0
O6 C:G5 2.9 4.6 1.0
K A:K104 3.5 5.1 0.8
C6 D:G5 3.6 5.2 1.0
C6 H:G5 3.6 5.5 1.0
C6 A:G5 3.7 3.4 1.0
C4 D:U6 3.7 9.8 1.0
C4 H:U6 3.7 8.7 1.0
C6 C:G5 3.7 4.8 1.0
C4 A:U6 3.7 5.8 1.0
C4 C:U6 3.7 5.5 1.0
N1 H:G5 3.9 5.8 1.0
N3 A:U6 3.9 6.3 1.0
N3 D:U6 3.9 10.2 1.0
N1 A:G5 3.9 3.4 1.0
N3 H:U6 3.9 8.0 1.0
N1 C:G5 3.9 4.8 1.0
N3 C:U6 3.9 5.7 1.0
N1 D:G5 4.0 4.8 1.0
C5 D:G5 4.8 5.5 1.0
C5 A:G5 4.8 3.6 1.0
C5 H:G5 4.8 6.0 1.0
C5 C:G5 4.8 4.9 1.0
C5 D:U6 5.0 10.5 1.0

Potassium binding site 2 out of 9 in 1n7b

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Potassium binding site 2 out of 9 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Rip-Radiation-Damage Induced Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K104

b:5.1
occ:0.80
 O6 D:G4 2.7 4.8 1.0
O6 A:G4 2.7 3.7 1.0
O6 H:G4 2.7 4.0 1.0
O6 C:G4 2.8 3.7 1.0
O6 C:G5 2.8 4.6 1.0
O6 A:G5 2.8 4.1 1.0
O6 H:G5 2.9 4.8 1.0
O6 D:G5 2.9 4.4 1.0
K A:K109 3.4 13.2 0.8
K A:K103 3.5 4.0 0.8
C6 D:G4 3.6 4.5 1.0
C6 C:G4 3.6 3.4 1.0
C6 H:G4 3.6 4.1 1.0
C6 A:G4 3.6 4.1 1.0
C6 C:G5 3.8 4.8 1.0
C6 A:G5 3.8 3.4 1.0
C6 H:G5 3.8 5.5 1.0
N1 D:G4 3.8 4.0 1.0
N1 A:G4 3.8 4.0 1.0
C6 D:G5 3.8 5.2 1.0
N1 C:G4 3.8 3.3 1.0
N1 H:G4 3.9 4.6 1.0
N1 C:G5 4.0 4.8 1.0
N1 A:G5 4.1 3.4 1.0
N1 H:G5 4.1 5.8 1.0
N1 D:G5 4.1 4.8 1.0
C5 C:G4 4.9 4.2 1.0
C5 D:G4 4.9 4.0 1.0
C5 H:G4 4.9 4.3 1.0
C5 A:G4 4.9 3.3 1.0

Potassium binding site 3 out of 9 in 1n7b

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Potassium binding site 3 out of 9 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Rip-Radiation-Damage Induced Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K105

b:8.2
occ:0.80
 O6 C:BGM2 2.8 3.4 1.0
O6 G:BGM2 2.8 4.0 1.0
O6 F:BGM2 2.9 3.2 1.0
O6 H:BGM2 2.9 3.1 1.0
O6 A:BGM2 2.9 4.6 1.0
O6 B:BGM2 2.9 3.5 1.0
O6 E:BGM2 2.9 3.7 1.0
O6 D:BGM2 2.9 3.3 1.0
K A:K108 3.6 10.2 0.8
K E:K106 3.6 11.4 0.8
C6 C:BGM2 3.7 3.9 1.0
C6 G:BGM2 3.7 3.9 1.0
C6 H:BGM2 3.7 3.4 1.0
C6 F:BGM2 3.7 3.3 1.0
C6 B:BGM2 3.7 3.4 1.0
C6 A:BGM2 3.8 4.4 1.0
C6 E:BGM2 3.8 3.8 1.0
C6 D:BGM2 3.8 3.7 1.0
N1 C:BGM2 4.0 4.0 1.0
N1 F:BGM2 4.0 3.4 1.0
N1 H:BGM2 4.0 3.8 1.0
N1 G:BGM2 4.0 3.8 1.0
N1 A:BGM2 4.0 3.0 1.0
N1 B:BGM2 4.0 3.5 1.0
N1 D:BGM2 4.1 4.0 1.0
N1 E:BGM2 4.1 3.0 1.0
C5 C:BGM2 4.9 3.1 1.0
C5 B:BGM2 4.9 3.3 1.0
C5 G:BGM2 4.9 3.3 1.0
C5 H:BGM2 4.9 4.0 1.0
C5 A:BGM2 4.9 4.3 1.0
C5 F:BGM2 4.9 4.2 1.0
C5 D:BGM2 5.0 3.5 1.0

Potassium binding site 4 out of 9 in 1n7b

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Potassium binding site 4 out of 9 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Rip-Radiation-Damage Induced Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K108

b:10.2
occ:0.80
 K A:K109 2.8 13.2 0.8
O6 A:BGM2 2.9 4.6 1.0
O6 D:BGM2 2.9 3.3 1.0
O6 C:BGM2 2.9 3.4 1.0
O6 H:BGM2 3.0 3.1 1.0
N1 C:A3 3.4 3.6 1.0
N1 A:A3 3.4 3.9 1.0
N1 H:A3 3.4 3.3 1.0
N1 D:A3 3.5 3.2 1.0
C2 A:A3 3.5 4.5 1.0
C2 C:A3 3.5 3.7 1.0
C2 D:A3 3.5 2.7 1.0
C2 H:A3 3.5 4.1 1.0
K A:K105 3.6 8.2 0.8
C6 D:BGM2 3.8 3.7 1.0
C6 A:BGM2 3.8 4.4 1.0
C6 H:BGM2 3.8 3.4 1.0
C6 C:BGM2 3.8 3.9 1.0
N1 H:BGM2 4.0 3.8 1.0
N1 A:BGM2 4.1 3.0 1.0
N1 C:BGM2 4.1 4.0 1.0
N1 D:BGM2 4.1 4.0 1.0
C6 C:A3 4.6 4.4 1.0
C6 A:A3 4.7 4.0 1.0
C6 H:A3 4.7 4.1 1.0
N3 A:A3 4.7 3.7 1.0
N3 C:A3 4.7 4.4 1.0
C6 D:A3 4.7 3.9 1.0
N3 H:A3 4.7 4.3 1.0
N3 D:A3 4.7 3.5 1.0
C5 D:BGM2 5.0 3.5 1.0
C5 C:BGM2 5.0 3.1 1.0
C5 H:BGM2 5.0 4.0 1.0
C5 A:BGM2 5.0 4.3 1.0

Potassium binding site 5 out of 9 in 1n7b

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Potassium binding site 5 out of 9 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Rip-Radiation-Damage Induced Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K109

b:13.2
occ:0.80
 K A:K108 2.8 10.2 0.8
O6 H:G4 3.1 4.0 1.0
O6 D:G4 3.1 4.8 1.0
O6 C:G4 3.1 3.7 1.0
O6 A:G4 3.1 3.7 1.0
C2 A:A3 3.4 4.5 1.0
C2 C:A3 3.4 3.7 1.0
C2 D:A3 3.4 2.7 1.0
N1 A:A3 3.4 3.9 1.0
C2 H:A3 3.4 4.1 1.0
N1 C:A3 3.4 3.6 1.0
N1 D:A3 3.4 3.2 1.0
N1 H:A3 3.4 3.3 1.0
K A:K104 3.4 5.1 0.8
C6 C:G4 3.9 3.4 1.0
C6 D:G4 3.9 4.5 1.0
C6 H:G4 3.9 4.1 1.0
C6 A:G4 4.0 4.1 1.0
N1 C:G4 4.2 3.3 1.0
N1 H:G4 4.2 4.6 1.0
N1 D:G4 4.2 4.0 1.0
N1 A:G4 4.2 4.0 1.0
N3 A:A3 4.5 3.7 1.0
N3 C:A3 4.5 4.4 1.0
N3 D:A3 4.5 3.5 1.0
N3 H:A3 4.5 4.3 1.0
C6 C:A3 4.6 4.4 1.0
C6 A:A3 4.6 4.0 1.0
C6 D:A3 4.7 3.9 1.0
C6 H:A3 4.7 4.1 1.0

Potassium binding site 6 out of 9 in 1n7b

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Potassium binding site 6 out of 9 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Rip-Radiation-Damage Induced Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K101

b:2.5
occ:0.80
 O4 F:U6 2.7 3.2 1.0
O4 B:U6 2.7 4.1 1.0
O4 G:U6 2.7 3.8 1.0
O4 E:U6 2.7 3.3 1.0
O6 E:G5 2.8 3.2 1.0
O6 B:G5 2.8 3.0 1.0
O6 G:G5 2.9 3.2 1.0
O6 F:G5 2.9 3.0 1.0
K B:K102 3.4 3.3 0.8
C6 E:G5 3.6 2.5 1.0
C6 F:G5 3.6 2.4 1.0
C6 G:G5 3.7 2.9 1.0
C4 F:U6 3.7 3.4 1.0
C4 G:U6 3.7 4.1 1.0
C6 B:G5 3.7 2.5 1.0
C4 B:U6 3.7 3.7 1.0
C4 E:U6 3.7 3.3 1.0
N3 G:U6 3.9 4.3 1.0
N1 E:G5 3.9 3.1 1.0
N3 E:U6 3.9 4.3 1.0
N3 F:U6 3.9 3.2 1.0
N1 F:G5 3.9 3.8 1.0
N1 B:G5 4.0 2.9 1.0
N3 B:U6 4.0 5.1 1.0
N1 G:G5 4.0 3.1 1.0
C5 E:G5 4.8 2.6 1.0
C5 F:G5 4.8 3.3 1.0
C5 G:G5 4.8 3.0 1.0
C5 B:G5 4.9 3.4 1.0

Potassium binding site 7 out of 9 in 1n7b

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Potassium binding site 7 out of 9 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Rip-Radiation-Damage Induced Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K102

b:3.3
occ:0.80
 O6 G:G4 2.8 3.1 1.0
O6 B:G4 2.8 3.6 1.0
O6 F:G4 2.8 2.7 1.0
O6 E:G4 2.8 2.8 1.0
O6 G:G5 2.8 3.2 1.0
O6 F:G5 2.8 3.0 1.0
O6 B:G5 2.8 3.0 1.0
O6 E:G5 2.9 3.2 1.0
K B:K101 3.4 2.5 0.8
K B:K107 3.4 11.0 0.8
C6 B:G4 3.6 3.1 1.0
C6 F:G4 3.6 2.7 1.0
C6 G:G4 3.6 3.1 1.0
C6 E:G4 3.6 2.7 1.0
C6 G:G5 3.7 2.9 1.0
C6 F:G5 3.8 2.4 1.0
N1 E:G4 3.8 2.4 1.0
N1 F:G4 3.8 3.1 1.0
C6 B:G5 3.8 2.5 1.0
N1 G:G4 3.8 3.4 1.0
N1 B:G4 3.8 3.4 1.0
C6 E:G5 3.8 2.5 1.0
N1 F:G5 4.0 3.8 1.0
N1 G:G5 4.1 3.1 1.0
N1 B:G5 4.1 2.9 1.0
N1 E:G5 4.1 3.1 1.0
C5 F:G4 4.9 2.8 1.0
C5 B:G4 4.9 2.8 1.0
C5 E:G4 4.9 3.1 1.0
C5 G:G4 4.9 2.2 1.0
C5 G:G5 5.0 3.0 1.0

Potassium binding site 8 out of 9 in 1n7b

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Potassium binding site 8 out of 9 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Rip-Radiation-Damage Induced Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K107

b:11.0
occ:0.80
 K E:K106 2.8 11.4 0.8
O6 F:G4 3.0 2.7 1.0
O6 G:G4 3.1 3.1 1.0
O6 E:G4 3.1 2.8 1.0
O6 B:G4 3.1 3.6 1.0
C2 F:A3 3.4 3.3 1.0
C2 G:A3 3.4 2.3 1.0
N1 G:A3 3.4 3.3 1.0
C2 B:A3 3.4 3.0 1.0
C2 E:A3 3.4 3.0 1.0
N1 B:A3 3.4 2.7 1.0
N1 F:A3 3.4 2.6 1.0
K B:K102 3.4 3.3 0.8
N1 E:A3 3.5 2.9 1.0
C6 G:G4 3.9 3.1 1.0
C6 F:G4 3.9 2.7 1.0
C6 B:G4 3.9 3.1 1.0
C6 E:G4 3.9 2.7 1.0
N1 F:G4 4.1 3.1 1.0
N1 G:G4 4.1 3.4 1.0
N1 E:G4 4.2 2.4 1.0
N1 B:G4 4.2 3.4 1.0
N3 G:A3 4.5 3.5 1.0
N3 F:A3 4.5 2.9 1.0
N3 B:A3 4.5 4.3 1.0
N3 E:A3 4.6 3.1 1.0
C6 G:A3 4.6 2.9 1.0
C6 B:A3 4.6 2.6 1.0
C6 F:A3 4.7 2.8 1.0
C6 E:A3 4.7 3.5 1.0

Potassium binding site 9 out of 9 in 1n7b

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Potassium binding site 9 out of 9 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Rip-Radiation-Damage Induced Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K106

b:11.4
occ:0.80
 K B:K107 2.8 11.0 0.8
O6 G:BGM2 2.9 4.0 1.0
O6 F:BGM2 2.9 3.2 1.0
O6 E:BGM2 3.0 3.7 1.0
O6 B:BGM2 3.0 3.5 1.0
N1 F:A3 3.4 2.6 1.0
N1 E:A3 3.4 2.9 1.0
N1 G:A3 3.5 3.3 1.0
C2 E:A3 3.5 3.0 1.0
N1 B:A3 3.5 2.7 1.0
C2 F:A3 3.5 3.3 1.0
C2 B:A3 3.5 3.0 1.0
C2 G:A3 3.6 2.3 1.0
K A:K105 3.6 8.2 0.8
C6 F:BGM2 3.8 3.3 1.0
C6 G:BGM2 3.8 3.9 1.0
C6 B:BGM2 3.8 3.4 1.0
C6 E:BGM2 3.8 3.8 1.0
N1 F:BGM2 4.0 3.4 1.0
N1 G:BGM2 4.1 3.8 1.0
N1 B:BGM2 4.1 3.5 1.0
N1 E:BGM2 4.1 3.0 1.0
C6 E:A3 4.6 3.5 1.0
C6 F:A3 4.7 2.8 1.0
N3 E:A3 4.7 3.1 1.0
C6 G:A3 4.7 2.9 1.0
N3 B:A3 4.7 4.3 1.0
C6 B:A3 4.7 2.6 1.0
N3 F:A3 4.7 2.9 1.0
N3 G:A3 4.7 3.5 1.0
C5 F:BGM2 5.0 4.2 1.0
C5 G:BGM2 5.0 3.3 1.0

Reference:

R.B.G.Ravelli, H.-K.S.Leiros, B.Pan, M.Caffrey, S.Mcsweeney. Specific Radiation-Damage Can Be Used to Solve Macromolecular Crystal Structures Structure V. 11 217 2003.
ISSN: ISSN 0969-2126
PubMed: 12575941
DOI: 10.1016/S0969-2126(03)00006-6
Page generated: Mon Aug 12 05:00:29 2024

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