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Zinc in PDB 3iew: Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Bound Ctp and Cdp

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

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

Protein crystallography data

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Bound Ctp and Cdp, PDB code: 3iew was solved by B.L.Staker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.703, 67.548, 60.152, 90.00, 95.85, 90.00
R / Rfree (%) 19.9 / 24.8

Zinc Binding Sites:

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

Zinc binding site 1 out of 3 in 3iew

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Bound Ctp and Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:39.8
occ:1.00
OD2 A:ASP10 2.1 28.7 1.0
NE2 A:HIS12 2.1 31.4 1.0
ND1 A:HIS44 2.2 25.4 1.0
O2B B:CTP901 2.2 58.0 1.0
O1G B:CTP901 2.7 64.6 1.0
CG A:ASP10 2.9 26.5 1.0
OD1 A:ASP10 3.1 27.2 1.0
CD2 A:HIS12 3.1 29.2 1.0
CE1 A:HIS12 3.1 32.1 1.0
CE1 A:HIS44 3.1 26.4 1.0
CG A:HIS44 3.2 22.9 1.0
PB B:CTP901 3.4 59.0 1.0
CB A:HIS44 3.5 21.1 1.0
O1B B:CTP901 3.7 58.1 1.0
O A:HOH219 3.8 25.6 1.0
PG B:CTP901 3.9 63.7 1.0
O3B B:CTP901 3.9 61.0 1.0
NZ B:LYS134 4.1 36.0 1.0
ND1 A:HIS12 4.2 30.4 1.0
CG A:HIS12 4.2 28.6 1.0
NE2 A:HIS44 4.3 25.8 1.0
CB A:ASP10 4.3 25.7 1.0
CD2 A:HIS44 4.3 22.9 1.0
O3G B:CTP901 4.6 64.3 1.0
O3A B:CTP901 4.8 55.7 1.0
O A:ASP40 4.8 24.2 1.0
CA A:VAL41 4.8 22.4 1.0
O A:VAL11 4.9 26.0 1.0

Zinc binding site 2 out of 3 in 3iew

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Bound Ctp and Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:73.4
occ:1.00
NE2 B:HIS12 1.9 39.1 1.0
ND1 B:HIS44 2.2 34.5 1.0
O2B C:CDP901 2.2 62.6 1.0
OD2 B:ASP10 2.2 33.4 1.0
CE1 B:HIS12 2.9 39.4 1.0
CE1 B:HIS44 2.9 35.1 1.0
CD2 B:HIS12 3.0 39.1 1.0
CG B:ASP10 3.1 30.5 1.0
OD1 B:ASP10 3.2 28.2 1.0
CG B:HIS44 3.3 31.1 1.0
O C:HOH196 3.5 39.1 1.0
PB C:CDP901 3.5 64.1 1.0
CB B:HIS44 3.7 29.1 1.0
O3B C:CDP901 4.0 64.6 1.0
ND1 B:HIS12 4.0 38.4 1.0
CG B:HIS12 4.1 36.8 1.0
NE2 B:HIS44 4.1 34.1 1.0
NZ C:LYS134 4.2 36.4 1.0
CD2 B:HIS44 4.3 33.6 1.0
O1B C:CDP901 4.4 64.6 1.0
CB B:ASP10 4.5 28.4 1.0
O3A C:CDP901 4.6 59.4 1.0
OE2 C:GLU137 4.8 40.8 1.0
O B:VAL11 4.8 31.8 1.0
CA B:VAL41 4.9 32.0 1.0

Zinc binding site 3 out of 3 in 3iew

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Bound Ctp and Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:72.5
occ:1.00
NE2 C:HIS12 2.1 36.7 1.0
ND1 C:HIS44 2.1 29.8 1.0
OD2 C:ASP10 2.3 29.6 1.0
CE1 C:HIS12 2.9 37.5 1.0
CG C:ASP10 3.0 26.8 1.0
CE1 C:HIS44 3.0 30.9 1.0
O2B A:CDP901 3.1 71.2 1.0
OD1 C:ASP10 3.1 24.6 1.0
CG C:HIS44 3.1 27.3 1.0
CD2 C:HIS12 3.2 35.5 1.0
O A:HOH221 3.4 45.2 1.0
O3B A:CDP901 3.4 72.4 1.0
CB C:HIS44 3.5 24.8 1.0
PB A:CDP901 3.8 72.4 1.0
ND1 C:HIS12 4.1 37.7 1.0
NE2 C:HIS44 4.1 32.4 1.0
CD2 C:HIS44 4.2 29.5 1.0
NZ A:LYS134 4.2 35.4 1.0
CG C:HIS12 4.2 33.5 1.0
CB C:ASP10 4.3 24.6 1.0
O1B A:CDP901 4.9 72.7 1.0
O C:VAL11 5.0 28.4 1.0

Reference:

D.W.Begley, R.C.Hartley, D.R.Davies, T.E.Edwards, J.T.Leonard, J.Abendroth, C.A.Burris, J.Bhandari, P.J.Myler, B.L.Staker, L.J.Stewart. Leveraging Structure Determination with Fragment Screening For Infectious Disease Drug Targets: Mecp Synthase From Burkholderia Pseudomallei. J Struct Funct Genomics V. 12 63 2011.
ISSN: ISSN 1345-711X
PubMed: 21359640
DOI: 10.1007/S10969-011-9102-6
Page generated: Wed Dec 16 04:26:16 2020

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