Atomistry » Cadmium » PDB 1jv4-1mwr » 1q8j
Atomistry »
  Cadmium »
    PDB 1jv4-1mwr »
      1q8j »

Cadmium in PDB 1q8j: Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+, Hcy, Methyltetrahydrofolate Complex)

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

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

Protein crystallography data

The structure of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+, Hcy, Methyltetrahydrofolate Complex), PDB code: 1q8j 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 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.980, 86.070, 125.820, 90.00, 100.30, 90.00
R / Rfree (%) 23.1 / 26.7

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+, Hcy, Methyltetrahydrofolate Complex) (pdb code 1q8j). 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+, Hcy, Methyltetrahydrofolate Complex), PDB code: 1q8j:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 1q8j

Go back to Cadmium Binding Sites List in 1q8j
Cadmium binding site 1 out of 2 in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+, Hcy, Methyltetrahydrofolate Complex)


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+, Hcy, Methyltetrahydrofolate Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd601

b:29.6
occ:1.00
SG A:CYS272 2.4 22.6 1.0
SG A:CYS273 2.5 27.7 1.0
SD A:HCS701 2.6 24.8 1.0
SG A:CYS207 2.7 28.0 1.0
CB A:CYS207 3.4 19.5 1.0
CG A:HCS701 3.6 26.8 1.0
N A:CYS273 3.6 26.4 1.0
CB A:CYS273 3.7 25.1 1.0
CB A:CYS272 3.7 23.1 1.0
OD1 A:ASN234 3.9 26.3 1.0
CB A:HCS701 4.0 27.0 1.0
CA A:CYS273 4.3 23.9 1.0
CA A:CYS207 4.3 21.3 1.0
ND2 A:ASN206 4.5 18.8 1.0
C A:CYS272 4.6 24.9 1.0
CA A:CYS272 4.6 22.5 1.0
OG1 A:THR147 4.8 19.7 1.0
N A:CYS207 4.9 18.6 1.0
CG A:ASN234 5.0 27.5 1.0

Cadmium binding site 2 out of 2 in 1q8j

Go back to Cadmium Binding Sites List in 1q8j
Cadmium binding site 2 out of 2 in the Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+, Hcy, Methyltetrahydrofolate Complex)


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+, Hcy, Methyltetrahydrofolate Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd602

b:34.6
occ:1.00
SD B:HCS702 2.3 32.4 1.0
SG B:CYS207 2.4 35.8 1.0
SG B:CYS272 2.5 31.6 1.0
SG B:CYS273 2.7 33.9 1.0
CB B:CYS207 3.3 35.0 1.0
CG B:HCS702 3.3 31.1 1.0
N B:CYS273 3.5 32.0 1.0
CB B:CYS273 3.5 33.8 1.0
CB B:HCS702 3.7 31.0 1.0
OD1 B:ASN234 3.8 47.3 1.0
CB B:CYS272 3.8 30.8 1.0
CA B:CYS273 4.1 34.1 1.0
CA B:CYS207 4.3 34.4 1.0
ND2 B:ASN206 4.5 24.7 1.0
C B:CYS272 4.6 33.0 1.0
CA B:CYS272 4.7 31.6 1.0
CG B:ASN234 4.8 45.8 1.0
OG1 B:THR147 4.8 27.9 1.0
N B:CYS207 4.9 31.4 1.0
ND2 B:ASN234 5.0 43.3 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 12:22:16 2020
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy