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Zinc 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:

Potassium (K) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Betaine-Homocysteine S-Methyltransferase From Homo Sapiens Complexed with Homocysteine, PDB code: 4m3p:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4m3p

Go back to Zinc Binding Sites List in 4m3p
Zinc 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 Zinc with other atoms in the Zn 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:Zn701

b:31.6
occ:1.00
 SD A:HCS703 2.4 35.1 1.0
SG A:CYS300 2.4 26.9 1.0
SG A:CYS217 2.4 27.8 1.0
SG A:CYS299 2.4 28.9 1.0
H A:CYS300 2.6 21.7 1.0
HG3 A:HCS703 2.8 36.0 1.0
HB2 A:CYS217 2.9 24.1 1.0
CG A:HCS703 3.1 36.0 1.0
CB A:CYS217 3.2 24.1 1.0
N A:CYS300 3.4 21.7 1.0
HB3 A:CYS299 3.5 25.3 1.0
HB2 A:CYS300 3.5 23.7 1.0
CB A:CYS300 3.5 23.7 1.0
CB A:CYS299 3.6 25.3 1.0
HB2 A:HCS703 3.7 34.2 1.0
HA A:CYS217 3.8 25.9 1.0
HG2 A:HCS703 3.9 36.0 1.0
HB3 A:CYS217 3.9 24.1 1.0
CB A:HCS703 4.0 34.2 1.0
CA A:CYS300 4.1 21.4 1.0
HD22 A:ASN216 4.1 28.5 1.0
CA A:CYS217 4.1 25.9 1.0
HD23 A:LEU249 4.2 22.0 1.0
HE1 A:TYR160 4.3 39.5 1.0
HD1 A:TYR160 4.3 37.2 1.0
HD21 A:LEU249 4.3 22.0 1.0
HB3 A:HCS703 4.3 34.2 1.0
HB2 A:CYS299 4.3 25.3 1.0
HB3 A:CYS300 4.4 23.7 1.0
C A:CYS299 4.4 22.3 1.0
HA A:CYS300 4.5 21.4 1.0
CA A:CYS299 4.5 22.8 1.0
HA A:CYS299 4.6 22.8 1.0
H A:HIS218 4.7 26.6 1.0
CD2 A:LEU249 4.7 22.0 1.0
ND2 A:ASN216 4.7 28.5 1.0
HZ A:PHE261 4.8 28.5 1.0
CE1 A:TYR160 4.8 39.5 1.0
CD1 A:TYR160 4.8 37.2 1.0
HD21 A:ASN216 4.8 28.5 1.0
O A:HOH808 4.9 25.9 1.0
N A:CYS217 4.9 24.9 1.0

Zinc binding site 2 out of 4 in 4m3p

Go back to Zinc Binding Sites List in 4m3p
Zinc 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 Zinc with other atoms in the Zn 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:Zn502

b:32.1
occ:1.00
 SD B:HCS504 2.3 38.4 1.0
SG B:CYS217 2.4 30.0 1.0
SG B:CYS300 2.4 24.3 1.0
SG B:CYS299 2.5 29.4 1.0
H B:CYS300 2.6 22.1 1.0
HB2 B:CYS217 2.9 27.0 1.0
CB B:CYS217 3.2 27.0 1.0
HG3 B:HCS504 3.4 36.8 1.0
N B:CYS300 3.4 22.1 1.0
CG B:HCS504 3.4 36.8 1.0
HB3 B:CYS299 3.5 23.0 1.0
HB2 B:CYS300 3.6 22.6 1.0
CB B:CYS300 3.6 22.6 1.0
HB2 B:HCS504 3.6 36.4 1.0
CB B:CYS299 3.7 23.0 1.0
HA B:CYS217 3.8 27.2 1.0
HB3 B:CYS217 3.9 27.0 1.0
CB B:HCS504 4.0 36.4 1.0
HD22 B:ASN216 4.1 30.0 1.0
CA B:CYS300 4.1 21.1 1.0
CA B:CYS217 4.1 27.2 1.0
HE1 B:TYR160 4.1 36.8 1.0
HD23 B:LEU249 4.2 21.4 1.0
HD1 B:TYR160 4.2 38.3 1.0
HG2 B:HCS504 4.3 36.8 1.0
HB3 B:HCS504 4.3 36.4 1.0
HD21 B:LEU249 4.3 21.4 1.0
HB3 B:CYS300 4.4 22.6 1.0
HB2 B:CYS299 4.4 23.0 1.0
C B:CYS299 4.4 20.9 1.0
HA B:CYS300 4.5 21.1 1.0
CA B:CYS299 4.5 21.4 1.0
HA B:CYS299 4.6 21.4 1.0
H B:HIS218 4.7 26.1 1.0
ND2 B:ASN216 4.7 30.0 1.0
CD2 B:LEU249 4.7 21.4 1.0
CE1 B:TYR160 4.7 36.8 1.0
HD21 B:ASN216 4.7 30.0 1.0
CD1 B:TYR160 4.7 38.3 1.0
O B:HOH642 4.7 26.5 1.0
HZ B:PHE261 4.8 23.6 1.0
N B:CYS217 4.9 25.6 1.0
HD22 B:LEU249 5.0 21.4 1.0

Zinc binding site 3 out of 4 in 4m3p

Go back to Zinc Binding Sites List in 4m3p
Zinc 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 Zinc with other atoms in the Zn 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:Zn501

b:25.1
occ:1.00
 SG C:CYS217 2.3 20.8 1.0
SG C:CYS300 2.4 19.4 1.0
SD C:HCS503 2.4 26.7 1.0
SG C:CYS299 2.5 23.7 1.0
H C:CYS300 2.6 19.0 1.0
HB2 C:CYS217 2.9 19.3 1.0
CB C:CYS217 3.1 19.3 1.0
HG3 C:HCS503 3.3 27.0 1.0
CG C:HCS503 3.5 27.0 1.0
HB2 C:CYS300 3.5 19.5 1.0
N C:CYS300 3.5 19.0 1.0
HB3 C:CYS299 3.5 20.8 1.0
CB C:CYS300 3.5 19.5 1.0
CB C:CYS299 3.6 20.8 1.0
HA C:CYS217 3.7 18.9 1.0
HB2 C:HCS503 3.8 26.1 1.0
HB3 C:CYS217 3.9 19.3 1.0
HD22 C:ASN216 3.9 21.9 1.0
HD23 C:LEU249 4.0 19.2 1.0
CA C:CYS217 4.0 18.9 1.0
CA C:CYS300 4.1 18.6 1.0
CB C:HCS503 4.1 26.1 1.0
HG2 C:HCS503 4.3 27.0 1.0
HD21 C:LEU249 4.3 19.2 1.0
HB2 C:CYS299 4.3 20.8 1.0
HB3 C:CYS300 4.3 19.5 1.0
HB3 C:HCS503 4.5 26.1 1.0
HA C:CYS300 4.5 18.6 1.0
C C:CYS299 4.5 18.3 1.0
HD1 C:TYR160 4.5 31.4 1.0
CA C:CYS299 4.5 17.9 1.0
ND2 C:ASN216 4.6 21.9 1.0
CD2 C:LEU249 4.6 19.2 1.0
HD21 C:ASN216 4.6 21.9 1.0
H C:HIS218 4.6 19.4 1.0
HE1 C:TYR160 4.6 31.0 1.0
HA C:CYS299 4.7 17.9 1.0
N C:CYS217 4.7 20.2 1.0
O C:HOH628 4.7 22.3 1.0
HZ C:PHE261 4.8 20.8 1.0
H C:CYS217 4.8 20.2 1.0
HD22 C:LEU249 4.9 19.2 1.0
CD1 C:TYR160 4.9 31.4 1.0
CE1 C:TYR160 5.0 31.0 1.0

Zinc binding site 4 out of 4 in 4m3p

Go back to Zinc Binding Sites List in 4m3p
Zinc 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 Zinc with other atoms in the Zn 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:Zn502

b:32.2
occ:1.00
 SG D:CYS217 2.3 28.0 1.0
SG D:CYS299 2.4 27.5 1.0
SG D:CYS300 2.4 25.0 1.0
SD D:HCS504 2.4 41.8 1.0
H D:CYS300 2.7 23.4 1.0
HB2 D:CYS217 2.9 26.0 1.0
CB D:CYS217 3.1 26.0 1.0
HB3 D:CYS299 3.5 23.8 1.0
N D:CYS300 3.5 23.4 1.0
HG3 D:HCS504 3.5 40.8 1.0
CG D:HCS504 3.5 40.8 1.0
CB D:CYS299 3.6 23.8 1.0
HB2 D:HCS504 3.6 39.3 1.0
CB D:CYS300 3.6 22.9 1.0
HB2 D:CYS300 3.6 22.9 1.0
HA D:CYS217 3.8 26.3 1.0
HB3 D:CYS217 3.9 26.0 1.0
CB D:HCS504 4.0 39.3 1.0
HD23 D:LEU249 4.1 21.2 1.0
CA D:CYS217 4.1 26.3 1.0
CA D:CYS300 4.1 21.7 1.0
HE1 D:TYR160 4.1 37.3 1.0
HD22 D:ASN216 4.2 32.2 1.0
HD21 D:LEU249 4.2 21.2 1.0
HD1 D:TYR160 4.3 38.1 1.0
HB2 D:CYS299 4.3 23.8 1.0
HB3 D:HCS504 4.3 39.3 1.0
HG2 D:HCS504 4.4 40.8 1.0
C D:CYS299 4.4 21.9 1.0
HB3 D:CYS300 4.4 22.9 1.0
CA D:CYS299 4.5 22.4 1.0
HA D:CYS300 4.5 21.7 1.0
CD2 D:LEU249 4.6 21.2 1.0
H D:HIS218 4.6 28.1 1.0
HA D:CYS299 4.6 22.4 1.0
O D:HOH622 4.7 25.1 1.0
CE1 D:TYR160 4.7 37.3 1.0
N D:CYS217 4.8 26.8 1.0
ND2 D:ASN216 4.8 32.2 1.0
CD1 D:TYR160 4.8 38.1 1.0
HZ D:PHE261 4.8 24.5 1.0
HD21 D:ASN216 4.9 32.2 1.0
H D:CYS217 4.9 26.8 1.0
HD22 D:LEU249 4.9 21.2 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: Sun Oct 27 02:16:28 2024

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