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Zinc in PDB 5giv: Crystal Structure of M32 Carboxypeptidase From Deinococcus Radiodurans R1

Enzymatic activity of Crystal Structure of M32 Carboxypeptidase From Deinococcus Radiodurans R1

All present enzymatic activity of Crystal Structure of M32 Carboxypeptidase From Deinococcus Radiodurans R1:
3.4.17.19;

Protein crystallography data

The structure of Crystal Structure of M32 Carboxypeptidase From Deinococcus Radiodurans R1, PDB code: 5giv was solved by B.Sharma, R.Singh, P.Yadav, B.Ghosh, A.Kumar, S.N.Jamdar, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.97 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 134.857, 256.632, 199.214, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 24.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of M32 Carboxypeptidase From Deinococcus Radiodurans R1 (pdb code 5giv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of M32 Carboxypeptidase From Deinococcus Radiodurans R1, PDB code: 5giv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5giv

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Zinc binding site 1 out of 6 in the Crystal Structure of M32 Carboxypeptidase From Deinococcus Radiodurans R1


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 M32 Carboxypeptidase From Deinococcus Radiodurans R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:24.4
occ:1.00
 O A:HOH737 2.0 20.4 1.0
OE2 A:GLU296 2.2 17.7 1.0
NE2 A:HIS270 2.2 17.3 1.0
NE2 A:HIS266 2.2 17.3 1.0
O A:HOH797 2.4 19.1 1.0
O A:HOH840 2.4 18.6 1.0
CD A:GLU296 3.1 17.8 1.0
CE1 A:HIS270 3.1 17.4 1.0
CE1 A:HIS266 3.2 17.2 1.0
CD2 A:HIS270 3.2 17.4 1.0
OE1 A:GLU296 3.2 17.8 1.0
CD2 A:HIS266 3.3 17.3 1.0
OG A:SER299 3.7 17.3 1.0
CB A:SER299 4.2 17.3 1.0
ND1 A:HIS270 4.3 17.4 1.0
ND1 A:HIS266 4.3 17.2 1.0
CG A:HIS270 4.3 17.4 1.0
CG A:HIS266 4.4 17.3 1.0
O A:HOH789 4.4 17.9 1.0
CG A:GLU296 4.5 17.9 1.0
OE2 A:GLU267 4.6 17.3 1.0
CB A:GLU296 4.9 17.8 1.0
CE1 A:TYR422 4.9 19.2 1.0
CA A:GLU296 5.0 17.8 1.0

Zinc binding site 2 out of 6 in 5giv

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Zinc binding site 2 out of 6 in the Crystal Structure of M32 Carboxypeptidase From Deinococcus Radiodurans R1


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 M32 Carboxypeptidase From Deinococcus Radiodurans R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:25.1
occ:1.00
 NE2 B:HIS270 2.2 18.6 1.0
NE2 B:HIS266 2.2 18.7 1.0
OE2 B:GLU296 2.2 18.6 1.0
O B:HOH827 2.2 18.8 1.0
O B:HOH843 2.3 25.5 1.0
O B:HOH759 2.4 18.8 1.0
CE1 B:HIS270 3.1 18.6 1.0
CD2 B:HIS270 3.2 18.6 1.0
CD B:GLU296 3.2 18.6 1.0
CD2 B:HIS266 3.2 18.7 1.0
CE1 B:HIS266 3.2 18.6 1.0
OE1 B:GLU296 3.4 18.6 1.0
OG B:SER299 3.7 18.5 1.0
CB B:SER299 4.2 18.5 1.0
ND1 B:HIS270 4.2 18.6 1.0
CG B:HIS270 4.3 18.6 1.0
ND1 B:HIS266 4.3 18.6 1.0
CG B:HIS266 4.3 18.7 1.0
O B:HOH770 4.5 18.9 1.0
OE1 B:GLU267 4.5 18.9 1.0
CG B:GLU296 4.6 18.5 1.0
CB B:GLU296 4.9 18.5 1.0
CE1 B:TYR422 5.0 19.2 1.0

Zinc binding site 3 out of 6 in 5giv

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Zinc binding site 3 out of 6 in the Crystal Structure of M32 Carboxypeptidase From Deinococcus Radiodurans R1


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 M32 Carboxypeptidase From Deinococcus Radiodurans R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn601

b:32.2
occ:1.00
 OE1 C:GLU296 2.2 20.9 1.0
NE2 C:HIS270 2.2 21.1 1.0
NE2 C:HIS266 2.2 20.8 1.0
O C:HOH787 2.3 22.4 1.0
O C:HOH843 2.4 21.2 1.0
CD C:GLU296 3.0 20.9 1.0
CE1 C:HIS266 3.2 20.7 1.0
CD2 C:HIS270 3.2 21.3 1.0
CE1 C:HIS270 3.2 20.9 1.0
OE2 C:GLU296 3.2 20.9 1.0
CD2 C:HIS266 3.2 20.8 1.0
OG C:SER299 3.8 20.5 1.0
ND1 C:HIS270 4.3 21.0 1.0
ND1 C:HIS266 4.3 20.6 1.0
CB C:SER299 4.3 20.4 1.0
CG C:HIS270 4.3 21.2 1.0
O C:HOH837 4.3 31.4 1.0
CG C:HIS266 4.4 20.6 1.0
OE2 C:GLU267 4.4 21.1 1.0
CG C:GLU296 4.5 20.8 1.0
CE1 C:TYR422 4.8 21.5 1.0
CB C:GLU296 4.9 20.8 1.0
CA C:GLU296 5.0 20.6 1.0

Zinc binding site 4 out of 6 in 5giv

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Zinc binding site 4 out of 6 in the Crystal Structure of M32 Carboxypeptidase From Deinococcus Radiodurans R1


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 M32 Carboxypeptidase From Deinococcus Radiodurans R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:25.6
occ:1.00
 NE2 D:HIS266 2.1 18.9 1.0
NE2 D:HIS270 2.2 18.9 1.0
O D:HOH769 2.3 19.3 1.0
OE2 D:GLU296 2.3 20.2 1.0
OXT D:ACT602 2.5 32.3 1.0
O D:HOH745 2.6 22.7 1.0
CE1 D:HIS266 3.1 19.0 1.0
CE1 D:HIS270 3.2 18.9 1.0
CD2 D:HIS270 3.2 18.8 1.0
CD2 D:HIS266 3.2 18.8 1.0
CD D:GLU296 3.2 20.4 1.0
OE1 D:GLU296 3.4 20.4 1.0
OG D:SER299 3.6 19.1 1.0
C D:ACT602 3.6 32.2 1.0
CB D:SER299 4.1 19.0 1.0
H1 D:ACT602 4.2 20.0 1.0
ND1 D:HIS266 4.2 19.0 1.0
ND1 D:HIS270 4.3 18.9 1.0
CG D:HIS266 4.3 18.9 1.0
CG D:HIS270 4.3 18.9 1.0
O D:ACT602 4.4 32.1 1.0
CH3 D:ACT602 4.5 32.1 1.0
OE2 D:GLU267 4.6 20.3 1.0
CG D:GLU296 4.6 20.5 1.0
O D:HOH867 4.8 29.3 1.0
H3 D:ACT602 4.9 20.0 1.0
CB D:GLU296 5.0 20.5 1.0

Zinc binding site 5 out of 6 in 5giv

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Zinc binding site 5 out of 6 in the Crystal Structure of M32 Carboxypeptidase From Deinococcus Radiodurans R1


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 M32 Carboxypeptidase From Deinococcus Radiodurans R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn601

b:33.4
occ:1.00
 NE2 E:HIS266 2.1 23.6 1.0
NE2 E:HIS270 2.3 23.9 1.0
OE1 E:GLU296 2.3 24.0 1.0
O E:HOH769 2.4 23.6 1.0
O E:HOH780 2.8 28.4 1.0
CE1 E:HIS266 3.1 23.6 1.0
CD E:GLU296 3.1 23.9 1.0
CD2 E:HIS266 3.1 23.5 1.0
CD2 E:HIS270 3.1 23.9 1.0
OE2 E:GLU296 3.2 23.8 1.0
CE1 E:HIS270 3.3 24.1 1.0
OG E:SER299 3.8 24.1 1.0
ND1 E:HIS266 4.2 23.6 1.0
CG E:HIS266 4.2 23.5 1.0
CB E:SER299 4.3 24.1 1.0
CG E:HIS270 4.3 24.1 1.0
ND1 E:HIS270 4.4 24.2 1.0
OE1 E:GLU267 4.4 25.8 1.0
O E:HOH721 4.5 23.4 1.0
CG E:GLU296 4.5 24.2 1.0

Zinc binding site 6 out of 6 in 5giv

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Zinc binding site 6 out of 6 in the Crystal Structure of M32 Carboxypeptidase From Deinococcus Radiodurans R1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of M32 Carboxypeptidase From Deinococcus Radiodurans R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn601

b:30.2
occ:1.00
 NE2 F:HIS270 2.1 23.0 1.0
O F:HOH779 2.2 22.5 1.0
NE2 F:HIS266 2.2 24.7 1.0
OE2 F:GLU296 2.2 28.1 1.0
O F:HOH762 2.4 20.4 1.0
CE1 F:HIS270 3.0 23.0 1.0
CD2 F:HIS270 3.1 23.2 1.0
CD2 F:HIS266 3.2 24.9 1.0
CE1 F:HIS266 3.2 24.4 1.0
CD F:GLU296 3.2 27.7 1.0
OE1 F:GLU296 3.5 27.5 1.0
OG F:SER299 3.6 23.5 1.0
CB F:SER299 4.1 23.7 1.0
ND1 F:HIS270 4.2 23.3 1.0
CG F:HIS270 4.2 23.4 1.0
ND1 F:HIS266 4.3 24.4 1.0
CG F:HIS266 4.3 24.7 1.0
O F:HOH782 4.4 20.3 1.0
OE1 F:GLU267 4.5 22.6 1.0
CG F:GLU296 4.6 27.6 1.0
CB F:GLU296 5.0 27.8 1.0

Reference:

B.Sharma, S.N.Jamdar, B.Ghosh, P.Yadav, A.Kumar, S.Kundu, V.D.Goyal, R.D.Makde. Active Site Gate of M32 Carboxypeptidases Illuminated By Crystal Structure and Molecular Dynamics Simulations Biochim. Biophys. Acta V.1865 1406 2017.
ISSN: ISSN 0006-3002
PubMed: 28844748
DOI: 10.1016/J.BBAPAP.2017.07.023
Page generated: Sun Oct 27 17:00:25 2024

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