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Cadmium in PDB 1q8a: Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+:L-Hcy Complex, Se-Met)

Enzymatic activity of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+:L-Hcy Complex, Se-Met)

All present enzymatic activity of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+:L-Hcy Complex, Se-Met):
2.1.1.13;

Protein crystallography data

The structure of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+:L-Hcy Complex, Se-Met), PDB code: 1q8a was solved by J.C.Evans, D.P.Huddler, M.T.Hilgers, G.Romanchuk, R.G.Matthews, M.L.Ludwig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.120, 86.190, 126.080, 90.00, 99.99, 90.00
R / Rfree (%) 21.4 / 24.2

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+:L-Hcy Complex, Se-Met) (pdb code 1q8a). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+:L-Hcy Complex, Se-Met), PDB code: 1q8a:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 1q8a

Go back to Cadmium Binding Sites List in 1q8a
Cadmium binding site 1 out of 2 in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+:L-Hcy Complex, Se-Met)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+:L-Hcy Complex, Se-Met) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd601

b:21.4
occ:1.00
 SG A:CYS272 2.4 16.4 1.0
SD A:HCS701 2.5 14.0 1.0
SG A:CYS273 2.6 23.0 1.0
SG A:CYS207 2.7 22.3 1.0
CB A:CYS207 3.4 16.6 1.0
CG A:HCS701 3.4 19.1 1.0
N A:CYS273 3.6 21.5 1.0
CB A:CYS273 3.7 20.3 1.0
CB A:CYS272 3.8 19.5 1.0
CB A:HCS701 3.9 17.2 1.0
OD1 A:ASN234 4.0 22.1 1.0
CA A:CYS273 4.2 20.7 1.0
CA A:CYS207 4.3 18.6 1.0
ND2 A:ASN206 4.4 13.8 1.0
C A:CYS272 4.6 21.2 1.0
CA A:CYS272 4.6 19.4 1.0
OG1 A:THR147 4.8 15.3 1.0
N A:CYS207 5.0 16.5 1.0

Cadmium binding site 2 out of 2 in 1q8a

Go back to Cadmium Binding Sites List in 1q8a
Cadmium binding site 2 out of 2 in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+:L-Hcy Complex, Se-Met)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+:L-Hcy Complex, Se-Met) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd602

b:23.7
occ:1.00
 SG B:CYS272 2.4 19.7 1.0
SG B:CYS207 2.5 30.6 1.0
SD B:HCS702 2.5 15.8 1.0
SG B:CYS273 2.6 25.9 1.0
CB B:CYS207 3.4 23.0 1.0
CG B:HCS702 3.4 21.4 1.0
N B:CYS273 3.6 21.9 1.0
CB B:CYS273 3.7 24.7 1.0
OD1 B:ASN234 3.7 36.5 1.0
CB B:CYS272 3.8 21.2 1.0
CB B:HCS702 3.9 18.9 1.0
CA B:CYS273 4.2 23.9 1.0
CA B:CYS207 4.4 23.7 1.0
ND2 B:ASN206 4.5 20.2 1.0
C B:CYS272 4.6 23.0 1.0
CA B:CYS272 4.6 21.4 1.0
CG B:ASN234 4.7 35.5 1.0
OG1 B:THR147 4.9 19.3 1.0

Reference:

J.C.Evans, D.P.Huddler, M.T.Hilgers, G.Romanchuk, R.G.Matthews, M.L.Ludwig. Structures of the N-Terminal Modules Imply Large Domain Motions During Catalysis By Methionine Synthase. Proc.Natl.Acad.Sci.Usa V. 101 3729 2004.
ISSN: ISSN 0027-8424
PubMed: 14752199
DOI: 10.1073/PNAS.0308082100
Page generated: Fri Aug 28 12:22:09 2020
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