Zinc in PDB 6sj3: Amidohydrolase, Ahs with 3-Hba

Protein crystallography data

The structure of Amidohydrolase, Ahs with 3-Hba, PDB code: 6sj3 was solved by J.H.Naismith, H.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 83.18 / 1.17
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 99.294, 117.339, 83.038, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 15.6

Other elements in 6sj3:

The structure of Amidohydrolase, Ahs with 3-Hba also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Amidohydrolase, Ahs with 3-Hba (pdb code 6sj3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Amidohydrolase, Ahs with 3-Hba, PDB code: 6sj3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6sj3

Go back to Zinc Binding Sites List in 6sj3
Zinc binding site 1 out of 4 in the Amidohydrolase, Ahs with 3-Hba


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Amidohydrolase, Ahs with 3-Hba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:11.2
occ:1.00
NE2 A:HIS77 2.0 11.3 1.0
O1' A:3HB501 2.0 12.1 1.0
NE2 A:HIS75 2.1 10.1 1.0
NE2 A:HIS253 2.1 11.2 1.0
OD1 A:ASP345 2.3 13.4 1.0
C1' A:3HB501 2.8 13.6 1.0
CE1 A:HIS77 3.0 13.6 1.0
O2' A:3HB501 3.0 15.0 1.0
CD2 A:HIS75 3.0 10.2 1.0
CD2 A:HIS253 3.0 11.5 1.0
CD2 A:HIS77 3.0 11.6 1.0
CE1 A:HIS75 3.1 11.1 1.0
CG A:ASP345 3.2 12.2 1.0
CE1 A:HIS253 3.2 14.1 1.0
OD2 A:ASP345 3.6 11.8 1.0
NE2 A:HIS290 4.0 10.8 1.0
O A:HOH938 4.0 22.4 1.0
ND1 A:HIS77 4.1 13.0 1.0
CG A:HIS77 4.2 11.2 1.0
C1 A:3HB501 4.2 12.5 1.0
CG A:HIS75 4.2 9.8 1.0
ND1 A:HIS75 4.2 11.3 1.0
CG A:HIS253 4.2 11.2 1.0
ND1 A:HIS253 4.3 14.0 1.0
CB A:ASP345 4.4 11.9 1.0
O A:HOH640 4.5 33.2 1.0
CA A:ASP345 4.5 12.1 1.0
CE1 A:HIS290 4.7 9.9 1.0
CD2 A:HIS290 4.8 10.4 1.0
C2 A:3HB501 4.9 12.3 1.0

Zinc binding site 2 out of 4 in 6sj3

Go back to Zinc Binding Sites List in 6sj3
Zinc binding site 2 out of 4 in the Amidohydrolase, Ahs with 3-Hba


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Amidohydrolase, Ahs with 3-Hba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:26.3
occ:1.00
O A:HOH999 2.0 18.0 1.0
O A:HOH745 2.1 12.0 1.0
O A:HOH992 4.1 25.7 1.0
O A:HOH827 4.2 13.0 1.0
O B:HOH973 4.2 12.7 1.0
O A:SER369 4.3 9.7 0.5
O A:HOH972 4.3 29.4 1.0
NH1 B:ARG258 4.3 10.7 1.0
O A:SER369 4.3 9.3 0.5
O A:HOH996 4.3 22.3 1.0
C A:SER369 4.9 8.7 0.5
C A:SER369 4.9 8.4 0.5
CA A:SER369 4.9 9.5 0.5
CA A:SER369 4.9 8.9 0.5
CZ B:ARG258 5.0 10.6 1.0

Zinc binding site 3 out of 4 in 6sj3

Go back to Zinc Binding Sites List in 6sj3
Zinc binding site 3 out of 4 in the Amidohydrolase, Ahs with 3-Hba


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Amidohydrolase, Ahs with 3-Hba within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn505

b:11.0
occ:1.00
NE2 B:HIS77 2.0 10.6 1.0
O2' B:3HB501 2.0 12.2 1.0
NE2 B:HIS75 2.1 9.9 1.0
NE2 B:HIS253 2.1 11.4 1.0
OD1 B:ASP345 2.3 14.5 1.0
C1' B:3HB501 2.8 12.8 1.0
O1' B:3HB501 2.9 14.0 1.0
CE1 B:HIS77 3.0 12.1 1.0
CD2 B:HIS75 3.0 9.9 1.0
CD2 B:HIS77 3.0 10.7 1.0
CD2 B:HIS253 3.0 10.9 1.0
CE1 B:HIS75 3.1 10.6 1.0
CE1 B:HIS253 3.2 11.7 1.0
CG B:ASP345 3.2 11.6 1.0
OD2 B:ASP345 3.6 11.8 1.0
NE2 B:HIS290 3.9 9.9 1.0
O B:HOH986 4.1 18.9 1.0
ND1 B:HIS77 4.1 12.7 1.0
CG B:HIS77 4.2 10.5 1.0
C1 B:3HB501 4.2 12.1 1.0
CG B:HIS75 4.2 9.3 1.0
ND1 B:HIS75 4.2 11.1 1.0
CG B:HIS253 4.2 10.0 1.0
ND1 B:HIS253 4.2 11.4 1.0
CB B:ASP345 4.4 11.6 1.0
O B:HOH712 4.5 33.8 1.0
CA B:ASP345 4.6 11.8 1.0
CE1 B:HIS290 4.7 9.6 1.0
O B:HOH861 4.7 24.4 1.0
CD2 B:HIS290 4.8 10.1 1.0
C2 B:3HB501 4.9 12.1 1.0

Zinc binding site 4 out of 4 in 6sj3

Go back to Zinc Binding Sites List in 6sj3
Zinc binding site 4 out of 4 in the Amidohydrolase, Ahs with 3-Hba


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Amidohydrolase, Ahs with 3-Hba within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn506

b:1.0
occ:1.00
O B:HOH848 2.0 17.4 1.0
O B:HOH962 2.7 42.6 1.0
O B:HOH1133 2.8 30.1 1.0
O B:HOH1106 3.2 18.1 1.0
OE1 B:GLU402 4.3 16.3 1.0
O B:HOH701 4.6 28.3 1.0
O B:HOH1057 4.6 19.1 1.0

Reference:

H.Song, C.Rao, Z.Deng, Y.Yi, J.H.Naismith. The Biosynthetic Pathway of the Benzoxazole in Nataxazole Proceeds Via An Unstable Ester and Has Synthetic Utility. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 31903677
DOI: 10.1002/ANIE.201915685
Page generated: Wed Dec 16 12:48:42 2020

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