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Zinc in PDB 4jnj: Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate

Protein crystallography data

The structure of Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate, PDB code: 4jnj was solved by D.Demonte, E.J.Drake, K.Hong Lim, A.M.Gulick, S.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.117, 64.058, 108.493, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 25.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate (pdb code 4jnj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate, PDB code: 4jnj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 4jnj

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Zinc binding site 1 out of 9 in the Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:22.6
occ:1.00
 ND1 C:HIS87 1.9 25.1 1.0
ND1 A:HIS87 2.0 21.7 1.0
OE2 C:GLU113 2.0 25.1 1.0
OE2 A:GLU113 2.0 26.2 1.0
CD C:GLU113 2.7 25.3 1.0
CD A:GLU113 2.8 23.2 1.0
CE1 C:HIS87 2.8 25.7 1.0
OE1 C:GLU113 2.8 21.5 1.0
OE1 A:GLU113 2.9 21.2 1.0
CG A:HIS87 3.0 22.2 1.0
CE1 A:HIS87 3.0 22.4 1.0
CG C:HIS87 3.0 26.2 1.0
CB A:HIS87 3.3 22.3 1.0
CB C:HIS87 3.5 26.3 1.0
O A:HOH357 3.8 27.5 1.0
CA A:HIS87 3.9 19.6 1.0
NE2 C:HIS87 3.9 26.8 1.0
CA C:HIS87 4.0 24.0 1.0
NE2 A:HIS87 4.1 21.4 1.0
CD2 C:HIS87 4.1 27.0 1.0
CD2 A:HIS87 4.1 22.9 1.0
CG C:GLU113 4.2 27.5 1.0
CG A:GLU113 4.2 24.4 1.0
O C:HOH309 4.3 27.8 1.0
OD1 C:ASN85 4.7 28.7 1.0
ND2 C:ASN85 4.8 24.9 1.0
C A:HIS87 4.8 21.1 1.0
O A:HIS87 4.9 18.5 1.0
C C:HIS87 4.9 28.0 1.0
N A:HIS87 5.0 19.4 1.0
ND2 A:ASN85 5.0 26.0 1.0

Zinc binding site 2 out of 9 in 4jnj

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Zinc binding site 2 out of 9 in the Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:20.2
occ:1.00
 N A:GLY12 2.0 20.9 1.0
OE2 A:GLU14 2.0 17.4 1.0
CD A:GLU14 2.7 21.1 1.0
OE1 A:GLU14 2.7 19.2 1.0
CA A:GLY12 3.0 20.5 1.0
C A:GLY12 3.8 24.9 1.0
O A:GLY12 4.0 27.5 1.0
CG A:GLU14 4.2 20.9 1.0
CB A:ALA35 4.3 23.0 1.0
N A:ALA13 4.8 25.6 1.0

Zinc binding site 3 out of 9 in 4jnj

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Zinc binding site 3 out of 9 in the Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:45.7
occ:1.00
 OD2 A:ASP36 2.3 32.8 1.0
O A:HOH364 2.4 33.1 1.0
O A:HOH311 2.7 33.4 1.0
CG A:ASP36 3.2 27.6 1.0
OD1 A:ASP36 3.3 29.8 1.0
CB A:ASN38 3.9 29.0 1.0
O A:HOH368 3.9 29.4 1.0
O A:HOH321 4.0 34.7 1.0
ND2 A:ASN38 4.1 32.6 1.0
O A:HOH304 4.1 29.1 1.0
CG A:ASN38 4.5 31.8 1.0
CB A:ASP36 4.6 26.7 1.0
CA A:GLY34 4.9 23.6 1.0

Zinc binding site 4 out of 9 in 4jnj

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Zinc binding site 4 out of 9 in the Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:66.2
occ:1.00
 OD2 B:ASP36 2.1 31.2 1.0
O B:HOH348 2.5 40.7 1.0
CG B:ASP36 2.9 30.1 1.0
OD1 B:ASP36 3.1 24.4 1.0
O B:HOH341 3.1 28.1 1.0
ND2 B:ASN38 3.6 25.1 0.5
CB B:ASN38 4.2 24.9 0.5
CB B:ASN38 4.3 24.8 0.5
CB B:ASP36 4.3 25.2 1.0
CG B:ASN38 4.5 25.6 0.5
ND2 B:ASN38 4.5 29.1 0.5
CA B:GLY34 4.5 20.4 1.0
O B:HOH323 4.5 29.5 1.0
CG B:ASN38 4.9 24.7 0.5

Zinc binding site 5 out of 9 in 4jnj

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Zinc binding site 5 out of 9 in the Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn203

b:35.2
occ:1.00
 OE2 B:GLU44 1.9 32.7 1.0
O B:HOH349 2.0 31.2 1.0
O B:HOH350 2.1 33.3 1.0
CD B:GLU44 2.9 26.3 1.0
OE1 B:GLU44 3.2 30.1 1.0
NH2 B:ARG46 3.8 24.9 1.0
O B:ASN51A 3.9 31.2 1.0
C B:ASN51A 4.1 27.8 1.0
CA B:ASN51A 4.2 22.8 1.0
CG B:GLU44 4.2 20.8 1.0
NE B:ARG46 4.4 24.3 1.0
CB B:ASN51A 4.4 26.1 1.0
CZ B:ARG46 4.5 24.9 1.0
OD1 B:ASN51A 5.0 31.2 1.0
N B:SER52 5.0 24.2 1.0

Zinc binding site 6 out of 9 in 4jnj

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Zinc binding site 6 out of 9 in the Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn204

b:18.4
occ:1.00
 OE2 B:GLU14 1.9 18.0 1.0
N B:GLY12 2.1 15.5 1.0
O B:HOH351 2.2 21.2 1.0
CD B:GLU14 2.7 16.8 1.0
OE1 B:GLU14 2.8 12.9 1.0
CA B:GLY12 3.0 17.2 1.0
C B:GLY12 3.8 14.7 1.0
O B:GLY12 4.0 15.6 1.0
CG B:GLU14 4.1 15.2 1.0
CB B:ALA35 4.7 18.0 1.0
N B:ALA13 4.9 14.4 1.0

Zinc binding site 7 out of 9 in 4jnj

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Zinc binding site 7 out of 9 in the Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:80.6
occ:1.00
 O12 C:BTN201 2.8 30.1 1.0
O11 C:BTN201 2.9 35.4 1.0
C11 C:BTN201 3.2 33.6 1.0
O C:HOH336 3.6 39.0 1.0
O C:CYS86 4.4 29.7 1.0
N C:GLY49 4.5 37.8 1.0
CB C:CYS86 4.6 27.4 1.0
C10 C:BTN201 4.7 29.0 1.0
CA C:GLY49 4.9 35.2 1.0
SG C:CYS86 4.9 29.7 1.0
OG C:SER88 5.0 23.3 1.0

Zinc binding site 8 out of 9 in 4jnj

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Zinc binding site 8 out of 9 in the Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:73.3
occ:1.00
 O D:HOH356 2.3 45.5 1.0
O12 D:BTN201 2.7 24.8 1.0
O D:HOH354 3.3 40.4 1.0
O11 D:BTN201 3.3 28.5 1.0
C11 D:BTN201 3.4 27.6 1.0
O D:CYS86 4.2 25.3 1.0
OG D:SER88 4.7 23.3 1.0
CB D:CYS86 4.8 26.1 1.0
C10 D:BTN201 4.8 25.4 1.0
O D:HOH353 5.0 40.9 1.0

Zinc binding site 9 out of 9 in 4jnj

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Zinc binding site 9 out of 9 in the Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn203

b:20.9
occ:1.00
 ND1 B:HIS87 1.9 21.1 1.0
OE2 B:GLU113 2.0 22.9 1.0
ND1 D:HIS87 2.1 23.7 1.0
OE2 D:GLU113 2.1 23.8 1.0
CD B:GLU113 2.7 18.6 1.0
OE1 B:GLU113 2.7 16.1 1.0
CE1 B:HIS87 2.7 18.9 1.0
CD D:GLU113 2.8 26.7 1.0
OE1 D:GLU113 2.9 23.9 1.0
CE1 D:HIS87 3.0 21.0 1.0
CG B:HIS87 3.1 23.1 1.0
CG D:HIS87 3.1 23.9 1.0
CB D:HIS87 3.5 20.1 1.0
CB B:HIS87 3.6 19.0 1.0
NE2 B:HIS87 3.9 25.1 1.0
CA B:HIS87 3.9 18.3 1.0
CA D:HIS87 4.0 19.8 1.0
CD2 B:HIS87 4.1 22.6 1.0
NE2 D:HIS87 4.1 22.0 1.0
O B:HOH311 4.1 25.8 1.0
CG B:GLU113 4.1 18.3 1.0
CG D:GLU113 4.2 26.4 1.0
CD2 D:HIS87 4.2 23.1 1.0
ND2 D:ASN85 4.6 19.2 1.0
OD1 B:ASN85 4.7 20.5 1.0
ND2 B:ASN85 4.7 21.3 1.0
C B:HIS87 4.9 18.9 1.0
C D:HIS87 4.9 23.5 1.0
N B:HIS87 4.9 17.0 1.0
OD1 D:ASN85 4.9 19.4 1.0
N D:HIS87 5.0 21.3 1.0

Reference:

D.Demonte, E.J.Drake, K.H.Lim, A.M.Gulick, S.Park. Structure-Based Engineering of Streptavidin Monomer with A Reduced Biotin Dissociation Rate. Proteins V. 81 1621 2013.
ISSN: ISSN 0887-3585
PubMed: 23670729
DOI: 10.1002/PROT.24320
Page generated: Sun Oct 27 01:22:47 2024

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