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Zinc in PDB 4xch: S-Ribosylhomocysteinase From Streptococcus Suis

Enzymatic activity of S-Ribosylhomocysteinase From Streptococcus Suis

All present enzymatic activity of S-Ribosylhomocysteinase From Streptococcus Suis:
4.4.1.21;

Protein crystallography data

The structure of S-Ribosylhomocysteinase From Streptococcus Suis, PDB code: 4xch was solved by Y.Wang, X.Mao, C.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.18 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.890, 86.250, 103.500, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 23.3

Zinc Binding Sites:

The binding sites of Zinc atom in the S-Ribosylhomocysteinase From Streptococcus Suis (pdb code 4xch). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the S-Ribosylhomocysteinase From Streptococcus Suis, PDB code: 4xch:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4xch

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Zinc binding site 1 out of 4 in the S-Ribosylhomocysteinase From Streptococcus Suis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of S-Ribosylhomocysteinase From Streptococcus Suis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:36.5
occ:1.00
NE2 A:HIS57 2.1 18.2 1.0
NE2 A:HIS61 2.2 24.9 1.0
SG A:CYS127 2.3 23.1 1.0
CE1 A:HIS61 2.8 27.9 1.0
CE1 A:HIS57 2.9 16.2 1.0
CD2 A:HIS57 3.2 18.2 1.0
CD2 A:HIS61 3.4 24.0 1.0
CB A:CYS127 3.5 19.1 1.0
NE2 A:HIS133 4.0 19.6 1.0
CB B:CYS82 4.0 18.0 1.0
ND1 A:HIS61 4.0 27.0 1.0
O A:HOH334 4.1 30.9 1.0
ND1 A:HIS57 4.1 18.1 1.0
CA A:CYS127 4.2 20.6 1.0
CG A:HIS57 4.3 18.4 1.0
CG A:HIS61 4.3 23.7 1.0
CE1 A:HIS133 4.4 19.7 1.0
N A:GLY128 4.5 18.7 1.0
O A:GLY121 4.6 28.3 1.0
OE2 A:GLU60 4.6 29.6 1.0
SG B:CYS82 4.7 19.7 1.0
C A:CYS127 4.8 19.3 1.0
N B:CYS82 4.8 14.9 1.0
CA B:CYS82 4.8 15.2 1.0

Zinc binding site 2 out of 4 in 4xch

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Zinc binding site 2 out of 4 in the S-Ribosylhomocysteinase From Streptococcus Suis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of S-Ribosylhomocysteinase From Streptococcus Suis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:37.4
occ:1.00
NE2 B:HIS61 2.2 24.1 1.0
NE2 B:HIS57 2.2 21.6 1.0
SG B:CYS127 2.4 20.1 1.0
O B:HOH330 2.4 39.8 1.0
CE1 B:HIS61 2.8 26.3 1.0
CE1 B:HIS57 3.0 19.1 1.0
CD2 B:HIS57 3.3 21.8 1.0
CD2 B:HIS61 3.4 26.9 1.0
CB B:CYS127 3.6 21.9 1.0
CB A:CYS82 4.0 22.2 1.0
ND1 B:HIS61 4.0 24.8 1.0
NE2 B:HIS133 4.0 19.2 1.0
ND1 B:HIS57 4.1 20.7 1.0
CA B:CYS127 4.3 23.8 1.0
CG B:HIS57 4.3 20.6 1.0
CG B:HIS61 4.3 24.2 1.0
CE1 B:HIS133 4.4 21.6 1.0
N B:GLY128 4.5 19.1 1.0
O B:GLY121 4.5 31.1 1.0
OE2 B:GLU60 4.7 34.4 1.0
CA A:CYS82 4.8 20.5 1.0
C B:CYS127 4.8 21.6 1.0
N A:CYS82 4.8 17.4 1.0
SG A:CYS82 4.8 21.9 1.0

Zinc binding site 3 out of 4 in 4xch

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Zinc binding site 3 out of 4 in the S-Ribosylhomocysteinase From Streptococcus Suis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of S-Ribosylhomocysteinase From Streptococcus Suis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:35.3
occ:1.00
NE2 C:HIS57 2.1 19.9 1.0
NE2 C:HIS61 2.2 24.7 1.0
SG C:CYS127 2.2 23.5 1.0
CE1 C:HIS57 2.8 20.4 1.0
CE1 C:HIS61 2.8 24.2 1.0
CD2 C:HIS57 3.2 17.3 1.0
CD2 C:HIS61 3.4 23.3 1.0
CB C:CYS127 3.5 24.8 1.0
NE2 C:HIS133 3.8 23.8 1.0
ND1 C:HIS57 4.0 19.7 1.0
ND1 C:HIS61 4.1 26.6 1.0
CB D:CYS82 4.1 21.9 1.0
CG C:HIS57 4.2 20.2 1.0
CA C:CYS127 4.2 24.2 1.0
CE1 C:HIS133 4.2 21.2 1.0
CG C:HIS61 4.3 25.7 1.0
OE2 C:GLU60 4.5 28.7 1.0
N C:GLY128 4.5 20.9 1.0
O C:GLY121 4.5 31.1 1.0
C C:CYS127 4.7 23.5 1.0
N D:CYS82 4.8 18.4 1.0
CA D:CYS82 4.8 16.6 1.0
SG D:CYS82 4.8 19.8 1.0
CD2 C:HIS133 5.0 20.6 1.0

Zinc binding site 4 out of 4 in 4xch

Go back to Zinc Binding Sites List in 4xch
Zinc binding site 4 out of 4 in the S-Ribosylhomocysteinase From Streptococcus Suis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of S-Ribosylhomocysteinase From Streptococcus Suis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:38.3
occ:1.00
NE2 D:HIS57 2.1 18.1 1.0
O D:HOH327 2.1 33.3 1.0
NE2 D:HIS61 2.2 24.8 1.0
SG D:CYS127 2.3 18.6 1.0
CE1 D:HIS61 2.7 25.2 1.0
CE1 D:HIS57 2.8 18.4 1.0
CD2 D:HIS57 3.2 18.0 1.0
CD2 D:HIS61 3.4 22.5 1.0
CB D:CYS127 3.7 25.0 1.0
NE2 D:HIS133 3.8 21.1 1.0
ND1 D:HIS61 3.9 26.0 1.0
ND1 D:HIS57 4.0 17.0 1.0
CB C:CYS82 4.0 17.0 1.0
CE1 D:HIS133 4.1 20.4 1.0
CG D:HIS57 4.2 18.3 1.0
CG D:HIS61 4.3 26.1 1.0
CA D:CYS127 4.3 26.6 1.0
O D:GLY121 4.3 33.0 1.0
N D:GLY128 4.5 21.3 1.0
OE1 D:GLU60 4.8 31.5 1.0
C D:CYS127 4.8 23.3 1.0
CA C:CYS82 4.9 16.5 1.0
SG C:CYS82 4.9 21.9 1.0
N D:ASN129 4.9 21.8 1.0
N C:CYS82 5.0 17.0 1.0

Reference:

Y.Wang, X.Mao, C.Lu. Crystal Structure of Luxs From Streptococcus Suis To Be Published.
Page generated: Wed Dec 16 05:54:12 2020

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