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Potassium in PDB 4m3p: Betaine-Homocysteine S-Methyltransferase From Homo Sapiens Complexed with Homocysteine

Enzymatic activity of Betaine-Homocysteine S-Methyltransferase From Homo Sapiens Complexed with Homocysteine

All present enzymatic activity of Betaine-Homocysteine S-Methyltransferase From Homo Sapiens Complexed with Homocysteine:
2.1.1.5;

Protein crystallography data

The structure of Betaine-Homocysteine S-Methyltransferase From Homo Sapiens Complexed with Homocysteine, PDB code: 4m3p was solved by M.Koutmos, K.Yamada, J.Mladkova, J.Paterova, C.E.Diamond, K.Tryon, P.Jungwirth, T.A.Garrow, J.Jiracek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.22 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.097, 102.617, 96.228, 90.00, 101.76, 90.00
R / Rfree (%) 18 / 21.9

Other elements in 4m3p:

The structure of Betaine-Homocysteine S-Methyltransferase From Homo Sapiens Complexed with Homocysteine also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Betaine-Homocysteine S-Methyltransferase From Homo Sapiens Complexed with Homocysteine (pdb code 4m3p). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Betaine-Homocysteine S-Methyltransferase From Homo Sapiens Complexed with Homocysteine, PDB code: 4m3p:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 4m3p

Go back to Potassium Binding Sites List in 4m3p
Potassium binding site 1 out of 4 in the Betaine-Homocysteine S-Methyltransferase From Homo Sapiens Complexed with Homocysteine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Betaine-Homocysteine S-Methyltransferase From Homo Sapiens Complexed with Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K702

b:23.1
occ:1.00
 O A:GLY298 2.7 20.4 1.0
O A:HOH945 2.7 31.1 1.0
O A:ASP26 2.8 23.8 1.0
O A:GLY27 2.9 25.4 1.0
OE1 A:GLN72 2.9 22.8 1.0
OD1 A:ASP26 2.9 28.4 1.0
O A:HOH825 3.0 36.7 1.0
OE1 A:GLN247 3.2 24.2 1.0
HE22 A:GLN247 3.4 25.3 1.0
C A:ASP26 3.5 24.4 1.0
O A:HOH831 3.6 25.0 1.0
CD A:GLN247 3.7 24.3 1.0
NE2 A:GLN247 3.7 25.3 1.0
C A:GLY27 3.7 22.6 1.0
H A:GLY298 3.8 22.6 1.0
HA A:CYS299 3.9 22.8 1.0
CD A:GLN72 3.9 24.0 1.0
C A:GLY298 3.9 21.8 1.0
HA2 A:GLY27 3.9 21.5 1.0
N A:GLY27 3.9 20.3 1.0
H A:ASP26 4.0 23.0 1.0
CA A:GLY27 4.1 21.5 1.0
CG A:ASP26 4.1 26.9 1.0
HB3 A:GLN247 4.2 26.7 1.0
HE21 A:GLN247 4.4 25.3 1.0
N A:ASP26 4.4 23.0 1.0
CA A:ASP26 4.4 22.3 1.0
HE22 A:GLN72 4.5 24.5 1.0
HG3 A:GLN72 4.5 23.6 1.0
H A:HCS703 4.5 32.9 1.0
H A:GLY27 4.5 20.3 1.0
HA2 A:GLY28 4.6 23.1 1.0
NE2 A:GLN72 4.6 24.5 1.0
N A:GLY298 4.6 22.6 1.0
O A:HCS703 4.6 33.5 1.0
CA A:CYS299 4.7 22.8 1.0
CG A:GLN72 4.7 23.6 1.0
N A:CYS299 4.8 22.5 1.0
CG A:GLN247 4.8 26.0 1.0
CB A:ASP26 4.8 25.0 1.0
N A:GLY28 4.8 22.9 1.0
CA A:GLY298 4.9 23.5 1.0
N A:HCS703 4.9 32.9 1.0
HB2 A:GLN72 4.9 22.6 1.0
H2 A:HCS703 5.0 32.9 1.0
CB A:GLN247 5.0 26.7 1.0
OD2 A:ASP26 5.0 28.6 1.0

Potassium binding site 2 out of 4 in 4m3p

Go back to Potassium Binding Sites List in 4m3p
Potassium binding site 2 out of 4 in the Betaine-Homocysteine S-Methyltransferase From Homo Sapiens Complexed with Homocysteine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Betaine-Homocysteine S-Methyltransferase From Homo Sapiens Complexed with Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K503

b:27.3
occ:1.00
 O B:GLY298 2.7 24.9 1.0
O B:HOH737 2.8 41.0 1.0
O B:GLY27 2.8 25.5 1.0
O B:ASP26 2.8 25.3 1.0
OD1 B:ASP26 2.8 25.9 1.0
O B:HOH701 2.9 39.7 1.0
OE1 B:GLN72 3.0 27.3 1.0
OE1 B:GLN247 3.1 24.7 1.0
HE22 B:GLN247 3.2 23.6 1.0
C B:ASP26 3.4 24.8 1.0
CD B:GLN247 3.5 24.3 1.0
NE2 B:GLN247 3.6 23.6 1.0
C B:GLY27 3.7 24.7 1.0
H B:GLY298 3.8 24.2 1.0
HA B:CYS299 3.8 21.4 1.0
O B:HOH619 3.8 31.7 1.0
C B:GLY298 3.9 24.4 1.0
CD B:GLN72 3.9 27.1 1.0
N B:GLY27 4.0 23.6 1.0
H B:ASP26 4.0 27.2 1.0
HA2 B:GLY27 4.0 24.4 1.0
CG B:ASP26 4.0 26.6 1.0
CA B:GLY27 4.1 24.4 1.0
HB3 B:GLN247 4.2 24.7 1.0
HE21 B:GLN247 4.3 23.6 1.0
N B:ASP26 4.3 27.2 1.0
CA B:ASP26 4.3 25.0 1.0
HG3 B:GLN72 4.5 27.1 1.0
O B:HCS504 4.5 31.6 1.0
N B:GLY298 4.6 24.2 1.0
HA2 B:GLY28 4.6 25.1 1.0
H B:HCS504 4.6 36.3 1.0
HE22 B:GLN72 4.6 28.3 1.0
H B:GLY27 4.6 23.6 1.0
CA B:CYS299 4.6 21.4 1.0
NE2 B:GLN72 4.7 28.3 1.0
N B:CYS299 4.7 21.6 1.0
CG B:GLN247 4.8 25.6 1.0
CB B:ASP26 4.8 24.6 1.0
CG B:GLN72 4.8 27.1 1.0
N B:GLY28 4.9 25.0 1.0
HB2 B:GLN72 4.9 27.0 1.0
CB B:GLN247 4.9 24.7 1.0
CA B:GLY298 4.9 23.5 1.0
N B:HCS504 4.9 36.3 1.0
OD2 B:ASP26 4.9 24.2 1.0
H2 B:HCS504 5.0 36.3 1.0

Potassium binding site 3 out of 4 in 4m3p

Go back to Potassium Binding Sites List in 4m3p
Potassium binding site 3 out of 4 in the Betaine-Homocysteine S-Methyltransferase From Homo Sapiens Complexed with Homocysteine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Betaine-Homocysteine S-Methyltransferase From Homo Sapiens Complexed with Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K502

b:20.9
occ:1.00
 O C:GLY298 2.7 16.4 1.0
O C:GLY27 2.8 19.9 1.0
OD1 C:ASP26 2.8 23.4 1.0
O C:HOH634 2.8 28.2 1.0
O C:ASP26 2.8 21.3 1.0
OE1 C:GLN72 2.9 23.6 1.0
O C:HOH658 2.9 29.5 1.0
OE1 C:GLN247 3.2 20.6 1.0
HE22 C:GLN247 3.3 21.8 1.0
C C:ASP26 3.5 19.5 1.0
C C:GLY27 3.6 21.4 1.0
NE2 C:GLN247 3.7 21.8 1.0
CD C:GLN247 3.7 22.6 1.0
O C:HOH606 3.7 22.4 1.0
CD C:GLN72 3.8 23.1 1.0
HA C:CYS299 3.8 17.9 1.0
H C:GLY298 3.8 18.6 1.0
HA2 C:GLY27 3.8 19.2 1.0
H C:ASP26 3.9 18.3 1.0
C C:GLY298 4.0 16.6 1.0
N C:GLY27 4.0 19.5 1.0
CG C:ASP26 4.0 21.0 1.0
CA C:GLY27 4.0 19.2 1.0
HB3 C:GLN247 4.2 20.4 1.0
HE21 C:GLN247 4.3 21.8 1.0
N C:ASP26 4.3 18.3 1.0
CA C:ASP26 4.3 18.7 1.0
HE22 C:GLN72 4.4 22.8 1.0
HG3 C:GLN72 4.4 21.3 1.0
H C:HCS503 4.5 26.3 1.0
NE2 C:GLN72 4.5 22.8 1.0
OXT C:HCS503 4.5 23.3 1.0
HA2 C:GLY28 4.6 20.7 1.0
H C:GLY27 4.6 19.5 1.0
N C:GLY298 4.6 18.6 1.0
CA C:CYS299 4.7 17.9 1.0
CG C:GLN72 4.7 21.3 1.0
CB C:ASP26 4.7 19.0 1.0
N C:GLY28 4.8 21.0 1.0
N C:CYS299 4.8 16.7 1.0
HB2 C:GLN72 4.8 20.2 1.0
N C:HCS503 4.8 26.3 1.0
CG C:GLN247 4.9 20.9 1.0
OD2 C:ASP26 4.9 22.8 1.0
CB C:GLN247 4.9 20.4 1.0
CA C:GLY298 4.9 17.6 1.0
H2 C:HCS503 4.9 26.3 1.0
HA3 C:GLY27 5.0 19.2 1.0

Potassium binding site 4 out of 4 in 4m3p

Go back to Potassium Binding Sites List in 4m3p
Potassium binding site 4 out of 4 in the Betaine-Homocysteine S-Methyltransferase From Homo Sapiens Complexed with Homocysteine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Betaine-Homocysteine S-Methyltransferase From Homo Sapiens Complexed with Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K503

b:27.0
occ:1.00
 O D:ASP26 2.7 23.6 1.0
O D:GLY298 2.8 25.4 1.0
OE1 D:GLN72 2.8 28.9 1.0
O D:GLY27 2.8 24.7 1.0
OD1 D:ASP26 2.8 29.0 1.0
O D:HOH684 3.0 39.7 1.0
OE1 D:GLN247 3.1 29.0 1.0
O D:HOH747 3.1 49.7 1.0
HE22 D:GLN247 3.2 27.0 1.0
C D:ASP26 3.4 23.6 1.0
CD D:GLN247 3.5 28.7 1.0
NE2 D:GLN247 3.6 27.0 1.0
C D:GLY27 3.7 26.0 1.0
O D:HOH627 3.7 26.9 1.0
CD D:GLN72 3.8 27.4 1.0
HA D:CYS299 3.8 22.4 1.0
H D:GLY298 3.8 24.2 1.0
HA2 D:GLY27 3.9 22.8 1.0
H D:ASP26 3.9 23.9 1.0
N D:GLY27 3.9 22.6 1.0
C D:GLY298 4.0 21.6 1.0
CG D:ASP26 4.0 26.4 1.0
CA D:GLY27 4.0 22.8 1.0
HB3 D:GLN247 4.2 26.5 1.0
H D:HCS504 4.2 38.7 1.0
HE21 D:GLN247 4.2 27.0 1.0
N D:ASP26 4.3 23.9 1.0
CA D:ASP26 4.3 24.2 1.0
HG3 D:GLN72 4.4 28.2 1.0
HE22 D:GLN72 4.5 27.4 1.0
H D:GLY27 4.6 22.6 1.0
NE2 D:GLN72 4.6 27.4 1.0
OXT D:HCS504 4.6 35.5 1.0
HA2 D:GLY28 4.6 23.6 1.0
N D:HCS504 4.6 38.7 1.0
CG D:GLN72 4.6 28.2 1.0
N D:GLY298 4.6 24.2 1.0
CA D:CYS299 4.7 22.4 1.0
H2 D:HCS504 4.7 38.7 1.0
CB D:ASP26 4.7 24.0 1.0
CG D:GLN247 4.8 28.6 1.0
N D:CYS299 4.8 20.8 1.0
HB2 D:GLN72 4.8 26.9 1.0
N D:GLY28 4.8 24.5 1.0
OD2 D:ASP26 4.9 27.8 1.0
CB D:GLN247 4.9 26.5 1.0
CA D:GLY298 5.0 23.6 1.0
HA3 D:GLY27 5.0 22.8 1.0

Reference:

J.Mladkova, J.Hladilkova, C.E.Diamond, K.Tryon, K.Yamada, T.A.Garrow, P.Jungwirth, M.Koutmos, J.Jiracek. Specific Potassium Ion Interactions Facilitate Homocysteine Binding to Betaine-Homocysteine S-Methyltransferase. Proteins V. 82 2552 2014.
ISSN: ISSN 0887-3585
PubMed: 24895213
DOI: 10.1002/PROT.24619
Page generated: Mon Aug 12 11:33:32 2024

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