Zinc in PDB 6j4b: Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate

Protein crystallography data

The structure of Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate, PDB code: 6j4b was solved by Y.Hou, B.Liu, K.Hu, R.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.78 / 1.58
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 43.627, 43.627, 99.973, 90.00, 90.00, 120.00
R / Rfree (%) 14.6 / 17.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate (pdb code 6j4b). 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 Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate, PDB code: 6j4b:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 6j4b

Go back to Zinc Binding Sites List in 6j4b
Zinc binding site 1 out of 5 in the Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate


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 Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:10.4
occ:1.00
O A:HOH316 1.9 9.3 1.0
OXT A:ACY209 2.0 11.8 1.0
O A:HOH332 2.0 9.5 1.0
NE2 A:HIS62 2.0 9.8 1.0
C A:ACY209 2.9 10.9 1.0
CE1 A:HIS62 2.9 10.6 1.0
CD2 A:HIS62 3.1 11.2 1.0
ZN A:ZN204 3.2 10.7 1.0
ZN A:ZN205 3.3 10.4 1.0
O A:ACY209 3.3 11.2 1.0
O3 A:GOL207 3.5 13.8 1.0
O2 A:GOL207 3.7 16.9 1.0
CE1 A:HIS25 3.7 9.4 1.0
OH A:TYR70 3.9 13.2 1.0
O A:HOH371 3.9 13.8 1.0
NE2 A:HIS25 4.0 8.2 1.0
ND1 A:HIS62 4.1 10.2 1.0
NE2 A:HIS107 4.1 9.4 1.0
NE2 A:HIS64 4.2 10.4 1.0
CG A:HIS62 4.2 11.1 1.0
CE1 A:HIS64 4.2 10.9 1.0
CH3 A:ACY209 4.2 11.6 1.0
C3 A:GOL207 4.2 14.9 1.0
CD2 A:HIS107 4.6 9.0 1.0
C2 A:GOL207 4.6 17.7 1.0
OXT A:ACY208 4.7 13.3 1.0
OE2 A:GLU68 4.9 12.6 1.0

Zinc binding site 2 out of 5 in 6j4b

Go back to Zinc Binding Sites List in 6j4b
Zinc binding site 2 out of 5 in the Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate


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 Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:14.7
occ:1.00
NE2 A:HIS26 2.1 9.6 1.0
CD2 A:HIS26 3.0 10.2 1.0
CE1 A:HIS26 3.0 8.9 1.0
O A:HOH365 4.0 20.5 1.0
ND1 A:HIS26 4.1 9.9 1.0
CG A:HIS26 4.2 8.8 1.0
O A:HOH350 4.2 28.6 1.0
OE1 A:GLN27 4.6 23.1 1.0
O A:HOH307 4.8 10.8 1.0
CG A:GLN27 5.0 17.2 1.0
O A:PRO57 5.0 13.2 1.0

Zinc binding site 3 out of 5 in 6j4b

Go back to Zinc Binding Sites List in 6j4b
Zinc binding site 3 out of 5 in the Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate


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 Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:17.6
occ:1.00
O A:HOH347 2.1 34.0 1.0
NE2 A:HIS91 2.1 19.1 1.0
CD2 A:HIS91 3.1 18.3 1.0
CE1 A:HIS91 3.1 17.3 1.0
ND1 A:HIS91 4.2 17.3 1.0
CG A:HIS91 4.2 16.3 1.0

Zinc binding site 4 out of 5 in 6j4b

Go back to Zinc Binding Sites List in 6j4b
Zinc binding site 4 out of 5 in the Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate


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 Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:10.7
occ:1.00
O A:HOH332 1.9 9.5 1.0
OXT A:ACY208 2.0 13.3 1.0
NE2 A:HIS25 2.0 8.2 1.0
O A:ACY209 2.0 11.2 1.0
C A:ACY208 2.7 15.2 1.0
O A:ACY208 2.8 14.8 1.0
C A:ACY209 2.9 10.9 1.0
CE1 A:HIS25 3.0 9.4 1.0
CD2 A:HIS25 3.1 9.4 1.0
OXT A:ACY209 3.2 11.8 1.0
ZN A:ZN201 3.2 10.4 1.0
O2 A:GOL207 3.8 16.9 1.0
CG2 A:VAL58 3.9 10.4 1.0
C3 A:GOL207 4.0 14.9 1.0
ND1 A:HIS25 4.1 8.5 1.0
CG A:HIS25 4.2 8.8 1.0
CH3 A:ACY208 4.2 14.0 1.0
CB A:ALA29 4.2 9.4 1.0
O3 A:GOL207 4.3 13.8 1.0
CH3 A:ACY209 4.3 11.6 1.0
O A:HOH371 4.4 13.8 1.0
NE2 A:HIS62 4.4 9.8 1.0
O1 A:GOL207 4.5 20.4 1.0
O A:HOH316 4.6 9.3 1.0
C2 A:GOL207 4.6 17.7 1.0
CE1 A:HIS62 4.8 10.6 1.0
CB A:VAL58 4.9 9.5 1.0

Zinc binding site 5 out of 5 in 6j4b

Go back to Zinc Binding Sites List in 6j4b
Zinc binding site 5 out of 5 in the Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate


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 Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:10.4
occ:1.00
OE1 A:GLU68 1.9 9.9 1.0
O A:HOH316 2.0 9.3 1.0
NE2 A:HIS64 2.0 10.4 1.0
NE2 A:HIS107 2.1 9.4 1.0
CD A:GLU68 2.7 10.9 1.0
OE2 A:GLU68 2.8 12.6 1.0
CD2 A:HIS64 2.9 11.4 1.0
CE1 A:HIS107 3.0 8.8 1.0
CE1 A:HIS64 3.1 10.9 1.0
CD2 A:HIS107 3.1 9.0 1.0
ZN A:ZN201 3.3 10.4 1.0
OH A:TYR70 3.8 13.2 1.0
CE1 A:TYR70 3.9 14.9 1.0
OXT A:ACY209 3.9 11.8 1.0
O3 A:GOL207 3.9 13.8 1.0
NE2 A:HIS62 4.0 9.8 1.0
CG A:GLU68 4.1 9.4 1.0
ND1 A:HIS107 4.1 8.7 1.0
CG A:HIS64 4.1 10.5 1.0
ND1 A:HIS64 4.2 10.7 1.0
CG A:HIS107 4.2 8.8 1.0
CZ A:TYR70 4.3 14.3 1.0
CD2 A:HIS62 4.4 11.2 1.0
CB A:GLU68 4.6 9.3 1.0
C A:ACY209 4.8 10.9 1.0
CG2 A:ILE101 4.8 12.0 1.0
O A:HOH317 4.8 15.1 1.0

Reference:

B.Liu, Y.Hou, X.Wang, X.Ma, S.Fang, T.Huang, Y.Chen, Z.Bai, S.Lin, R.Zhang, K.Hu. Structural Basis of the Mechanism of Beta-Methyl Epimerization By Enzyme Marh. Org.Biomol.Chem. V. 17 9605 2019.
ISSN: ESSN 1477-0539
PubMed: 31681917
DOI: 10.1039/C9OB01996K
Page generated: Wed Dec 16 12:02:38 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy