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Zinc in PDB 4z3z: Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc

Protein crystallography data

The structure of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc, PDB code: 4z3z was solved by T.Weinert, J.W.Kung, S.Weidenweber, S.G.Huwiler, M.Boll, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.51 / 2.67
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 124.240, 117.430, 143.080, 90.00, 111.04, 90.00
R / Rfree (%) 23.2 / 27.4

Other elements in 4z3z:

The structure of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc also contains other interesting chemical elements:

Tungsten (W) 4 atoms
Magnesium (Mg) 4 atoms
Iron (Fe) 64 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc (pdb code 4z3z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc, PDB code: 4z3z:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4z3z

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Zinc binding site 1 out of 4 in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn707

b:67.0
occ:0.18
OE1 A:GLU257 2.0 0.3 1.0
OE2 A:GLU257 2.0 0.9 1.0
OE1 A:GLU251 2.0 0.0 1.0
NE2 A:HIS255 2.1 0.9 1.0
ND1 A:HIS260 2.1 0.3 1.0
CD A:GLU257 2.1 0.3 1.0
OE2 A:GLU251 2.5 0.5 1.0
CD A:GLU251 2.6 0.6 1.0
CE1 A:HIS260 2.8 0.4 1.0
CE1 A:HIS255 2.9 0.6 1.0
CD2 A:HIS255 3.2 0.8 1.0
CG A:HIS260 3.2 1.0 1.0
CG A:GLU257 3.5 0.3 1.0
CB A:HIS260 3.8 0.0 1.0
CD1 A:LEU326 4.0 0.1 1.0
NE2 A:HIS260 4.0 0.2 1.0
ND1 A:HIS255 4.1 0.1 1.0
CG A:GLU251 4.1 0.1 1.0
CD2 A:HIS260 4.2 0.6 1.0
CG A:HIS255 4.2 0.5 1.0
CB A:GLU257 4.3 1.0 1.0
CA A:GLU257 4.3 0.4 1.0
NZ A:LYS325 4.6 0.5 1.0
CD1 A:ILE242 4.7 0.9 1.0
CG A:LEU326 4.7 0.7 1.0
CD2 A:LEU326 4.7 0.4 1.0
CB A:GLU251 5.0 0.4 1.0

Zinc binding site 2 out of 4 in 4z3z

Go back to Zinc Binding Sites List in 4z3z
Zinc binding site 2 out of 4 in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn707

b:40.1
occ:0.26
OE2 B:GLU257 2.0 0.2 1.0
OE1 B:GLU257 2.0 0.6 1.0
OE1 B:GLU251 2.0 85.4 1.0
NE2 B:HIS255 2.1 0.3 1.0
ND1 B:HIS260 2.1 0.7 1.0
CD B:GLU257 2.1 0.1 1.0
OE2 B:GLU251 2.5 79.0 1.0
CD B:GLU251 2.6 82.5 1.0
CE1 B:HIS260 2.8 0.4 1.0
CE1 B:HIS255 2.9 0.2 1.0
CD2 B:HIS255 3.2 0.3 1.0
CG B:HIS260 3.2 0.7 1.0
CG B:GLU257 3.5 0.2 1.0
CB B:HIS260 3.8 0.1 1.0
CD1 B:LEU326 3.9 75.9 1.0
NE2 B:HIS260 4.0 0.4 1.0
CG B:GLU251 4.1 83.1 1.0
ND1 B:HIS255 4.1 0.6 1.0
CD2 B:HIS260 4.2 0.3 1.0
CG B:HIS255 4.3 0.4 1.0
CB B:GLU257 4.3 0.0 1.0
CA B:GLU257 4.3 0.3 1.0
NZ B:LYS325 4.5 72.4 1.0
CG B:LEU326 4.7 75.1 1.0
CD1 B:ILE242 4.7 0.8 1.0
CD2 B:LEU326 4.7 74.5 1.0
CB B:GLU251 4.9 83.3 1.0

Zinc binding site 3 out of 4 in 4z3z

Go back to Zinc Binding Sites List in 4z3z
Zinc binding site 3 out of 4 in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn707

b:76.6
occ:0.55
OE2 C:GLU257 2.0 87.1 1.0
OE1 C:GLU257 2.0 88.3 1.0
OE1 C:GLU251 2.0 68.1 1.0
ND1 C:HIS260 2.1 77.0 1.0
NE2 C:HIS255 2.1 0.8 1.0
CD C:GLU257 2.1 85.7 1.0
OE2 C:GLU251 2.5 66.9 1.0
CD C:GLU251 2.5 67.4 1.0
CE1 C:HIS260 2.8 77.0 1.0
CE1 C:HIS255 2.9 0.7 1.0
CD2 C:HIS255 3.2 0.5 1.0
CG C:HIS260 3.2 79.1 1.0
CG C:GLU257 3.5 82.6 1.0
CB C:HIS260 3.8 79.3 1.0
CD1 C:LEU326 3.9 59.9 1.0
NE2 C:HIS260 4.0 78.5 1.0
CG C:GLU251 4.0 68.5 1.0
ND1 C:HIS255 4.1 0.2 1.0
CD2 C:HIS260 4.2 79.8 1.0
CG C:HIS255 4.3 0.6 1.0
CB C:GLU257 4.3 81.4 1.0
CA C:GLU257 4.3 82.8 1.0
NZ C:LYS325 4.5 59.4 1.0
CG C:LEU326 4.6 61.0 1.0
CD2 C:LEU326 4.7 60.1 1.0
CD1 C:ILE242 4.7 96.7 1.0
CB C:GLU251 4.9 65.5 1.0

Zinc binding site 4 out of 4 in 4z3z

Go back to Zinc Binding Sites List in 4z3z
Zinc binding site 4 out of 4 in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn707

b:90.0
occ:0.47
OE1 D:GLU251 2.0 89.3 1.0
OE1 D:GLU257 2.0 94.1 1.0
OE2 D:GLU257 2.0 97.4 1.0
NE2 D:HIS255 2.0 0.4 1.0
ND1 D:HIS260 2.0 0.1 1.0
CD D:GLU257 2.2 96.1 1.0
OE2 D:GLU251 2.6 85.5 1.0
CD D:GLU251 2.6 86.0 1.0
CE1 D:HIS260 2.8 0.9 1.0
CE1 D:HIS255 2.9 0.9 1.0
CD2 D:HIS255 3.2 0.1 1.0
CG D:HIS260 3.2 0.1 1.0
CG D:GLU257 3.5 98.2 1.0
CB D:HIS260 3.8 0.8 1.0
NE2 D:HIS260 4.0 0.2 1.0
CD1 D:LEU326 4.0 83.6 1.0
ND1 D:HIS255 4.0 0.6 1.0
CG D:GLU251 4.1 82.2 1.0
CD2 D:HIS260 4.2 0.9 1.0
CG D:HIS255 4.2 0.4 1.0
CB D:GLU257 4.3 99.7 1.0
CA D:GLU257 4.3 0.3 1.0
NZ D:LYS325 4.6 73.5 1.0
CD1 D:ILE242 4.6 0.8 1.0
CG D:LEU326 4.7 80.0 1.0
CD2 D:LEU326 4.8 81.6 1.0
CB D:GLU251 5.0 80.0 1.0
N D:GLU257 5.0 0.5 1.0

Reference:

T.Weinert, S.G.Huwiler, J.W.Kung, S.Weidenweber, P.Hellwig, H.J.Stark, T.Biskup, S.Weber, J.J.Cotelesage, G.N.George, U.Ermler, M.Boll. Structural Basis of Enzymatic Benzene Ring Reduction. Nat.Chem.Biol. V. 11 586 2015.
ISSN: ESSN 1552-4469
PubMed: 26120796
DOI: 10.1038/NCHEMBIO.1849
Page generated: Wed Dec 16 05:58:46 2020

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