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

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

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

Protein crystallography data

The structure of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+, PDB code: 3bol 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) 47.62 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.626, 85.841, 125.587, 90.00, 100.67, 90.00
R / Rfree (%) 19.3 / 22.8

Other elements in 3bol:

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

Zinc binding site 1 out of 3 in 3bol

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


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+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:21.2
occ:1.00
 OD1 A:ASN234 2.1 15.3 1.0
SG A:CYS207 2.2 18.0 1.0
SG A:CYS273 2.3 21.8 1.0
SG A:CYS272 2.4 17.5 1.0
CB A:CYS207 3.1 14.8 1.0
CG A:ASN234 3.1 17.2 1.0
N A:CYS273 3.3 16.8 1.0
CB A:CYS273 3.3 17.7 1.0
CA A:CYS207 3.4 15.4 1.0
CB A:CYS272 3.4 16.4 1.0
ND2 A:ASN234 3.5 17.7 1.0
CA A:CYS273 3.9 17.2 1.0
O A:HOH1061 4.1 40.6 1.0
N A:CYS207 4.3 14.5 1.0
C A:CYS272 4.3 16.9 1.0
N A:SER208 4.3 16.7 1.0
CA A:CYS272 4.4 15.8 1.0
O A:HOH738 4.4 27.8 1.0
C A:CYS207 4.4 15.7 1.0
O A:HOH774 4.5 28.2 1.0
CB A:ASN234 4.5 16.5 1.0
CA A:ASN234 4.8 15.2 1.0

Zinc binding site 2 out of 3 in 3bol

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


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+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:29.7
occ:0.70
 ZN B:ZN703 1.9 12.9 0.3
SG B:CYS272 2.2 27.3 1.0
SG B:CYS273 2.4 32.7 1.0
SD B:HCS710 2.5 22.2 0.7
SG B:CYS207 2.7 31.7 1.0
CG B:HCS710 3.3 21.6 0.7
N B:CYS273 3.4 24.9 1.0
CB B:CYS207 3.5 26.2 1.0
CB B:CYS272 3.6 24.4 1.0
CB B:CYS273 3.6 26.0 1.0
OD1 B:ASN234 3.7 33.4 1.0
CB B:HCS710 3.9 22.2 0.7
CA B:CYS273 4.1 26.4 1.0
CA B:CYS207 4.3 26.4 1.0
CA B:CYS272 4.4 24.1 1.0
C B:CYS272 4.4 24.3 1.0
ND2 B:ASN206 4.4 17.9 1.0
CG B:ASN234 4.8 31.6 1.0
OG1 B:THR147 4.9 20.3 1.0
N B:CYS207 5.0 23.9 1.0

Zinc binding site 3 out of 3 in 3bol

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima Complexed with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:12.9
occ:0.30
 SG B:CYS207 1.7 31.7 1.0
ZN B:ZN702 1.9 29.7 0.7
OD1 B:ASN234 2.1 33.4 1.0
CB B:CYS207 2.7 26.2 1.0
SG B:CYS273 2.9 32.7 1.0
SG B:CYS272 3.0 27.3 1.0
CG B:ASN234 3.1 31.6 1.0
CA B:CYS207 3.1 26.4 1.0
CB B:CYS273 3.3 26.0 1.0
ND2 B:ASN234 3.4 30.2 1.0
N B:CYS273 3.6 24.9 1.0
CB B:CYS272 3.6 24.4 1.0
N B:SER208 4.0 27.5 1.0
SD B:HCS710 4.1 22.2 0.7
C B:CYS207 4.1 26.3 1.0
CA B:CYS273 4.1 26.4 1.0
N B:CYS207 4.1 23.9 1.0
O B:HOH1036 4.2 44.3 1.0
CB B:ASN234 4.4 28.3 1.0
C B:CYS272 4.6 24.3 1.0
CA B:CYS272 4.7 24.1 1.0
CA B:ASN234 4.8 27.6 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 04:09:23 2020

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