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Zinc in PDB 3rpd: The Structure of A B12-Independent Methionine Synthase From Shewanella Sp. W3-18-1 in Complex with Selenomethionine.

Enzymatic activity of The Structure of A B12-Independent Methionine Synthase From Shewanella Sp. W3-18-1 in Complex with Selenomethionine.

All present enzymatic activity of The Structure of A B12-Independent Methionine Synthase From Shewanella Sp. W3-18-1 in Complex with Selenomethionine.:
2.1.1.14;

Protein crystallography data

The structure of The Structure of A B12-Independent Methionine Synthase From Shewanella Sp. W3-18-1 in Complex with Selenomethionine., PDB code: 3rpd was solved by M.E.Cuff, H.Li, C.Hatzos-Skintges, C.Tesar, J.Bearden, A.Clancy, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.50 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.099, 89.371, 86.526, 90.00, 92.45, 90.00
R / Rfree (%) 16.4 / 18.9

Zinc Binding Sites:

The binding sites of Zinc atom in the The Structure of A B12-Independent Methionine Synthase From Shewanella Sp. W3-18-1 in Complex with Selenomethionine. (pdb code 3rpd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Structure of A B12-Independent Methionine Synthase From Shewanella Sp. W3-18-1 in Complex with Selenomethionine., PDB code: 3rpd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3rpd

Go back to Zinc Binding Sites List in 3rpd
Zinc binding site 1 out of 2 in the The Structure of A B12-Independent Methionine Synthase From Shewanella Sp. W3-18-1 in Complex with Selenomethionine.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of A B12-Independent Methionine Synthase From Shewanella Sp. W3-18-1 in Complex with Selenomethionine. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn355

b:11.5
occ:1.00
NE2 A:HIS221 2.1 10.6 1.0
SG A:CYS322 2.2 11.3 1.0
SG A:CYS223 2.3 12.3 1.0
SE A:MSE356 2.5 13.3 1.0
CD2 A:HIS221 3.0 10.8 1.0
CE1 A:HIS221 3.1 11.9 1.0
CB A:CYS223 3.2 11.8 1.0
CB A:CYS322 3.3 10.6 1.0
CE A:MSE356 3.3 13.0 1.0
CG A:MSE356 3.5 12.8 1.0
CA A:CYS322 3.8 10.1 1.0
CB A:MSE356 4.0 11.3 1.0
CG A:HIS221 4.2 10.1 1.0
O A:ASN321 4.2 10.5 1.0
ND1 A:HIS221 4.2 10.8 1.0
CA A:CYS223 4.6 12.0 1.0
N A:GLY323 4.6 10.8 1.0
N A:GLY225 4.8 13.5 1.0
CA A:GLY225 4.8 14.1 1.0
C A:CYS322 4.8 10.2 1.0
N A:CYS223 4.8 11.7 1.0
N A:CYS322 4.9 9.9 1.0
C A:ASN321 5.0 9.4 1.0
C A:GLY225 5.0 13.8 1.0

Zinc binding site 2 out of 2 in 3rpd

Go back to Zinc Binding Sites List in 3rpd
Zinc binding site 2 out of 2 in the The Structure of A B12-Independent Methionine Synthase From Shewanella Sp. W3-18-1 in Complex with Selenomethionine.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of A B12-Independent Methionine Synthase From Shewanella Sp. W3-18-1 in Complex with Selenomethionine. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn355

b:10.3
occ:1.00
NE2 B:HIS221 2.1 8.6 1.0
SG B:CYS322 2.3 10.6 1.0
SG B:CYS223 2.3 10.4 1.0
SE B:MSE356 2.5 12.3 1.0
CD2 B:HIS221 3.0 8.1 1.0
CE1 B:HIS221 3.1 8.5 1.0
CB B:CYS223 3.3 9.8 1.0
CB B:CYS322 3.3 9.4 1.0
CE B:MSE356 3.3 13.2 1.0
CG B:MSE356 3.6 9.9 1.0
CA B:CYS322 3.8 9.6 1.0
CB B:MSE356 4.0 9.9 1.0
CG B:HIS221 4.2 8.2 1.0
O B:ASN321 4.2 9.2 1.0
ND1 B:HIS221 4.2 9.1 1.0
CA B:CYS223 4.6 9.7 1.0
N B:GLY323 4.6 10.2 1.0
N B:GLY225 4.7 11.3 1.0
C B:CYS322 4.8 10.0 1.0
CA B:GLY225 4.8 10.5 1.0
N B:CYS223 4.8 9.1 1.0
N B:CYS322 4.9 9.1 1.0
C B:GLY225 5.0 10.4 1.0
C B:ASN321 5.0 9.8 1.0

Reference:

M.E.Cuff, H.Li, C.Hatzos-Skintges, C.Tesar, J.Bearden, A.Clancy, A.Joachimiak. The Structure of A B12-Independent Methionine Synthase From Shewanella Sp. W3-18-1 in Complex with Selenomethionine. To Be Published.
Page generated: Wed Dec 16 04:47:43 2020

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