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Zinc in PDB 3ome: Crystal Structure of A Probable Enoyl-Coa Hydratase From Mycobacterium Smegmatis

Enzymatic activity of Crystal Structure of A Probable Enoyl-Coa Hydratase From Mycobacterium Smegmatis

All present enzymatic activity of Crystal Structure of A Probable Enoyl-Coa Hydratase From Mycobacterium Smegmatis:
4.2.1.17;

Protein crystallography data

The structure of Crystal Structure of A Probable Enoyl-Coa Hydratase From Mycobacterium Smegmatis, PDB code: 3ome 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 / 2.05
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 145.220, 86.650, 140.050, 90.00, 97.93, 90.00
R / Rfree (%) 14.5 / 17.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Probable Enoyl-Coa Hydratase From Mycobacterium Smegmatis (pdb code 3ome). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of A Probable Enoyl-Coa Hydratase From Mycobacterium Smegmatis, PDB code: 3ome:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3ome

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Zinc binding site 1 out of 6 in the Crystal Structure of A Probable Enoyl-Coa Hydratase From Mycobacterium Smegmatis


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 Probable Enoyl-Coa Hydratase From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:36.8
occ:1.00
 OE2 A:GLU144 2.2 27.8 1.0
NE2 A:HIS233 2.2 25.2 1.0
NE2 A:HIS237 2.3 31.9 1.0
OE1 A:GLU83 2.3 30.8 1.0
O A:HOH741 2.3 16.3 1.0
OE2 A:GLU83 2.4 31.0 1.0
CD A:GLU83 2.6 28.8 1.0
CD A:GLU144 3.1 29.1 1.0
CE1 A:HIS233 3.1 26.6 1.0
CE1 A:HIS237 3.2 33.6 1.0
CD2 A:HIS233 3.2 26.6 1.0
CD2 A:HIS237 3.3 32.3 1.0
CG A:GLU144 3.6 27.6 1.0
O A:HOH742 3.7 29.0 1.0
O A:HOH740 4.0 22.2 1.0
OE1 A:GLU144 4.1 28.7 1.0
CG A:GLU83 4.2 28.5 1.0
ND1 A:HIS233 4.3 24.4 1.0
ND1 A:HIS237 4.3 32.9 1.0
CG A:HIS233 4.3 25.4 1.0
CG A:HIS237 4.4 31.2 1.0
O A:HOH661 4.6 29.0 1.0
NE2 A:GLN234 4.6 28.2 1.0
CD2 A:TYR87 4.9 34.2 1.0
CE2 A:TYR87 4.9 35.9 1.0
CB A:GLU83 4.9 28.6 1.0

Zinc binding site 2 out of 6 in 3ome

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Zinc binding site 2 out of 6 in the Crystal Structure of A Probable Enoyl-Coa Hydratase From Mycobacterium Smegmatis


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 Probable Enoyl-Coa Hydratase From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn300

b:42.0
occ:1.00
 OE1 B:GLU83 2.2 32.4 1.0
NE2 B:HIS233 2.2 29.4 1.0
NE2 B:HIS237 2.2 35.7 1.0
OE2 B:GLU144 2.2 32.6 1.0
OE2 B:GLU83 2.4 34.8 1.0
O B:HOH468 2.5 20.6 1.0
CD B:GLU83 2.6 34.0 1.0
CE1 B:HIS233 3.2 29.8 1.0
CE1 B:HIS237 3.2 37.9 1.0
CD2 B:HIS233 3.2 29.5 1.0
CD2 B:HIS237 3.2 35.6 1.0
CD B:GLU144 3.2 32.8 1.0
CG B:GLU144 3.7 32.4 1.0
O B:HOH522 3.7 19.0 1.0
O B:HOH523 3.9 21.0 1.0
CG B:GLU83 4.1 34.0 1.0
OE1 B:GLU144 4.3 30.8 1.0
ND1 B:HIS233 4.3 28.3 1.0
ND1 B:HIS237 4.3 38.6 1.0
CG B:HIS233 4.3 28.0 1.0
CG B:HIS237 4.3 35.5 1.0
O B:HOH446 4.5 26.8 1.0
NE2 B:GLN234 4.7 30.6 1.0
CB B:GLU83 4.9 32.8 1.0
CD2 B:TYR87 4.9 36.8 1.0
CE2 B:TYR87 5.0 38.3 1.0

Zinc binding site 3 out of 6 in 3ome

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Zinc binding site 3 out of 6 in the Crystal Structure of A Probable Enoyl-Coa Hydratase From Mycobacterium Smegmatis


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 Probable Enoyl-Coa Hydratase From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn300

b:29.5
occ:1.00
 OE2 C:GLU144 2.1 22.8 1.0
NE2 C:HIS233 2.2 22.9 1.0
NE2 C:HIS237 2.2 23.1 1.0
O C:HOH459 2.3 13.6 1.0
OE2 C:GLU83 2.3 21.3 1.0
OE1 C:GLU83 2.3 22.6 1.0
CD C:GLU83 2.6 22.6 1.0
CD C:GLU144 3.1 25.1 1.0
CD2 C:HIS233 3.1 24.4 1.0
CE1 C:HIS233 3.2 22.0 1.0
CD2 C:HIS237 3.2 24.3 1.0
CE1 C:HIS237 3.2 25.9 1.0
CG C:GLU144 3.6 24.0 1.0
O C:HOH458 3.9 21.1 1.0
O C:HOH457 4.0 22.4 1.0
CG C:GLU83 4.1 22.9 1.0
OE1 C:GLU144 4.1 23.9 1.0
ND1 C:HIS233 4.3 21.5 1.0
CG C:HIS233 4.3 21.2 1.0
ND1 C:HIS237 4.3 27.1 1.0
CG C:HIS237 4.3 25.3 1.0
O C:HOH454 4.5 18.6 1.0
NE2 C:GLN234 4.6 19.9 1.0
CB C:GLU83 4.8 22.3 1.0
CD2 C:TYR87 4.9 22.9 1.0
CE2 C:TYR87 4.9 24.3 1.0

Zinc binding site 4 out of 6 in 3ome

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Zinc binding site 4 out of 6 in the Crystal Structure of A Probable Enoyl-Coa Hydratase From Mycobacterium Smegmatis


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 Probable Enoyl-Coa Hydratase From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn300

b:37.2
occ:1.00
 NE2 D:HIS237 2.2 32.8 1.0
NE2 D:HIS233 2.2 26.3 1.0
OE2 D:GLU144 2.2 30.1 1.0
OE2 D:GLU83 2.2 35.1 1.0
OE1 D:GLU83 2.3 31.1 1.0
O D:HOH470 2.4 13.6 1.0
CD D:GLU83 2.6 32.4 1.0
CE1 D:HIS233 3.1 26.3 1.0
CE1 D:HIS237 3.2 29.4 1.0
CD D:GLU144 3.2 30.3 1.0
CD2 D:HIS237 3.2 29.3 1.0
CD2 D:HIS233 3.2 26.0 1.0
O D:HOH524 3.6 35.8 1.0
CG D:GLU144 3.6 29.8 1.0
O D:HOH469 3.9 12.5 1.0
CG D:GLU83 4.1 32.1 1.0
OE1 D:GLU144 4.2 29.2 1.0
ND1 D:HIS233 4.3 24.3 1.0
ND1 D:HIS237 4.3 31.5 1.0
CG D:HIS237 4.3 29.5 1.0
CG D:HIS233 4.3 24.8 1.0
O D:HOH663 4.6 23.6 1.0
NE2 D:GLN234 4.6 27.2 1.0
CB D:GLU83 4.9 30.9 1.0
CD2 D:TYR87 4.9 35.0 1.0
CE2 D:TYR87 5.0 35.4 1.0

Zinc binding site 5 out of 6 in 3ome

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Zinc binding site 5 out of 6 in the Crystal Structure of A Probable Enoyl-Coa Hydratase From Mycobacterium Smegmatis


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 Probable Enoyl-Coa Hydratase From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn300

b:40.4
occ:1.00
 NE2 E:HIS237 2.2 35.3 1.0
OE2 E:GLU144 2.2 32.1 1.0
NE2 E:HIS233 2.3 29.5 1.0
OE1 E:GLU83 2.3 33.0 1.0
OE2 E:GLU83 2.3 29.5 1.0
O E:HOH492 2.4 16.4 1.0
CD E:GLU83 2.6 31.1 1.0
CE1 E:HIS237 3.0 37.4 1.0
CD2 E:HIS233 3.2 29.2 1.0
CD E:GLU144 3.2 33.4 1.0
CD2 E:HIS237 3.3 34.8 1.0
CE1 E:HIS233 3.3 32.2 1.0
CG E:GLU144 3.6 31.6 1.0
O E:HOH525 3.8 30.8 1.0
O E:HOH493 4.0 23.6 1.0
CG E:GLU83 4.1 32.1 1.0
ND1 E:HIS237 4.2 37.3 1.0
OE1 E:GLU144 4.2 32.1 1.0
CG E:HIS237 4.3 36.0 1.0
CG E:HIS233 4.4 27.2 1.0
ND1 E:HIS233 4.4 28.3 1.0
NE2 E:GLN234 4.6 30.3 1.0
CB E:GLU83 4.9 31.0 1.0
CD2 E:TYR87 4.9 34.1 1.0
CE2 E:TYR87 5.0 33.1 1.0

Zinc binding site 6 out of 6 in 3ome

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Zinc binding site 6 out of 6 in the Crystal Structure of A Probable Enoyl-Coa Hydratase From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of A Probable Enoyl-Coa Hydratase From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn300

b:41.7
occ:1.00
 NE2 F:HIS237 2.2 34.8 1.0
NE2 F:HIS233 2.2 30.8 1.0
OE1 F:GLU83 2.3 36.6 1.0
OE2 F:GLU144 2.3 34.8 1.0
OE2 F:GLU83 2.4 31.5 1.0
O F:HOH498 2.4 16.4 1.0
CD F:GLU83 2.6 32.5 1.0
CE1 F:HIS237 3.1 33.0 1.0
CD2 F:HIS233 3.1 30.2 1.0
CD2 F:HIS237 3.2 31.1 1.0
CD F:GLU144 3.2 34.6 1.0
CE1 F:HIS233 3.2 33.7 1.0
CG F:GLU144 3.6 33.1 1.0
O F:HOH728 3.7 28.0 1.0
O F:HOH665 4.1 24.2 1.0
CG F:GLU83 4.1 33.8 1.0
ND1 F:HIS237 4.2 33.4 1.0
OE1 F:GLU144 4.3 34.2 1.0
CG F:HIS233 4.3 29.2 1.0
CG F:HIS237 4.3 31.0 1.0
ND1 F:HIS233 4.3 27.5 1.0
O F:HOH662 4.4 24.1 1.0
NE2 F:GLN234 4.6 33.0 1.0
CB F:GLU83 4.9 33.5 1.0
CD2 F:TYR87 4.9 38.6 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: Sat Oct 26 11:01:17 2024

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