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Zinc in PDB 3rpc: The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008

Protein crystallography data

The structure of The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008, PDB code: 3rpc was solved by K.Tan, N.Marshall, S.Clancy, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.859, 97.104, 123.352, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18.2

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008 (pdb code 3rpc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008, PDB code: 3rpc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3rpc

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Zinc binding site 1 out of 8 in the The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:17.6
occ:0.66
 O A:HOH1177 2.0 22.0 1.0
NE2 A:HIS129 2.1 17.6 1.0
NE2 A:HIS69 2.2 16.1 1.0
ND1 A:HIS71 2.3 19.5 1.0
OD2 A:ASP165 2.4 16.3 1.0
CD2 A:HIS129 3.0 21.4 1.0
CE1 A:HIS129 3.2 18.3 1.0
CD2 A:HIS69 3.2 16.1 1.0
CE1 A:HIS71 3.2 21.8 1.0
CE1 A:HIS69 3.3 18.3 1.0
CG A:HIS71 3.3 22.0 1.0
ZN A:ZN302 3.3 16.5 0.7
CG A:ASP165 3.4 17.0 1.0
CB A:HIS71 3.6 18.3 1.0
CB A:ASP165 3.8 14.6 1.0
NE2 A:HIS74 4.0 16.3 1.0
CD2 A:HIS74 4.0 14.2 1.0
O A:HOH521 4.1 17.0 1.0
O A:HOH406 4.1 37.7 1.0
CG A:HIS129 4.2 18.1 1.0
ND1 A:HIS129 4.2 18.2 1.0
CG A:HIS69 4.3 13.2 1.0
ND1 A:HIS69 4.4 16.1 1.0
OD1 A:ASP73 4.4 17.4 1.0
NE2 A:HIS71 4.4 21.5 1.0
CD2 A:HIS71 4.4 22.3 1.0
OD1 A:ASP165 4.5 17.0 1.0
OD2 A:ASP73 4.8 20.0 1.0
CE1 A:HIS74 4.9 16.3 1.0

Zinc binding site 2 out of 8 in 3rpc

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Zinc binding site 2 out of 8 in the The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:16.5
occ:0.71
 OD2 A:ASP165 2.1 16.3 1.0
NE2 A:HIS74 2.2 16.3 1.0
NE2 A:HIS223 2.3 16.4 1.0
O A:HOH1177 2.3 22.0 1.0
OD2 A:ASP73 2.4 20.0 1.0
O A:HOH521 2.6 17.0 1.0
CG A:ASP165 3.0 17.0 1.0
CD2 A:HIS74 3.1 14.2 1.0
CE1 A:HIS223 3.1 18.4 1.0
OD1 A:ASP165 3.2 17.0 1.0
CE1 A:HIS74 3.3 16.3 1.0
ZN A:ZN301 3.3 17.6 0.7
CD2 A:HIS223 3.3 15.0 1.0
CG A:ASP73 3.3 17.6 1.0
OD1 A:ASP73 3.6 17.4 1.0
CG A:HIS74 4.3 13.7 1.0
ND1 A:HIS223 4.3 15.5 1.0
ND1 A:HIS74 4.3 15.6 1.0
NE2 A:HIS69 4.4 16.1 1.0
CG A:HIS223 4.4 14.0 1.0
CB A:ASP165 4.5 14.6 1.0
O A:HOH406 4.5 37.7 1.0
CE1 A:HIS69 4.6 18.3 1.0
NE2 A:HIS129 4.6 17.6 1.0
CB A:ASP73 4.7 17.5 1.0
CE1 A:HIS129 4.8 18.3 1.0
ND2 A:ASN9 4.8 16.9 1.0
CG2 A:ILE201 5.0 15.7 1.0

Zinc binding site 3 out of 8 in 3rpc

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Zinc binding site 3 out of 8 in the The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:20.2
occ:0.61
 O B:HOH1178 2.0 22.3 1.0
NE2 B:HIS69 2.1 16.1 1.0
NE2 B:HIS129 2.2 20.2 1.0
OD2 B:ASP165 2.3 18.8 1.0
ND1 B:HIS71 2.4 23.6 1.0
CD2 B:HIS129 3.0 21.8 1.0
CD2 B:HIS69 3.1 20.5 1.0
CE1 B:HIS69 3.1 16.5 1.0
CE1 B:HIS129 3.3 21.0 1.0
ZN B:ZN302 3.3 17.6 0.7
CE1 B:HIS71 3.3 23.6 1.0
CG B:HIS71 3.4 21.6 1.0
CG B:ASP165 3.4 18.0 1.0
CB B:HIS71 3.6 18.5 1.0
CB B:ASP165 3.8 15.9 1.0
NE2 B:HIS74 3.8 18.6 1.0
CD2 B:HIS74 4.0 19.5 1.0
O B:HOH520 4.0 18.5 1.0
O B:HOH917 4.1 33.3 1.0
CG B:HIS129 4.2 20.6 1.0
ND1 B:HIS69 4.2 17.5 1.0
CG B:HIS69 4.3 16.9 1.0
OD1 B:ASP73 4.3 20.9 1.0
ND1 B:HIS129 4.3 22.5 1.0
NE2 B:HIS71 4.4 24.9 1.0
OD1 B:ASP165 4.5 18.2 1.0
CD2 B:HIS71 4.5 26.5 1.0
CE1 B:HIS74 4.7 18.3 1.0
OD2 B:ASP73 4.7 22.4 1.0
CG B:HIS74 4.9 16.3 1.0
CG B:ASP73 4.9 21.0 1.0

Zinc binding site 4 out of 8 in 3rpc

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Zinc binding site 4 out of 8 in the The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:17.6
occ:0.70
 OD2 B:ASP165 2.2 18.8 1.0
NE2 B:HIS74 2.2 18.6 1.0
O B:HOH1178 2.3 22.3 1.0
NE2 B:HIS223 2.3 16.8 1.0
OD2 B:ASP73 2.4 22.4 1.0
O B:HOH520 2.5 18.5 1.0
CG B:ASP165 3.0 18.0 1.0
CD2 B:HIS74 3.1 19.5 1.0
CE1 B:HIS223 3.1 17.9 1.0
OD1 B:ASP165 3.2 18.2 1.0
CE1 B:HIS74 3.2 18.3 1.0
ZN B:ZN301 3.3 20.2 0.6
CG B:ASP73 3.3 21.0 1.0
CD2 B:HIS223 3.4 17.5 1.0
OD1 B:ASP73 3.6 20.9 1.0
CG B:HIS74 4.3 16.3 1.0
ND1 B:HIS223 4.3 17.3 1.0
ND1 B:HIS74 4.3 16.3 1.0
O B:HOH917 4.3 33.3 1.0
NE2 B:HIS69 4.4 16.1 1.0
CG B:HIS223 4.5 16.9 1.0
CB B:ASP165 4.5 15.9 1.0
CE1 B:HIS69 4.5 16.5 1.0
NE2 B:HIS129 4.5 20.2 1.0
CB B:ASP73 4.7 17.9 1.0
CE1 B:HIS129 4.7 21.0 1.0
ND2 B:ASN9 4.7 18.7 1.0
CG2 B:ILE201 5.0 16.1 1.0

Zinc binding site 5 out of 8 in 3rpc

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Zinc binding site 5 out of 8 in the The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:15.9
occ:0.69
 O C:HOH1175 2.0 22.3 1.0
NE2 C:HIS129 2.2 14.9 1.0
NE2 C:HIS69 2.2 16.3 1.0
OD2 C:ASP165 2.3 17.6 1.0
ND1 C:HIS71 2.3 19.9 1.0
CD2 C:HIS129 3.1 17.6 1.0
CE1 C:HIS129 3.1 16.4 1.0
CD2 C:HIS69 3.1 15.6 1.0
CE1 C:HIS71 3.2 19.2 1.0
CE1 C:HIS69 3.2 17.0 1.0
CG C:HIS71 3.3 17.9 1.0
ZN C:ZN302 3.3 16.4 0.7
CG C:ASP165 3.4 15.3 1.0
CB C:HIS71 3.6 17.8 1.0
CB C:ASP165 3.8 18.0 1.0
NE2 C:HIS74 3.9 15.2 1.0
O C:HOH275 4.0 15.9 1.0
CD2 C:HIS74 4.0 14.8 1.0
ND1 C:HIS129 4.2 15.8 1.0
CG C:HIS129 4.2 17.2 1.0
ND1 C:HIS69 4.3 15.1 1.0
CG C:HIS69 4.3 13.8 1.0
OD1 C:ASP73 4.3 19.8 1.0
NE2 C:HIS71 4.3 18.3 1.0
CD2 C:HIS71 4.4 20.2 1.0
OD1 C:ASP165 4.4 15.8 1.0
CE1 C:HIS74 4.8 14.7 1.0
O C:HOH1252 4.8 49.3 1.0
OD2 C:ASP73 4.8 20.7 1.0
CG C:HIS74 5.0 13.9 1.0

Zinc binding site 6 out of 8 in 3rpc

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Zinc binding site 6 out of 8 in the The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:16.4
occ:0.70
 NE2 C:HIS74 2.2 15.2 1.0
OD2 C:ASP165 2.2 17.6 1.0
O C:HOH1175 2.2 22.3 1.0
NE2 C:HIS223 2.2 18.1 1.0
OD2 C:ASP73 2.4 20.7 1.0
O C:HOH275 2.6 15.9 1.0
CG C:ASP165 3.0 15.3 1.0
CE1 C:HIS223 3.1 17.1 1.0
CD2 C:HIS74 3.1 14.8 1.0
OD1 C:ASP165 3.2 15.8 1.0
CE1 C:HIS74 3.2 14.7 1.0
CD2 C:HIS223 3.3 16.0 1.0
ZN C:ZN301 3.3 15.9 0.7
CG C:ASP73 3.3 18.8 1.0
OD1 C:ASP73 3.6 19.8 1.0
ND1 C:HIS223 4.3 16.2 1.0
CG C:HIS74 4.3 13.9 1.0
ND1 C:HIS74 4.3 15.5 1.0
CG C:HIS223 4.4 15.9 1.0
NE2 C:HIS69 4.4 16.3 1.0
CB C:ASP165 4.5 18.0 1.0
CE1 C:HIS69 4.5 17.0 1.0
NE2 C:HIS129 4.6 14.9 1.0
CB C:ASP73 4.7 16.5 1.0
CE1 C:HIS129 4.8 16.4 1.0
ND2 C:ASN9 4.8 17.7 1.0
CG2 C:ILE201 5.0 14.7 1.0

Zinc binding site 7 out of 8 in 3rpc

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Zinc binding site 7 out of 8 in the The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:19.3
occ:0.66
 O D:HOH1176 2.0 22.9 1.0
NE2 D:HIS129 2.2 20.7 1.0
NE2 D:HIS69 2.2 18.4 1.0
ND1 D:HIS71 2.4 22.3 1.0
OD1 D:ASP165 2.4 18.6 1.0
CD2 D:HIS129 3.1 19.8 1.0
CD2 D:HIS69 3.1 20.5 1.0
CE1 D:HIS129 3.2 19.4 1.0
CE1 D:HIS69 3.2 19.8 1.0
CE1 D:HIS71 3.3 21.8 1.0
ZN D:ZN302 3.3 17.9 0.7
CG D:HIS71 3.3 20.9 1.0
CG D:ASP165 3.4 19.2 1.0
CB D:HIS71 3.6 19.8 1.0
CB D:ASP165 3.8 17.7 1.0
NE2 D:HIS74 3.9 16.8 1.0
O D:HOH313 4.0 18.6 1.0
CD2 D:HIS74 4.0 17.8 1.0
O D:HOH1047 4.0 36.7 1.0
CG D:HIS129 4.2 17.4 1.0
ND1 D:HIS129 4.3 16.9 1.0
OD1 D:ASP73 4.3 21.8 1.0
CG D:HIS69 4.3 17.4 1.0
ND1 D:HIS69 4.3 19.0 1.0
NE2 D:HIS71 4.4 22.0 1.0
CD2 D:HIS71 4.5 21.9 1.0
OD2 D:ASP165 4.5 17.4 1.0
OD2 D:ASP73 4.8 22.8 1.0
CE1 D:HIS74 4.8 17.9 1.0
CG D:HIS74 5.0 17.4 1.0
CG D:ASP73 5.0 23.6 1.0

Zinc binding site 8 out of 8 in 3rpc

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Zinc binding site 8 out of 8 in the The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:17.9
occ:0.69
 NE2 D:HIS74 2.2 16.8 1.0
OD1 D:ASP165 2.2 18.6 1.0
NE2 D:HIS223 2.3 17.5 1.0
O D:HOH1176 2.3 22.9 1.0
OD2 D:ASP73 2.4 22.8 1.0
O D:HOH313 2.5 18.6 1.0
CG D:ASP165 3.1 19.2 1.0
CD2 D:HIS74 3.1 17.8 1.0
CE1 D:HIS223 3.1 21.5 1.0
OD2 D:ASP165 3.2 17.4 1.0
CE1 D:HIS74 3.2 17.9 1.0
ZN D:ZN301 3.3 19.3 0.7
CD2 D:HIS223 3.3 20.1 1.0
CG D:ASP73 3.3 23.6 1.0
OD1 D:ASP73 3.6 21.8 1.0
CG D:HIS74 4.3 17.4 1.0
ND1 D:HIS74 4.3 18.0 1.0
ND1 D:HIS223 4.3 19.1 1.0
NE2 D:HIS69 4.4 18.4 1.0
O D:HOH1047 4.4 36.7 1.0
CG D:HIS223 4.4 18.2 1.0
CB D:ASP165 4.5 17.7 1.0
CE1 D:HIS69 4.5 19.8 1.0
NE2 D:HIS129 4.6 20.7 1.0
CB D:ASP73 4.7 21.3 1.0
CE1 D:HIS129 4.8 19.4 1.0
ND2 D:ASN9 4.8 20.7 1.0
CG2 D:ILE201 4.9 18.7 1.0

Reference:

K.Tan, N.Marshall, S.Clancy, A.Joachimiak. The Crystal Structure of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008 To Be Published.
Page generated: Sat Oct 26 14:59:01 2024

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