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Zinc in PDB 3vfj: The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier

Protein crystallography data

The structure of The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier, PDB code: 3vfj was solved by N.J.Economou, S.D.Weeks, K.C.Grasty, P.J.Loll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.89 / 2.05
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 40.320, 123.610, 156.740, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 23.1

Other elements in 3vfj:

The structure of The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier also contains other interesting chemical elements:

Arsenic (As) 2 atoms
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier (pdb code 3vfj). 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 Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier, PDB code: 3vfj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3vfj

Go back to Zinc Binding Sites List in 3vfj
Zinc binding site 1 out of 8 in the The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:29.9
occ:1.00
OXT A:ACT410 2.1 29.4 1.0
OE2 A:GLU111 2.1 29.6 1.0
CD A:GLU111 2.8 30.3 1.0
OE1 A:GLU111 2.9 28.4 1.0
C A:ACT410 3.0 29.4 1.0
O A:ACT410 3.1 27.0 1.0
O A:HOH618 3.5 35.0 1.0
CG A:GLU111 4.1 25.9 1.0
O A:HOH591 4.2 30.8 1.0
O A:HOH554 4.3 29.9 1.0
CH3 A:ACT410 4.4 24.2 1.0
CB A:ALA63 4.8 24.1 1.0

Zinc binding site 2 out of 8 in 3vfj

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Zinc binding site 2 out of 8 in the The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:42.6
occ:1.00
O A:HOH547 2.1 36.3 1.0
OD2 A:ASP65 2.3 37.4 1.0
OD1 A:ASP65 2.6 30.3 1.0
CG A:ASP65 2.8 30.2 1.0
O A:HOH603 4.2 39.7 1.0
CB A:ASP65 4.3 27.7 1.0
CB A:ALA63 4.4 24.1 1.0
SD A:MET330 4.6 44.9 1.0
O A:HOH575 4.8 40.3 1.0
NE1 A:TRP62 4.8 27.7 1.0
N A:ARG66 5.0 24.5 1.0

Zinc binding site 3 out of 8 in 3vfj

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Zinc binding site 3 out of 8 in the The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:42.2
occ:0.50
OE1 A:GLU291 2.1 40.4 1.0
OE2 A:GLU288 2.2 44.7 1.0
OE1 A:GLU288 2.6 40.1 1.0
CD A:GLU288 2.8 40.1 1.0
CD A:GLU291 2.9 39.2 1.0
OE2 A:GLU291 3.0 40.8 1.0
O A:HOH616 3.7 39.2 1.0
O A:HOH590 4.2 36.3 1.0
CG A:GLU288 4.2 37.5 1.0
CG A:GLU291 4.3 34.1 1.0
NZ A:LYS295 4.6 46.0 1.0
CB A:GLU291 4.8 28.9 1.0
CA A:GLU288 4.9 30.5 1.0

Zinc binding site 4 out of 8 in 3vfj

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Zinc binding site 4 out of 8 in the The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:75.3
occ:1.00
OE1 A:GLU359 2.3 55.6 1.0
O A:HOH621 2.4 49.3 1.0
OD1 A:ASP363 2.6 44.6 1.0
OD2 A:ASP363 2.7 44.0 1.0
CG A:ASP363 3.0 44.4 1.0
CD A:GLU359 3.2 53.4 1.0
CG A:GLU359 3.5 48.8 1.0
CE A:LYS362 4.2 51.8 1.0
NZ A:LYS362 4.3 58.5 1.0
OE2 A:GLU359 4.3 53.5 1.0
NE2 A:GLN355 4.4 45.5 1.0
CB A:ASP363 4.5 39.0 1.0
O A:GLU359 4.5 38.5 1.0
CB A:GLU359 4.9 43.5 1.0

Zinc binding site 5 out of 8 in 3vfj

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Zinc binding site 5 out of 8 in the The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:35.3
occ:1.00
OE1 A:GLU172 2.1 35.1 1.0
O A:HOH614 2.1 30.9 1.0
OD2 A:ASP177 2.1 34.5 1.0
CD A:GLU172 3.0 39.6 1.0
CG A:ASP177 3.1 30.8 1.0
OE2 A:GLU172 3.3 43.2 1.0
CB A:ASP177 3.3 28.0 1.0
O A:HOH646 4.0 41.4 1.0
OD1 A:ASP177 4.2 31.0 1.0
OD2 A:ASP180 4.3 38.4 1.0
CG A:GLU172 4.4 39.5 1.0
CB A:ASP180 4.4 32.8 1.0
CA A:ASP177 4.8 28.6 1.0
CG A:ASP180 4.9 35.3 1.0

Zinc binding site 6 out of 8 in 3vfj

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Zinc binding site 6 out of 8 in the The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:42.2
occ:1.00
NE2 A:HIS203 2.1 34.0 1.0
O A:HOH533 2.3 34.4 1.0
O A:HOH615 2.5 39.8 1.0
O A:HOH532 2.8 36.0 1.0
CD2 A:HIS203 2.9 30.2 1.0
O A:HOH628 3.0 39.9 1.0
CE1 A:HIS203 3.2 33.1 1.0
CB A:PRO133 3.9 26.8 1.0
ND2 A:ASN201 3.9 36.3 1.0
CB A:ASN201 4.1 36.4 1.0
CG A:HIS203 4.1 31.2 1.0
ND1 A:HIS203 4.3 31.2 1.0
CG A:ASN201 4.4 38.8 1.0
CG A:PRO133 4.7 30.5 1.0
CA A:PRO133 4.9 29.8 1.0

Zinc binding site 7 out of 8 in 3vfj

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Zinc binding site 7 out of 8 in the The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:38.6
occ:0.53
O A:HOH594 2.2 37.1 1.0
ND1 A:HIS39 2.2 33.6 1.0
O A:HIS39 2.3 34.2 1.0
CE1 A:HIS39 2.9 36.4 1.0
CG A:HIS39 3.3 30.5 1.0
C A:HIS39 3.4 30.3 1.0
CB A:HIS39 3.8 31.1 1.0
NE2 A:HIS39 4.1 37.4 1.0
CA A:HIS39 4.2 29.9 1.0
CD2 A:HIS39 4.2 32.8 1.0
O A:HOH582 4.4 32.7 1.0
N A:PRO40 4.4 29.9 1.0
C A:PRO40 4.5 34.4 1.0
N A:ASP41 4.6 32.0 1.0
O A:HOH638 4.6 37.0 1.0
CA A:PRO40 4.6 30.8 1.0
N A:HIS39 4.8 28.2 1.0
CA A:GLY13 4.9 28.2 1.0
O A:PRO40 5.0 31.9 1.0

Zinc binding site 8 out of 8 in 3vfj

Go back to Zinc Binding Sites List in 3vfj
Zinc binding site 8 out of 8 in the The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Structure of Monodechloro-Teicoplanin in Complex with Its Ligand, Using Mbp As A Ligand Carrier within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:74.0
occ:0.84
OD2 A:ASP82 2.4 40.5 1.0
CG A:ASP82 3.3 43.2 1.0
OD1 A:ASP82 3.6 43.1 1.0
O A:HOH560 4.1 41.0 1.0
O A:HOH559 4.3 37.6 1.0
CB A:ASP82 4.7 39.1 1.0
CB A:ALA84 4.8 42.0 1.0

Reference:

N.J.Economou, I.J.Zentner, E.Lazo, J.Jakoncic, V.Stojanoff, S.D.Weeks, K.C.Grasty, S.Cocklin, P.J.Loll. Structure of the Complex Between Teicoplanin and A Bacterial Cell-Wall Peptide: Use of A Carrier-Protein Approach. Acta Crystallogr.,Sect.D V. 69 520 2013.
ISSN: ISSN 0907-4449
PubMed: 23519660
DOI: 10.1107/S0907444912050469
Page generated: Wed Dec 16 04:56:09 2020

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