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Potassium in PDB 2irf: Crystal Structure of An Irf-2/Dna Complex.

Protein crystallography data

The structure of Crystal Structure of An Irf-2/Dna Complex., PDB code: 2irf was solved by Y.Fujii, T.Shimizu, M.Kusumoto, Y.Kyogoku, T.Taniguchi, T.Hakoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.20
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 132.300, 132.300, 296.500, 90.00, 90.00, 120.00
R / Rfree (%) 20.2 / 24.3

Other elements in 2irf:

The structure of Crystal Structure of An Irf-2/Dna Complex. also contains other interesting chemical elements:

Iodine (I) 6 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of An Irf-2/Dna Complex. (pdb code 2irf). 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 An Irf-2/Dna Complex., PDB code: 2irf:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 2irf

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Potassium binding site 1 out of 6 in the Crystal Structure of An Irf-2/Dna Complex.


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 An Irf-2/Dna Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K4001

b:25.6
occ:1.00
 O G:ILE91 2.7 22.5 1.0
O G:LEU88 2.7 19.9 1.0
O G:ASN86 2.8 14.7 1.0
O G:MET85 2.8 14.3 1.0
C G:ASN86 3.4 11.5 1.0
CA G:ASN86 3.7 12.4 1.0
C G:LEU88 3.8 17.3 1.0
N G:LEU88 3.8 16.4 1.0
C G:MET85 3.9 13.0 1.0
C G:ILE91 3.9 23.5 1.0
CA G:LEU88 4.2 16.0 1.0
N G:ASN86 4.3 13.3 1.0
N G:SER87 4.3 13.1 1.0
CB G:LEU88 4.4 15.6 1.0
C G:SER87 4.4 13.0 1.0
CA G:GLU92 4.5 29.4 1.0
N G:GLU92 4.7 25.5 1.0
CA G:SER87 4.8 12.6 1.0
CA G:ILE91 4.9 22.2 1.0
N G:PRO89 4.9 18.7 1.0
N G:ILE91 4.9 21.9 1.0

Potassium binding site 2 out of 6 in 2irf

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Potassium binding site 2 out of 6 in the Crystal Structure of An Irf-2/Dna Complex.


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 An Irf-2/Dna Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K4006

b:31.9
occ:1.00
 O H:ILE291 2.7 30.2 1.0
O H:MET285 2.8 13.6 1.0
O H:LEU288 2.9 22.7 1.0
O H:ASN286 3.3 24.3 1.0
O H:HOH3176 3.6 21.2 1.0
C H:ASN286 3.7 20.6 1.0
C H:ILE291 3.9 27.7 1.0
C H:MET285 3.9 17.0 1.0
C H:LEU288 4.0 24.6 1.0
CA H:ASN286 4.0 17.9 1.0
N H:LEU288 4.2 21.2 1.0
N H:ASN286 4.4 18.1 1.0
CA H:LEU288 4.4 20.9 1.0
CA H:GLU292 4.5 26.1 1.0
CB H:LEU288 4.6 22.0 1.0
N H:SER287 4.6 20.6 1.0
N H:GLU292 4.7 26.1 1.0
C H:SER287 4.7 20.9 1.0
O H:HOH3110 4.7 20.2 1.0
CA H:ILE291 4.9 27.2 1.0
N H:ILE291 5.0 30.9 1.0

Potassium binding site 3 out of 6 in 2irf

Go back to Potassium Binding Sites List in 2irf
Potassium binding site 3 out of 6 in the Crystal Structure of An Irf-2/Dna Complex.


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 An Irf-2/Dna Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K4003

b:28.5
occ:1.00
 O I:ILE491 2.6 26.2 1.0
O I:LEU488 2.7 23.6 1.0
O I:MET485 2.8 22.1 1.0
O I:ASN486 2.9 17.0 1.0
C I:ASN486 3.5 18.8 1.0
C I:LEU488 3.8 23.0 1.0
C I:ILE491 3.9 28.1 1.0
CA I:ASN486 3.9 19.4 1.0
C I:MET485 3.9 19.0 1.0
N I:LEU488 4.0 17.9 1.0
CA I:LEU488 4.2 20.0 1.0
CB I:LEU488 4.3 19.7 1.0
N I:ASN486 4.4 19.1 1.0
N I:SER487 4.4 18.6 1.0
C I:SER487 4.5 20.4 1.0
CA I:GLU492 4.6 33.9 1.0
N I:GLU492 4.7 31.2 1.0
N I:ILE491 4.8 28.9 1.0
CA I:ILE491 4.8 25.7 1.0
CA I:SER487 4.9 19.1 1.0
N I:PRO489 4.9 25.2 1.0

Potassium binding site 4 out of 6 in 2irf

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Potassium binding site 4 out of 6 in the Crystal Structure of An Irf-2/Dna Complex.


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 An Irf-2/Dna Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K4005

b:35.3
occ:1.00
 O J:LEU688 2.7 27.0 1.0
O J:ILE691 2.7 38.7 1.0
O J:MET685 2.8 22.2 1.0
O J:ASN686 2.9 22.9 1.0
C J:ASN686 3.3 21.8 1.0
CA J:ASN686 3.7 19.6 1.0
C J:LEU688 3.8 30.5 1.0
C J:MET685 3.8 18.5 1.0
N J:LEU688 3.9 27.4 1.0
C J:ILE691 3.9 36.0 1.0
N J:SER687 4.1 24.7 1.0
CA J:LEU688 4.2 28.7 1.0
C J:SER687 4.2 24.3 1.0
N J:ASN686 4.3 19.5 1.0
CA J:GLU692 4.3 40.3 1.0
CB J:LEU688 4.4 25.7 1.0
N J:GLU692 4.5 38.4 1.0
CA J:SER687 4.6 24.3 1.0
O J:SER687 4.8 23.2 1.0
N J:PRO689 4.9 34.5 1.0

Potassium binding site 5 out of 6 in 2irf

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Potassium binding site 5 out of 6 in the Crystal Structure of An Irf-2/Dna Complex.


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 An Irf-2/Dna Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
K:K4004

b:27.8
occ:1.00
 O K:ILE891 2.7 33.9 1.0
O K:LEU888 2.7 22.1 1.0
O K:MET885 2.8 21.9 1.0
O K:ASN886 3.1 15.0 1.0
C K:ASN886 3.5 16.1 1.0
C K:LEU888 3.8 16.9 1.0
C K:ILE891 3.8 31.2 1.0
CA K:ASN886 3.9 14.9 1.0
C K:MET885 3.9 18.4 1.0
N K:LEU888 4.0 15.9 1.0
CA K:LEU888 4.2 16.0 1.0
CB K:LEU888 4.3 12.8 1.0
CA K:GLU892 4.3 33.6 1.0
N K:ASN886 4.3 17.6 1.0
N K:SER887 4.4 17.4 1.0
N K:GLU892 4.5 31.3 1.0
C K:SER887 4.5 16.2 1.0
CB K:GLU892 4.7 39.5 1.0
O K:HOH3246 4.8 33.4 1.0
CA K:ILE891 4.9 28.4 1.0
N K:PRO889 4.9 19.4 1.0
N K:ILE891 5.0 30.0 1.0
CA K:SER887 5.0 18.4 1.0
CB K:ILE891 5.0 25.3 1.0

Potassium binding site 6 out of 6 in 2irf

Go back to Potassium Binding Sites List in 2irf
Potassium binding site 6 out of 6 in the Crystal Structure of An Irf-2/Dna Complex.


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 An Irf-2/Dna Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K4002

b:28.0
occ:1.00
 O L:LEU2088 2.7 22.9 1.0
O L:ILE2091 2.8 32.6 1.0
O L:MET2085 2.8 14.3 1.0
O L:ASN2086 3.1 18.5 1.0
C L:ASN2086 3.6 15.5 1.0
C L:LEU2088 3.8 21.6 1.0
CA L:ASN2086 3.9 16.6 1.0
C L:MET2085 3.9 13.5 1.0
C L:ILE2091 3.9 30.4 1.0
N L:LEU2088 4.1 20.9 1.0
CA L:LEU2088 4.3 18.7 1.0
CB L:LEU2088 4.3 18.5 1.0
N L:ASN2086 4.3 14.9 1.0
CA L:GLU2092 4.5 34.4 1.0
N L:SER2087 4.5 17.7 1.0
C L:SER2087 4.5 19.8 1.0
N L:GLU2092 4.7 31.7 1.0
N L:PRO2089 5.0 24.6 1.0
N L:ILE2091 5.0 27.3 1.0
CA L:ILE2091 5.0 27.4 1.0

Reference:

Y.Fujii, T.Shimizu, M.Kusumoto, Y.Kyogoku, T.Taniguchi, T.Hakoshima. Crystal Structure of An Irf-Dna Complex Reveals Novel Dna Recognition and Cooperative Binding to A Tandem Repeat of Core Sequences. Embo J. V. 18 5028 1999.
ISSN: ISSN 0261-4189
PubMed: 10487755
DOI: 10.1093/EMBOJ/18.18.5028
Page generated: Mon Aug 12 06:42:03 2024

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