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Potassium in PDB 2qyo: Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah

Enzymatic activity of Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah

All present enzymatic activity of Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah:
2.1.1.46;

Protein crystallography data

The structure of Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah, PDB code: 2qyo was solved by C.Wang, X.-H.Yu, C.-J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.57 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.540, 82.049, 101.034, 90.00, 101.94, 90.00
R / Rfree (%) 21.4 / 24.5

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Potassium atom in the Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah (pdb code 2qyo). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 13 binding sites of Potassium where determined in the Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah, PDB code: 2qyo:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 13 in 2qyo

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Potassium binding site 1 out of 13 in the Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah


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 Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K358

b:28.2
occ:1.00
 ND1 A:HIS262 2.4 28.9 1.0
OE1 A:GLU323 2.4 16.4 1.0
OD1 A:ASP293 2.4 26.4 1.0
O A:HOH703 2.5 4.6 1.0
OE2 A:GLU323 2.6 19.5 1.0
CD A:GLU323 2.9 19.2 1.0
CG A:HIS262 3.1 25.2 1.0
CB A:HIS262 3.2 24.6 1.0
CG A:ASP293 3.3 23.6 1.0
CE1 A:HIS262 3.4 27.2 1.0
N A:MET294 3.9 17.1 1.0
OD2 A:ASP293 4.0 21.6 1.0
O A:HOH705 4.0 16.2 1.0
CB A:ASP293 4.1 18.3 1.0
CD2 A:HIS262 4.3 27.9 1.0
CB A:MET294 4.3 16.8 1.0
CG A:GLU323 4.4 19.0 1.0
NE2 A:HIS262 4.4 28.3 1.0
CA A:ASP293 4.5 17.8 1.0
CA A:HIS262 4.7 21.7 1.0
CD1 A:ILE316 4.7 28.5 1.0
C A:ASP293 4.8 17.2 1.0
CA A:MET294 4.8 17.1 1.0

Potassium binding site 2 out of 13 in 2qyo

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Potassium binding site 2 out of 13 in the Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah


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 Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K359

b:23.7
occ:1.00
 CB A:ARG8 3.7 32.8 1.0
N A:LYS9 3.8 29.6 1.0
CA A:ARG8 3.8 32.1 1.0
NH1 A:ARG8 4.0 30.7 1.0
CG A:GLU12 4.0 32.1 1.0
CG A:ARG8 4.1 33.6 1.0
CB A:GLU12 4.2 25.6 1.0
C A:ARG8 4.4 30.6 1.0
CD A:ARG8 4.5 32.1 1.0
CG A:LYS9 4.6 35.6 1.0
CB A:LYS9 4.6 33.3 1.0
CA A:LYS9 4.8 30.0 1.0
CD A:GLU12 5.0 34.2 1.0
N A:ARG8 5.0 34.9 1.0

Potassium binding site 3 out of 13 in 2qyo

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Potassium binding site 3 out of 13 in the Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah


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 Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K360

b:23.9
occ:1.00
 N A:LEU101 3.6 17.4 1.0
CB A:ALA100 3.8 21.7 1.0
CA A:ALA100 3.9 18.5 1.0
C A:LYS50 4.1 25.1 1.0
N A:PRO51 4.1 24.3 1.0
CG2 A:ILE45 4.1 19.9 1.0
C A:ALA100 4.3 18.4 1.0
CD A:PRO51 4.3 22.7 1.0
CA A:LYS50 4.3 26.2 1.0
O A:LYS50 4.4 25.4 1.0
CG A:LEU101 4.5 20.5 1.0
CB A:LEU101 4.5 18.6 1.0
CG A:PRO51 4.5 23.3 1.0
CA A:PRO51 4.6 24.1 1.0
CA A:LEU101 4.6 18.9 1.0
CD1 A:LEU101 4.7 23.0 1.0
N A:LYS50 4.7 27.2 1.0
O A:LEU101 5.0 18.5 1.0

Potassium binding site 4 out of 13 in 2qyo

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Potassium binding site 4 out of 13 in the Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah


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 Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K361

b:14.0
occ:1.00
 CG A:PRO118 3.6 20.2 1.0
N A:GLY111 3.8 23.7 1.0
CB A:CYS115 4.0 18.0 1.0
SG A:CYS115 4.0 20.1 1.0
CD A:PRO118 4.1 19.4 1.0
O A:HOH766 4.2 28.2 1.0
CA A:LYS110 4.2 21.7 1.0
CB A:LYS110 4.4 23.5 1.0
C A:LYS110 4.5 22.4 1.0
CG A:LYS110 4.7 26.3 1.0
O A:CYS115 4.7 19.2 1.0
CA A:GLY111 4.8 24.8 1.0
O A:HOH752 4.8 36.3 1.0
CB A:ASP171 4.8 27.3 1.0
CG A:ASP171 4.9 30.8 1.0
OG A:SER175 4.9 23.4 1.0
O A:THR112 5.0 22.2 1.0

Potassium binding site 5 out of 13 in 2qyo

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Potassium binding site 5 out of 13 in the Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah


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 Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K362

b:15.0
occ:1.00
 OG1 A:THR145 3.3 23.2 1.0
N A:LEU155 3.7 45.6 1.0
CB A:ASP154 3.9 43.4 1.0
CA A:ASP154 3.9 42.9 1.0
CB A:THR145 4.0 22.2 1.0
CG2 A:THR145 4.0 22.6 1.0
CD2 A:PHE147 4.1 27.4 1.0
CG A:LEU155 4.1 48.3 1.0
C A:ASP154 4.3 43.7 1.0
CB A:PHE147 4.4 25.6 1.0
CB A:LEU155 4.4 48.2 1.0
CG1 A:VAL319 4.6 26.7 1.0
CD1 A:LEU155 4.6 49.6 1.0
CA A:LEU155 4.7 46.5 1.0
CG A:PHE147 4.7 25.7 1.0
CB A:VAL319 4.9 26.4 1.0

Potassium binding site 6 out of 13 in 2qyo

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Potassium binding site 6 out of 13 in the Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah


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 Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K363

b:7.1
occ:1.00
 O A:HOH788 3.3 21.6 1.0
O A:HOH751 3.5 34.2 1.0
CD1 A:ILE247 4.1 26.6 1.0
CB A:ASP244 4.2 22.0 1.0
N A:ASP244 4.3 23.5 1.0
O A:HOH732 4.5 23.9 1.0
CA A:GLY243 4.6 23.8 1.0
C A:GLY243 4.6 24.8 1.0
CA A:ASP244 4.9 21.8 1.0

Potassium binding site 7 out of 13 in 2qyo

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Potassium binding site 7 out of 13 in the Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K364

b:16.1
occ:1.00
 O A:HOH734 3.1 23.0 1.0
N A:GLU327 3.8 23.5 1.0
N A:GLU326 3.9 21.4 1.0
CB A:ASN325 3.9 20.8 1.0
CG A:ASN325 4.0 21.6 1.0
ND2 A:ASN325 4.1 20.6 1.0
O A:ILE296 4.1 18.8 1.0
CB A:GLU327 4.2 28.1 1.0
CB A:GLU326 4.2 21.9 1.0
CA A:ASN297 4.4 23.4 1.0
CA A:GLU326 4.4 22.5 1.0
OD1 A:ASN325 4.4 26.4 1.0
OD1 A:ASN297 4.4 24.4 1.0
CG A:ASN297 4.5 24.8 1.0
C A:GLU326 4.6 22.9 1.0
C A:ASN325 4.6 19.6 1.0
CE A:LYS299 4.6 47.9 1.0
CA A:GLU327 4.6 24.7 1.0
CA A:ASN325 4.8 18.8 1.0
CB A:ASN297 4.8 23.0 1.0
ND2 A:ASN297 4.9 23.9 1.0
NZ A:LYS299 4.9 50.4 1.0

Potassium binding site 8 out of 13 in 2qyo

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Potassium binding site 8 out of 13 in the Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K365

b:45.1
occ:1.00
 CA A:LYS137 4.1 23.4 1.0
CG A:LYS136 4.4 24.1 1.0
CE A:LYS136 4.4 28.9 1.0
CD1 A:TYR140 4.4 20.0 1.0
N A:LYS137 4.4 19.7 1.0
CB A:LYS137 4.5 25.8 1.0
CD A:LYS136 4.7 25.7 1.0
O A:LYS136 4.8 17.7 1.0
C A:LYS136 4.8 19.8 1.0
CG A:LYS137 4.8 30.6 1.0
CB A:TYR140 4.9 22.2 1.0
CG A:TYR140 4.9 22.3 1.0

Potassium binding site 9 out of 13 in 2qyo

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Potassium binding site 9 out of 13 in the Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K358

b:27.6
occ:1.00
 O B:HOH782 3.1 9.1 1.0
N B:GLU298 3.5 18.5 1.0
NH2 A:ARG76 3.7 26.8 1.0
CB B:ASN325 3.8 27.1 1.0
CA B:ASN297 4.0 18.9 1.0
CG B:GLU298 4.1 25.9 1.0
CG B:ASN325 4.2 30.5 1.0
C B:ASN297 4.2 18.8 1.0
O B:ILE296 4.3 17.4 1.0
OD1 B:ASN325 4.4 34.0 1.0
CB B:GLU298 4.4 22.1 1.0
N B:ASN297 4.4 18.1 1.0
OE2 B:GLU298 4.5 29.2 1.0
CA B:GLU298 4.5 20.2 1.0
C B:ILE296 4.6 17.0 1.0
CG2 B:ILE296 4.7 13.5 1.0
CD B:GLU298 4.7 28.8 1.0
ND2 B:ASN325 4.9 33.2 1.0
CZ A:ARG76 5.0 26.4 1.0

Potassium binding site 10 out of 13 in 2qyo

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Potassium binding site 10 out of 13 in the Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Crystal Structure of Isoflavone O-Methyltransferase Homolog in Complex with Biochanin A and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K359

b:15.6
occ:1.00
 N B:LEU155 3.5 32.3 1.0
OG1 B:THR145 3.7 21.9 1.0
CB B:LEU155 3.9 33.4 1.0
CG2 B:THR145 4.1 20.2 1.0
CD2 B:PHE147 4.1 28.6 1.0
CB B:ASP154 4.1 35.4 1.0
CB B:THR145 4.1 20.9 1.0
CA B:ASP154 4.2 32.9 1.0
CG1 B:VAL319 4.2 24.9 1.0
OD2 B:ASP154 4.3 38.0 1.0
C B:ASP154 4.3 33.0 1.0
CA B:LEU155 4.3 32.0 1.0
CG B:ASP154 4.4 39.1 1.0
CB B:VAL319 4.6 24.9 1.0
CB B:PHE147 4.6 24.4 1.0
CG B:PHE147 4.8 27.6 1.0
CA B:VAL319 4.9 24.9 1.0

Reference:

C.Wang, X.-H.Yu, C.-J.Liu. Crystal Structures of Medicago Truncatula Isoflavone O-Methyltransferase Reveal Conserved Surface Binding Motifs Critical For Enzymatic Activity To Be Published.
Page generated: Mon Aug 12 06:56:59 2024

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