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Zinc in PDB 3f0f: Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp

Enzymatic activity of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp

All present enzymatic activity of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp:
4.6.1.12;

Protein crystallography data

The structure of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp, PDB code: 3f0f was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.078, 66.457, 131.465, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24.6

Other elements in 3f0f:

The structure of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp (pdb code 3f0f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp, PDB code: 3f0f:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3f0f

Go back to Zinc Binding Sites List in 3f0f
Zinc binding site 1 out of 3 in the Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn165

b:34.2
occ:1.00
 OD2 A:ASP10 2.0 25.8 1.0
NE2 A:HIS12 2.1 24.5 1.0
ND1 A:HIS44 2.2 23.4 1.0
O3 A:GOL163 2.2 24.9 1.0
CG A:ASP10 2.8 24.8 1.0
C3 A:GOL163 2.8 33.5 1.0
OD1 A:ASP10 2.8 23.6 1.0
CD2 A:HIS12 3.0 25.3 1.0
CE1 A:HIS44 3.1 22.0 1.0
CE1 A:HIS12 3.1 25.4 1.0
CG A:HIS44 3.1 22.1 1.0
CB A:HIS44 3.5 21.8 1.0
NE2 A:HIS44 4.2 21.6 1.0
CG A:HIS12 4.2 26.0 1.0
ND1 A:HIS12 4.2 25.7 1.0
CB A:ASP10 4.2 24.0 1.0
C2 A:GOL163 4.2 36.1 1.0
CD2 A:HIS44 4.2 22.2 1.0
NZ B:LYS134 4.3 24.3 1.0
O A:HOH211 4.4 14.9 1.0
CA A:VAL41 4.8 22.4 1.0
O A:ASP40 4.8 23.4 1.0
O2 A:GOL163 4.9 37.8 1.0
O A:VAL11 4.9 25.2 1.0

Zinc binding site 2 out of 3 in 3f0f

Go back to Zinc Binding Sites List in 3f0f
Zinc binding site 2 out of 3 in the Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn163

b:55.4
occ:1.00
 OD2 B:ASP10 2.1 22.2 1.0
ND1 B:HIS44 2.1 24.4 1.0
O C:HOH198 2.1 40.0 1.0
NE2 B:HIS12 2.3 27.1 1.0
CG B:ASP10 2.8 22.3 1.0
OD1 B:ASP10 3.0 20.7 1.0
CE1 B:HIS44 3.0 24.2 1.0
CG B:HIS44 3.1 23.2 1.0
CD2 B:HIS12 3.2 27.0 1.0
CE1 B:HIS12 3.3 27.1 1.0
CB B:HIS44 3.5 21.8 1.0
O B:HOH215 4.0 38.3 1.0
NE2 B:HIS44 4.2 25.6 1.0
NZ C:LYS134 4.2 30.1 1.0
CB B:ASP10 4.2 22.1 1.0
CD2 B:HIS44 4.2 23.5 1.0
CG B:HIS12 4.3 27.1 1.0
ND1 B:HIS12 4.3 28.1 1.0
CA B:VAL41 4.8 23.0 1.0
O B:ASP40 4.8 24.1 1.0

Zinc binding site 3 out of 3 in 3f0f

Go back to Zinc Binding Sites List in 3f0f
Zinc binding site 3 out of 3 in the Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn164

b:51.0
occ:1.00
 O A:HOH203 2.0 30.8 1.0
ND1 C:HIS44 2.0 30.4 1.0
OD2 C:ASP10 2.2 28.7 1.0
NE2 C:HIS12 2.2 35.7 1.0
CG C:ASP10 2.9 27.4 1.0
CE1 C:HIS44 2.9 31.1 1.0
OD1 C:ASP10 3.0 27.9 1.0
CG C:HIS44 3.1 29.1 1.0
CD2 C:HIS12 3.1 35.5 1.0
CE1 C:HIS12 3.2 35.8 1.0
CB C:HIS44 3.5 27.3 1.0
NE2 C:HIS44 4.1 31.5 1.0
CD2 C:HIS44 4.1 30.4 1.0
NZ A:LYS134 4.2 32.7 1.0
CB C:ASP10 4.3 26.8 1.0
CG C:HIS12 4.3 34.1 1.0
ND1 C:HIS12 4.3 35.6 1.0
O A:HOH224 4.4 51.1 1.0
O C:HOH186 4.7 34.6 1.0
CA C:VAL41 4.8 30.0 1.0
O C:VAL11 4.9 29.8 1.0
O C:ASP40 4.9 31.9 1.0
CA C:HIS44 5.0 27.0 1.0

Reference:

L.Baugh, L.A.Gallagher, R.Patrapuvich, M.C.Clifton, A.S.Gardberg, T.E.Edwards, B.Armour, D.W.Begley, S.H.Dieterich, D.M.Dranow, J.Abendroth, J.W.Fairman, D.Fox, B.L.Staker, I.Phan, A.Gillespie, R.Choi, S.Nakazawa-Hewitt, M.T.Nguyen, A.Napuli, L.Barrett, G.W.Buchko, R.Stacy, P.J.Myler, L.J.Stewart, C.Manoil, W.C.Van Voorhis. Combining Functional and Structural Genomics to Sample the Essential Burkholderia Structome. Plos One V. 8 53851 2013.
ISSN: ESSN 1932-6203
PubMed: 23382856
DOI: 10.1371/JOURNAL.PONE.0053851
Page generated: Thu Oct 24 13:00:38 2024

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