Atomistry » Zinc » PDB 5hmy-5i1r » 5i0p
Atomistry »
  Zinc »
    PDB 5hmy-5i1r »
      5i0p »

Zinc in PDB 5i0p: Crystal Structure of A Beta-Lactamase Domain Protein From Burkholderia Ambifaria

Protein crystallography data

The structure of Crystal Structure of A Beta-Lactamase Domain Protein From Burkholderia Ambifaria, PDB code: 5i0p was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.94 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.170, 141.230, 236.990, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 22.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Beta-Lactamase Domain Protein From Burkholderia Ambifaria (pdb code 5i0p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of A Beta-Lactamase Domain Protein From Burkholderia Ambifaria, PDB code: 5i0p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5i0p

Go back to Zinc Binding Sites List in 5i0p
Zinc binding site 1 out of 8 in the Crystal Structure of A Beta-Lactamase Domain Protein From Burkholderia Ambifaria


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 A Beta-Lactamase Domain Protein From Burkholderia Ambifaria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:50.7
occ:1.00
ND1 A:HIS96 2.1 40.3 1.0
OD2 A:ASP224 2.1 39.7 1.0
NE2 A:HIS205 2.3 24.0 1.0
NE2 A:HIS94 2.4 24.4 1.0
CE1 A:HIS205 3.0 25.4 1.0
CE1 A:HIS96 3.0 36.0 1.0
CG A:HIS96 3.1 31.5 1.0
CG A:ASP224 3.2 23.9 1.0
CD2 A:HIS94 3.3 22.1 1.0
CD2 A:HIS205 3.4 27.1 1.0
CE1 A:HIS94 3.4 20.7 1.0
CB A:HIS96 3.4 25.8 1.0
ZN A:ZN401 3.5 37.1 1.0
CB A:ASP224 3.9 20.2 1.0
NE2 A:HIS96 4.2 33.2 1.0
OD1 A:ASP224 4.2 28.0 1.0
NE2 A:HIS99 4.2 24.0 1.0
CD2 A:HIS96 4.2 37.3 1.0
ND1 A:HIS205 4.2 25.9 1.0
CD2 A:HIS99 4.3 19.0 1.0
CG A:HIS205 4.4 25.2 1.0
CG A:HIS94 4.5 25.6 1.0
ND1 A:HIS94 4.5 25.5 1.0
OD2 A:ASP98 4.8 34.9 1.0
CA A:HIS96 4.9 27.6 1.0

Zinc binding site 2 out of 8 in 5i0p

Go back to Zinc Binding Sites List in 5i0p
Zinc binding site 2 out of 8 in the Crystal Structure of A Beta-Lactamase Domain Protein From Burkholderia Ambifaria


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 A Beta-Lactamase Domain Protein From Burkholderia Ambifaria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:37.1
occ:1.00
NE2 A:HIS269 2.3 26.4 1.0
NE2 A:HIS99 2.3 24.0 1.0
OD2 A:ASP224 2.4 39.7 1.0
OD1 A:ASP224 2.5 28.0 1.0
OD1 A:ASP98 2.7 39.9 1.0
CG A:ASP224 2.8 23.9 1.0
CD2 A:HIS99 3.1 19.0 1.0
CE1 A:HIS269 3.2 21.9 1.0
CD2 A:HIS269 3.3 21.2 1.0
CE1 A:HIS99 3.4 19.0 1.0
ZN A:ZN400 3.5 50.7 1.0
CG A:ASP98 3.6 34.7 1.0
OD2 A:ASP98 3.8 34.9 1.0
CB A:ASP224 4.3 20.2 1.0
CG A:HIS99 4.3 30.4 1.0
ND1 A:HIS269 4.4 26.6 1.0
ND1 A:HIS99 4.4 28.0 1.0
CG A:HIS269 4.4 26.5 1.0
CE1 A:HIS94 4.4 20.7 1.0
NE2 A:HIS94 4.4 24.4 1.0
CD2 A:LEU40 4.6 44.2 1.0
CD1 A:ILE43 4.7 18.7 1.0
CB A:SER268 4.8 25.5 1.0
CB A:ASP98 4.9 27.6 1.0

Zinc binding site 3 out of 8 in 5i0p

Go back to Zinc Binding Sites List in 5i0p
Zinc binding site 3 out of 8 in the Crystal Structure of A Beta-Lactamase Domain Protein From Burkholderia Ambifaria


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 A Beta-Lactamase Domain Protein From Burkholderia Ambifaria within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn400

b:57.9
occ:1.00
ND1 B:HIS96 2.1 55.0 1.0
OD2 B:ASP224 2.1 48.6 1.0
NE2 B:HIS94 2.3 39.8 1.0
NE2 B:HIS205 2.3 30.6 1.0
CG B:HIS96 3.0 49.6 1.0
CE1 B:HIS96 3.1 45.5 1.0
CE1 B:HIS205 3.1 31.4 1.0
CE1 B:HIS94 3.2 35.6 1.0
CG B:ASP224 3.3 38.9 1.0
CD2 B:HIS94 3.3 35.0 1.0
CB B:HIS96 3.3 32.9 1.0
ZN B:ZN401 3.4 38.8 1.0
CD2 B:HIS205 3.4 30.2 1.0
NE2 B:HIS99 3.8 48.4 1.0
CB B:ASP224 3.9 23.6 1.0
CD2 B:HIS99 4.0 31.5 1.0
NE2 B:HIS96 4.2 44.9 1.0
CD2 B:HIS96 4.2 48.0 1.0
OD1 B:ASP224 4.3 36.8 1.0
ND1 B:HIS205 4.3 33.1 1.0
ND1 B:HIS94 4.4 34.6 1.0
CG B:HIS94 4.4 32.4 1.0
CG B:HIS205 4.4 32.2 1.0
OD2 B:ASP98 4.7 54.5 1.0
CA B:HIS96 4.8 35.1 1.0
CE1 B:HIS99 4.9 35.3 1.0

Zinc binding site 4 out of 8 in 5i0p

Go back to Zinc Binding Sites List in 5i0p
Zinc binding site 4 out of 8 in the Crystal Structure of A Beta-Lactamase Domain Protein From Burkholderia Ambifaria


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 A Beta-Lactamase Domain Protein From Burkholderia Ambifaria within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:38.8
occ:1.00
NE2 B:HIS99 2.2 48.4 1.0
OD2 B:ASP224 2.3 48.6 1.0
NE2 B:HIS269 2.4 35.5 1.0
OD1 B:ASP98 2.5 50.7 1.0
OD1 B:ASP224 2.6 36.8 1.0
CG B:ASP224 2.8 38.9 1.0
CD2 B:HIS99 3.1 31.5 1.0
CE1 B:HIS99 3.2 35.3 1.0
CE1 B:HIS269 3.3 30.8 1.0
ZN B:ZN400 3.4 57.9 1.0
CD2 B:HIS269 3.4 33.8 1.0
CG B:ASP98 3.4 49.3 1.0
OD2 B:ASP98 3.7 54.5 1.0
CG B:HIS99 4.2 42.9 1.0
ND1 B:HIS99 4.3 36.8 1.0
CB B:ASP224 4.3 23.6 1.0
ND1 B:HIS269 4.4 32.8 1.0
CE1 B:HIS94 4.4 35.6 1.0
NE2 B:HIS94 4.5 39.8 1.0
CD1 B:ILE43 4.5 34.0 1.0
CG B:HIS269 4.5 34.3 1.0
CB B:SER268 4.7 37.8 1.0
CB B:ASP98 4.8 37.6 1.0

Zinc binding site 5 out of 8 in 5i0p

Go back to Zinc Binding Sites List in 5i0p
Zinc binding site 5 out of 8 in the Crystal Structure of A Beta-Lactamase Domain Protein From Burkholderia Ambifaria


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 A Beta-Lactamase Domain Protein From Burkholderia Ambifaria within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn400

b:43.2
occ:1.00
OD2 C:ASP224 2.1 40.2 1.0
ND1 C:HIS96 2.1 43.2 1.0
NE2 C:HIS94 2.3 24.3 1.0
NE2 C:HIS205 2.3 27.0 1.0
CE1 C:HIS96 3.0 34.3 1.0
CG C:HIS96 3.1 39.0 1.0
CE1 C:HIS205 3.2 24.5 1.0
CD2 C:HIS94 3.2 20.5 1.0
CG C:ASP224 3.2 30.3 1.0
CE1 C:HIS94 3.2 19.8 1.0
O C:HOH593 3.2 54.6 1.0
CD2 C:HIS205 3.4 27.0 1.0
CB C:HIS96 3.5 32.2 1.0
ZN C:ZN401 3.5 36.8 1.0
CB C:ASP224 3.8 23.9 1.0
NE2 C:HIS99 4.1 21.5 1.0
NE2 C:HIS96 4.2 36.4 1.0
OD1 C:ASP224 4.2 29.3 1.0
CD2 C:HIS96 4.2 37.0 1.0
CD2 C:HIS99 4.3 23.0 1.0
ND1 C:HIS205 4.3 27.1 1.0
ND1 C:HIS94 4.3 19.1 1.0
CG C:HIS94 4.4 25.8 1.0
CG C:HIS205 4.5 24.2 1.0
OD2 C:ASP98 5.0 34.0 1.0
CA C:HIS96 5.0 28.7 1.0

Zinc binding site 6 out of 8 in 5i0p

Go back to Zinc Binding Sites List in 5i0p
Zinc binding site 6 out of 8 in the Crystal Structure of A Beta-Lactamase Domain Protein From Burkholderia Ambifaria


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 A Beta-Lactamase Domain Protein From Burkholderia Ambifaria within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:36.8
occ:1.00
NE2 C:HIS269 2.3 19.2 1.0
NE2 C:HIS99 2.3 21.5 1.0
OD2 C:ASP224 2.4 40.2 1.0
OD1 C:ASP224 2.7 29.3 1.0
OD1 C:ASP98 2.8 36.3 1.0
CG C:ASP224 2.9 30.3 1.0
CD2 C:HIS99 3.1 23.0 1.0
CE1 C:HIS269 3.1 20.3 1.0
O C:HOH593 3.2 54.6 1.0
CD2 C:HIS269 3.3 24.2 1.0
CE1 C:HIS99 3.4 21.9 1.0
ZN C:ZN400 3.5 43.2 1.0
CG C:ASP98 3.6 33.4 1.0
OD2 C:ASP98 3.8 34.0 1.0
ND1 C:HIS269 4.3 27.4 1.0
CG C:HIS99 4.4 24.7 1.0
CB C:ASP224 4.4 23.9 1.0
CG C:HIS269 4.4 19.9 1.0
CE1 C:HIS94 4.4 19.8 1.0
ND1 C:HIS99 4.4 24.6 1.0
NE2 C:HIS94 4.5 24.3 1.0
CD1 C:ILE43 4.6 19.2 1.0
CB C:SER268 4.7 20.7 1.0
CD2 C:LEU40 4.8 42.0 1.0
CB C:ASP98 5.0 27.1 1.0

Zinc binding site 7 out of 8 in 5i0p

Go back to Zinc Binding Sites List in 5i0p
Zinc binding site 7 out of 8 in the Crystal Structure of A Beta-Lactamase Domain Protein From Burkholderia Ambifaria


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of A Beta-Lactamase Domain Protein From Burkholderia Ambifaria within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn400

b:47.5
occ:1.00
ND1 D:HIS96 2.1 41.9 1.0
OD1 D:ASP224 2.1 45.4 1.0
NE2 D:HIS205 2.3 26.4 1.0
NE2 D:HIS94 2.3 22.7 1.0
CE1 D:HIS96 3.0 40.0 1.0
CE1 D:HIS205 3.1 16.8 1.0
CG D:HIS96 3.1 35.3 1.0
CD2 D:HIS94 3.2 26.2 1.0
CG D:ASP224 3.2 27.8 1.0
O D:HOH603 3.3 43.0 1.0
CE1 D:HIS94 3.3 21.9 1.0
ZN D:ZN401 3.3 38.4 1.0
CD2 D:HIS205 3.4 22.9 1.0
CB D:HIS96 3.5 27.2 1.0
CB D:ASP224 3.7 25.0 1.0
NE2 D:HIS99 3.9 31.4 1.0
NE2 D:HIS96 4.1 38.1 1.0
CD2 D:HIS99 4.2 24.6 1.0
CD2 D:HIS96 4.2 40.7 1.0
OD2 D:ASP224 4.2 35.9 1.0
ND1 D:HIS205 4.3 29.3 1.0
CG D:HIS94 4.4 25.9 1.0
ND1 D:HIS94 4.4 30.1 1.0
CG D:HIS205 4.4 23.0 1.0
CE1 D:HIS99 4.8 21.4 1.0
CA D:HIS96 4.9 23.1 1.0
OD2 D:ASP98 5.0 38.4 1.0

Zinc binding site 8 out of 8 in 5i0p

Go back to Zinc Binding Sites List in 5i0p
Zinc binding site 8 out of 8 in the Crystal Structure of A Beta-Lactamase Domain Protein From Burkholderia Ambifaria


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of A Beta-Lactamase Domain Protein From Burkholderia Ambifaria within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:38.4
occ:1.00
OD1 D:ASP224 2.1 45.4 1.0
NE2 D:HIS99 2.1 31.4 1.0
NE2 D:HIS269 2.3 22.5 1.0
OD2 D:ASP224 2.7 35.9 1.0
CG D:ASP224 2.7 27.8 1.0
OD1 D:ASP98 2.9 34.2 1.0
CD2 D:HIS99 3.0 24.6 1.0
CE1 D:HIS99 3.1 21.4 1.0
CE1 D:HIS269 3.2 20.0 1.0
CD2 D:HIS269 3.3 27.2 1.0
ZN D:ZN400 3.3 47.5 1.0
CG D:ASP98 3.8 37.6 1.0
O D:HOH603 3.8 43.0 1.0
OD2 D:ASP98 3.9 38.4 1.0
ND1 D:HIS99 4.2 27.9 1.0
CG D:HIS99 4.2 21.7 1.0
CB D:ASP224 4.2 25.0 1.0
NE2 D:HIS94 4.3 22.7 1.0
ND1 D:HIS269 4.3 26.8 1.0
CE1 D:HIS94 4.4 21.9 1.0
CG D:HIS269 4.4 30.5 1.0
CD1 D:ILE43 4.7 21.5 1.0
CB D:SER268 4.8 21.4 1.0

Reference:

D.M.Dranow, J.Abendroth, D.Lorimer, T.E.Edwards. Crystal Structure of A Beta-Lactamase Domain Protein From Burkholderia Ambifaria To Be Published.
Page generated: Wed Dec 16 06:21:09 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy