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Cadmium in PDB 1q85: Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+ Complex, Se-Met)

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

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

Protein crystallography data

The structure of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+ Complex, Se-Met), PDB code: 1q85 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 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.300, 86.170, 125.880, 90.00, 100.39, 90.00
R / Rfree (%) 24.3 / 28.3

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+ Complex, Se-Met) (pdb code 1q85). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+ Complex, Se-Met), PDB code: 1q85:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 1q85

Go back to Cadmium Binding Sites List in 1q85
Cadmium binding site 1 out of 3 in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+ 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+ Complex, Se-Met) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd601

b:41.1
occ:1.00
SG A:CYS272 2.5 28.1 1.0
SG A:CYS207 2.5 33.6 1.0
SG A:CYS273 2.8 16.7 1.0
OD1 A:ASN234 3.2 29.8 1.0
N A:CYS273 3.3 30.7 1.0
O A:HOH662 3.3 14.7 1.0
CB A:CYS207 3.4 26.5 1.0
CB A:CYS273 3.4 24.8 1.0
CB A:CYS272 3.5 29.7 1.0
O A:HOH665 3.7 6.0 1.0
CA A:CYS207 4.0 25.8 1.0
CA A:CYS273 4.0 27.5 1.0
CG A:ASN234 4.3 28.6 1.0
C A:CYS272 4.4 31.0 1.0
O A:HOH663 4.4 20.5 1.0
CA A:CYS272 4.5 29.6 1.0
ND2 A:ASN234 4.6 30.6 1.0
N A:CYS207 4.6 22.9 1.0
ND2 A:ASN206 4.7 20.3 1.0

Cadmium binding site 2 out of 3 in 1q85

Go back to Cadmium Binding Sites List in 1q85
Cadmium binding site 2 out of 3 in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+ 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+ Complex, Se-Met) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd603

b:45.5
occ:1.00
OD2 A:ASP253 2.5 33.1 1.0
OD1 A:ASP253 2.6 28.4 1.0
CG A:ASP253 2.8 30.3 1.0
CB A:ASP253 4.3 29.6 1.0
O A:HOH640 4.5 35.8 1.0

Cadmium binding site 3 out of 3 in 1q85

Go back to Cadmium Binding Sites List in 1q85
Cadmium binding site 3 out of 3 in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+ Complex, Se-Met)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+ Complex, Se-Met) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd602

b:58.9
occ:1.00
SG B:CYS272 2.6 47.0 1.0
SG B:CYS207 2.7 43.4 1.0
ND2 B:ASN234 3.0 49.5 1.0
CB B:CYS207 3.2 39.6 1.0
CB B:CYS273 3.2 44.0 1.0
O B:HOH633 3.2 23.5 1.0
SG B:CYS273 3.3 25.3 1.0
N B:CYS273 3.4 48.5 1.0
CB B:CYS272 3.5 47.6 1.0
CA B:CYS207 3.8 41.0 1.0
CG B:ASN234 3.9 49.4 1.0
OD1 B:ASN234 3.9 46.5 1.0
CA B:CYS273 3.9 47.5 1.0
C B:CYS272 4.4 48.7 1.0
N B:CYS207 4.5 40.3 1.0
CA B:CYS272 4.5 48.1 1.0
O B:HOH634 4.5 17.6 1.0
ND2 B:ASN206 4.7 38.4 1.0
N B:SER208 4.9 43.2 1.0
C B:CYS207 5.0 41.8 1.0
O B:CYS273 5.0 51.4 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: Wed Oct 28 09:55:32 2020
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