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Zinc in PDB 2cye: Crystal Structure of Thioesterase Complexed with Coenzyme A and Zn From Thermus Thermophilus HB8

Protein crystallography data

The structure of Crystal Structure of Thioesterase Complexed with Coenzyme A and Zn From Thermus Thermophilus HB8, PDB code: 2cye was solved by T.Hosaka, M.Kato-Murayama, K.Murayama, S.Kishishita, N.Handa, M.Shirouzu, S.Yokoyama, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.05 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 89.530, 55.817, 110.147, 90.00, 102.42, 90.00
R / Rfree (%) 20.8 / 24.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Thioesterase Complexed with Coenzyme A and Zn From Thermus Thermophilus HB8 (pdb code 2cye). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Thioesterase Complexed with Coenzyme A and Zn From Thermus Thermophilus HB8, PDB code: 2cye:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2cye

Go back to Zinc Binding Sites List in 2cye
Zinc binding site 1 out of 4 in the Crystal Structure of Thioesterase Complexed with Coenzyme A and Zn From Thermus Thermophilus HB8


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 Thioesterase Complexed with Coenzyme A and Zn From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:13.7
occ:1.00
NE2 A:HIS22 2.1 10.8 1.0
OE2 C:GLU50 2.2 13.7 1.0
OD1 A:ASP18 2.3 9.5 1.0
S1P C:COA602 2.4 11.2 1.0
OE1 C:GLU50 2.7 11.1 1.0
CD C:GLU50 2.8 11.2 1.0
CD2 A:HIS22 3.1 10.1 1.0
CE1 A:HIS22 3.1 11.8 1.0
C2P C:COA602 3.1 17.1 1.0
CG A:ASP18 3.2 7.2 1.0
O A:HOH1012 3.3 8.5 1.0
CB A:ASP18 3.6 7.5 1.0
OD2 A:ASP18 4.2 7.9 1.0
ND1 A:HIS22 4.2 13.8 1.0
CG A:HIS22 4.2 8.7 1.0
CG C:GLU50 4.2 9.5 1.0
O C:HOH1022 4.4 13.5 1.0
O C:HOH1012 4.5 11.7 1.0
C3P C:COA602 4.6 10.6 1.0
CG1 C:VAL54 4.9 9.0 1.0
O A:VAL23 4.9 6.7 1.0
O C:PHE53 5.0 10.3 1.0
O C:HOH1006 5.0 12.8 1.0

Zinc binding site 2 out of 4 in 2cye

Go back to Zinc Binding Sites List in 2cye
Zinc binding site 2 out of 4 in the Crystal Structure of Thioesterase Complexed with Coenzyme A and Zn From Thermus Thermophilus HB8


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 Thioesterase Complexed with Coenzyme A and Zn From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:11.3
occ:1.00
NE2 B:HIS22 2.1 11.1 1.0
OE1 D:GLU50 2.1 10.4 1.0
OD2 B:ASP18 2.2 8.2 1.0
S1P B:COA601 2.4 9.9 1.0
OE2 D:GLU50 2.7 10.5 1.0
CD D:GLU50 2.7 9.8 1.0
CD2 B:HIS22 2.9 7.9 1.0
CG B:ASP18 3.2 3.7 1.0
CE1 B:HIS22 3.2 12.8 1.0
C2P B:COA601 3.2 9.2 1.0
O B:HOH1004 3.5 9.1 1.0
CB B:ASP18 3.6 4.9 1.0
CG B:HIS22 4.1 7.2 1.0
CG D:GLU50 4.2 11.4 1.0
OD1 B:ASP18 4.2 8.1 1.0
ND1 B:HIS22 4.2 9.8 1.0
O D:HOH1017 4.5 13.9 1.0
O D:HOH1023 4.6 17.5 1.0
C3P B:COA601 4.7 11.8 1.0
O B:VAL23 4.9 7.1 1.0
CB D:GLU50 5.0 9.5 1.0
CG1 D:VAL54 5.0 21.0 1.0

Zinc binding site 3 out of 4 in 2cye

Go back to Zinc Binding Sites List in 2cye
Zinc binding site 3 out of 4 in the Crystal Structure of Thioesterase Complexed with Coenzyme A and Zn From Thermus Thermophilus HB8


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 Thioesterase Complexed with Coenzyme A and Zn From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1003

b:8.9
occ:1.00
OE2 A:GLU50 2.1 9.3 1.0
NE2 C:HIS22 2.1 9.5 1.0
OD2 C:ASP18 2.1 9.7 1.0
S1P C:COA603 2.4 10.5 1.0
OE1 A:GLU50 2.7 16.6 1.0
CD A:GLU50 2.7 13.0 1.0
CD2 C:HIS22 3.0 6.5 1.0
CG C:ASP18 3.1 11.6 1.0
CE1 C:HIS22 3.2 12.1 1.0
C2P C:COA603 3.2 11.8 1.0
O C:HOH1010 3.4 9.0 1.0
CB C:ASP18 3.6 9.7 1.0
OD1 C:ASP18 4.2 11.9 1.0
CG C:HIS22 4.2 7.8 1.0
CG A:GLU50 4.2 11.4 1.0
ND1 C:HIS22 4.2 11.5 1.0
O A:HOH1017 4.3 13.4 1.0
O C:HOH1020 4.5 13.4 1.0
C3P C:COA603 4.7 9.7 1.0
O A:HOH1041 4.8 12.3 1.0
O A:PHE53 4.9 11.4 1.0
CB A:GLU50 5.0 11.1 1.0

Zinc binding site 4 out of 4 in 2cye

Go back to Zinc Binding Sites List in 2cye
Zinc binding site 4 out of 4 in the Crystal Structure of Thioesterase Complexed with Coenzyme A and Zn From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Thioesterase Complexed with Coenzyme A and Zn From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1004

b:9.5
occ:1.00
OE2 B:GLU50 2.0 8.1 1.0
NE2 D:HIS22 2.1 9.4 1.0
OD1 D:ASP18 2.2 9.5 1.0
S1P B:COA604 2.4 11.1 1.0
OE1 B:GLU50 2.6 7.6 1.0
CD B:GLU50 2.6 8.6 1.0
CD2 D:HIS22 3.0 8.0 1.0
C2P B:COA604 3.1 7.2 1.0
CG D:ASP18 3.1 10.2 1.0
CE1 D:HIS22 3.2 13.1 1.0
O D:HOH1008 3.4 11.5 1.0
CB D:ASP18 3.5 7.6 1.0
CG B:GLU50 4.1 15.4 1.0
CG D:HIS22 4.2 11.5 1.0
OD2 D:ASP18 4.2 9.8 1.0
ND1 D:HIS22 4.2 11.1 1.0
O B:HOH1051 4.3 16.4 1.0
O B:HOH1020 4.4 12.3 1.0
C3P B:COA604 4.6 10.4 1.0
O B:HOH1050 4.7 15.8 1.0
CG1 B:VAL54 4.7 6.8 1.0
O B:PHE53 4.8 11.9 1.0
CB B:GLU50 4.9 8.8 1.0
O D:VAL23 4.9 5.6 1.0
CA B:VAL54 5.0 8.3 1.0

Reference:

T.Hosaka, K.Murayama, M.Kato-Murayama, A.Urushibata, R.Akasaka, T.Terada, M.Shirouzu, S.Kuramitsu, S.Yokoyama. Structure of the Putative Thioesterase Protein TTHA1846 From Thermus Thermophilus HB8 Complexed with Coenzyme A and A Zinc Ion. Acta Crystallogr.,Sect.D V. 65 767 2009.
ISSN: ISSN 0907-4449
PubMed: 19622860
DOI: 10.1107/S0907444909015601
Page generated: Wed Dec 16 03:20:34 2020

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