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Potassium in PDB 2dv6: Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans

Enzymatic activity of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans

All present enzymatic activity of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans:
1.7.2.1;

Protein crystallography data

The structure of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans, PDB code: 2dv6 was solved by M.Nojiri, Y.Xie, T.Yamamoto, T.Inoue, S.Suzuki, Y.Kai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.20
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 162.551, 162.551, 148.970, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 16.5

Other elements in 2dv6:

The structure of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans also contains other interesting chemical elements:

Copper (Cu) 18 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans (pdb code 2dv6). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans, PDB code: 2dv6:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 2dv6

Go back to Potassium Binding Sites List in 2dv6
Potassium binding site 1 out of 6 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2503

b:30.4
occ:1.00
O A:HOH2607 2.3 36.5 1.0
O A:LYS404 2.4 29.9 1.0
O A:HOH2555 2.4 30.0 1.0
OD2 A:ASP406 2.4 37.5 1.0
O B:HOH3563 2.5 28.2 1.0
OE2 A:GLU369 2.5 30.4 1.0
OE1 A:GLU369 2.6 30.3 1.0
CD A:GLU369 2.9 30.0 1.0
CG A:ASP406 3.5 35.9 1.0
C A:LYS404 3.6 31.3 1.0
OD1 A:ASP406 4.0 36.9 1.0
CG2 B:THR227 4.2 29.4 1.0
N A:ASP406 4.3 32.8 1.0
N A:LYS404 4.4 31.1 1.0
CG A:GLU369 4.5 27.7 1.0
CA A:LYS404 4.5 32.1 1.0
O A:ILE370 4.5 24.7 1.0
N A:ILE405 4.5 31.1 1.0
OD1 A:ASP372 4.6 28.1 1.0
CA A:ILE405 4.6 32.3 1.0
O A:HOH2553 4.7 32.2 1.0
CB A:ASP406 4.7 34.4 1.0
CB A:LYS404 4.8 33.7 1.0
CB A:PHE403 4.8 27.1 1.0
OD2 A:ASP372 4.8 27.4 1.0
OG1 B:THR227 4.9 29.6 1.0
CD1 B:ILE252 4.9 25.8 1.0
N A:ILE370 4.9 25.0 1.0
C A:ILE405 4.9 32.5 1.0

Potassium binding site 2 out of 6 in 2dv6

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Potassium binding site 2 out of 6 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K3503

b:33.9
occ:1.00
OD1 B:ASP406 2.4 37.7 1.0
O B:LYS404 2.4 30.8 1.0
O B:HOH3640 2.4 40.6 1.0
O B:HOH3530 2.4 28.3 1.0
O C:HOH4538 2.4 30.5 1.0
OE2 B:GLU369 2.5 30.9 1.0
OE1 B:GLU369 2.6 31.5 1.0
CD B:GLU369 2.9 32.5 1.0
CG B:ASP406 3.5 37.5 1.0
C B:LYS404 3.6 31.6 1.0
OD2 B:ASP406 3.9 37.8 1.0
CG2 C:THR227 4.2 34.0 1.0
N B:ASP406 4.4 35.8 1.0
N B:LYS404 4.4 30.2 1.0
CG B:GLU369 4.5 30.5 1.0
CA B:LYS404 4.5 31.8 1.0
O B:ILE370 4.5 27.7 1.0
N B:ILE405 4.6 32.4 1.0
CA B:ILE405 4.6 33.9 1.0
CD1 C:ILE252 4.6 26.7 1.0
O B:HOH3504 4.7 28.2 1.0
OD1 B:ASP372 4.7 27.3 1.0
CB B:LYS404 4.7 32.9 1.0
CB B:ASP406 4.7 36.4 1.0
OG1 C:THR227 4.8 35.7 1.0
OD2 B:ASP372 4.8 30.0 1.0
N B:ILE370 4.9 28.0 1.0
CB B:PHE403 4.9 27.6 1.0
C B:ILE405 5.0 35.0 1.0

Potassium binding site 3 out of 6 in 2dv6

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Potassium binding site 3 out of 6 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K4503

b:26.2
occ:1.00
OD1 C:ASP406 2.2 34.8 1.0
O C:HOH4515 2.4 30.4 1.0
O A:HOH2549 2.4 31.2 1.0
O C:LYS404 2.4 29.0 1.0
OE2 C:GLU369 2.4 25.4 1.0
O C:HOH4565 2.4 33.0 1.0
OE1 C:GLU369 2.5 28.9 1.0
CD C:GLU369 2.9 27.8 1.0
CG C:ASP406 3.4 33.3 1.0
C C:LYS404 3.6 29.1 1.0
OD2 C:ASP406 4.0 34.2 1.0
N C:ASP406 4.2 30.7 1.0
CG2 A:THR227 4.2 28.1 1.0
CG C:GLU369 4.4 26.7 1.0
CA C:ILE405 4.5 29.3 1.0
N C:ILE405 4.5 29.1 1.0
CB C:ASP406 4.5 31.9 1.0
CA C:LYS404 4.6 29.1 1.0
N C:LYS404 4.6 27.8 1.0
O C:ILE370 4.6 27.5 1.0
O C:HOH4505 4.6 21.9 1.0
OG1 A:THR227 4.7 30.4 1.0
OD1 C:ASP372 4.7 27.1 1.0
CB C:LYS404 4.8 30.8 1.0
OD2 C:ASP372 4.8 26.4 1.0
C C:ILE405 4.8 30.3 1.0
CD1 A:ILE252 4.8 26.4 1.0
CB C:PHE403 4.9 21.9 1.0
N C:ILE370 4.9 26.1 1.0
CA C:ASP406 5.0 31.3 1.0

Potassium binding site 4 out of 6 in 2dv6

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Potassium binding site 4 out of 6 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K5503

b:27.0
occ:1.00
O D:HOH5557 2.3 23.9 1.0
O D:LYS404 2.4 29.1 1.0
OD1 D:ASP406 2.4 33.0 1.0
O D:HOH5667 2.5 34.8 1.0
OE2 D:GLU369 2.5 24.5 1.0
O E:HOH6532 2.5 26.1 1.0
OE1 D:GLU369 2.5 28.8 1.0
CD D:GLU369 2.9 27.0 1.0
CG D:ASP406 3.5 32.0 1.0
C D:LYS404 3.6 30.1 1.0
OD2 D:ASP406 4.0 32.8 1.0
CG2 E:THR227 4.3 27.2 1.0
N D:LYS404 4.4 29.0 1.0
CG D:GLU369 4.4 25.2 1.0
N D:ASP406 4.4 30.0 1.0
CA D:LYS404 4.5 30.2 1.0
O D:ILE370 4.5 22.2 1.0
N D:ILE405 4.5 30.9 1.0
O D:HOH5523 4.6 27.9 1.0
CA D:ILE405 4.6 31.1 1.0
OD1 D:ASP372 4.7 31.2 1.0
CB D:LYS404 4.7 32.1 1.0
CB D:ASP406 4.7 29.9 1.0
CB D:PHE403 4.8 23.3 1.0
OG1 E:THR227 4.9 29.4 1.0
N D:ILE370 4.9 20.6 1.0
C D:ILE405 4.9 30.6 1.0
OD2 D:ASP372 4.9 31.3 1.0
CD1 E:ILE252 4.9 24.9 1.0

Potassium binding site 5 out of 6 in 2dv6

Go back to Potassium Binding Sites List in 2dv6
Potassium binding site 5 out of 6 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K6503

b:25.1
occ:1.00
OD1 E:ASP406 2.3 32.0 1.0
O E:LYS404 2.4 22.3 1.0
O E:HOH6642 2.4 32.3 1.0
OE1 E:GLU369 2.4 26.9 1.0
O F:HOH7569 2.4 23.8 1.0
O E:HOH6523 2.5 21.4 1.0
OE2 E:GLU369 2.6 26.9 1.0
CD E:GLU369 2.8 26.8 1.0
CG E:ASP406 3.4 30.8 1.0
C E:LYS404 3.6 24.1 1.0
OD2 E:ASP406 3.9 33.9 1.0
CG2 F:THR227 4.3 26.3 1.0
CG E:GLU369 4.4 25.0 1.0
N E:ASP406 4.4 27.7 1.0
N E:LYS404 4.4 23.9 1.0
CA E:LYS404 4.4 25.2 1.0
O E:ILE370 4.5 23.3 1.0
N E:ILE405 4.5 25.2 1.0
CB E:LYS404 4.6 27.3 1.0
CA E:ILE405 4.6 26.6 1.0
CB E:ASP406 4.6 29.2 1.0
O E:HOH6507 4.7 24.1 1.0
CD1 F:ILE252 4.7 23.2 1.0
OD1 E:ASP372 4.8 24.9 1.0
OD2 E:ASP372 4.8 26.0 1.0
OG1 F:THR227 4.8 25.8 1.0
CB E:PHE403 4.9 21.5 1.0
C E:ILE405 4.9 27.4 1.0
N E:ILE370 5.0 22.4 1.0

Potassium binding site 6 out of 6 in 2dv6

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Potassium binding site 6 out of 6 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K7503

b:27.4
occ:1.00
O D:HOH5654 2.3 35.5 1.0
OD1 F:ASP406 2.4 34.8 1.0
O F:HOH7639 2.4 36.2 1.0
O F:HOH7566 2.4 25.7 1.0
O F:LYS404 2.4 25.3 1.0
OE2 F:GLU369 2.5 26.6 1.0
OE1 F:GLU369 2.5 24.2 1.0
CD F:GLU369 2.8 26.8 1.0
CG F:ASP406 3.5 34.7 1.0
C F:LYS404 3.6 26.5 1.0
OD2 F:ASP406 4.1 35.8 1.0
N F:ASP406 4.3 30.7 1.0
N F:LYS404 4.3 25.4 1.0
CG F:GLU369 4.4 25.7 1.0
CG2 D:THR227 4.4 26.5 1.0
CA F:LYS404 4.4 27.4 1.0
O F:ILE370 4.5 23.8 1.0
N F:ILE405 4.5 27.7 1.0
CB F:ASP406 4.6 32.2 1.0
CA F:ILE405 4.6 29.5 1.0
O F:HOH7527 4.6 27.4 1.0
CB F:LYS404 4.7 29.0 1.0
OD1 F:ASP372 4.8 26.7 1.0
CB F:PHE403 4.8 22.9 1.0
OG1 D:THR227 4.8 29.6 1.0
CD1 D:ILE252 4.8 25.2 1.0
OD2 F:ASP372 4.9 28.6 1.0
C F:ILE405 4.9 30.6 1.0
N F:ILE370 4.9 25.0 1.0

Reference:

M.Nojiri, Y.Xie, T.Inoue, T.Yamamoto, H.Matsumura, K.Kataoka, Deligeer, K.Yamaguchi, Y.Kai, S.Suzuki. Structure and Function of A Hexameric Copper-Containing Nitrite Reductase. Proc.Natl.Acad.Sci.Usa V. 104 4315 2007.
ISSN: ISSN 0027-8424
PubMed: 17360521
DOI: 10.1073/PNAS.0609195104
Page generated: Sun Dec 13 23:09:29 2020

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