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Arsenic in PDB 5xko: Crystal Structure of Native MSMEG3575 Deaminase From Mycobacterium Smegmatis

Protein crystallography data

The structure of Crystal Structure of Native MSMEG3575 Deaminase From Mycobacterium Smegmatis, PDB code: 5xko was solved by V.M.Gaded, R.Anand, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.80 / 1.89
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 63.262, 108.335, 53.261, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 17.8

Other elements in 5xko:

The structure of Crystal Structure of Native MSMEG3575 Deaminase From Mycobacterium Smegmatis also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of Native MSMEG3575 Deaminase From Mycobacterium Smegmatis (pdb code 5xko). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 2 binding sites of Arsenic where determined in the Crystal Structure of Native MSMEG3575 Deaminase From Mycobacterium Smegmatis, PDB code: 5xko:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 5xko

Go back to Arsenic Binding Sites List in 5xko
Arsenic binding site 1 out of 2 in the Crystal Structure of Native MSMEG3575 Deaminase From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of Native MSMEG3575 Deaminase From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As201

b:9.8
occ:1.00
AS A:CAC201 0.0 9.8 1.0
O2 A:CAC201 1.7 9.9 1.0
O1 A:CAC201 1.7 8.3 1.0
C1 A:CAC201 1.9 10.2 1.0
C2 A:CAC201 2.0 9.2 1.0
ZN A:ZN203 3.3 12.2 0.8
OE1 A:GLU58 3.6 10.2 1.0
OE2 A:GLU58 3.8 13.2 1.0
ND1 A:HIS56 3.8 10.2 1.0
O A:HOH372 3.9 11.5 1.0
CD A:GLU58 4.0 10.1 1.0
N A:CYS86 4.1 7.5 1.0
CD1 A:PHE29 4.1 9.4 1.0
CE1 A:HIS56 4.3 10.4 1.0
CE1 A:PHE29 4.4 9.9 1.0
CG A:HIS56 4.4 10.0 1.0
CG A:PHE29 4.4 9.6 1.0
CB A:CYS86 4.5 8.1 1.0
O A:GLU84 4.6 8.6 1.0
CA A:HIS85 4.7 7.3 1.0
CB A:HIS56 4.7 9.5 1.0
O A:HOH436 4.7 22.4 1.0
SG A:CYS86 4.7 8.2 1.0
O A:HOH350 4.8 14.0 1.0
C A:HIS85 4.8 7.4 1.0
SG A:CYS89 4.8 9.6 1.0
CB A:PHE29 4.8 9.2 1.0
O A:GLY83 4.9 8.7 1.0
O A:HOH366 4.9 12.5 1.0
CA A:CYS86 4.9 7.8 1.0
CZ A:PHE29 4.9 10.3 1.0
CD2 A:PHE29 5.0 9.8 1.0

Arsenic binding site 2 out of 2 in 5xko

Go back to Arsenic Binding Sites List in 5xko
Arsenic binding site 2 out of 2 in the Crystal Structure of Native MSMEG3575 Deaminase From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of Native MSMEG3575 Deaminase From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As201

b:8.2
occ:1.00
AS B:CAC201 0.0 8.2 1.0
O1 B:CAC201 1.7 7.7 1.0
O2 B:CAC201 1.7 8.0 1.0
C1 B:CAC201 1.9 8.4 1.0
C2 B:CAC201 1.9 8.2 1.0
ZN B:ZN202 3.3 11.2 0.8
OE1 B:GLU58 3.5 9.2 1.0
OE2 B:GLU58 3.7 12.7 1.0
ND1 B:HIS56 3.8 8.7 1.0
O B:HOH356 3.9 10.6 1.0
CD B:GLU58 3.9 10.1 1.0
N B:CYS86 4.0 7.3 1.0
CD1 B:PHE29 4.1 8.8 1.0
O B:HOH435 4.2 14.0 1.0
CE1 B:PHE29 4.3 8.8 1.0
CG B:PHE29 4.4 8.7 1.0
CE1 B:HIS56 4.4 9.2 1.0
CB B:CYS86 4.4 8.0 1.0
O B:GLU84 4.5 7.7 1.0
CG B:HIS56 4.5 8.8 1.0
O B:HOH363 4.7 12.5 1.0
SG B:CYS86 4.7 7.1 1.0
CA B:HIS85 4.8 6.9 1.0
CB B:HIS56 4.8 8.7 1.0
CB B:PHE29 4.8 7.7 1.0
C B:HIS85 4.9 6.7 1.0
SG B:CYS89 4.9 8.3 1.0
CA B:CYS86 4.9 7.5 1.0
CZ B:PHE29 4.9 8.8 1.0
CD2 B:PHE29 4.9 9.6 1.0
O B:GLY83 4.9 8.1 1.0
O B:HOH318 4.9 17.1 1.0

Reference:

V.Gaded, R.Anand. Selective Deamination of Mutagens By A Mycobacterial Enzyme J. Am. Chem. Soc. V. 139 10762 2017.
ISSN: ESSN 1520-5126
PubMed: 28708393
DOI: 10.1021/JACS.7B04967
Page generated: Sat Dec 12 01:48:09 2020

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