Zinc in PDB 8wlv: Crystal Structure of P122A_MSD in Complex with 5-Azauracil

Protein crystallography data

The structure of Crystal Structure of P122A_MSD in Complex with 5-Azauracil, PDB code: 8wlv was solved by S.Porathoor, R.Anand, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.01 / 1.96
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.67, 109.47, 64.32, 90, 98.96, 90
R / Rfree (%) 19 / 22.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of P122A_MSD in Complex with 5-Azauracil (pdb code 8wlv). 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 P122A_MSD in Complex with 5-Azauracil, PDB code: 8wlv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8wlv

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Zinc binding site 1 out of 4 in the Crystal Structure of P122A_MSD in Complex with 5-Azauracil


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 P122A_MSD in Complex with 5-Azauracil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:25.2
occ:1.00
 O A:HOH310 2.0 25.2 1.0
ND1 A:HIS56 2.1 24.2 1.0
SG A:CYS89 2.3 26.5 1.0
SG A:CYS86 2.3 26.4 1.0
CE1 A:HIS56 3.1 24.5 1.0
CG A:HIS56 3.1 23.9 1.0
CB A:CYS89 3.3 23.9 1.0
CB A:CYS86 3.4 23.2 1.0
CB A:HIS56 3.4 22.6 1.0
CAD A:WHC201 3.5 34.3 1.0
NAE A:WHC201 3.6 30.7 1.0
OE2 A:GLU58 3.8 34.2 1.0
N A:CYS86 3.8 25.6 1.0
NAC A:WHC201 3.9 30.4 1.0
N A:CYS89 4.1 26.9 1.0
CAF A:WHC201 4.1 30.0 1.0
CA A:CYS86 4.1 25.5 1.0
OE1 A:GLU58 4.2 27.3 1.0
CE A:MET88 4.2 30.3 1.0
NE2 A:HIS56 4.2 24.0 1.0
CD2 A:HIS56 4.2 24.5 1.0
CA A:CYS89 4.3 25.1 1.0
CAB A:WHC201 4.3 31.2 1.0
CD A:GLU58 4.3 31.5 1.0
NAH A:WHC201 4.4 28.7 1.0
C A:CYS86 4.6 23.4 1.0
O A:CYS86 4.7 23.1 1.0
CB A:MET88 4.8 25.5 1.0
OAG A:WHC201 4.8 26.9 1.0
NE1 B:TRP95 4.9 29.3 1.0
CA A:HIS56 4.9 22.8 1.0
C A:HIS85 5.0 26.3 1.0

Zinc binding site 2 out of 4 in 8wlv

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Zinc binding site 2 out of 4 in the Crystal Structure of P122A_MSD in Complex with 5-Azauracil


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 P122A_MSD in Complex with 5-Azauracil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn204

b:25.8
occ:1.00
 O B:HOH308 1.9 30.2 1.0
ND1 B:HIS56 2.1 21.9 1.0
SG B:CYS89 2.3 28.1 1.0
SG B:CYS86 2.3 24.9 1.0
CE1 B:HIS56 3.0 22.4 1.0
CG B:HIS56 3.1 21.5 1.0
CB B:CYS89 3.2 28.8 1.0
CAD B:WHC201 3.3 32.3 1.0
CB B:HIS56 3.4 21.9 1.0
CB B:CYS86 3.4 26.5 1.0
NAC B:WHC201 3.7 29.0 1.0
NAE B:WHC201 3.7 30.0 1.0
N B:CYS86 3.8 26.8 1.0
CE B:MET88 4.0 28.1 1.0
N B:CYS89 4.0 26.1 1.0
CA B:CYS86 4.1 26.3 1.0
NE2 B:HIS56 4.2 24.0 1.0
OE2 B:GLU58 4.2 37.1 1.0
CA B:CYS89 4.2 26.8 1.0
CAB B:WHC201 4.2 27.2 1.0
CD2 B:HIS56 4.2 23.2 1.0
CAF B:WHC201 4.3 30.9 1.0
OE1 B:GLU58 4.3 26.6 1.0
NAH B:WHC201 4.5 28.3 1.0
CD B:GLU58 4.5 34.5 1.0
O B:CYS86 4.6 23.6 1.0
C B:CYS86 4.6 28.9 1.0
CB B:MET88 4.7 23.6 1.0
NE1 A:TRP95 4.9 24.5 1.0
C B:HIS85 4.9 27.4 1.0
CA B:HIS56 5.0 24.7 1.0
OAA B:WHC201 5.0 26.9 1.0

Zinc binding site 3 out of 4 in 8wlv

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Zinc binding site 3 out of 4 in the Crystal Structure of P122A_MSD in Complex with 5-Azauracil


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 P122A_MSD in Complex with 5-Azauracil within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn204

b:25.6
occ:1.00
 O C:HOH302 2.0 24.7 1.0
ND1 C:HIS56 2.0 25.8 1.0
SG C:CYS89 2.2 27.5 1.0
SG C:CYS86 2.3 23.7 1.0
CE1 C:HIS56 3.0 26.2 1.0
CG C:HIS56 3.1 26.2 1.0
CB C:CYS89 3.3 27.9 1.0
CB C:HIS56 3.4 25.5 1.0
CB C:CYS86 3.5 28.9 1.0
CAD C:WHC201 3.5 34.5 1.0
NAC C:WHC201 3.7 29.7 1.0
N C:CYS86 3.8 25.8 1.0
NAE C:WHC201 3.9 36.4 1.0
CE C:MET88 4.0 28.8 1.0
N C:CYS89 4.0 22.6 1.0
OE2 C:GLU58 4.1 48.5 1.0
NE2 C:HIS56 4.1 25.7 1.0
CAB C:WHC201 4.1 33.8 1.0
CD2 C:HIS56 4.2 24.8 1.0
CA C:CYS86 4.2 28.1 1.0
CA C:CYS89 4.3 24.9 1.0
OE1 C:GLU58 4.3 38.8 1.0
CAF C:WHC201 4.3 32.6 1.0
NAH C:WHC201 4.4 31.6 1.0
CD C:GLU58 4.4 37.1 1.0
O C:CYS86 4.6 25.2 1.0
C C:CYS86 4.7 29.1 1.0
CB C:MET88 4.8 24.8 1.0
OAA C:WHC201 4.8 32.4 1.0
CA C:HIS56 4.9 23.5 1.0
C C:HIS85 4.9 27.1 1.0
NE1 D:TRP95 5.0 28.6 1.0

Zinc binding site 4 out of 4 in 8wlv

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Zinc binding site 4 out of 4 in the Crystal Structure of P122A_MSD in Complex with 5-Azauracil


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 P122A_MSD in Complex with 5-Azauracil within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn203

b:26.6
occ:1.00
 O D:HOH302 2.0 31.5 1.0
ND1 D:HIS56 2.1 24.1 1.0
SG D:CYS89 2.3 27.0 1.0
SG D:CYS86 2.4 26.4 1.0
CE1 D:HIS56 3.0 24.6 1.0
CG D:HIS56 3.1 24.4 1.0
CB D:CYS89 3.3 25.0 1.0
CAD D:WHC201 3.4 32.1 1.0
CB D:CYS86 3.4 25.5 1.0
CB D:HIS56 3.4 21.9 1.0
NAE D:WHC201 3.7 32.5 1.0
NAC D:WHC201 3.7 28.9 1.0
N D:CYS86 3.9 25.4 1.0
N D:CYS89 4.0 24.7 1.0
CE D:MET88 4.0 30.9 1.0
OE2 D:GLU58 4.1 43.4 1.0
CA D:CYS86 4.2 25.1 1.0
NE2 D:HIS56 4.2 25.4 1.0
CD2 D:HIS56 4.2 25.8 1.0
CAF D:WHC201 4.2 30.2 1.0
OE1 D:GLU58 4.2 28.3 1.0
CAB D:WHC201 4.2 30.6 1.0
CA D:CYS89 4.3 25.6 1.0
CD D:GLU58 4.4 34.1 1.0
NAH D:WHC201 4.5 29.6 1.0
O D:CYS86 4.5 26.2 1.0
C D:CYS86 4.6 29.1 1.0
CB D:MET88 4.7 25.7 1.0
NE1 C:TRP95 4.9 27.6 1.0
C D:HIS85 4.9 26.9 1.0
OAG D:WHC201 5.0 30.2 1.0
CA D:HIS56 5.0 25.1 1.0

Reference:

S.Porathoor, R.Anand. Crystal Structure of P122A_MSD in Complex with 5-Azauracil To Be Published.
Page generated: Thu Oct 31 13:32:17 2024

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