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Zinc in PDB 3bof: Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine

Enzymatic activity of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine

All present enzymatic activity of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine:
2.1.1.13;

Protein crystallography data

The structure of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine, PDB code: 3bof was solved by M.Koutmos, J.L.Smith, M.L.Ludwig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.68 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.067, 86.308, 125.879, 90.00, 100.03, 90.00
R / Rfree (%) 19.5 / 22.2

Other elements in 3bof:

The structure of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine also contains other interesting chemical elements:

Potassium (K) 2 atoms
Yttrium (Y) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine (pdb code 3bof). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine, PDB code: 3bof:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3bof

Go back to Zinc Binding Sites List in 3bof
Zinc binding site 1 out of 2 in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:14.6
occ:1.00
SG A:CYS272 2.3 12.9 1.0
SD A:HCS711 2.3 12.5 1.0
SG A:CYS273 2.4 16.1 1.0
SG A:CYS207 2.4 15.7 1.0
CB A:CYS207 3.3 12.4 1.0
CG A:HCS711 3.3 13.2 1.0
N A:CYS273 3.5 15.0 1.0
CB A:CYS272 3.6 13.4 1.0
CB A:CYS273 3.6 13.3 1.0
CB A:HCS711 3.7 11.5 1.0
OD1 A:ASN234 4.1 17.4 1.0
CA A:CYS273 4.2 13.5 1.0
CA A:CYS207 4.3 13.9 1.0
ND2 A:ASN206 4.3 11.0 1.0
O A:HOH1121 4.4 28.3 1.0
C A:CYS272 4.4 14.6 1.0
CA A:CYS272 4.4 13.4 1.0
OG1 A:THR147 4.7 10.8 1.0
O A:HOH724 4.9 13.5 1.0
N A:CYS207 5.0 12.9 1.0
CG2 A:THR147 5.0 12.3 1.0
O A:HOH1122 5.0 36.7 1.0

Zinc binding site 2 out of 2 in 3bof

Go back to Zinc Binding Sites List in 3bof
Zinc binding site 2 out of 2 in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ and Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:20.2
occ:1.00
SG B:CYS207 2.3 21.8 1.0
SD B:HCS712 2.3 17.5 1.0
SG B:CYS272 2.3 19.1 1.0
SG B:CYS273 2.5 21.2 1.0
CB B:CYS207 3.2 19.4 1.0
CG B:HCS712 3.3 17.4 1.0
N B:CYS273 3.5 19.4 1.0
CB B:CYS273 3.5 20.8 1.0
CB B:CYS272 3.6 19.0 1.0
CB B:HCS712 3.8 18.2 1.0
CA B:CYS273 4.1 20.1 1.0
CA B:CYS207 4.3 19.5 1.0
ND2 B:ASN206 4.4 17.0 1.0
C B:CYS272 4.5 19.3 1.0
CA B:CYS272 4.5 18.8 1.0
OG1 B:THR147 4.7 17.2 1.0
N B:CYS207 5.0 19.2 1.0
O B:HOH769 5.0 22.5 1.0

Reference:

M.Koutmos, R.Pejchal, T.M.Bomer, R.G.Matthews, J.L.Smith, M.L.Ludwig. Metal Active Site Elasticity Linked to Activation of Homocysteine in Methionine Synthases. Proc.Natl.Acad.Sci.Usa V. 105 3286 2008.
ISSN: ISSN 0027-8424
PubMed: 18296644
DOI: 10.1073/PNAS.0709960105
Page generated: Wed Dec 16 04:09:24 2020

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