Zinc in PDB 5xkr: Crystal Structure of MSMEG3575 in Complex with Benzoguanamine

Protein crystallography data

The structure of Crystal Structure of MSMEG3575 in Complex with Benzoguanamine, PDB code: 5xkr 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) 108.57 / 1.38
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.076, 63.446, 108.573, 90.00, 89.99, 90.00
R / Rfree (%) 12.8 / 15.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of MSMEG3575 in Complex with Benzoguanamine (pdb code 5xkr). 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 MSMEG3575 in Complex with Benzoguanamine, PDB code: 5xkr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5xkr

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Zinc binding site 1 out of 4 in the Crystal Structure of MSMEG3575 in Complex with Benzoguanamine


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 MSMEG3575 in Complex with Benzoguanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:10.1
occ:0.98
 O A:HOH319 2.0 11.4 1.0
ND1 A:HIS56 2.0 9.4 1.0
SG A:CYS89 2.3 10.8 1.0
SG A:CYS86 2.3 9.8 1.0
CE1 A:HIS56 2.9 9.7 1.0
CG A:HIS56 3.1 10.0 1.0
CB A:CYS89 3.3 9.7 1.0
CB A:CYS86 3.4 10.2 1.0
CB A:HIS56 3.5 11.0 1.0
N A:CYS86 3.8 9.8 1.0
OE2 A:GLU58 3.8 19.8 1.0
CE A:MET88 4.0 12.1 1.0
N A:CYS89 4.0 9.5 1.0
N4 A:BZE201 4.1 11.2 1.0
NE2 A:HIS56 4.1 10.9 1.0
CA A:CYS86 4.1 9.9 1.0
OE1 A:GLU58 4.2 14.6 1.0
N13 A:BZE201 4.2 12.4 1.0
CD2 A:HIS56 4.2 11.2 1.0
CA A:CYS89 4.3 10.2 1.0
CD A:GLU58 4.3 16.4 1.0
C8 A:BZE201 4.4 11.3 1.0
O A:CYS86 4.6 8.9 1.0
C A:CYS86 4.6 9.2 1.0
CB A:MET88 4.7 9.5 1.0
NE1 B:TRP95 4.8 10.3 1.0
C1 A:BZE201 4.9 11.3 1.0
C A:HIS85 4.9 10.7 1.0

Zinc binding site 2 out of 4 in 5xkr

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Zinc binding site 2 out of 4 in the Crystal Structure of MSMEG3575 in Complex with Benzoguanamine


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 MSMEG3575 in Complex with Benzoguanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:9.5
occ:1.00
 ND1 B:HIS56 2.0 8.7 1.0
O B:HOH310 2.0 10.6 1.0
SG B:CYS89 2.3 10.1 1.0
SG B:CYS86 2.3 9.3 1.0
CE1 B:HIS56 3.0 9.7 1.0
CG B:HIS56 3.1 9.4 1.0
CB B:CYS89 3.3 9.5 1.0
CB B:CYS86 3.4 8.8 1.0
CB B:HIS56 3.5 9.8 1.0
OE2 B:GLU58 3.8 14.2 0.8
N B:CYS86 3.8 8.7 1.0
CE B:MET88 4.0 13.7 1.0
N B:CYS89 4.0 8.8 1.0
N3 B:BZE201 4.0 10.3 1.0
NE2 B:HIS56 4.1 10.2 1.0
CA B:CYS86 4.1 8.8 1.0
OE1 B:GLU58 4.1 12.4 1.0
N12 B:BZE201 4.2 11.0 1.0
CD2 B:HIS56 4.2 10.1 1.0
CA B:CYS89 4.3 9.2 1.0
CD B:GLU58 4.3 15.2 1.0
C7 B:BZE201 4.4 10.2 1.0
O B:CYS86 4.5 8.5 1.0
C B:CYS86 4.6 8.9 1.0
CB B:MET88 4.7 9.9 1.0
NE1 A:TRP95 4.8 9.9 1.0
C1 B:BZE201 4.9 10.4 1.0
C B:HIS85 4.9 8.9 1.0

Zinc binding site 3 out of 4 in 5xkr

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Zinc binding site 3 out of 4 in the Crystal Structure of MSMEG3575 in Complex with Benzoguanamine


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 MSMEG3575 in Complex with Benzoguanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn203

b:9.3
occ:0.98
 O C:HOH319 2.0 10.6 1.0
ND1 C:HIS56 2.0 8.8 1.0
SG C:CYS89 2.3 10.2 1.0
SG C:CYS86 2.3 9.4 1.0
CE1 C:HIS56 2.9 9.6 1.0
CG C:HIS56 3.1 9.2 1.0
CB C:CYS89 3.2 9.3 1.0
CB C:CYS86 3.4 8.6 1.0
CB C:HIS56 3.5 9.8 1.0
N C:CYS86 3.8 8.7 1.0
OE2 C:GLU58 3.8 14.4 0.8
N C:CYS89 4.0 8.7 1.0
CE C:MET88 4.0 14.0 1.0
N4 C:BZE202 4.0 10.2 1.0
CA C:CYS86 4.1 8.8 1.0
NE2 C:HIS56 4.1 10.4 1.0
OE1 C:GLU58 4.1 12.4 1.0
N13 C:BZE202 4.1 10.6 1.0
CD2 C:HIS56 4.2 10.0 1.0
CA C:CYS89 4.3 9.1 1.0
CD C:GLU58 4.3 15.2 1.0
C8 C:BZE202 4.4 10.2 1.0
O C:CYS86 4.5 8.6 1.0
C C:CYS86 4.6 9.0 1.0
CB C:MET88 4.7 9.8 1.0
NE1 D:TRP95 4.8 9.8 1.0
C1 C:BZE202 4.9 10.5 1.0
C C:HIS85 4.9 9.0 1.0

Zinc binding site 4 out of 4 in 5xkr

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Zinc binding site 4 out of 4 in the Crystal Structure of MSMEG3575 in Complex with Benzoguanamine


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 MSMEG3575 in Complex with Benzoguanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:10.2
occ:1.00
 O D:HOH318 2.0 11.5 1.0
ND1 D:HIS56 2.0 9.4 1.0
SG D:CYS89 2.3 11.0 1.0
SG D:CYS86 2.3 9.9 1.0
CE1 D:HIS56 2.9 9.9 1.0
CG D:HIS56 3.1 9.7 1.0
CB D:CYS89 3.3 10.1 1.0
CB D:CYS86 3.4 10.0 1.0
CB D:HIS56 3.5 10.5 1.0
N D:CYS86 3.8 9.6 1.0
OE2 D:GLU58 3.8 20.0 1.0
N D:CYS89 4.0 9.6 1.0
CE D:MET88 4.0 12.2 1.0
N3 D:BZE202 4.1 10.8 1.0
CA D:CYS86 4.1 9.5 1.0
NE2 D:HIS56 4.1 10.9 1.0
OE1 D:GLU58 4.1 14.7 1.0
N12 D:BZE202 4.2 12.1 1.0
CD2 D:HIS56 4.2 11.1 1.0
CA D:CYS89 4.3 10.3 1.0
CD D:GLU58 4.3 16.2 1.0
C7 D:BZE202 4.4 10.9 1.0
O D:CYS86 4.6 8.8 1.0
C D:CYS86 4.6 8.9 1.0
CB D:MET88 4.7 9.5 1.0
NE1 C:TRP95 4.8 10.1 1.0
C1 D:BZE202 4.9 11.1 1.0
C D:HIS85 4.9 10.3 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: Wed Dec 16 11:20:38 2020

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