Zinc in PDB 6dxs: Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate

Enzymatic activity of Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate

All present enzymatic activity of Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate:
4.2.1.83;

Protein crystallography data

The structure of Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate, PDB code: 6dxs was solved by M.F.Mabanglo, F.M.Raushel, T.N.Hogancamp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.63 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.689, 78.253, 136.216, 90.00, 89.98, 90.00
R / Rfree (%) 20.2 / 26.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate (pdb code 6dxs). 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 the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate, PDB code: 6dxs:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6dxs

Go back to Zinc Binding Sites List in 6dxs
Zinc binding site 1 out of 4 in the Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate


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 the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:26.4
occ:1.00
 NE2 A:HIS8 2.2 18.6 1.0
O01 A:HJ7402 2.3 33.3 1.0
O05 A:HJ7402 2.3 24.5 1.0
NE2 A:HIS178 2.4 20.7 1.0
NE2 A:HIS10 2.5 23.3 1.0
CE1 A:HIS8 2.8 18.6 1.0
CD2 A:HIS10 2.9 22.0 1.0
C02 A:HJ7402 3.0 32.5 1.0
C03 A:HJ7402 3.0 28.6 1.0
CE1 A:HIS178 3.2 21.9 1.0
CD2 A:HIS8 3.4 19.2 1.0
CD2 A:HIS178 3.5 22.5 1.0
CG A:GLN284 3.7 23.9 1.0
CE1 A:HIS10 3.8 20.3 1.0
ND1 A:HIS8 4.0 20.5 1.0
CB A:ALA72 4.1 20.8 1.0
CG A:HIS10 4.2 22.7 1.0
O04 A:HJ7402 4.3 25.1 1.0
CG A:HIS8 4.3 21.5 1.0
ND1 A:HIS178 4.4 22.5 1.0
NE2 A:GLN284 4.5 26.7 1.0
CG A:HIS178 4.5 23.5 1.0
CD A:GLN284 4.5 25.1 1.0
C06 A:HJ7402 4.5 33.2 1.0
ND1 A:HIS10 4.6 20.2 1.0
NE2 A:HIS223 4.6 22.2 1.0
CB A:GLN284 4.8 19.5 1.0
CE2 A:TYR194 4.8 18.3 1.0
O10 A:HJ7402 5.0 35.3 1.0

Zinc binding site 2 out of 4 in 6dxs

Go back to Zinc Binding Sites List in 6dxs
Zinc binding site 2 out of 4 in the Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate


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 the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:27.0
occ:1.00
 NE2 B:HIS10 2.0 17.5 1.0
NE2 B:HIS8 2.1 20.9 1.0
O05 B:HJ7402 2.2 30.9 1.0
NE2 B:HIS178 2.2 22.0 1.0
O01 B:HJ7402 2.8 37.8 1.0
CD2 B:HIS178 2.8 22.4 1.0
CE1 B:HIS8 3.0 21.8 1.0
CD2 B:HIS10 3.0 17.5 1.0
CE1 B:HIS10 3.0 17.5 1.0
C03 B:HJ7402 3.1 33.0 1.0
CD2 B:HIS8 3.2 20.3 1.0
C02 B:HJ7402 3.3 33.5 1.0
CE1 B:HIS178 3.4 21.1 1.0
CG B:GLN284 3.8 26.2 1.0
CG B:HIS178 4.1 20.9 1.0
ND1 B:HIS10 4.1 21.5 1.0
CG B:HIS10 4.1 19.2 1.0
ND1 B:HIS8 4.1 18.4 1.0
NE2 B:HIS223 4.2 18.1 1.0
O04 B:HJ7402 4.3 32.7 1.0
CG B:HIS8 4.3 19.6 1.0
ND1 B:HIS178 4.3 20.6 1.0
CB B:ALA72 4.3 25.4 1.0
CD B:GLN284 4.5 31.2 1.0
C06 B:HJ7402 4.7 30.4 1.0
CE1 B:HIS223 4.7 18.3 1.0
OE1 B:GLN284 4.8 27.9 1.0
SD B:MET176 4.9 18.6 1.0
CE2 B:TYR194 5.0 24.2 1.0

Zinc binding site 3 out of 4 in 6dxs

Go back to Zinc Binding Sites List in 6dxs
Zinc binding site 3 out of 4 in the Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate


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 the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:30.4
occ:1.00
 NE2 C:HIS8 2.0 20.9 1.0
CE1 C:HIS10 2.0 25.9 1.0
NE2 C:HIS10 2.3 25.7 1.0
NE2 C:HIS178 2.3 24.8 1.0
O05 C:HJ7402 2.7 22.7 1.0
O01 C:HJ7402 2.8 33.4 1.0
CE1 C:HIS8 2.9 22.9 1.0
CD2 C:HIS178 2.9 25.8 1.0
CD2 C:HIS8 3.1 23.1 1.0
ND1 C:HIS10 3.3 27.3 1.0
C03 C:HJ7402 3.4 25.6 1.0
CE1 C:HIS178 3.4 26.3 1.0
C02 C:HJ7402 3.5 31.2 1.0
CD2 C:HIS10 3.7 25.6 1.0
CG C:GLN284 3.9 21.9 1.0
ND1 C:HIS8 4.0 20.1 1.0
CG C:HIS178 4.1 25.3 1.0
CG C:HIS10 4.1 26.4 1.0
CG C:HIS8 4.1 23.7 1.0
ND1 C:HIS178 4.3 24.8 1.0
CB C:ALA72 4.4 26.4 1.0
O04 C:HJ7402 4.5 26.6 1.0
NE2 C:HIS223 4.5 21.1 1.0
O C:HOH505 4.7 29.5 1.0
CD C:GLN284 4.7 24.2 1.0
SD C:MET176 4.7 26.4 1.0
O C:HOH530 4.9 27.3 1.0
C06 C:HJ7402 4.9 32.9 1.0
O10 C:HJ7402 5.0 29.8 1.0
CB C:GLN284 5.0 20.8 1.0

Zinc binding site 4 out of 4 in 6dxs

Go back to Zinc Binding Sites List in 6dxs
Zinc binding site 4 out of 4 in the Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate


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 the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:27.6
occ:1.00
 O01 D:HJ7402 1.9 28.4 1.0
NE2 D:HIS8 2.4 23.3 1.0
NE2 D:HIS178 2.4 20.2 1.0
O04 D:HJ7402 2.4 22.0 1.0
C02 D:HJ7402 2.7 31.8 1.0
C03 D:HJ7402 2.9 26.8 1.0
NE2 D:HIS10 3.0 27.5 1.0
CE1 D:HIS8 3.2 21.9 1.0
CE1 D:HIS178 3.4 20.9 1.0
CD2 D:HIS178 3.4 19.6 1.0
CD2 D:HIS10 3.5 27.9 1.0
CD2 D:HIS8 3.5 22.0 1.0
CG D:GLN284 3.8 24.7 1.0
CE1 D:HIS10 3.9 28.8 1.0
C06 D:HJ7402 4.2 31.6 1.0
O05 D:HJ7402 4.2 24.4 1.0
ND1 D:HIS8 4.4 22.8 1.0
O10 D:HJ7402 4.4 38.3 1.0
C08 D:HJ7402 4.5 37.0 1.0
CG D:HIS10 4.5 25.8 1.0
ND1 D:HIS178 4.5 18.9 1.0
NE2 D:GLN284 4.5 28.4 1.0
CB D:ALA72 4.5 26.1 1.0
CD D:GLN284 4.5 27.0 1.0
CG D:HIS8 4.5 18.0 1.0
CG D:HIS178 4.5 21.0 1.0
ND1 D:HIS10 4.7 27.0 1.0
CB D:GLN284 4.7 23.8 1.0
CE2 D:TYR194 4.7 18.8 1.0
NE2 D:HIS223 4.8 21.8 1.0
O09 D:HJ7402 4.8 39.2 1.0
O D:HOH548 4.8 23.5 1.0
C07 D:HJ7402 4.8 31.6 1.0
H061 D:HJ7402 4.8 37.9 1.0

Reference:

T.N.Hogancamp, M.F.Mabanglo, F.M.Raushel. Structure and Reaction Mechanism of the Ligj Hydratase: An Enzyme Critical For the Bacterial Degradation of Lignin in the Protocatechuate 4,5-Cleavage Pathway. Biochemistry V. 57 5841 2018.
ISSN: ISSN 1520-4995
PubMed: 30207699
DOI: 10.1021/ACS.BIOCHEM.8B00713
Page generated: Mon Oct 28 19:56:21 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy