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Zinc in PDB 4l99: Structure of the Rbp From Lactococcal Phage 1358 in Complex with Glycerol

Protein crystallography data

The structure of Structure of the Rbp From Lactococcal Phage 1358 in Complex with Glycerol, PDB code: 4l99 was solved by C.Farenc, S.Spinelli, C.Bebeacua, D.Tremblay, I.Orlov, S.Blangy, B.P.Klaholz, S.Moineau, C.Cambillau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.21 / 2.20
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 166.210, 166.210, 166.210, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 20.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Rbp From Lactococcal Phage 1358 in Complex with Glycerol (pdb code 4l99). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of the Rbp From Lactococcal Phage 1358 in Complex with Glycerol, PDB code: 4l99:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4l99

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Zinc binding site 1 out of 6 in the Structure of the Rbp From Lactococcal Phage 1358 in Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Rbp From Lactococcal Phage 1358 in Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:0.9
occ:0.33
OE2 A:GLU377 4.5 68.1 1.0

Zinc binding site 2 out of 6 in 4l99

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Zinc binding site 2 out of 6 in the Structure of the Rbp From Lactococcal Phage 1358 in Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Rbp From Lactococcal Phage 1358 in Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:63.7
occ:1.00
OD1 A:ASP133 2.0 47.3 1.0
NZ A:LYS338 2.1 56.1 1.0
NE2 A:HIS303 2.4 42.8 1.0
O A:HOH743 2.5 47.8 1.0
O A:HOH534 2.7 38.9 1.0
CE A:LYS338 2.8 47.5 1.0
CG A:ASP133 3.0 46.1 1.0
CD A:LYS338 3.0 36.1 1.0
OD2 A:ASP133 3.2 49.3 1.0
CD2 A:HIS303 3.3 42.6 1.0
CE1 A:HIS303 3.4 41.4 1.0
O A:GLU301 4.3 40.9 1.0
CB A:ASP133 4.3 41.4 1.0
CG A:HIS303 4.4 40.9 1.0
CG A:LYS338 4.4 36.4 1.0
ND1 A:HIS303 4.4 41.9 1.0
O A:HOH533 4.7 35.5 1.0
O A:ARG132 4.7 43.0 1.0
CA A:ASP133 4.9 40.2 1.0

Zinc binding site 3 out of 6 in 4l99

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Zinc binding site 3 out of 6 in the Structure of the Rbp From Lactococcal Phage 1358 in Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Rbp From Lactococcal Phage 1358 in Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:0.7
occ:0.50
OE2 A:GLU16 2.2 65.5 1.0
OG A:SER20 2.5 62.5 1.0
ND1 A:HIS137 3.1 66.3 1.0
CB A:SER20 3.3 60.2 1.0
CD A:GLU16 3.5 97.0 1.0
O A:HOH755 3.6 75.5 1.0
CB A:HIS137 3.6 60.3 1.0
CG A:HIS137 3.7 64.2 1.0
O A:HOH791 3.9 63.6 1.0
CE1 A:HIS137 4.1 65.8 1.0
O A:HOH768 4.2 66.4 1.0
OE1 A:GLU16 4.3 0.8 1.0
CA A:SER20 4.4 56.4 1.0
CG A:GLU16 4.4 80.3 1.0
CA A:HIS137 4.5 59.2 1.0
O A:GLU16 4.8 72.1 1.0
CD2 A:HIS137 4.8 66.4 1.0
O A:HIS137 4.9 66.1 1.0

Zinc binding site 4 out of 6 in 4l99

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Zinc binding site 4 out of 6 in the Structure of the Rbp From Lactococcal Phage 1358 in Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Rbp From Lactococcal Phage 1358 in Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:0.0
occ:0.30
OE2 B:GLU377 3.8 64.1 1.0
OE1 B:GLU377 4.3 69.7 1.0
CD B:GLU377 4.4 69.4 1.0
O B:HOH663 4.8 55.4 1.0

Zinc binding site 5 out of 6 in 4l99

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Zinc binding site 5 out of 6 in the Structure of the Rbp From Lactococcal Phage 1358 in Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Rbp From Lactococcal Phage 1358 in Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:76.6
occ:0.50
OE2 B:GLU16 1.9 0.2 1.0
OG B:SER20 2.3 69.9 1.0
ND1 B:HIS137 2.4 77.6 1.0
CD B:GLU16 2.9 0.3 1.0
OE1 B:GLU16 3.3 0.7 1.0
CG B:HIS137 3.3 75.4 1.0
CE1 B:HIS137 3.4 77.2 1.0
CB B:SER20 3.5 63.1 1.0
CB B:HIS137 3.5 71.1 1.0
O B:HOH734 3.9 80.3 1.0
O B:HOH900 4.0 72.8 1.0
CG B:GLU16 4.2 85.8 1.0
O B:GLU16 4.2 74.2 1.0
CA B:HIS137 4.3 69.7 1.0
CA B:SER20 4.4 59.6 1.0
CD2 B:HIS137 4.4 77.7 1.0
NE2 B:HIS137 4.5 77.6 1.0
N B:SER20 4.9 59.4 1.0

Zinc binding site 6 out of 6 in 4l99

Go back to Zinc Binding Sites List in 4l99
Zinc binding site 6 out of 6 in the Structure of the Rbp From Lactococcal Phage 1358 in Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Rbp From Lactococcal Phage 1358 in Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:49.9
occ:0.50
NZ B:LYS338 1.9 0.2 1.0
OD1 B:ASP133 2.1 56.7 1.0
CE B:LYS338 2.4 85.1 1.0
NE2 B:HIS303 2.5 54.3 1.0
CD B:LYS338 2.8 64.2 1.0
CG B:ASP133 3.0 54.0 1.0
OD2 B:ASP133 3.2 54.9 1.0
CD2 B:HIS303 3.3 53.7 1.0
CE1 B:HIS303 3.4 53.6 1.0
O B:GLU301 4.1 50.8 1.0
CG B:LYS338 4.2 48.6 1.0
CB B:ASP133 4.4 49.3 1.0
CG B:HIS303 4.4 51.5 1.0
ND1 B:HIS303 4.5 53.7 1.0
O B:HOH669 4.8 56.0 1.0
O B:ARG132 4.8 48.7 1.0
CA B:ASP133 5.0 47.8 1.0
CB B:ALA300 5.0 47.4 1.0
CB B:LYS338 5.0 40.7 1.0

Reference:

C.Farenc, S.Spinelli, C.Bebeacua, D.Tremblay, I.Orlov, S.Blangy, B.P.Klaholz, S.Moineau, C.Cambillau. A Virulent Siphophage Cyoem Structure and Host Recognition and Infection Mechanism To Be Published.
Page generated: Wed Dec 16 05:31:31 2020

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