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Zinc in PDB 4hdt: Crystal Structure of A Carnitinyl-Coa Dehydratase From Mycobacterium Thermoresistibile

Protein crystallography data

The structure of Crystal Structure of A Carnitinyl-Coa Dehydratase From Mycobacterium Thermoresistibile, PDB code: 4hdt 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) 45.45 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.200, 62.400, 56.880, 90.00, 109.59, 90.00
R / Rfree (%) 16 / 18.9

Other elements in 4hdt:

The structure of Crystal Structure of A Carnitinyl-Coa Dehydratase From Mycobacterium Thermoresistibile also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Carnitinyl-Coa Dehydratase From Mycobacterium Thermoresistibile (pdb code 4hdt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of A Carnitinyl-Coa Dehydratase From Mycobacterium Thermoresistibile, PDB code: 4hdt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 4hdt

Go back to Zinc Binding Sites List in 4hdt
Zinc binding site 1 out of 5 in the Crystal Structure of A Carnitinyl-Coa Dehydratase From Mycobacterium Thermoresistibile


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 A Carnitinyl-Coa Dehydratase From Mycobacterium Thermoresistibile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:15.3
occ:1.00
OE2 A:GLU46 1.9 17.5 1.0
OE1 A:GLU348 2.0 21.9 1.0
NE2 A:HIS97 2.1 12.0 1.0
CL A:CL405 2.3 15.8 1.0
CD A:GLU46 2.6 18.0 1.0
OE1 A:GLU46 2.6 18.0 1.0
CD A:GLU348 2.8 23.7 1.0
CD2 A:HIS97 3.0 11.4 1.0
OE2 A:GLU348 3.0 23.1 1.0
CE1 A:HIS97 3.1 12.2 1.0
O A:HOH665 4.0 34.5 1.0
O A:HOH765 4.0 36.1 1.0
CG A:GLU46 4.1 18.1 1.0
CG A:HIS97 4.2 10.9 1.0
CG A:GLU348 4.2 26.6 1.0
ND1 A:HIS97 4.2 11.6 1.0
CD A:PRO102 4.4 13.8 1.0
NH2 A:ARG100 4.6 13.6 1.0
CD1 A:TYR101 4.8 12.4 1.0
NE A:ARG100 4.9 13.3 1.0
CE1 A:TYR101 5.0 12.9 1.0

Zinc binding site 2 out of 5 in 4hdt

Go back to Zinc Binding Sites List in 4hdt
Zinc binding site 2 out of 5 in the Crystal Structure of A Carnitinyl-Coa Dehydratase From Mycobacterium Thermoresistibile


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 A Carnitinyl-Coa Dehydratase From Mycobacterium Thermoresistibile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:15.8
occ:1.00
OE1 A:GLU61 1.9 16.2 1.0
NE2 A:HIS189 2.0 16.1 1.0
O A:HOH670 2.0 21.6 1.0
CD A:GLU61 2.8 16.2 1.0
CE1 A:HIS189 3.0 15.5 1.0
CD2 A:HIS189 3.0 16.9 1.0
OE2 A:GLU61 3.1 16.7 1.0
O A:HOH720 3.6 26.8 1.0
ND1 A:HIS189 4.1 15.4 1.0
CG A:HIS189 4.1 16.1 1.0
O A:HOH719 4.2 34.0 1.0
CG A:GLU61 4.2 15.8 1.0
CB A:GLU61 4.6 14.8 1.0
O A:HIS189 4.8 20.7 1.0
CA A:GLU61 4.8 13.9 1.0
OD2 A:ASP193 4.9 26.2 1.0

Zinc binding site 3 out of 5 in 4hdt

Go back to Zinc Binding Sites List in 4hdt
Zinc binding site 3 out of 5 in the Crystal Structure of A Carnitinyl-Coa Dehydratase From Mycobacterium Thermoresistibile


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 A Carnitinyl-Coa Dehydratase From Mycobacterium Thermoresistibile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:13.5
occ:1.00
OE1 A:GLU83 1.9 16.4 1.0
ND1 A:HIS32 2.1 11.9 1.0
CD A:GLU83 2.7 16.1 1.0
OE2 A:GLU83 2.8 16.9 1.0
CE1 A:HIS32 2.9 12.0 1.0
CG A:HIS32 3.2 11.4 1.0
CB A:HIS32 3.8 11.4 1.0
NE2 A:HIS32 4.1 11.5 1.0
CG A:GLU83 4.2 16.1 1.0
CD2 A:HIS32 4.3 11.1 1.0
CB A:GLU83 4.8 16.3 1.0

Zinc binding site 4 out of 5 in 4hdt

Go back to Zinc Binding Sites List in 4hdt
Zinc binding site 4 out of 5 in the Crystal Structure of A Carnitinyl-Coa Dehydratase From Mycobacterium Thermoresistibile


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 A Carnitinyl-Coa Dehydratase From Mycobacterium Thermoresistibile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:36.5
occ:1.00
ND1 A:HIS75 2.1 27.6 1.0
CE1 A:HIS75 2.9 28.5 1.0
CG A:HIS75 3.2 26.1 1.0
CB A:HIS75 3.7 23.6 1.0
NE2 A:HIS75 4.1 28.3 1.0
CD2 A:HIS75 4.2 27.8 1.0
O A:HOH614 4.5 24.9 1.0
CG1 A:VAL71 4.8 28.9 1.0
O A:VAL71 4.9 25.6 1.0

Zinc binding site 5 out of 5 in 4hdt

Go back to Zinc Binding Sites List in 4hdt
Zinc binding site 5 out of 5 in the Crystal Structure of A Carnitinyl-Coa Dehydratase From Mycobacterium Thermoresistibile


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Carnitinyl-Coa Dehydratase From Mycobacterium Thermoresistibile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:42.9
occ:1.00
O A:HOH690 2.2 29.5 1.0
OD2 A:ASP193 2.4 26.2 1.0
CB A:ASP193 2.7 28.2 1.0
O A:HOH583 2.8 22.9 1.0
CG A:ASP193 2.9 28.6 1.0
N A:ASP193 3.8 27.5 1.0
CA A:ASP193 3.8 27.2 1.0
C A:ASP190 3.9 27.4 1.0
O A:ASP190 3.9 28.5 1.0
N A:GLU194 4.0 26.2 1.0
OD1 A:ASP193 4.2 29.9 1.0
CA A:ASP190 4.3 25.6 1.0
N A:LYS191 4.3 28.1 1.0
C A:ASP193 4.3 26.0 1.0
CA A:LYS191 4.4 28.6 1.0
NH2 A:ARG197 4.4 34.8 1.0
C A:LYS191 4.6 28.9 1.0
NH1 A:ARG197 4.6 33.9 1.0
N A:ILE192 4.6 28.0 1.0
O A:HIS189 4.9 20.7 1.0
C A:ILE192 5.0 27.6 1.0
CZ A:ARG197 5.0 33.8 1.0

Reference:

L.Baugh, I.Phan, D.W.Begley, M.C.Clifton, B.Armour, D.M.Dranow, B.M.Taylor, M.M.Muruthi, J.Abendroth, J.W.Fairman, D.Fox, S.H.Dieterich, B.L.Staker, A.S.Gardberg, R.Choi, S.N.Hewitt, A.J.Napuli, J.Myers, L.K.Barrett, Y.Zhang, M.Ferrell, E.Mundt, K.Thompkins, N.Tran, S.Lyons-Abbott, A.Abramov, A.Sekar, D.Serbzhinskiy, D.Lorimer, G.W.Buchko, R.Stacy, L.J.Stewart, T.E.Edwards, W.C.Van Voorhis, P.J.Myler. Increasing the Structural Coverage of Tuberculosis Drug Targets. Tuberculosis (Edinb) V. 95 142 2015.
ISSN: ISSN 1472-9792
PubMed: 25613812
DOI: 10.1016/J.TUBE.2014.12.003
Page generated: Wed Dec 16 05:22:04 2020

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